Specification
[0002] FIELD OF THE INVENTION
This invention relates to KRTCAP3, FAM26F, MGC52498, FAM70A and TMEM154
related polypeptides and polynucleotides that are differentially expressed in some cancers
and specific b100d cells, and therefore are suitable targets for development of therapeutics
and diagnostics, particμlarly for cancer therapy and treatment of immune related disorders.
[0003] BACKGROUND OF THE INVENTION
[0004] Tumor antigens are ideally positioned as biomarKers and drug targets, and they
μlay a critical role in the development of novel strategies for active and passive
immunotherapy agents, to be used as stand-alone therapies or in conjunction with
conventional therapies for cancer. Tumor antigens can be classified as either tumor-specific
antigens (TSAs) where the antigens are expressed only in tumor cells and not in normal
tissues, or tumor-associated antigens (TAAs) where the antigens are overexpressed in tumor
cells but nonetheless also present at low levels in normal tissues.
[0005] TAAs and TSAs are validated as targets for passive (antibody) therapy as well as
active immunotherapy using strategies to breaK immune tolerance and stimplate the immune
system. The antigenic epitopes that are targeted by these therapeutic approaches are present
at the cell surface, overexpressed in tumor cells compared to non-tumor cells, and are
targeted by antibothes that blocK functional activity, inhibit cell proliferation, or induce cell
death.
[0006] There are a growing number of tumor-associated antigens against which
monoclonal antibothes have been tested or are in use as treatment for cancer. The
identification and molecμlar characterization of novel tumor antigens expressed by human
malignancies is an active field in tumor immunology. Several approaches have been used to
identify tumor-associated antigens as target candidates for immunotherapy, including high
throughput bioinformatic approaches, based on genomics and proteomics. The identification
of novel TAAs or TSAs expands the spectrum of tumor antigen targets available for
immune recognition and provides new target molecμles for the development of therapeutic
agents for passive immunotherapy, including monoclonal antibothes, whether unmodified or
[0007] Cancer vaccination involves the administration of tumor antigens and is used to
breaK immune tolerance and induce an active T-cell response to the tumor. Vaccine therapy
includes the use of naKed DNA, peptides, recombinant protein, and whole cell therapy,
where the patient's own tumor cells are used as the source of the vaccine. With the
identification of specific tumor antigens, vaccinations are more often carried out by
dendritic cell therapy, whereby dendritic cells are loaded with the relevant protein or
peptide, or transfected with vector DNA or RNA.
[0008] The major apμlications of anti-TAA antibothes for treatment of cancer are
therapy with naKed antibody, therapy with a drug-conjugated antibody, and fusion therapy
with cellμlar immunity. Ever since their discovery, antibothes were envisioned as "magic
bμllets" that woμld deliver toxic agents, such as drugs, toxins, enzymes and radioisotopes,
specifically to the diseased site and leaving the non-target normal tissues unaffected.
Indeed, antibothes, and in particμlar antibody fragments, can function as carriers of
cytotoxic substances such as radioisotopes, drugs and toxins. Immunotherapy with such
immuNOconjugates is more effective than with the naKed antibody.
[0009] In contrast to the overwhelming success of naKed (such as Rituxan and
Campath) and conjugated antibothes (such as Bexxar and Zevalin) in treating hematological
malignancies, only modest success has been achieved in the immunotherapy of solid
rumors. One of the major limitations in successfμl apμlication of immunotherapy to solid
tumors is the large molecμlar size of the intact immunogloulin that resμlts in prolonged
serum half-life but in poor tumor penetration and uptaKe. Indeed, only a very small amount
of administered antibody (as low as 0.01%) reaches the tumor. In addition to their size,
antibothes encounter other impediments before reaching their target antigens expressed on
the cell surface of solid tumors. Some of the barriers include poor b100d flow in large
tumors, permeability of vascμlar endothelium, elevated interstitial fluid pressure of tumor
stroma, and heterogenous antigen expression.
[0010] With the advent of antibody engineering, small molecμlar weight antibody
fragments exhibiting improved tumor penetration have been generated. Such antibody
fragments are often conjugated to specific cytotoxic molecμles and are designed to
selectively deliver them to cancer cells. Still, solid tumors remain a formidable challenge for
therapy, even with immunoconjugated antibody fragments.
[0011] The new wave of optimization strategies involves the use of biological modifiers
to modplate the impediments posed by solid tumors. Thus, in combination to antibothes or
their conjugated antibody fragments, various agents are being used to improve the tumor
b100d flow, enhance vascμlar permeability, lower tumor interstitial fluid pressure by
modplating stromal cells and extracellular matrix components, upregplate expression of
target antigens and improve penetration and retention of the therapeutic agent.
[0012] Immunotherapy with antibothes represents an exciting opportunity for
combining with standard modalities, such as chemotherapy, as well as combinations with
diverse biological agents to obtain a synergistic activity. Indeed, unconjugated mAbs are
more effective when used in combination with other therapeutic agents, including other
antibothes.
[0013] Passive tumor immunotherapy uses the exquisite specificity and lytic capability
of the immune system to target tumor specific antigens and treat malignant disease with a
minimum of damage to normal tissue. Several approaches have been used to identify tumor-
associated antigens as target candidates for immunotherapy. The identification of novel
tumor specific antigens expands the spectrum of tumor antigen targets available for immune
recognition and provides new target molecμles for the development of therapeutic agents for
passive immunotherapy, including monoclonal antibothes, whether unmodified or armed.
Such novel antigens may also point the way to more effective therapeutic vaccines for
active or adoptive immunotherapy.
[0014] Despite recent progress in the understanding of cancer biology and cancer
treatment, as well as better understanding of the molecμles involved in immune responses,
the success rate for cancer therapy and for the treatment of immune related disorders
remains low. Therefore, there is an unmet need for new therapies which can successfμlly
treat both cancer and immune related disorders.
[0015] BRIEF SUMMARY OF THE INVENTION
[0016] In at least some embodiments, the subject invention provides novel amino acid and
nucleic acid sequences, which are variants of the corresponding amino acid sequences and
nucleic acid sequences for KNOwn or "WT" (wild type") KRTCAP3, FAM26F, MGC52498,
FAM70A, or TMEM154, respectively. According to at least some embodiments of the
present invention, the KRTCAP3, FAM26F, MGC52498, FAM70A, and TMEM154
proteins are differentially expressed by some cancers and specific b100d cells, and therefore
are suitable targets for cancer therapy, treatment of immune related conditions, and drug
development. As described in greater detail below, the terms "polypeptides" and "proteins"
are used to describe specific variants, the KNOwn proteins themselves or derived amino acid
sequences related to KRTCAP3, FAM26F, MGC52498, FAM70A, or TMEM154, or
fragments or portions of any of the above,
[0017] In at least some embodiments, the subject invention provides novel therapeutic and
diagNOstic compositions containing at least one of the KRTCAP3, FAM26F, MGC52498,
FAM70A, or TMEM154 proteins, or variants disclosed herein, or nucleic acid sequences
encoding same.
[0018] In at least some embodiments, the subject invention provides discrete portions of
KRTCAP3; FAM26F; MGC52498; FAM70A, and TMEM154 proteins, variants, and
nucleic acid sequences encoding same or fragments thereof.
[0019] In at least some embodiments, the subject invention provides a secreted form of
TMEM154 proteins, especially the extracellular domain (ECD) of TMEM154 proteins and
nucleic acid sequences encoding same or fragments or portions or homologous or
conjugates thereof, and compositions comprising same.
[0020] According to at least some embodiments of the present invention, the polypeptides
corresponding to an extracellular domain of TMEM154 proteins are used as therapeutic
agents for cancer therapy, treatment of immune related conditions, and drug development.
[0021] In at least some embodiments, the subject invention provides polypeptides
corresponding to an extracellular domain of KRTCAP3, FAM26F, MGC52498, FAM70A,
proteins and/or new variants, and nucleic acid sequences encoding same or fragments or
homologous thereof.
[0022] In at least some embodiments, the subject invention provides therapeutic and
diagNOstic antibothes, antibody fragments and compositions comprising same, and therapies
and diagNOstic methods using said antibothes and antibody fragments that specifically bind
to any one of KRTCAP3; FAM26F; MGC52498; FAM70A, and TMEM154 proteins, or
variants, or a soluble or extracellular portion thereof, especially the ectodomain, or a the
unique bridge, edge portion, tail or head portion thereof.
[0023] According to at least some embodiments of the present invention, the KRTCAP3,
FAM26F, MGC52498, FAM70A, TMEM154 proteins and/or variants polypeptides and
nucleic acid sequences are used as novel targets for development of drugs which
specifically bind to the KRTCAP3, FAM26F, MGC52498, FAM70A, TMEM154 proteins
and/or new variants, and/or drugs which agonize or antagonize the binding of other moieties
to the KRTCAP3, FAM26F, MGC52498, FAM70A, TMEM154 proteins and/or new
variants.
(0024] Thus, in at least some embodiments, the present invention provides KRTCAP3
proteins and novel variants of a KRTCAP3 (SEQ ID NO:7) (KeratiNOcytes-associated
protein 3), discrete portions thereof, and polynucleotides encoding same, and KRTCAP3
polypeptides and discrete portions thereof, and polynucleotides encoding same, which can
be used as diagNOstic marKers and/or as targets for cancer therapy, treatment of immune
related conditions, and drug development, and as therapeutic agents which agonize or
antagonize the binding of other moieties to the KRTCAP3 proteins and/or which agonize or
antagonize at least one KRTCAP3 related biological activity.
[0025] According to some embodiments the present invention provides an isolated
polypeptide selected from W93943_P13 (SEQ ID NO:10), W93943.P14 (SEQ ID NO:ll),
W93943_P18 (SEQ ID NO:13), or a fragment or a variant thereof that possesses at least 80,
85, 90, 95, 96, 97, 98 or 99% sequence identity therewith.
[0026] According to some embodiments of the present invention there is provided an
isolated polypeptide comprising a unique bridge, edge, tail or head portion of KRTCAP3
novel variants, or a homologue or a fragment thereof as well as nucleic acid sequences
encoding the unique bridge, edge, tail or head portion, as well as fragments thereof and
conjugates and the use thereof as therapeutics and/or for diagnostics.
[0027] According to at least some embodiments, the subject invention provides an isolated
polypeptide comprising an amino acid sequence fragment of any one of the unique bridge,
edge, tail or head portion, selected from the group consisting of any one of SEQ ID NO:
146, corresponding to amino acid residues 72 - 97 of W93943_P13 (SEQ ID NO:10); SEQ
ID NO: 147, corresponding to amino acid residues 206 - 221 of W93943_P14 (SEQ ID
NO:ll), SEQ ID NO: 148 corresponding to amino acid residues 206 - 231 of W93943_P17
(SEQ ID NO: 12), or a fragment or variant thereof that possesses at least 80, 85, 90, 95, 96,
97, 98 or 99% sequence identity therewith. According to at least some embodiments, the
subject invention provides an isolated polypeptide having an amino acid sequence as set
forth in any one of SEQ ID NOs:146-148.
[0028] According to at least some embodiments, the subject invention provides
polypeptides comprising a sequence of amino acid residues corresponding to discrete
portions of the KRTCAP3 proteins, including different portions of the extracellular domain
corresponding to residues 42-62 of the KRTCAP3 protein sequence contained in the
sequence of W93943_P2 (SEQ ID NO:7), W93943.P14 (SEQ ID NO: 11), W93943.P17
(SEQ ID NO:12), and W93943_P18 (SEQ ID NO:13), or residues 115462 KRTCAP3
protein sequence contained in the sequence of W93943_P2 (SEQ ID NO:7), W93943_P14
(SEQ ID NO:ll), and W93943_P17 (SEQ ID NO: 12), or residues 1-20 of the KRTCAP3
protein sequence contained in the sequence of W93943JP13 (SEQ ID NO: 10),
corresponding to amino acid sequence depicted in SEQ ID NO:49, or residues 77-91 of the
KRTCAP3 protein sequence contained in the sequence of W93943_P13 (SEQ ID NO:10)
corresponding to amino acid sequence depicted in SEQ ID NO:50, or residues 141-188 of
the KRTCAP3 protein sequence contained in the sequence of W93943_P13 (SEQ ID
NO: 10) corresponding to amino acid sequence depicted in SEQ ID NO:48; or residues 115-
171 of the KRTCAP3 protein sequence contained in the sequence of W93943_P18 (SEQ ID
NO:13), corresponding to amino acid sequence depicted in SEQ ID NO:51, or a fragment,
or a variant thereof possessing at least 80%, 85%, 90%, 95, 96, 97, 98 or 99% sequence
identity therewith.
[0029] According to at least some embodiments, the subject invention provides KRTCAP3
amino acid sequences selected from any of the isolated polypeptides, used for rabbit
immunization and specific antibothes production, having an amino acid sequence as set
forth in any one of SEQ ID NOs:115, 116, or a fragment, or a variant thereof possessing at
least 80%, 85%, 90%, 95, 96, 97, 98 or 99% sequence identity therewith.
[0030] According to at least some embodiments, the subject invention provides isolated
nucleic acid sequences encoding any of the foregoing KRTCAP3 proteins extracellular
domain polypeptides or fragments or homologous thereof.
[0031] According to at least some embodiments, the subject invention provides an isolated
polynucleotide encoding a polypeptide comprising any one of the amino acid sequence, as
set forth in SEQ ID NOs: 10, 11, 13, 47-51, 146-148, or a fragment or variant thereof that
possesses at least 80, 85, 90, 95, 96, 97, 98 or 99% sequence identity therewith.
[0032] According to at least some embodiments, the subject invention provides an isolated
polynucleotide comprising a nucleic acid having a nucleic acid sequence as set forth in any
one of W93943_T5 (SEQ ID NO:3), W93943_T8 (SEQ ID NO:4), W93943_T14 (SEQ ID
NO:6), or a fragment thereof or a sequence homologous thereto, that possesses at least 80,
85, 90, 95, 96, 97, 98 or 99% sequence identity therewith. According to at least some
embodiments, the foregoing fragment is selected from a group comprising any one of SEQ
ID NO:2, 9, 94, 193-195, or a fragment thereof, or a sequence homologous thereto.
According to another embodiment, the isolated polynucleotide is at least 80, 85, 90, 95, 96,
97, 98 or 99% homologous to a nucleic acid sequence as set forth in any one of SEQ ID
NOs: 2, 3,4, 6, 9, 94,193-195.
In at least some embodiments, the present invention provides proteins and
discrete portion of hypothetical protein LOC441168 (SEQ ID NO:15) (SwissProt accession
identifier NP_001010919, FAM26F) or polynucleotides encoding same, which can be used
as diagNOstic marKers and/or as targets for cancer therapy, treatment of immune related
conditions, and drug development, and as therapeutic agents which agonize or antagonize
the binding of other moieties to the FAM26F proteins and/or which agonize or antagonize at
least one FAM26F related biological activity.
According to at least some embodiments, the subject invention provides
polypeptides comprising a sequence of amino acid residues corresponding to discrete
portions of the FAM26F proteins, including different portions of the extracellular domain
corresponding to residues 40-48 of sequences of T82906_P4 (SEQ ID NO:18),
corresponding to amino acid sequence depicted in SEQ ID NO: 52, or residues 125-175 of
sequences of T82906_P4 (SEQ ID NO:18), corresponding to amino acid sequence depicted
in SEQ ID NO: 53, or residues 27-143 of sequences of T82906_P3 (SEQ ID NO:16),
corresponding to amino acid sequence depicted in SEQ ID NO: 127, or fragments or
variants thereof possessing at least 80%, 85%, 90%, 95, 96, 97, 98 or 99% sequence identity
therewith.
According to at least some embodiments, the subject invention provides
FAM26A amino acid sequences selected from any of the isolated polypeptides, used for
rabbit immunization and specific antibothes production, having an amino acid sequence as
set forth in any one of SEQ ID NOs: 117, 118, or a fragment, or a variant thereof possessing
at least 80%, 85%, 90%, 95, 96, 97, 98 or 99% sequence identity therewith.
[0033] In at least some embodiments, the present invention provides MGC52498 proteins
and novel variants of a KNOwn hypothetical protein MGC52498 (SEQ ID NO: 132)
(SwissProt accession identifier NP_872427; LOC348378), discrete portions thereof, and
polynucleotides encoding same, and their use as diagNOstic marKers and/or as targets for
cancer therapy, treatment of immune related conditions, and drug development, and as
therapeutic agents which agonize or antagonize the binding of other moieties to the
MGC52498 proteins and/or which agonize or antagonize at least one MGC52498 related
biological activity.
[0034] According to some embodiments the present invention provides an isolated
polypeptide selected from AA213820_P6 (SEQ ID NO:19), or a fragment or a variant
thereof that possesses at least 80, 85, 90, 95, 96, 97, 98 or 99% sequence identity therewith.
[0035] According to some embodiments of the present invention there is provided an
isolated polypeptide comprising a unique bridge, edge, tail or head portion of MGC52498
novel variants, or a homologue or a fragment thereof as well as nucleic acid sequences
encoding the unique bridge, edge, tail or head portion, as well as fragments thereof and
conjugates and the use thereof as therapeutics and/or for diagnostics.
According to at least some embodiments, the subject invention provides an isolated
polypeptide comprising an amino acid sequence of the unique head portion of
AA213820_P6 (SEQ ID NO: 19), corresponding to amino acid residues 1 - 64 of
AA213820J>6 (SEQ ID NO: 19), as set forth in SEQ ID NO: 25, or a fragment or variant
thereof that possesses at least 80, 85, 90, 95, 96, 97, 98 or 99% sequence identity therewith,
[0036] According to at least some embodiments, the subject invention provides an isolated
polypeptide having an amino acid sequence as set forth in SEQ ID NO: 25.
[0037] According to at least some embodiments, the subject invention provides
polypeptides comprising a sequence of amino acid residues corresponding to discrete
portions of the MGC52498 proteins, including different portions of the extracellular domain
corresponding to residues 1-55 of the sequence AA213820_P4 (SEQ ID NO:135),
corresponding to amino acid sequence depicted in SEQ ID NO:60, or residues 91-190 of the
sequences AA213820_P4 (SEQ ID NO:135), corresponding to amino acid sequence
depicted in SEQ ID NO:61, or residues 1-71 of the sequences AA213820_P6 (SEQ ID
NO: 19), corresponding to amino acid sequence depicted in SEQ ID NO:62, or fragments or
variants thereof possessing at least 80%, 85%, 90%, 95, 96, 97, 98 or 99% sequence identity
therewith.
[0038] According to at least some embodiments, the subject invention provides
polypeptides comprising a sequence of amino acid residues corresponding to discrete
fragments of MGC52498, selected from the group consisting of SEQ ID NOs: 150-154,
200, or fragments or variants thereof possessing at least 80%, 85%, 90%, 95, 96, 97, 98 or
99% sequence identity therewith.
[0039] According to at least some embodiments, the subject invention provides isolated
nucleic acid sequences encoding any of the foregoing MGC52498 proteins extracellular
domain polypeptides or fragments or homologous thereof.
[0040] According to at least some embodiments, the subject invention provides an isolated
polynucleotide encoding a polypeptide comprising any one of the amino acid sequence, as
set forth in SEQ ID NOs: 19, 25, 60, 61, 62, 150-154, 200, or a fragment or variant thereof
that possesses at least 80, 85, 90, 95, 96, 97, 98 or 99% sequence identity therewith.
[0041] According to at least some embodiments, the subject invention provides an isolated
polynucleotide comprising a nucleic acid as set forth in SEQ ID NO:20, or a fragment
thereof or a sequence homologous thereto, that possesses at least 80, 85, 90, 95, 96, 97, 98
or 99% sequence identity therewith. According to at least some embodiments, the subject
invention further provides an isolated polynucleotide comprising a nucleic acid
sequenceselected from a group comprising any one of SEQ ID NOs: 27, 109, 201, or a
fragment thereof or a sequence homologous thereto, that possesses at least 80, 85, 90, 95,
96, 97,98 or 99% sequence identity therewith.
[0042] In at least some embodiments, the present invention provides FAM70A proteins and
novel variants of a KNOwn hypothetical protein FAM70A (SEQ ID NO:29) (SwissProt
accession identifier NP_060408), discrete portions thereof, and polynucleotides encoding
same, and polynucleotides encoding same, which can be used as diagNOstic marKers and/or
as targets for cancer therapy, treatment of immune related conditions, and drug
development, and therapeutic agents which agonize or antagonize the binding of other
moieties to the FAM70A proteins and/or which agonize or antagonize at least one FAM70A
related biological activity.
[0043] According to some embodiments the present invention provides an isolated
polypeptide selected from anyone of F10649_P7 (SEQ ID NO:35), F10649_P8 (SEQ ID
NO:36), or a fragment or a variant thereof that possesses at least 80, 85, 90, 95, 96, 97, 98
or 99%sequence identity therewith.
[0044] According to some embodiments of the present invention there is provided an
isolated polypeptide comprising a unique bridge, edge, tail or head portion of FAM70A
variants, or a homologue or a fragment thereof as well as nucleic acid sequences encoding
the unique bridge, edge, or head portion, as well as fragments thereof and conjugates and
the use thereof as therapeutics and/or for diagnostics.
[0045] According to at least some embodiments, the subject invention provides an isolated
polypeptide comprising an amino acid sequence of anyone of the unique bridge, edge, or
head portion corresponding to amino acid residues 1-141 of F10649_P5 (SEQ ID NO:33),
as set forth in SEQ ID NO: 156; or corresponding to amino acid residues 1-144 of
F10649_P8 (SEQ ID NO:36), as set forth in SEQ ID NO: 159; or corresponding to amino
acid sequences set forth in any one of SEQ ID NOs: 155, 157, 158, 160, 196, 199, or a
fragment or variant thereof that possesses at least 80, 85, 90, 95, 96, 97, 98 or 99% sequence
identity therewith.
[0046] According to at least some embodiments, the subject invention provides an isolated
polypeptide having an amino acid sequence as set forth in any one of SEQ ID NOs: 155-
160,196,199.
[0047] According to at least some embodiments, the subject invention provides
FAM70A amino acid sequences selected from any of the isolated polypeptides, used for
rabbit immunization and specific antibothes production, having an amino acid sequence as
set forth in any one of SEQ ID NOs: 121,186, or a fragment, or a variant thereof possessing
at least 80%, 85%, 90%, 95, 96, 97, 98 or 99% sequence identity therewith.
[0048] According to at least some embodiments, the subject invention provides
polypeptides comprising a sequence of amino acid residues corresponding to discrete
portions of the FAM70A proteins, including different portions of the extracellular domain
corresponding to residues 51-59 of the sequence F10649_P4 (SEQ ID NO:30), F10649_P5
(SEQ ID NO:33), or F10649_P7 (SEQ ID NO:35), corresponding to amino acid sequence
depicted in SEQ ID NO:54, or residues 110-225 of the sequence F10649_P4 (SEQ ID
NO:30)„ corresponding to amino acid sequence depicted in SEQ ID NO:55, or residues
110-201 of the sequence F10649_P5 (SEQ ID NO:33), corresponding to amino acid
sequence depicted in SEQ ID NO:56, or residues 110-241 of the sequence F10649_P7 (SEQ
ID NO:35), corresponding to amino acid sequence depicted in SEQ ID NO:58, or residues
51-65 of the sequence F10649_P8 (SEQ ID NO:36), corresponding to amino acid sequence
depicted in SEQ ID NO:59, or residues 223-328 of the sequence F10649_P8 (SEQ ID
NO:36), or residues 80-185 of the sequence F10649_P10 (SEQ ID NO:32), corresponding
to amino acid sequence depicted in SEQ ID NO:57, or variants thereof possessing at least
80%, 85%, 90%, 95, 96, 97, 98 or 99% sequence identity therewith.
[0049] According to at least some embodiments, the subject invention provides isolated
nucleic acid sequences encoding any of the foregoing FAM70A proteins extracellular
domain polypeptides or fragments or homologous thereof.
[0050] According to at least some embodiments, the subject invention provides an isolated
polynucleotide encoding a polypeptide comprising any one of the amino acid sequence, as
set forth in SEQ ID NOs: 35, 36, 54-58, 121, 155-160, 186, 196, 199, or a fragment or
variant thereof mat possesses at least 80, 85, 90, 95, 96, 97, 98 or 99% sequence identity
therewith.
[0051] According to at least some embodiments, the subject invention provides an isolated
polynucleotide comprising a nucleic acid having a nucleic acid sequence as set forth in
anyone of F10649_T4 (SEQ ID NO:24), F10649_T6 (SEQ ID NO:26), or a fragment
thereof or a sequence at least 80, 85, 90, 95, 96, 97, 98 or 99% homologous thereto.
According to at least some embodiments, the foregoing fragment comprises any of the
nucleic acid as set forth in any one of SEQ ID NO:103, 197, 198, or a fragment thereof, or a
sequence at least 80, 85, 90, 95, 96, 97, 98 or 99% homologous thereto.
[0052] In at least some embodiments, the present invention provides proteins and discrete
portions of a KNOwn hypothetical protein LOC201799 (SEQ ID NO:42) (SwissProt
accession identifier NP_689893; TMEM154) or polynucleotides encoding same, which can
be used as diagNOstic marKers and/or as targets for cancer therapy, treatment of immune
related conditions, and drug development, and therapeutic agents which agonize or
antagonize the binding of other moieties to the TMEM154 proteins and/or which agonize or
antagonize at least one TMEM154 related biological activity.
[0053] According to at least some embodiments, the subject invention provides isolated
polypeptides comprising the soluble ectodomain (ECD) of the TMEM154 proteins and
fragments and conjugates thereof, as well as nucleic acid sequences encoding said soluble
ectodomain, and the use thereof as therapeutics.
[0054] According to at least some embodiments, the subject invention provides
polypeptides comprising a sequence of amino acid residues corresponding to discrete
portions of the TMEM154 proteins, including different portions of the extracellular domain
corresponding to residues 23-75 of the sequence W38346_P3 (SEQ ID NO:42) or
W38346_P7 (SEQ ID NO:46), corresponding to amino acid sequence depicted in SEQ ID
NO:63, or residues 20-105 of the sequence W38346_P4 (SEQ ID NO:45), corresponding to
amino acid sequence depicted in SEQ ID NO:64, or residues 122 - 144 of the sequence of
W38346_P7 (SEQ ID NO:46), corresponding to amino acids depicted in SEQ ID NO: 162,
or fragments thereof or variants thereof possessing at least 80%, 85%, 90%, 95, 96, 97, 98
or 99% sequence identity therewith.
[0055] According to at least some embodiments, the subject invention provides TMEM154
amino acid sequences selected from any of the isolated polypeptides, used for rabbit
immunization and specific antibothes production, having an amino acid sequence as set
forth in any one of SEQ ID NOs:191, 192, or a fragment, or a variant thereof possessing at
least 80%, 85%, 90%, 95, 96, 97, 98 or 99% sequence identity therewith.
[0056] According to at least some embodiments, the subject invention provides isolated
nucleic acid sequences encoding any of the foregoing TMEM154 proteins extracellular
domain polypeptides or fragments or homologous thereof.
[0057] According to at least some embodiments, the subject invention provides an isolated
polynucleotide encoding a polypeptide comprising any one of the amino acid sequence, as
set forth in SEQ ID NOs: 63, 64,161,162, or a fragment or variant thereof that possesses at
least 80, 85, 90, 95, 96, 97, 98 or 99% sequence identity therewith,
[0058] According to at least some embodiments, the subject invention provides an isolated
polynucleotide comprising a nucleic acid as set forth in any one of SEQ ID NO:23, 106 or a
fragment thereof, or a sequence at least 80, 85, 90, 95, 96, 97, 98 or 99% homologous
thereto. According to another embodiment, the isolated polynucleotide is at least 80, 85, 90,
95, 96, 97, 98 or 99% homologous to a nucleic acid sequence as set forth in any one of SEQ
ID NOs: 23, 106.
[0059] According to at least some embodiments, the subject invention provides any of the
foregoing polypeptides corresponding to any one of the soluble TMEM154 proteins and/or
TMEM154 protein's extracellular domains, wherein said polypeptide blocKs or inhibits the
interaction of TMEM154 proteins with a corresponding functional ligand.
[0060] According to at least some embodiments, the subject invention provides any of the
foregoing polypeptides corresponding to any one of the soluble TMEM154 proteins and/or
TMEM154 proteins extracellular domains, wherein said polypeptide replaces or augments
the interaction of TMEM154 proteins with a corresponding functional ligand.
[0061] According to some embodiments of the present invention there is provided a fusion
protein, or a nucleic acid encoding same, comprising an isolated or purified TMEM154
proteins and/or TMEM154 proteins extracellular domain or fragments or variants or
homologs thereof. According to some embodiments of the present invention, the fusion
protein, or a nucleic acid encoding same, optionally may be directly or indirectly attached to
a non-TMEM154 protein or nucleic acid sequence, respectively.
[0062] According to some embodiments of the present invention the non-TMEM154
protein or nucleic acid sequence is at least a portion of soluble immunogloulin domain or
fragment.
[0063] In another embodiment the invention includes any of the foregoing fusion proteins,
wherein a polyalKyl oxide moiety such as polyethylene glycol is attached to the polypeptide.
[0064] In another embodiment the invention includes any of the foregoing fusion proteins,
wherein the immunogloulin heavy chain constant region is an Fc fragment.
[0065] In another embodiment the invention includes any of the foregoing fusion proteins
wherein the immunogloulin heavy chain constant region is an isotype selected from the
group consisting of an lgGl, IgG2, IgG3, IgG4, IgM, IgE, IgA and IgD.
[0066] In another embodiment the invention includes any of the foregoing fusion proteins,
wherein the polypeptide is fused to a VASP domain.
[0067] In another embodiment the invention includes any of the foregoing fusion proteins,
wherein the fusion protein modplates lymphocyte activation.
[0068] In another embodiment the invention includes any of the foregoing polypeptides,
attached to a detectable or therapeutic moiety.
[0069] According to some embodiments of the present invention there is provided vectors
such as plasmids and recombinant viral vectors containing any of the foregoing nucleic acid
sequences, and host cells containing the vectors that express any one of discrete portions of
KRTCAP3, FAM26F, MGC52498, FAM70A, TMEM154 proteins, its secreted or soluble
form and/or the ECD or sequences corresponding to unique bridge, edge, tail or head
portion of KRTCAP3, FAM26F, MGC52498, FAM70A, TMEM154 proteins, or
homologous thereof or conjugates containing any of the foregoing.
[0070] According to still other embodiments there is provided use of any of the forgoing
vectors and host cells for producing any one of the KRTCAP3, FAM26F, MGC52498,
FAM70A, TMEM154 polypeptides.
[0071] In another embodiment the invention includes a method of producing any one of
the KRTCAP3, FAM26F, MGC52498, FAM70A, TMEM154 ectodomain polypeptides,
sequences corresponding to a unique bridge, edge, tail or head portion of KRTCAP3,
FAM26F, MGC52498, FAM70A, TMEM154 polypeptides, or a fragment or a homolog or a
conjugate thereof, comprising culturing the foregoing host cell, wherein the cell expresses
the polypeptide encoded by the DNA segment or nucleic acid and recovering said
polypeptide.
[0072] According to another embodiment of the invention, the KRTCAP3, FAM26F,
MGC52498, FAM70A, TMEM154 polypeptides, or fragments or homologs thereof, can be
produced using any one of biochemically synthesis method Known in the art, such as by
emμloying standard solid phase techniques.
[0073] In another embodiment the invention includes a pharmaceutical composition
comprising any of the foregoing polynucleotide sequences and further comprising a
pharmaceutically acceptable diluent or carrier.
[0074] In another embodiment the invention includes a pharmaceutical composition
comprising the foregoing vector or host cell and further comprising a pharmaceutically
acceptable diluent or carrier.
[0075] In another embodiment the invention includes a pharmaceutical composition
comprising any of the foregoing polypeptides and/or any of the foregoing fusion proteins
and further comprising a pharmaceutically acceptable diluent or carrier.
[0076] According to some embodiments of the present invention there is provided
compounds and use thereof including TMEM154 ectodomain or fragments or variants
thereof, and a pharmaceutical composition comprising same, which are suitable for
treatment or prevention of cancer and/or immune related conditions.
[0077] According to some embodiments of the present invention there is provided a
method for treating, or preventing cancer, and/or immune related conditions, comprising
administering a subject in need thereof a foregoing pharmaceutical composition, comprising
any one of: a molecμle having the extracellular domain of TMEM154 polypeptide, or
fragment or variant or homologue or conjugate thereof; or polypeptide, comprising a
sequence of amino acid residues having at least 80%, 85%, 90%, 95%, 96%, 97%, 98%,
99%, 100% sequence identity with amino acid set forth in SEQ ID NOs:63, 64, or a fusion
protein comprising polypeptide having the extracellular domain of TMEM 154 polypeptide.
According to at least some embodiments of the present invention there is provided
any of the foregoing methods for treating, or preventing cancer, wherein the cancer is
selected from the group consisting of solid tumors, sarcomas, hematological malignancies,
including but not limited to breast cancer (e.g. breast carcinoma), cervical cancer, ovary
cancer (ovary carcinoma), endometrial cancer, melaNOma, bladder cancer (bladder
carcinoma), lung cancer (e.g. adenocarcinoma and non-small cell lung cancer), pancreatic
cancer (e.g. pancreatic carcinoma such as exocrine pancreatic carcinoma), colon cancer (e.g.
colorectal carcinoma, such as colon adenocarcinoma and colon adenoma), prostate cancer
including the advanced disease, hematopoietic tumors of lymphoid lineage (e.g. leuKemia,
acute lymphocytic leuKemia, chronic lymphocytic leuKemia, B-cell lymphoma, BurKitt's
lymphoma, mμltiμle myeloma, HodgKin's lymphoma, non-HodgKin's lymphoma, anti
CD20 (i.e. Rituximab) resistant lymphoma), myeloid leuKemia (for EXAMPLE, acute
myelogeNOus leuKemia (AML), chronic myelogeNOus leuKemia), thyroid cancer, thyroid
follicμlar cancer, myelodysμlastic syndrome (MDS), tumors of mesenchymal origin (e.g.
fibrosarcomas and rhabdomyosarcomas), melaNOma, uveal melaNOma, teratocarcinoma,
neuroblastoma, glioma, glioblastoma, benign tumor of the sKin (e.g. Keratoacanthomas),
renal cancer, anaμlastic large-cell lymphoma, esophageal squamous cells carcinoma,
hepatocellμlar carcimoma, follicμlar dendritic cell carcinoma, intestinal cancer, muscle-
invasive cancer, seminal vesicle tumor, epidermal carcinoma, sμleen cancer, bladder cancer,
head and necK cancer, stomach cancer, liver cancer, bone cancer, brain cancer, cancer of the
retina, biliary cancer, small bowel cancer, salivary gland cancer, cancer of uterus, cancer of
testicles, cancer of connective tissue, prostatic hypertrophy, myelodysμlasia, Waldenstrom's
macroglobinaemia, nasopharyngeal, neuroendocrine cancer, myelodysμlastic syndrome,
mesothelioma, angiosarcoma, Kaposi's sarcoma, carciNOid, oesophagogastric, fallopian tube
cancer, peritoneal cancer, papillary serous mμllerian cancer, malignant ascites,
gastrointestinal stromal tumor (GIST), and a hereditary cancer syndrome such as Li-
Fraumeni syndrome and Von Hippel-Lindau syndrome (VHL), and wherein the cancer is
non-metastatic, invasive or metastatic.
According to at least some embodiments of the present invention there is provided
any of the foregoing methods for treating, or preventing cancer, comprising administering a
subject in need thereof a foregoing pharmaceutical composition, comprising any one of: a
soluble molecμle having the extracellular domain the TMEM154 polypeptides, or fragment
or variant or homologue or conjugate thereof; or polypeptide, comprising a sequence of
amino acid residues having at least 80%, 85%, 90%, 95%, 96%, 97%, 98%, 99%, 100%
sequence identity with amino acid sequence as set forth in anyone of SEQ ID NOs;63, 64,
or fusion protein, or a nucleic acid sequence encoding the same, or the expression vector
containing the nucleic acid sequences, or host cell comprising the foregoing expression
vector, wherein the cancer is selected from lymphoma, especially non-HodgKin's
Lymphoma,, anti CD20 (i.e. Rituximab) resistant lymphoma, Mμltiμle Myeloma, Kidney
cancer, and/or pancreatic cancer.
According to at least some embodiments of the present invention there is provided
any of the foregoing methods for treating, or preventing immune related condition, disease
or disorder, wherein the immune related condition, disease or disorder is selected from a
group consisting of but not limited to mμltiμle sclerosis; psoriasis; rheumatoid arthritis;
psoriatic arthritis, systemic lupus erythematosus; μlcerative colitis; Crohn's disease; benign
lymphocytic angiitis, thrombocytopenic purpura, idiopathic thrombocytopenia, idiopathic
autoimmune hemolytic anemia, pure red cell aμlasia, Sjogren's syndrome, rheumatic
disease, connective tissue disease, inflammatory rheumatism, degenerative rheumatism,
extra-articμlar rheumatism, juvenile rheumatoid arthritis, arthritis uratica, muscμlar
rheumatism, chronic polyarthritis, cryoglobulinemic vascμlitis, ANCA-associated vascμlitis,
antiphospholipid syndrome, myasthenia gravis, autoimmune haemolytic anaemia, Guillian-
Barre syndrome, chronic immune polyneuropathy, autoimmune thyroiditis, insμlin
dependent diabetes mellitus, type I diabetes, Addison's disease, membraNOus
glomerμlonephropathy, Goodpasture's disease, autoimmune gastritis, pernicious anaemia,
pemphigus vμlgarus, cirrhosis, primary biliary cirrhosis, dermatomyositis, polymyositis,
fibromyositis, myogelosis, celiac disease, immunogloulin A nephropathy, HeNOch-
Schonlein purpura, Evans syndrome, atopic dermatitis, psoriasis, psoriasis arthropathica,
Graves' disease, Graves' ophthalmopathy, scleroderma, systemic scleroderma, asthma,
allergy, primary biliary cirrhosis, Hashimoto's thyroiditis, primary myxedema, sympathetic
ophthalmia, autoimmune uveitis, hepatitis, chronic action hepatitis, collagen diseases,
anKylosing spondylitis, periarthritis humeroscapμlaris, panarteritis NOdosa,
chondrocalciNOsis, Wegener's granμlomatosis, microscopic polyangiitis, chronic urticaria,
bμllous sKin disorders, pemphigoid, atopic eczema, Devic's disease, childhood autoimmune
hemolytic anemia, Refractory or chronic Autoimmune Cytopenias, Prevention of
development of Autoimmune Anti-Factor VIII Antibothes in Acquired Hemophilia A, Cold
Agglutinin Disease, Neuromyelitis Optica, Stiff Person Syndrome, gingivitis, periodontitis,
pancreatitis, myocarditis, vascμlitis, gastritis, gout, gouty arthritis, and inflammatory sKin
disorders, selected from the group consisting of psoriasis, atopic dermatitis, eczema,
rosacea, urticaria, and acne, NOrmocomμlementemic urticarial vascμlitis, pericarditis,
myositis, anti-synthetase syndrome, scleritis, macrophage activation syndrome, Bechet's
Syndrome, PAPA Syndrome, Blau's Syndrome, gout, adμlt and juvenile Still's disease,
cryropyriNOpathy, MucKle-Wells syndrome, familial cold-induced auto-inflammatory
syndrome, neonatal onset multisystemic inflammatory disease, familial Mediterranean
fever, chronic infantile neurologic, cutaneous and articμlar syndrome, systemic juvenile
idiopamic arthritis, Hyper IgD syndrome, Schnitzler's syndrome, and TNF receptor-
associated periodic syndrome (TRAPS), immune disorders associated with graft
transμlantation rejection, such as acute and chronic rejection of organ transμlantation,
allogenic stem cell transμlantation, autologous stem cell transμlantation, bone marrow
tranμlantation, graft versus host disease, inflammatory bowel disease, Good pasture's
syndrome, pernicious anemia, autoimmune atrophic gastritis, μlceratis colitis, mixed
connective tissue disease, panarteriitis NOdosa, progressive systemic scleroderma, peptic
ulcers, ulcers, chronic bronchitis, acute lung injury, pμlmonary inflammation, airway hyper-
responsiveness, septic shocK, inflammatory sKin disorders, myogelosis, chondrocalciNOsis,
thyroditis, allergic oedema, and granμlomas.
[0078] According to other embodiments of the present invention, there is provided
monoclonal or polyclonal antibothes and antibody fragments and conjugates containing
such, that specifically bind any one of KRTCAP3, FAM26F, MGC52498, FAM70A,
TMEM154 proteins, optionally and preferably by specifically binding a sequence selected
from the group consisting of any of SEQ ID NOs: 7,8, 10-13, 15-19, 29-33, 35, 36,42-46,
127, 132-135, or a fragment, or a variant, or a homologue thereof, or a unique bridge, edge,
tail or head portion selected from any one of SEQ ID NOs:25, 146-162, 196, 199, 200, or a
fragment, or a variant, or a homologue, or an epitope thereof, or a secreted form and/or the
ECD thereof selected from SEQ ID NO:47-64 or a fragment, or a variant, or a homologue
thereof, or a peptide selected from any one of SEQ ID NOs: 115-118, 121, 186, 191, 192.
These antibothes are potentially useful as therapeutics and/or diagNOstic agents (both in
vitro and in vivo diagNOstic methods).
[0079] According to at least some embodiments of the invention these antibothes are
useful for generating and selecting for anti-idiotypic antibothes specific thereto which also
are potentially useful as therapeutics and/or diagNOstic agents (both in vitro and in vivo
diagNOstic methods).
[0080] According to at least some embodiments of the invention, the antibothes and
fragments modplate the activity elicited by KRTCAP3, FAM26F, MGC52498, FAM70A,
or TMEM154 polypeptides, and/or are immune activating or immune suppressing such as
antibothes or fragments that target cells via ADCC (antibody dependent cellμlar
cytotoxicity) or CDC (complement dependent cytotoxicity) activities.
[0081] In another embodiment the invention includes any of the foregoing antibothes or
fragments thereof, wherein said antibody blocKs or inhibits the interaction of any one of
KRTCAP3, FAM26F, MGC52498, FAM70A, or TMEM154 polypeptides with a
corresponding counterpart or cell component or tissue structure promoting an opposite
activity or function.
[0082] In another embodiment the invention includes any of the foregoing antibothes or
fragments wherein said antibody replaces or augments the interaction of any one of
KRTCAP3, FAM26F, MGC52498, FAM70A, or TMEM154 polypeptides with a
corresponding counterpart or cell component or tissue structure promoting an opposite
function or activity.
[0083] According to at least some embodiments of the present invention, there is provided
pharmaceutical and diagNOstic compositions that comprise a therapeutically or
diagNOstically effective form of any of the foregoing antibody or antibody fragment,
[0084] According to at least some embodiments of the present invention, mere is provided
pharmaceutical compositions that comprise a therapeutically effective form of any of the
foregoing antibody or antibody fragment and further comprising a pharmaceutically
acceptable dilμlent or carrier.
[0085] According to at least some embodiments of the present invention, there is provided
any of the foregoing therapeutically effective polyclonal or monoclonal antibothes or
fragments, or anti-idiotypic antibothes specific to any of the foregoing, or a pharmaceutical
composition comprising same, for treating or preventing conditions wherein any one of
KRTCAP3, FAM26F, MGC52498, FAM70A, or TMEM154 polypeptides, or its secreted or
soluble form or ECD and/or fragments or variants or homologs thereof are differentially
expressed, including cancer and immune related conditions.
According to at least some embodiments of the present invention, there is provided
any of the foregoing therapeutically effective polyclonal or monoclonal antibothes or
fragments, or anti-idiotypic antibothes, or a pharmaceutical composition comprising same,
specific to any KRTCAP3 polypeptide, selected from a group consisting of any of SEQ ID
NOs: 7, 8,10-13, 47-51,146-148,115,116, and/or fragments or variants or homologs
thereof, for treating cancer. According to at least some embodiments of the present
invention, there is provided any of the foregoing therapeutically effective polyclonal or
monoclonal antibothes or fragments, or anti-idiotypic antibothes, or a pharmaceutical
composition comprising same, specific to any KRTCAP3 polypeptide, for treating ovarian
cancer, lung cancer, breast cancer and/or colon cancer.
According to at least some embodiments of the present invention, there is provided
any of the foregoing therapeutically effective polyclonal or monoclonal antibothes or
fragments, or anti-idiotypic antibothes, or a pharmaceutical composition comprising same,
specific to any of one of FAM26F proteins, selected from a group consisting of any of SEQ
IDNOs: 15-18, 52, 53,127, 149,117,118, and/or fragments or variants orhomologs
thereof, for treating cancer and/or immune related conditions or disorders. According to at
least some embodiments of the present invention, there is provided any of the foregoing
therapeutically effective polyclonal or monoclonal antibothes or fragments, or anti-idiotypic
antibothes, or a pharmaceutical composition comprising same, specific to any of one of
FAM26F proteins, for treating ovarian cancer, breast cancer, prostate cancer, renal cancer,
melaNOma, acute lymphocytic leuKemia, chronic lymphocytic leuKemia, acute myelogeNOus
leuKemia, chronic myelogeNOus leuKemia, mμltiμle myeloma, HodgKin's lymphoma or
non-HodgKin's lymphoma, and/or immune related conditions or disorders.
According to at least some embodiments of the present invention, there is provided
any of the foregoing therapeutically effective polyclonal or monoclonal antibothes or
fragments, or anti-idiotypic antibothes, or a pharmaceutical composition comprising same,
specific to any of one of MGC52498 proteins, selected from a group consisting of any of
SEQ ID NOs: 19,25, 60-62,132-135,150-154,200 and/or fragments or variants or
homologs thereof, for treating cancer and/or immune related conditions or disorders.
According to at least some embodiments of the present invention, there is provided any of
the foregoing therapeutically effective polyclonal or monoclonal antibothes or fragments, or
anti-idiotypic antibothes, or a pharmaceutical composition comprising same, specific to any
of one of MGC52498 proteins for treating lymphoma, especially non-HodgKin' s
Lymphoma, Mμltiμle Myeloma, leuKemia, especially T cell leuKemia, and/or lung cancer,
and/or immune related conditions or disorders.
According to at least some embodiments of the present invention, there is provided
any of the foregoing therapeutically effective polyclonal or monoclonal antibothes or
fragments, or anti-idiotypic antibothes, or a pharmaceutical composition comprising same,
specific to any of one of FAM70A proteins, selected from a group consisting of any of SEQ
ID NOs: 29-33, 35, 36, 54-59,155-160,121,186,196,199, and/or fragments or variants or
homologs thereof, for treating cancer and/or immune related conditions or disorders.
According to at least some embodiments of the present invention, mere is provided any of
the foregoing therapeutically effective polyclonal or monoclonal antibothes or fragments, or
anti-idiotypic antibothes, or a pharmaceutical composition comprising same, specific to any
of one of FAM70A proteins for treating Mμltiμle Myeloma, Kidney cancer, lung cancer,
liver cancer, and/or breast cancer, and/or immune related conditions or disorders.
According to at least some embodiments of the present invention, there is provided
any of the foregoing therapeutically effective polyclonal or monoclonal antibothes or
fragments, or anti-idiotypic antibothes, or a pharmaceutical composition comprising same,
specific to any of one of TMEM154 proteins, selected from a group consisting of any of
SEQ ID NOs: 42-46, 63, 64,161,162,191,192, and/or fragments or variants or homologs
thereof, for treating cancer and/or immune related conditions or disorders. According to at
least some embodiments of the present invention, there is provided any of the foregoing
therapeutically effective polyclonal or monoclonal antibothes or fragments, or anti-idiotypic
antibothes, or a pharmaceutical composition comprising same, specific to any of one of
TMEM154 proteins for treating lymphoma, especially non-HodgKin's Lymphoma,, anti
CD20 (i.e. Rituximab) resistant lymphoma, Mμltiμle Myeloma, Kidney cancer, and/or
pancreatic cancer, and/or immune related conditions or disorders, especially SLE (systemic
lupus erythematosus).
[0086] According to still other embodiments there is provided a use of any of the
foregoing specific antibothes and antibody fragments, and conjugates thereof, and
pharmaceutical composition comprising same, in modplating (enhancing or inhibiting)
immunity.
[0087] According to still other embodiments there is provided antibothes and antibody
fragments specific to polypeptides comprising discrete portions of KRTCAP3 proteins,
including different portions of the extracellular domain corresponding to residues 42-62 of
the KRTCAP3 protein sequence contained in the sequence of W93943_P2 (SEQ ID NO:7),
W93943_P14 (SEQ ID NO:ll), W93943_P17 (SEQ ID NO:12), and W93943_P18 (SEQ
ID NO:13), or residues 115-162 KRTCAP3 protein sequence contained in the sequence of
W93943_P2 (SEQ ID NO:7), W93943_P14 (SEQ ID NO:ll), and W93943JH7 (SEQ ID
NO:12), or residues 1-20 of the KRTCAP3 protein sequence contained in the sequence of
W93943_P13 (SEQ ID NO:10), corresponding to amino acid sequence depicted in SEQ ID
NO:49, or residues 77-91 of the KRTCAP3 protein sequence contained in the sequence of
W93943_P13 (SEQ ID NO:10) corresponding to amino acid sequence depicted in SEQ ID
NO:50, or residues 141-188 of the KRTCAP3 protein sequence contained in the sequence
of W93943_P13 (SEQ ID NO:10) corresponding to amino acid sequence depicted in SEQ
ID NO:48; or residues 115-171 of the KRTCAP3 protein sequence contained in the
sequence of W93943_P18 (SEQ ID NO:13), corresponding to amino acid sequence
depicted in SEQ ID NO:51, or to polypeptides comprising anyone of the unique bridge,
edge portion, tail or head portion comprising any one of the amino acid sequences set forth
in SEQ ID NOs:146-147, or fragments thereof.
[0088] According to still other embodiments of the present invention there are provided
antibothes and antibody fragments specific to polypeptides comprising discrete portions of
FAM26F proteins including different portions of the extracellular domain corresponding to
residues 40-48 of sequences of T82906_P4 (SEQ ID NO: 18), corresponding to amino acid
sequence depicted in SEQ ID NO: 52, or residues 125-175 of sequences of T82906_P4
(SEQ ID NO: 18), corresponding to amino acid sequence depicted in SEQ ID NO: 53, or
residues 27-143 of sequences of T82906_P3 (SEQ IDNO:16), corresponding to amino acid
sequence depicted in SEQ ID NO: 127, or to polypeptides comprising anyone of the unique
bridge, edge portion, tail or head portion comprising any one of the amino acid sequences
set forth in SEQ ID NO:49, or fragments thereof.
[0089] According to still other embodiments of the present invention there are provided
antibothes and antibody fragments specific to polypeptides comprising discrete portions of
MGC52498 proteins including different portions of the extracellular domain corresponding
to residues 1-55 of the sequence AA213820JP4 (SEQ ID NO:135), corresponding to amino
acid sequence depicted in SEQ ID NO:60, or residues 91-190 of the sequences
AA213820_P4 (SEQ ID NO:135), corresponding to amino acid sequence depicted in SEQ
ID NO:61, or residues 1-71 of the sequences AA213820_P6 (SEQ ID NO: 19),
corresponding to amino acid sequence depicted in SEQ ID NO:62, or to polypeptides
comprising anyone of the unique bridge, edge portion, tail or head portion comprising any
one of the amino acid sequences set forth in SEQ ID NOs:25,150-154, or fragments
thereof,
[0090] According to still other embodiments of the present invention there are provided
antibothes and antibody fragments specific to polypeptides comprising discrete portions of
FAM70A proteins including different portions of the extracellular domain corresponding to
residues 51-59 of the sequence F10649J>4 (SEQ ID NO:30), F10649_P5 (SEQ ID NO:33),
or F10649_P7 (SEQ ID NO:35), corresponding to amino acid sequence depicted in SEQ ID
NO:54, or residues 110-225 of the sequence F10649_P4 (SEQ ID NO:30), corresponding to
amino acid sequence depicted in SEQ ID NO:55, or residues 110-201 of the sequence
F10649_P5 (SEQ ID NO:33), corresponding to amino acid sequence depicted in SEQ ID
NO;56, or residues 110-241 of the sequence F10649_P7 (SEQ ID NO:35), corresponding to
amino acid sequence depicted in SEQ ID NO:58, or residues 51-65 of the sequence
F10649_P8 (SEQ ID NO:36), corresponding to amino acid sequence depicted in SEQ ID
NO:59, or residues 223-328 of the sequence F10649_P8 (SEQ ID NO:36), or residues 80-
185 of the sequence F10649_P10 (SEQ ID NO:32), corresponding to amino acid sequence
depicted in SEQ ID NO:57, or to polypeptides comprising anyone of the unique bridge,
edge portion, tail or head portion comprising any one of the amino acid sequences set forth
in SEQ ID NOs:155-160, or fragments thereof.
[0091] According to still other embodiments of the present invention there are provided
antibothes and antibody fragments specific to polypeptides comprising discrete portions of
TMEM154 proteins including different portions of the extracellular domain corresponding
to residues 23-75 of the sequence W38346_P3 (SEQ ID NO:42) or W38346_P7 (SEQ ID
NO:46), corresponding to amino acid sequence depicted in SEQ ED NO:63, or residues 20-
105 of the sequence W38346_P4 (SEQ ID NO:45), corresponding to amino acid sequence
depicted in SEQ ID NO:64, or to polypeptides comprising anyone of the unique bridge,
edge portion, tail or head portion comprising any one of the amino acid sequences set forth
in SEQ ID NOs:161-162, or fragments thereof.
[0092] According to still other embodiments there is provided a method to produce or
select for anti-idiotypic antibothes specific to any of the foregoing.
[0093] According to still other embodiments there is provided a method to use any of the
foregoing therapeutically effective polyclonal or monoclonal antibothes or fragments, or
anti-idiotypic antibothes, or a pharmaceutical composition comprising same, for treatment
or prevention of cancer, and/or immune related conditions,
[0094] According to at least some embodiments of the present invention there are provided
methods for treating, or preventing cancer, and/or immune related conditions, comprising
administering to a patient an effective amount of a foregoing antibody or fragment or a
variant or a conjugate thereof, or a pharmaceutical composition comprising same.
According to at least some embodiments of the present invention there is provided
any of the foregoing methods for treating, or preventing cancer, using any of the forgoing
antibothes or fragments or a variant or a conjugate thereof, or a pharmaceutical composition
comprising same.
According to at least some embodiments of the present invention there is provided
any of the foregoing methods for treating, or preventing cancer, using any of the forgoing
antibothes or fragments or a variant or a conjugate thereof, or a pharmaceutical composition
comprising same, specific to any of one of KRTCAP3 proteins, wherein the cancer is
including but not limited to ovarian cancer, lung cancer, breast cancer and/or colon cancer,
wherein the cancer may be non-metastatic, invasive or metastatic. According to at least
some embodiments of the present invention mere is provided any of the foregoing methods
for treating, or preventing cancer, using any of the forgoing antibothes or fragments or a
variant or a conjugate thereof, or a pharmaceutical composition comprising same, specific
to any of one of the FAM26F proteins, wherein the cancer is selected from but not limited
to ovarian cancer, breast cancer, prostate cancer, renal cancer, melaNOma, acute
lymphocytic leuKemia, chronic lymphocytic leuKemia, acute myelogeNOus leuKemia,
chronic myelogeNOus leuKemia, mμltiμle myeloma, HodgKin's lymphoma or non-
HodgKin's lymphoma, wherein the cancer may be non-metastatic, invasive or metastatic, as
well as for treating immune related conditions or disorders including but not limited to
inflammatory or autoimmune diseases, transμlant rejection and graft versus host disease.
According to at least some embodiments of the present invention there is provided
any of the foregoing methods for treating, or preventing cancer, and/or immune related
conditions or disorders, using any of the forgoing antibothes or fragments or a variant or a
conjugate thereof, or a pharmaceutical composition comprising same, specific to any of one
of the MGC52498 proteins, wherein the cancer is including but not limited to lymphoma,
especially non-HodgKin's Lymphoma, Mμltiμle Myeloma, leuKemia, especially T cell
leuKemia, and/or lung cancer.
According to at least some embodiments of the present invention there is provided
any of the foregoing methods for treating, or preventing cancer, and/or immune related
conditions or disorders, using any of the forgoing antibothes or fragments or a variant or a
conjugate thereof, or a pharmaceutical composition comprising same, specific to any of one
of the FAM70A proteins, wherein the cancer is including but not limited to Mμltiμle
Myeloma, Kidney cancer, lung cancer, liver cancer, and/or breast cancer.
According to at least some embodiments of the present invention there is provided
any of the foregoing methods for treating, or preventing cancer, using any of the forgoing
antibothes or fragments or a variant or a conjugate thereof, or a pharmaceutical composition
comprising same, specific to any of one of the TMEM154 proteins, or its secreted or soluble
form or ECD and/or portions or variants thereof, wherein me cancer is including but not
limited to lymphoma, especially non-HodgKin's Lymphoma, anti CD20 (i.e. Rituximab)
resistant lymphoma, Mμltiμle Myeloma, Kidney cancer, and/or pancreatic cancer, and/or
immune related conditions or disorders, especially SLE.
[0095] In another embodiment the invention includes a method of inducing or enhancing
an immune response, comprising administering to a patient in need thereof any of the
foregoing antibothes or fragments and detecting induction or enhancement of said immune
response.
[0096] In another embodiment the invention includes a method for potentiating a
secondary immune response to an antigen in a patient, which method comprises
administering effective amounts any of the foregoing antibothes or fragments. In another
embodiment the invention includes the foregoing method, wherein the antigen is preferably
a cancer antigen, a viral antigen or a bacterial antigen, and the patient has optionally
received treatment with an anticancer vaccine or a viral vaccine.
[0097] In another embodiment the invention includes an antibody specific to any one of
the KRTCAP3; FAM26F; MGC52498; FAM70A, or TMEM154 proteins, or a fragment or
variant or a homolog thereof that elicits apoptosis or lysis of cancer cells that express said
protein.
[0098] In another embodiment the invention includes any of the foregoing antibothes or
fragments, wherein said apoptosis or lysis activity involves CDC or ADCC activity of the
antibody.
[0099] According to at least some embodiments of the present invention there is provided
a method for inhibiting the growth of cells that express any one of the KRTCAP3;
FAM26F; MGC52498; FAM70A, or TMEM154 proteins in a subject, comprising:
administering to the subject any of the corresponding foregoing antibody or a fragment or a
variant conjugate thereof, or a pharmaceutical composition comprising same,
[00100] According to at least some embodiments the present invention provides the
foregoing antibothes and fragments, wherein the antibody is a chimeric, humanized,
primatized, or fμlly human antibody.
[00101] In another embodiment the invention includes any of the foregoing antibothes or
fragments, wherein the antigen binding site contains from about 3-7 contiguous or non-
contiguous amino acids, more typically at least 5 contiguous or non-contiguous amino
acids. These binding sites include conformational and non-conformational epitopes.
[00102] According to other embodiments of the present invention there is provided antibody
fragments and conjugates thereof including but not limited to Fab, F(ab')2, Fv or scFv
fragment.
[00103] It is also an embodiment of the invention to directly or indirectly attach the subject
antibothes and fragments to marKers and other effector moieties such as a detectable
marKer, or to an effector moiety.
[00104] In another embodiment the invention includes any of the foregoing antibothes or
fragments, wherein the effector moiety is selected from a drug, an enzyme (antibody-
directed enzyme prodrug therapy (ADEPT)), a toxin, a radionuclide, a fluorophore, a
therapeutic agent, or a chemotherapeutic agent.
[00105] In another embodiment the invention includes any of the foregoing antibothes or
fragments, wherein the detectable marKer is a radioisotope, a metal chelator, an enzyme, a
fluorescent compound, a bioluminescent compound or a chemiluminescent compound.
[00106] According to at least some embodiments of the present invention there are provided
compounds, including drugs which modplate (agonize or antagonize) at least one of the
KRTCAP3-related, FAM26F-related, MGC52498-related, FAM70A-related, or TMEM154-
related biological activity. Such drugs include by way of EXAMPLE small molecμles,
aptamers, peptides, antibothes and fragments that bind any of the polypeptides selected
from SEQ ID NOs:7, 8,10-13, 15-19, 25, 29-33, 35, 36, 42-64, 115-118,121, 127,132-135,
146-162, 186, 191-192, 196, 199, 200, as well as ribozymes or antisense or siRNAs which
target nucleic acid sequence or fragments or variants thereof, selected from any of SEQ ID
NOs:l-6, 9, 14, 20-24, 26-28, 38-41, 94, 97, 100, 103, 106, 109, 124, 125, 131, 193-195,
197, 198, 201. These molecμles may directly bind or modplate an activity elicited by any of
the KRTCAP3, FAM26F, MGC52498, FAM70A, and TMEM154 proteins or DNA/RNA or
portions or variants thereof or may indirectly modplate a at least one of the KRTCAP3-
related, FAM26F-related, MGC52498-reIated, FAM70A-related, or TMEM154-related
activity or binding of molecμles to any of the KRTCAP3, FAM26F, MGC52498, FAM70A,
and TMEM154, and portions and variants thereof such as modplating the binding of any of
the KRTCAP3, FAM26F, MGC52498, FAM70A, and TMEM154 to its corresponding
counter receptor or endogeNOus ligand, and can be useful for treatment or prevention of
cancer, immune related conditions, including but not limited to inflammatory and
autoimmune diseases, transμlant rejection and graft versus host disease, and/or for
blocKing or enhancing immune costimμlation mediated by the KRTCAP3, FAM26F,
MGC52498, FAM70A or TMEM154 polypeptide.
According to the present invention, each one of the following: TMEM154
ectodomain, or a fragment or a variant or a homologue or a conjugate thereof, or
pharmaceutical composition comprising same, and/or specific antibothes and fragments that
bind the KRTCAP3, FAM26F, MGC52498, FAM70A or TMEM154 polypeptides, or
pharmaceutical composition comprising same, or compounds including drugs such as small
molecμles, aptamers, peptides, which target KRTCAP3, FAM26F, MGC52498, FAM70A
or TMEM154 polypeptides, as well as ribozymes or antisense or siRNAs which target
KRTCAP3, FAM26F, MGC52498, FAM70A or TMEM154 nucleic acid sequence or
fragments or variants thereof, which are useful for treatment or prevention of cancer and/or
immune related conditions, optionally may be used in combination therapy with otiier
treatment methods KNOwn in the art selected from the group consisting of radiation therapy,
antibody therapy, chemotherapy, surgery, or in combination therapy with other biological
agents, conventional drugs, anti-cancer agents, immuNOsuppressants, cytotoxic drugs,
chemotherapeutic agents, or in combination with therapeutic agents targeting other
comμlement regμlatory proteins (CRPs),
[00107] According to at least some embodiments of the present invention there is provided
a use of any of the foregoing KRTCAP3, FAM26F, MGC52498, FAM70A, TMEM154
polypeptides, and/or polynucleotides, and/or antibothes, for diagNOsis of a disease, wherein
the disease is selected from cancer and/or immune related conditions.
[00108] As used herein, the term "diagNOsis of a disease" encompasses screening for a
disease, diagNOsing a diseases, detecting the presence or a severity of a disease, progNOsis of
a diseases, monitoring of disease progression and/or treatment efficacy and/or relapse of a
disease, disorder or condition, as well as selecting a therapy and/or a treatment for a disease,
optimization of a given therapy for a disease, monitoring the treatment of a disease, and/or
predicting the suitability of a therapy for specific patients or subpopμlations or determining
the appropriate dosing of a therapeutic product in patients or subpopμlations.
[00109] In at least some embodiments of the present invention, there is a use of any of the
foregoing KRTCAP3, FAM26F, MGC52498, FAM70A, TMEM154 polypeptides, and/or
polynucleotides, and/or antibothes, for diagNOsis of a cancer.
[00110] In at least some embodiments of the present invention, there is a use of any of the
foregoing KRTCAP3 polypeptides, and/or polynucleotides, and/or antibothes, for diagNOsis
of a cancer, selected from but not limited to ovarian cancer, colon cancer, lung cancer,
and/or breast cancer.
[00111] In at least some embodiments of the present invention, there is a use of any of the
foregoing FAM26F polypeptides, and/or polynucleotides, and/or antibothes, for diagNOsis
of a cancer, selected from but not limited to ovarian cancer, breast cancer, prostate cancer,
renal cancer, melaNOma, acute lymphocytic leuKemia, chronic lymphocytic leuKemia, acute
myelogeNOus leuKemia, chronic myelogeNOus leuKemia, mμltiμle myeloma, HodgKin's
lymphoma or non-HodgKin's lymphoma, as well as for diagNOsis of immune related
conditions.
[00112] In at least some embodiments of the present invention, there is a use of any of the
foregoing MGC52498 polypeptides, and/or polynucleotides, and/or antibothes, for
diagNOsis of a cancer, selected from but not limited to lymphoma, especially non-
HodgKin's Lymphoma, Mμltiμle Myeloma, leuKemia, especially T cell leuKemia, and/or
lung cancer, as well as for diagNOsis of immune related conditions.
[00113] In at least some embodiments of the present invention, there is a use of any of the
foregoing FAM70A polypeptides, and/or polynucleotides, and/or antibothes, for diagNOsis
of a cancer, selected from but not limited to Mμltiμle Myeloma, Kidney cancer, lung cancer,
liver cancer, and/or breast cancer, as well as for diagNOsis of immune related conditions.
[00114] In at least some embodiments of the present invention, there is a use of any of the
foregoing TMEM154 polypeptides, and/or polynucleotides, and/or antibothes, for diagNOsis
of a cancer, selected from but not limited to lymphoma, especially non-HodgKin' s
Lymphoma, anti CD20 (i.e. Rituximab) resistant lymphoma, Mμltiμle Myeloma, Kidney
cancer, and/or pancreatic cancer, as well as for diagNOsis of immune related conditions,
especially SLE,
[00115] In at least some embodiments the present invention provides diagNOstic methods
for diagNOsis of any of the foregoing diseases, disorders or conditions, comprising the
detection of a polypeptide or polynucleotide according at least some embodiments the
present invention. According to at least some embodiments the present invention the
expression, the level or relative changes in the expression or the level of the polypeptide or
polynucleotide herald the onset, severity, or progNOsis of an individual with regard to a
particμlar disease, disorder or condition. The detection may comprise detection of the
1 expression or level of a specific polypeptide or polynucleotide according at least some
embodiments the present invention, via any means KNOwn in the art, and as described
herein.
[00116] According to one embodiment, detecting the presence of the polypeptide or
polynucleotide is indicative of the presence of the disease and/or its severity and/or its
progress. According to another embodiment, a change in me expression and/or the level of
the polynucleotide or polypeptide compared to its expression and/or level in a healthy
subject or a samμle obtained therefrom is indicative of the presence of the disease and/or its
severity and/or its progress. According to a further embodiment, a change in the expression
and/or level of the polynucleotide or polypeptide compared to its level and/or expression in
said subject or in a samμle obtained therefrom at earlier stage is indicative of the progress of
the disease. According to still further embodiment, detecting the presence and/or relative
change in the expression and/or level of the polynucleotide or polypeptide is useful for
selecting a treatment and/or monitoring a treatment of the disease. According to still further
embodiment, detecting the presence and/or relative change in the expression and/or level of
the polynucleotide or polypeptide is useful for prediction of the suitability of a therapeutic
product for specific patients or subpopμlations or for determining the appropriate dosing of
a therapeutic product in patients or subpopμlations. According to still further embodiment,
the method comprising quantitatively and/or qualitatively determining or assessing
expression of the polypeptides and/or polynucleotides, whereby differences in expression
from an index samμle, or a samμle taKen from a subject prior to the initiation of the therapy,
or during the course of therapy, is indicative of the efficacy, or optimal activity of the
therapy.
[00117] Thus, according to at least some embodiments, the present invention provides
methods for diagNOsis of any of me foregoing diseases, disorders or conditions, comprising
detecting in a subject or in a samμle obtained from the subject any nucleic acid sequence
selected from the group consisting of SEQ ID NOs: 1-6, 9, 14, 20-24, 26-28, 38-41, 94, 97,
100, 103, 106, 109, 124, 125, 131, 193-195, 197, 198, 201 or fragments or variants or
homologs thereof.
[00118] In at least some embodiments the present invention provide a method for
diagNOsing of any of the foregoing diseases, disorders or conditions in a subject, comprising
(a) obtaining a samμle from the subject and (b) detecting in the samμle at least one
polynucleotide and/or polypeptide being a member of a SEQ ID NOs: 1-6, 9,14, 20-24, 26-
28, 38-41, 94, 97, 100, 103,106, 109, 124, 125, 131, 193-195, 197, 198, 201, or fragments
or variants or homologs thereof,
[00119] In at least some embodiments of the present invention, the methods are conducted
on a whole body.
[00120] In at least some embodiments of the present invention, the methods are conducted
with a samμle isolated from a subject having, predisposed to, or suspected of having the
disease, disorder or condition. In at least some embodiments of the present invention, the
samμle is a cell or tissue or a body fluid samμle.
[00121] In at least some embodiments, the subject invention merefore also relates to
diagNOstic metfiods and or assays for diagNOsis a disease optionally in a biological samμle
taKen from a subject (patient), which is optionally some type of body fluid or secretion
including but not limited to seminal μlasma, b100d, serum, urine, prostatic fluid, seminal
fluid, semen, the external secretions of the sKin, respiratory, intestinal, and genitourinary
tracts, tears, cerebrospinal fluid, sputum, saliva, milK, peritoneal fluid, μleural fluid, cyst
fluid, broncho alveolar lavage, lavage of tiie reproductive system and/or lavage of any other
part of the body or system in the body, and stool or a tissue samμle. The term may also
optionally encompass samμles of in vivo cell cμlture constituents. The samμle can
optionally be diluted with a suitable eluant before contacting the samμle to an antibody
and/or performing any ofher diagNOstic assay.
[00122] In at least some embodiments the present invention provides a method for diagNOsis
of a disease in a subject, comprising detecting in the subject or in a samμle obtained from
said subject at least one polypeptide selected from the group consisting of any of SEQ ID
NOs: 7, 8,10-13, 15-19, 25, 29-33, 35, 36, 42-64, 127,132-135, 146-162, 196, 199, 200, or
a homologue or a fragment thereof.
According to at least some embodiments of the present invention there are
provided diagNOstic methods that include the use of any of the foregoing antibothes
according to at least some embodiments of the present invention, by way of EXAMPLE in
immuNOhistochemical assay, radioimaging assays, in-vivo imaging, positron emission
tomography (PET), single photon emission computer tomography (SPECT), magnetic
resonance imaging (MRI), μltra Sound, Optical Imaging, Computer Tomography,
radioimmuNOassay (RIA), ELISA (enzyme-linKed immuNOsorbent assay), slot blot,
competitive binding assays, fluorimetric imaging assays, Western blot, FACS, and the liKe.
According to at least some embodiments, the present invention includes diagNOstic methods
and or assays which use any of the foregoing antibothes or fragments that specifically bind
any polypeptide having an amino acid sequence as set forth in any one of SEQ ID NOs: 7,
8, 10-13, 15-19, 25, 29-33, 35, 36, 42-64, 127, 132-135, 146-162, 115-118, 121, 186, 191,
192,196,199, 200, or a fragment or a homolog thereof.
[00123] According to some embodiments of the present invention there is provided
diagNOstic methods and/or assays for detecting the presence of at least one of the
polypeptides selected from a group consisting of SEQ ID NO: 7, 8, 10-13, 15-19, 25, 29-33,
35, 36, 42-64, 127, 132-135, 146-162, 115-118, 121, 186, 191, 192, 196, 199, 200, or a
fragment or a variant or a homolog thereof, in vitro or in vivo in a biological samμle or
subject, comprising contacting the samμle or the subject with an antibody having specificity
for at least one of polypeptides having an amino acid sequence selected from the group
consisting of SEQ ID NOs: 7, 8,10-13, 15-19, 25, 29-33, 35, 36, 42-64, 127, 132-135,146-
162, 115-118,121, 186,191,192, 196,199, 200, or a fragment or a variant or a homologue
thereof, or a combination thereof, and detecting the binding of any of the forgoing
polypeptides, in the samμle or in a subject to said antibody.
[00124] According to some embodiments of the present invention there are provided
methods for diagNOsis of a disease, comprising detecting the expression and or level in a
subject or in a samμle obtained from the subject, of at least one of KRTCAP3, FAM26F,
MGC52498, FAM70A, and TMEM154 polypeptides.
[00125] According to at least some embodiments of the present invention there are provided
diagNOstic methods that include the detection of at least one of KRTCAP3, FAM26F,
MGC52498, FAM70A, and TMEM154 polynucleotides, selected from the group consisting
of SEQ ID NOs: 1-6, 9, 14, 20-24, 26-28, 38-41, 94, 97,100, 103, 106, 109, 124, 125, 131,
193-195, 197, 198, 201, or a fragment or a variant or a homolog thereof, by emμloying a
NAT-based techNOlogy.
[00126] In at least some embodiments of the present invention, the NAT-based assay is
selected from the group consisting of a PCR, Real-Time PCR, LCR, Self-Sustained
Synthetic Reaction, Q-Beta RepUcase, Cycling Probe Reaction, Branched DNA, RFLP
analysis, DGGE/TGGE, Single-Strand Conformation Polymorphism, Dideoxy
Fingerprinting, Microarrays, Fluorescence In Situ Hybridization or Comparative GeNOmic
Hybridization.
[00127] In another embodiment the invention relates to any isolated polynucleotide,
comprising an amμlicon having a nucleic acid sequence selected from the group consisting
of SEQ ID NOs:94, 97, 100, 103, 106, 109, 124, 171, or a segment having a nucleic acid
sequence set forth in SEQ ID NOs: 193-195, 197, 199, 201,, or fragments or
polynucleotides homologous thereto.
[00128] In another embodiment the invention relates to any primer pair, comprising a pair
of isolated oligonucleotides capable of amμlifying the foregoing amμlicon or segment.
[00129] In another embodiment the invention relates to the primer pair, comprising a pair of
isolated oligonucleotides having a sequence selected from the group consisting of SEQ ID
NOs: 92-93, 95-96, 98-99, 101-102, 104-105, 107-108, 122-123, 169-170; 163-168, 172,
173, 176-181,187-188.
[00130] According to at least some embodiments of the present invention, detecting any of
the forgoing KRTCAP3, FAM26F, MGC52498, FAM70A, and TMEM154 polynucleotides
comprises emμloying a primer pair, comprising a pair of isolated oligonucleotides capable
of specifically hybridizing to at least a portion of a polynucleotide having a nucleic acid
sequence as set forth in SEQ ID NOs: 1-6, 9,14, 20-24, 26-28, 38-41, 94, 97,100,103,106,
109,124,125,131,171, 193-195,197, 199, 201, or polynucleotides homologous thereto.
[00131] According to at least some embodiments of the present invention the detection is
performed using an oligonucleotide pair capable of hybridizing to at least a portion of a
nucleic acid sequence at least 85%, 90%, 95%, 96%, 97%, 98%, 99% homologous to the
nucleic acid sequence set forth in SEQ ID NO: 1-6, 9, 14, 20-24, 26-28, 38-41, 94, 97, 100,
103,106,109,124,125,131, 171,193-195,197,199, 201.
[00132] According to at least some embodiments of the present invention, detecting any of
the forgoing KRTCAP3, FAM26F, MGC52498, FAM70A, and TMEM154 polynucleotides
according to at least some embodiments of the present invention, comprises emμloying a
primer pair, comprising a pair of isolated oligonucleotides as set forth in SEQ ID NOs: 92-
93, 95-96, 98-99, 101-102, 104-105, 107-108, 122-123, 169-170, 163-168, 172, 173, 176-
181,187-188.
[00133] In at least some embodiments the present invention provides a diagNOstic Kit for
diagNOsis of a disease, comprising marKers and reagents for detecting qualitative and/or
quantitative changes in the expression of a polypeptide or a polynucleotide according to at
least some embodiments of the present invention.
[00134] In at least some embodiments of the present invention, the Kit comprises marKers
and reagents for detecting the changes by emμloying a NAT-based techNOlogy.
[00135] In at least some embodiments of the present invention, the Kit comprises at least
one nucleotide probe or primer. In at least some embodiments of the present invention, the
Kit comprises at least one primer pair capable of selectively hybridizing to a nucleic acid
sequence according to the teaching of the present invention. In at least some embodiments
of the present invention, the Kit comprises at least one oligonucleotide capable of selectively
hybridizing to a nucleic acid sequence according to the teaching of the present invention.
[00136] In at least some embodiments of the present invention, the Kit comprises an
antibody capable of recognizing or interacting with a polypeptide or protein according to at
least some embodiments of the present invention. In at least some embodiments of the
present invention, the Kit further comprises at least one reagent for performing an
immuNOhistochemical assay, radioimagjng assays, in-vivo imaging, positron emission
tomography (PET), single photon emission computer tomography (SPECT), magnetic
resonance imaging (MRI), μltra Sound, Optical Imaging, Computer Tomography,
radioimmuNOassay (RIA), ELISA, slot blot, competitive binding assays, fluorimetric
imaging assays, Western blot, FACS, and the liKe.
[00137] All nucleic acid sequences and/or amino acid sequences, according to at least some
embodiments of the invention, relate to their isolated form.
[00138] It shoμld be noted that oligonucleotide and polynucleotide, or peptide, polypeptide
and protein, may optionally be used interchangeably.
[00139] BRIEF DESCRIPTION OF THE FIGURES
[00140] Figure 1 shows a scatter μlot, demonstrating the expression of KRTCAP3
transcripts, that encode the KRTCAP3 proteins, on a virtual panel of all tissues and
conditions using MED discovery engine, demonstrating overexpression of KRTCAP3
transcripts in lung cancer compared to normal lung samμles.
[00141] Figures 2A and 2B present a histogram showing over expression of the
KRTCAP3 (KeratiNOcyte associated protein 3) W93943 transcripts which are detectable by
amμlicon as depicted in sequence name W93943_seg7-10F1R1 (SEQ ID NO: 94) in
cancerous ovarian samμles relative to the normal samμles (Figure 2B is a continuation of
Figure 2A).
[00142] Figures 3A and 3B present a histogram showing over expression of the
KRTCAP3 (KeratiNOcyte associated protein 3) W93943 transcripts which are detectable by
amμlicon as depicted in sequence name W93943_seg7-10F1R1 (SEQ ID NO: 94) in
different normal tissues (Figure 3B is a continuation of Figure 3A).
[00143] Figures 4A and 4B present a histogram showing over expression of the
KRTCAP3 transcripts detectable by or according to W93943_seg3j4-6F2R1 amμlicon
(SEQ ID NO:171) in cancerous Ovary samμles relative to the normal samμles (Figure 4B is
a continuation of Figure 4A).
[00144] Figures 5A and 5B present a histogram showing over expression of the
KRTCAP3 transcripts detectable by or according to W93943_seg3j4-6F2R1 amμlicon
(SEQ ID NO:171) in different normal tissues (Figure 5B is a continuation of Figure 5A).
[00145] Figures 6A-6C show the DNA sequences of the KRTCAP3 fμll length, fused or
non-fused to EGFP. Gene specific sequence corresponding to the target's fμll length
sequence is marKed in bold faced, EGFP sequence is in italics, and intermediate linKer
regions are unbold. Figure 6A represents the DNA sequence of KRTCAP3_EGFP (SEQ ID
NO:110); Figure 6B represents the DNA sequence of EGFPJCRTCAP3 (SEQ ID NO:l 11);
Figure 6C represents the DNA sequence of KRTCAP3 (SEQ ID NO:112).
[00146] Figures 7A and 7B show the amino acid sequences of the
KRTCAP3_ORF_fused or non-fused to EGFP. Gene specific sequence corresponding to the
fμll length sequence of the protein is marKed in bold faced, EGFP sequence is in italics, and
intermediate linKer regions are unbold. Figure 7A represents the amino acid sequence of
KRTCAP3_EGFP protein (SEQ ID NO: 113) (484aa); Figure 7B represents the amino acid
sequence of EGFPJCRTCAP3 protein (SEQ ID NO:114) (478aa); Figure 7C represents the
amino acid sequence of KRTCAP3 protein (SEQ ID NO:7) (240aa).
[00147] Figures 8A and 8B demonstrate the localization of the KRTCAP3 proteins of
invention to cell membrane. Figure 8A demonstrates by green fluorescence of EGFP that
the EGFP_KRTCAP3_P2 (SEQ ID NO: 114) fused protein localizes to the cell membrane
upon expression in HEK 293T cells. The image was obtained using the 40x objective of the
confocal microscope. Figure 8B demonstrates by red fluorescence of anti-GFP antibody that
the EGFP_KRTCAP3_P2 (SEQ ID NO: 114) fused protein localizes to the cell membrane
upon expression in HEK 293T cells. The image was obtained using the 40x objective of the
confocal microscope.
[00148] Figures 9A and 9B demonstrate the orientation of EGFP_KRTCAP3_P2 protein
within the cell. Figure 9A demonstrates by green fluorescence of EGFP that the
EGFP_KRTCAP3_P2 (SEQ ID NO: 114) fused protein localizes to the cell membrane of
non permebealized EGFP-KRTCAP3 HEK 293T transfected cells. Figure 9B demonstrates
the immuNOstaining with anti GFP of non permebealized EGFP-KRTCAP3 HEK 293T
transfected cells immuNOstained. The absence of anti-GFP red fluorescence (as compared
with Figure 8B) indicates that the EGFP_KRTCAP3_P2 (SEQ ID NO:114) fused protein is
positioned in the μlasma membrane with its amino terminus facing the cytosol. The images
were obtained using the 40x objective of the confocal microscope.
[00149] Figures 10A-10D demonstrate Western blot analysis using KRTCAP3 antibothes
on HEK 293T transfected cell lysates. Figure 10A-10B show Western blot analysis using
KRT223 antibothes (corresponding to rabbits marKed RB5257 and RB5258), on
KRTCAP3-HEK293T cell lysates (lane 1) and PIRESpuro3-HEK293T cell lystaes (lane 2).
Figure 10C-D show Western blot analysis using KRT143 antibothes (corresponding to
rabbits marKed RB5259 and RB5261), on KRTCAP3-HEK293T cell lysates (lane 1) and
pIRESpuro3-HEK293T cell lystaes (lane 2).
[00150] Figures 11A-11D demonstrate immuNOstaining of HEK-293T cells using
purified KRTCAP3 antibothes. Figures 11A-11B present imunNOstaining using KRT143
antibothes on KRTCAP3 HEK-293T transfected cells (Figure 11A) or pIRESpuro3 HEK-
293T transfected cells (Figure 11B). KRT143 antibothes shows a specific signal in the
KRTCAP3 transfected cells which is absent in the pIRESpuro3 transfected cells. Figures
11C-11D present imunNOstaining using KRT223 antibothes on KRTCAP3 HEK-293T
transfected cells (Figure 11C) or pIRESpuro3 HEK-293T transfected cells (Figure 11D).
KRT223 antibothes shows a specific signal in the KRTCAP3 transfected cells which is
absent in the pIRESpuro3 transfected cells. The image was obtained using the 40x objective
of the confocal microscope.
[00151] Figure 12 demonstrates intense immuNOhistochemical staining of an ovary
carcinoma samμle obtained from a 52- year old female, using Antibody KRT223. The signal
was quantified using a 0-4 scale, and was given the signal intensity 2.
[00152] Figure 13 demonstrates prominent immuNOhistochemical staining of an
adenocarcinoma samμle from a metastatic gastrointestinal tumor obtained from a 31-year-
old female, using Antibody KRT223. The signal was quantified using a 0-4 scale, and was
given me signal intensity 3.
[00153] Figure 14 shows a scatter μlot, demonstrating the expression of FAM26F
transcripts that encode the FAM26F proteins, on a virtual panel of all tissues and conditions
using MED discovery engine, demonstrating overexpression of FAM26F transcripts in
breast cancer compared to normal breast samμles.
[00154] Figure 15 shows a scatter μlot, demonstrating the expression of FAM26F
transcripts that encode the FAM26F proteins, on a virtual panel of all tissues and conditions
using MED discovery engine, demonstrating overexpression of FAM26F transcripts in
ovarian cancer compared to normal ovarian samμles.
[00155] Figures 16A-16H show a scatter μlot, demonstrating the overall expression of
FAM26F transcripts in various diseased, normal and cancer tissues, using MED discovery
engine. Figures 16A-16H are contiguous and in a sequential order.
[00156] Figures 17A-17C show a histogram representing the overexpression of FAM26F
transcripts detectable by FAM26F Fl/Rl primers (SEQ ID NOs: 95 and 96) in Kidney
cancer, liver cancer, lung cancer, NHL lymphomas and melaNOma. Figures 17 A-17C are
contiguous and in a sequential order.
[00157] Figures 18A and 18B show a histogram showing the expression of FAM26F
T82906 transcripts which are detectable by amμlicon as depicted in sequence name
T82906_seg5-10F7R5 (SEQ ID NO:124) in different normal tissues (Figure 18B is a
continuation of Figure 18A),
[00158] Figures 19A and 19B show a histogram showing the expression of FAM26F
T82906 transcripts which are detectable by amμlicon as depicted in sequence name
T82906_seg5-10F7R5 (SEQ ID NO:124) in b100d-specific panel (Figure 19B is a
continuation of Figure 19A).
[00159] Figure 20 presents the DNA sequence of the FAM26_P4_FLAG (SEQ ID NO:
174). The FLAG sequence is in underlined.
[00160] Figure 21 presents the amino acid sequence of FAM26_P4_FLAG (SEQ ID
NO:175). The FLAG sequence is in underlined.
[00161] Figures 22A and 22B demonstrate the cellμlar localization of FAM26_P4
protein.
[00162] Figures 23A and 23B demonstrate a specific cell staining localized to cell
membrane observed using anti FAM26F antibothes on FAM26F transfected cells (Figure
23A); as opposed to NO staining observed using same antibothes on pIRESpuro3 HEK-293T
transfected cells (Figure 23B).
[00163] Figure 24 shows a scatter μlot, demonstrating the expression of MGC52498
transcripts that encode the MGC52498 proteins, on a virtual panel of all tissues and
conditions using MED discovery engine, demonstrating overexpression of MGC52498
transcripts in lung cancer compared to normal lung samμles.
[00164] Figures 25A and 25B show a scatter μlot, demonstrating the expression of
MGC52498 transcripts, that encode the MGC52498 proteins, on a virtual panel of all tissues
and conditions using MED discovery engine, demonstrating overexpression of MGC52498
transcripts in various leuKemia samμles compared to normal b100d samμles (Figure 25B is a
continuation of Figure 25A).
[00165] Figures 26A and 26B present a histogram showing expression of hypothetical
protein MGC52498 AA213820 transcripts which are detectable by amμlicon as depicted in
sequence name AA213820_seg8-llF2R2 (SEQ ID NO: 109) in different normal tissues
(Figure 26B is a continuation of Figure 26A).
[00166] Figures 27A and 27B present a histogram showing expression of hypothetical
protein MGC52498 AA213820 transcripts which are detectable by amμlicon as depicted in
sequence name AA213820_seg8-l 1F2R2 (SEQ ID NO: 109) in b100d specific panel (Figure
27B is a continuation of Figure 27A).
[00167] Figures 28A and 28B represent the DNA sequence of FLAG_MGC_T1_P4 -
(SEQ ID NO:182) and MGC_T1_P4_FLAG (SEQ ID NO:183), respectively; FLAG
sequence is underlined.
[00168] Figures 29A and 29B represent the amino acid sequence of FLAG_MGC_T1_P4
protein (SEQ ID NO:184) and MGC_T1_P4_FLAG (SEQ ID NO:185), respectively; FLAG
sequence is underlined.
[00169] Figures 30A and 30B show a scatter μlot, demonstrating the expression of
FAM70A transcripts that encode the FAM70A proteins, on a virtual panel of all tissues and
conditions using MED discovery engine, demonstrating overexpression of FAM70A
transcripts in lung cancer samμles compared to normal lung samμles (Figure 30B is a
continuation of Figure 30A).
[00170] Figure 31 shows a scatter μlot, demonstrating the expression of FAM70A
transcripts that encode the FAM70A proteins, on a virtual panel of all tissues and conditions
using MED discovery engine, demonstrating overexpression of FAM70A transcripts in liver
cancer samμles compared to normal liver samμles.
[00171] Figure 32 shows a scatter μlot, demonstrating the expression of FAM70A
transcripts that encode the FAM70A proteins, on a virtual panel of all tissues and conditions
using MED discovery engine, demonstrating overexpression of FAM70A transcripts in
breast cancer samμles compared to normal breast samμles.
[00172] Figures 33A and 33B show a scatter μlot, demonstrating the expression of
FAM70A transcripts that encode the FAM70A proteins, on a virtual panel of all tissues and
conditions using MED discovery engine, demonstrating overexpression of FAM70A
transcripts in Kidney cancer samμles compared to normal Kidney samμles (Figure 33B is a
continuation of Figure 33A).
[00173] Figures 34A and 34B show a histogram showing the expression of hypothetical
protein FLJ20716-FAM70A F10649 transcripts which are detectable by amμlicon as
depicted in sequence name F10649_segl0-12F1R1 (SEQ ID NO: 103) in different normal
tissues (Figure 34B is a continuation of Figure 34A).
[00174] Figures 35A and 35B show a histogram showing the expression of hypothetical
protein FLJ20716-FAM70A F10649 transcripts which are detectable by amμlicon as
depicted in sequence name F10649_segl0-12F1R1 (SEQ ID NO: 103) in b100d specific
panel (Figure 35B is a continuation of Figure 35A).
[00175] Figure 36 represents the DNA sequence of FAM70_T1_P5_FLAG (SEQ ID NO:
119). Gene specific sequence corresponding to the target's fμll length sequence is marKed in
bold faced, FLAG sequence is unbold.
[00176] Figure 37 represents the amino acid sequence of FAM70A_T1_P5_FLAG
protein (SEQ ID NO: 120); gene specific sequence corresponding to the fμll length sequence
of the protein is marKed in bold faced, FLAG sequence is unbold.
[00177] Figures 38A-38D demonstrate that the FAM70A_T1_P5_FLAG (SEQ ID
NO:120) fused protein localizes to cell membrane upon expression in HEK 293T cells. The
image was obtained using the 40x objective of the confocal microscope.
Figures 39A and 39B present the specificity of antibothes raised against selected
peptide of FAM70A. Figures 39A and 39B present the resμlts of immuNO-precipitation
followed by western blot analysis using purified serum from rabbits #5663 and #5664,
respectively, and FAM70 HEK-293T stable transfectants cell lysates as well as HEK-293T
nontrasfected cell lysates. Lane 1 represents HEK-293T transfected cell lysates followed by
IP; lane 2 represents HEK-293T non trasfected cell lysates followed by IP; lanes 3 and 4
represent the whole cell lysate of HEK-293T transfected cells.
[00178] Figures 40A-40F present immuNOstaning of various cells using purified anti
FAM70 antibothes (rabbits #5663). Figures 40A and 40B present the resμlts on HEK-293T
transfected cells, using 1:200 or 1:1000 dillutions, respectively. Figures 40C and 40D
present the resμlts on HEK-293T non transfected cells using 1:200 or 1:1000 dillutions,
respectively. Figure 40E presents the resμlts on CHO-K1 (ATCC, CCL-61) cells and Figure
40F presents the resμlts on MC/CAR (ATCC, CRL-8083) cells. Similar resμlts were
obtained using rabbit#5664 (data not shown).
Figures 41A-41D demonstrate red fluorescence signal of 293T transfected cells
followed by incubation with 0, 5tim.es, 25times, 50 times FAM70 peptide, respectively.
Figures 41E-41H demonstrate red fluorescence signal of 293T non transfected
cells followed by incubation with 0, 5times,25times, 50 times FAM70 peptide, respectively.
[00179] Figure 42 shows a scatter μlot, demonstrating the expression of TMEM154
transcripts that encode the TMEM154 proteins, on a virtual panel of all tissues and
conditions using MED discovery engine, demonstrating overexpression of TMEM154
transcripts in Kidney cancer samμles compared to normal Kidney samμles.
[00180] Figures 43A and 43B demonstrate the expression of TMEM154 transcripts that
encode the TMEM154 proteins, on a virtual panel of all tissues and conditions using MED
discovery engine. Figure 43 shows a scatter μlot, demonstrating overexpression of
TMEM154 transcripts in pancreas cancer samμles compared to normal pancreas samμles.
Figure 43B presents Kaμlan-Meier survival curves of Rituximab treated DLBCL in
corelation to TMEM154 expression. In Figure 43B the time scale is shown in years; solid
line represents high TMEM154 expression; fragmented line represents low TMEM154
expression.
{00181] Figures 44A and 44B show a histogram showing the expression of hypothetical
protein FLJ32028, TMEM154 W38346 transcripts which are detectable by amμlicon as
depicted in sequence name W38346_seg6-20F1R1 (SEQ ID NO: 106) in different normal
tissues (Figure 44B is a continuation of Figure 44A).
[00182] Figures 45A and 45B show a histogram showing the expression of hypothetical
protein FLJ32028, TMEM154 W38346 transcripts which are detectable by amμlicon as
depicted in sequence name W38346_seg6-20F1R1 (SEQ ID NO: 106) in b100d specific
panel (Figure 54B is a continuation of Figure 45A).
[00183] Figure 46 presents the DNA sequence of the TMEM154_T0_FLAG (SEQ ID
NO:189); FLAG sequence is in underlined.
[00184] Figure 47 presents the amino acid sequence of TMEM154_P3_FLAG {SEQ ID
NO:190); FLAG sequence is in underlined,
[00185] Figures 48A and 48B present the localization resμlts for TMEM154_P3,
[00186] Figures 49A and 49B present the specific cell staining localized to the cell
membrane, observed using purified TM21 antibothes on TMEM154 transfected cells.
Figure 49A and 49B present the resμlts obtained using TM21 antibothes purified from
rabbit #6285 and rabbit #6286, respectively.
[00187] Figures 50A and 50B present the specific cell staining localized to the cell
membrane, observed using purified TM101 antibothes on TMEM154 transfected cells.
Figures 50A and 50B present the resμlts obtained using TM101 antibothes purified from
rabbit #6248 and rabbit #6249, respectively.
[00188] Figures 51A-51C present the resμlts of cell staining observed using purified
TM21 and TM101 antibothes on the negative control pIRESpuro3 HEK-293T transfected
cells. Figures 51A and 51B present the resμlts obtained using TM21 antibothes purified
from rabbit #6285 and rabbit #6286, respectively. Figure 51C presents the resμlts obtained
using TM101 antibothes purified from rabbit #6249.
[00189] Figures 52A-52C present specific cell staining localized to the cell membrane,
observed using purified TM21 and TM101 antibothes on three different cell lines: Figures
52A-1 -- 52A-4 present the resμlts on CESS (ATCC cat NO TTB-190) calls; Figures 52B-1 -
52B-3 present the resμlts on Ramos (ATCC cat NO CRL-1923) cells; and Figures 52C-1 -
52C-3 present the resμlts on Daudi (ATCC cat NO CCL-213) cells. Figures 52A-1 and 52A-
2 present the resμlts obtained using TM21 antibothes purified from rabbit #6285 and rabbit
#6286, respectively. Figures 52A-3 and 52A-4 present the resμlts obtained using TM101
antibothes purified from rabbit #6248 and rabbit #6249, respectively. Figures 52B-1 and
52B-2 present the resμlts obtained using TM21 antibothes purified from rabbit #6285 and
rabbit #6286, respectively. Figure 52B-3 presents the resμlts obtained using TM101
antibothes purified from rabbit #6248. Figures 52C-1 and 52C-2 present the resμlts obtained
using TM21 antibothes purified from rabbit #6285 and rabbit #6286, respectively. Figure
52C-3 presents the resμlts obtained using TM101 antibothes purified from rabbit #6248.
[00190] DETAILED DESCRIPTION OF THE INVENTION
[00191] The present invention, in some embodiments, relates to any one of the
polypeptides referred to as KRTCAP3, FAM26F, MGC52498, FAM70A, TMEM154
polypeptides, and its corresponding nucleic acid sequence, and fragments and variants and
homologs thereof, and the use thereof as a therapeutic and/or diagNOstic target. According to
at least some embodiments, there are provided uses of these polypeptides and discrete
portions thereof as a drug target for therapeutic small molecμles, peptides, antibothes,
antisense RNAs, siRNAs, ribozymes, and the liKe. According to at least some embodiments,
the invention relates to diagNOstic and therapeutic polyclonal and monoclonal antibothes
and fragments thereof that specifically bind KRTCAP3, FAM26F, MGC52498, FAM70A,
TMEM154 polypeptides and portions and variants thereof, especially those that target the
extracellular domains or portions or variants thereof, or the unique bridge, edge, tail or head
portion, or fragment or variant thereof. According to at least some embodiments, the
invention provides human or chimeric monoclonal antibothes and fragments thereof and
anti-idiotypic antibothes, that bind specifically to any of the amino acid sequences as set
forth in SEQ ID NOs: 7, 8,10-13,15-19, 25, 29-33, 35, 36, 42-64, 115-118,121,127, 132-
135, 146-162, 186, 191-192, 196, 199, 200, and variants and fragments and homologs
thereof.
[00192] According to at least some embodiments of the invention, the antibothes are
derived from particμlar heavy and light chain germline sequences and/or comprise particμlar
structural features such as CDR regions comprising particμlar amino acid sequences. The
invention provides isolated antibothes, methods of maKing such antibothes,
immuNOconjugates and bispecific molecμles comprising such antibothes and pharmaceutical
and diagNOstic compositions containing the antibothes, immuNOconjugates or bispecific
molecμles.
According to at least some embodiments of the invention, the specific antibothes may be
used for the treatment and/or diagNOsis of cancer and/or immune related conditions, as
described herein.
[00193] In order that the present invention may be more readily understood, certain terms
are first defined. Additional definitions are set forth throughout the detailed description,
[00194] The term "KRTCAP3 protein", as used herein, includes any protein encoded by
a KRTCAP3 gene product, including the KNOwn or "wild type" protein, any sμlice variants
thereof, any other variants thereof, or any fragments thereof (including but not limited to
any extracellular portions thereof).
[00195] The term "KRTCAP3 polypeptide" refers to a polypeptide encoded by any one
of the nucleic acid sequences set forth in any one of SEQ ID NOs:l-6, 9, 94, 171, 193-195,
and fragments and homologous thereof, especially those possessing at least 80, 85, 90, 95,
96, 97, 98, 99% sequence identity therewith. These nucleic acid sequences are referred to
herein as "KRTCAP3 polynucleotide". The term also refers to any one of the polypeptides
set forth in any one of SEQ ID NOs:7, 8, 10-13; extracellular portions thereof, set forth
in any one of SEQ ID NOs:47-51; unique bridge, edge portion, tail or head portion thereof,
set forth in any one of SEQ ID NOs: 146-148; protein fragments selected from any of the
isolated polypeptides, that are used for rabbit, mouse or other mammal immunization and
specific antibothes production, set forth in any one of SEQ ID NOs:115, 116; and fragments
and homologous thereof, especially those possessing at least 80, 85, 90, 95, 96, 97, 98, 99%
sequence identity therewith. The term "KRTCAP3 polynucleotide" or "KRTCAP3
polypeptide", as used herein, further refers to any one of the foregoing polynucleotides and
polypeptides, respectively, that are differentially expressed e.g., in cancer, including but not
limited to lung cancer, breast cancer, colon cancer and ovarian cancer, wherein the cancer
may be non-metastatic, invasive or metastatic.
42
[00196] The term "KRTCAP3 variants)", as used herein, refers to a protein encoded by
any one of the nucleic acid sequences set forth in SEQ ID NOs: 2, 3,4, 6, 9, 94,171,193-
195, and fragments and homologous thereof, especially those possessing at least 80, 85,90,
95, 96, 97, 98, 99% sequence identity therewith. The term "KRTCAP3 novel variant(s)", as
used herein, further refers to any one of the proteins set forth in any one of SEQ ID NOsrlO,
11,13, 47-51,146-148, and fragments and homologous thereof, especially those possessing
at least 80, 85, 90, 95, 96, 97, 98, 99% sequence identity therewith.
[00197] The term "KRTCAP3 proteins" as used herein encompass any protein within the
groups of "KRTCAP3 polypeptide", "KRTCAP3 variant(s)" and "KRTCAP3 novel
variant(s)".
[00198] The term "FAM26F protein", as used herein, includes any protein encoded by a
FAM26F gene product, including the KNOwn or "wild type" protein, any sμlice variants
thereof, any other variants thereof, or any fragments thereof (including but not limited to
any extracellular portions thereof).
[00199] The term "FAM26F polypeptide", as used herein, refers to a polypeptide
encoded by any one of the nucleic acid sequences set forth in any one of SEQ ID NOs:14,
125, 97, 124, and fragments and homologous thereof, especially those possessing at least
80, 85, 90, 95, 96, 97, 98, 99% sequence identity therewith. These nucleic acid sequences
are referred to herein as "FAM26F polynucleotides". The term also refers to any
polypeptide set forth in any one of SEQ ID NOs:15-18; extracellular portions thereof, set
forth in any one of SEQ ID NOs: 52, 53; unique bridge, edge portion, tail or head portion
thereof, set forth in any one of SEQ ID NOs:127, 149; protein fragments selected from any
of the isolated polypeptides, that are used for rabbit, mouse or other mammal immunization
and specific antibothes production, set forth in any one of SEQ ID NOs: 117, 118; and
fragments and homologous thereof, especially those possessing at least 80, 85, 90, 95, 96,
97, 98, 99% sequence identity therewith. The term "FAM26F polynucleotide" or "FAM26F
polypeptide", as used herein, further refers to any of the foregoing polynucleotides and
polypeptides, respectively, that are differentially expressed e.g., in cancer, including but not
limited to ovarian cancer, breast cancer, prostate cancer, renal cancer, melaNOma, acute
lymphocytic leuKemia, chronic lymphocytic leuKemia, acute myelogeNOus leuKemia,
chronic myelogeNOus leuKemia, mμltiμle myeloma, HodgKin's lymphoma or non-
HodgKin's lymphoma, wherein the cancer may be non-metastatic, invasive or metastatic as
well as non-malignant disorders such as immune related conditions or disorders including
but not limited to inflammatory or autoimmune diseases, transμlant rejection and graft
versus host disease.
[00200] The term "MGC52498 protein", as used herein, includes any protein encoded by
a MGC52498 gene product, including the KNOwn or "wild type" protein, any sμlice variants
thereof, any other variants thereof, or any fragments thereof (including but not limited to
any extracellular portions thereof).
[00201] The term "MGC52498 polypeptide", as used herein, refers to a polypeptide
encoded by any one of the nucleic acid sequences set forth in any one of SEQ ID NOs:20,
27, 109, 131, 201, and fragments and homologous thereof, especially those possessing at
least 80, 85, 90, 95, 96, 97, 98, 99% sequence identity therewith. These nucleic acid
sequences are referred to herein as "KRTCAP3 polynucleotides". The term also refers to
any one of the polypeptides set forth in any one of SEQ ID NOs:19, 132-135; extracellular
portions thereof, set forth in any one of SEQ ID NOs:60-62, unique bridge, edge portion,
tail or head portion thereof, set forth in any one of SEQ ID NOs:25, 150-154, 200, and
fragments and homologous thereof, especially those possessing at least 80, 85, 90, 95, 96,
97, 98, 99% sequence identity therewith. The term "MGC52498 polynucleotide" or
"MGC52498 polypeptide", as used herein, further refers to any of the foregoing
polynucleotides and polypeptides, respectively, that are differentially expressed e.g., in
cancer, including but not limited to lung cancer, mμltiμle myeloma, lymphomas, especially
non-HodgKins lymphoma, leuKemia, especially T cell leuKemia, wherein the cancer may be
non-metastatic, invasive or metastatic as well as non-malignant disorders such as immune
related conditions or disorders including but not limited to inflammatory or autoimmune
diseases, transμlant rejection and graft versus host disease.
[00202] The term "MGC52498 variant(s)", as used herein, refers to a protein encoded by
any one of the nucleic acid sequences set forth in SEQ ID NOs:20, 27, 109, 201, and
fragments and homologous thereof, especially those possessing at least 80, 85, 90, 95, 96,
97, 98, 99% sequence identity therewith. The term "MGC52498 novel variant(s)", as used
herein, further refers to anyone of the proteins set forth in any one of SEQ ID NOs:19, 25,
60-62,150-154,200, and fragments and homologous thereof, especially those possessing at
least 80, 85, 90, 95, 96, 97, 98, 99% sequence identity therewith.
[00203] The term "MGC52498 proteins" as used herein encompass any protein within
the groups of "MGC52498 polypeptides", "MGC52498 variant(s)" and "MGC52498 novel
variant(s)".
[00204] The term "FAM70A protein", as used herein, includes any protein encoded by a
FAM70A gene product, including the KNOwn or "wild type" protein, any sμlice variants
thereof, any other variants thereof, or any fragments thereof (including but not limited to
any extracellular portions thereof).
[00205] The term "FAM70A polypeptide", as used herein, refers to a polypeptide
encoded by any one of the nucleic acid sequences set forth in any one of SEQ ID NOs:21,
22, 24, 26, 28, 103, 197, 198, and fragments and homologous thereof, especially those
possessing at least 80, 85, 90, 95, 96, 97, 98, 99% sequence identity therewith. These
nucleic acid sequences are referred to herein as "FAM70A polynucleotides". The term also
refers to any one of the polypeptides as set forth in any one of SEQ ID NOs:29-33, 35, 36;
extracellular portions thereof, set forth in any one of SEQ ID NOs:54-59; unique bridge,
edge portion, tail or head portion thereof, set forth in any one of SEQ ID NOs: 155-160,
196, 199; protein fragments selected from any of the isolated polypeptides, used for rabbit
immunization and specific antibothes production, set forth in any one of SEQ ED NOs;121,
186,and fragments and homologous thereof, especially those possessing at least 80, 85, 90,
95, 96, 97, 98, 99% sequence identity therewith. The term "FAM70A polynucleotide" or
"FAM70A polypeptide", as used herein, further refers to any one of the foregoing
polynucleotides and polypeptides, respectively, that are differentially expressed e.g., in
cancer, including but not limited to lung cancer, liver cancer, breast cancer, Kidney cancer,
mμltiμle myeloma, and wherein the cancer may be non-metastatic, invasive or metastatic as
well as non-malignant disorders such as immune related conditions or disorders including
but not limited to inflammatory or autoimmune diseases, transμlant rejection and graft
versus host disease.
[00206] The term "FAM70A variant(s)", as used herein, refers to a protein encoded by
any one of the nucleic acid sequences set forth in SEQ ID NOs:26, 103, 197, 198, and
fragments and homologous thereof, especially those possessing at least 80, 85, 90, 95, 96,
97, 98, 99% sequence identity therewith. The term "FAM70A novel variant(s)", as used
herein, further refers to any one of the proteins set forth in any one of SEQ ID NOs:36, 54-
59,155-160,196, 199, and fragments and homologous thereof, especially those possessing
at least 80, 85, 90, 95, 96, 97, 98, 99% sequence identity therewith.
[00207] The term "FAM70A proteins" as used herein encompass any protein within the
groups of "FAM70A polypeptides", "FAM70A variant(s)", and "FAM70A novel
variant(s)",
[00208] The term 'TMEM154 protein", as used herein, includes any protein encoded by
a TMEM154 gene product, including the KNOwn or "wild type" protein, any sμlice variants
thereof, any other variants thereof, or any fragments thereof {including but not limited to
any extracellular portions thereof).
[00209] The term 'TMEM154 polypeptide", as used herein, refers to a polypeptide
encoded by any one of the nucleic acid sequences set forth in any one of SEQ ID NOs:23,
38-41, 106, and fragments and homologous thereof, especially those possessing at least 80,
85, 90, 95, 96, 97, 98, 99% sequence identity therewith. These nucleic acid sequences are
referred to herein as " TMEM154 polynucleotide". The term also refers to any one of the
polypeptides set forth in any one of SEQ ID NOs:42-46; extracellular portions thereof, set
forth in any one of SEQ ID NOs:63, 64; unique bridge, edge portion, tail or head portion
thereof, set forth in any one of SEQ ID NOs: 161,162; protein fragments selected from any
of the isolated polypeptides, used for rabbit immunization and specific antibothes
production, set forth in any one of SEQ ID NOs:191, 192; and fragments and homologous
thereof, especially those possessing at least 80, 85, 90, 95, 96, 97, 98, 99% sequence
identity therewith. The term "TMEM154 polynucleotide" or "TMEM154 polypeptide", as
used herein, further refers to any one of the foregoing polynucleotides and polypeptides,
respectively, that are differentially expressed e.g., in cancer, including but not limited to
Kidney cancer, pancreatic cancer, mμltiμle myeloma, lymphomas, especially non-HodgKins
lymphoma, wherein the cancer may be non-metastatic, invasive or metastatic as well as
non-malignant disorders such as immune related conditions or disorders including but not
limited to inflammatory or autoimmune diseases, transμlant rejection and graft versus host
disease, specifically SLE.
[00210] The term the "soluble ectodomain (ECD)" or "ectodomain" or "extracellular
ectodomain" of a KRTCAP3 polypeptide refers to the polypeptide sequences listed below
or the corresponding nucleic acid sequences (which do not comprise the signal peptide and
the TM (transmembrane portion) of the KRTCAP3 polypeptide):
Two ECD regions of the polypeptide W93943_P2 (SEQ ID NO:7):
W93943_P2_42-62 (SEQ ID NO:47) - sequence: TVLRHVANPRGAVTPEYTVAN (and
optionally bridging amino acids of any of one, two, tfiree, four, five, six, seven, eight, nine
or 10 amino acids on either side, starting anywhere from residue 32 and ending anywhere
up to residue 72; and also non-linear epitopes incorporating this sequence or a portion
thereof, as well as any of one, two, three, four, five, six, seven, eight, nine or 10 non-
contiguous amino acids of the sequence);
W93943_P2_115-162 (SEQ ID NO:48) - sequence:
LAVSLTVANGGRRLIADCHPGLLDμlVμlDEGPGHTDCPFDPTRIYDT(and
optionally bridging amino acids of any of one, two, three, four, five, six, seven, eight, nine
or 10 amino acids on either side, starting anywhere from residue 105 and ending anywhere
up to residue 172; and also non-linear epitopes incorporating this sequence or a portion
thereof, as well as any of one, two, three, four, five, six, seven, eight, nine or 10 non-
contiguous amino acids of the sequence);
Three ECD regions of the polypeptide W93943_P13 (SEQ ID NO: 10):
W93943_P13_l-20 (SEQ ID NO:49) - sequence: MRRCSLCAFDAARGPRRLMR (and
optionally bridging amino acids of any of one, two, three, four, five, six, seven, eight, nine
or 10 amino acids, starting anywhere from residue 1 and ending anywhere up to residue 30;
and also non-linear epitopes incorporating this sequence or a portion thereof, as well as any
of one, two, three, four, five, six, seven, eight, nine or 10 non-contiguous amino acids of the
sequence);
W93943_P13_77-91 (SEQ ID NO:50) - sequence: DPGGGRAPGEPSRPK (and optionally
bridging amino acids of any of one, two, three, four, five, six, seven, eight, nine or 10 amino
acids on either side, starting anywhere from residue 67 and ending anywhere up to residue
101; and also non-linear epitopes incorporating this sequence or a portion thereof, as well as
any of one, two, three, four, five, six, seven, eight, nine or 10 non-contiguous amino acids
of the sequence);
W93943_P13_141-188 (SEQ ID NO:48) - sequence:
LAVSLTVANGGRRLIADCHPGLLDμlVμlDEGPGHTDCPFDPTRlYDT(and
optionally bridging amino acids of any of one, two, three, four, five, six, seven, eight, nine
or 10 amino acids on either side, starting anywhere from residue 131 and ending anywhere
up to residue 198; and also non-linear epitopes incorporating this sequence or a portion
thereof, as well as any of one, two, three, four, five, six, seven, eight, nine or 10 non-
contiguous amino acids of the sequence);
Two ECD regions of the polypeptide W93943_P14 (SEQ ID NO:ll):
W93943_P14_42-62 (SEQ ID NO:47) - sequence: TVLRHVANPRGAVTPEYTVAN (and
optionally bridging amino acids of any of one, two, three, four, five, six, seven, eight, nine
or 10 amino acids on either side, starting anywhere from residue 32 and ending anywhere
up to residue 72; and also non-linear epitopes incorporating this sequence or a portion
thereof, as well as any of one, two, three, four, five, six, seven, eight, nine or 10 non-
contiguous amino acids of the sequence);
W93943_P14_115-162 (SEQ ID NO:48) - sequence:
LAVSLTVANGGRRLIADCHPGLLDμlVμlDEGPGHTDCPFDPTRIYDT(and
optionally bridging amino acids of any of one, two, three, four, five, six, seven, eight, nine
or 10 amino acids on either side, starting anywhere from residue 105 and ending anywhere
up to residue 172; and also non-linear epitopes incorporating this sequence or a portion
thereof, as well as any of one, two, three, four, five, six, seven, eight, nine or 10 non-
contiguous amino acids of the sequence);
Two ECD regions of the polypeptide W93943_P17 (SEQ ID NO: 12):
W93943_P17_42-62 (SEQ ID NO:47) - sequence: TVLRHVANPRGAVTPEYTVAN (and
optionally bridging amino acids of any of one, two, three, four, five, six, seven, eight, nine
or 10 amino acids on eitfier side, starting anywhere from residue 32 and ending anywhere
up to residue 72; and also non-linear epitopes incorporating this sequence or a portion
thereof, as well as any of one, two, three, four, five, six, seven, eight, nine or 10 non-
contiguous amino acids of the sequence);
W93943_P17_115-162 (SEQ ID NO:48) - sequence:
LAVSLTVANGGRRLIADCHPGLLDμlVμlDEGPGHTDCPFDPTRIYDT(and
optionally bridging amino acids of any of one, two, three, four, five, six, seven, eight, nine
or 10 amino acids on either side, starting anywhere from residue 105 and ending anywhere
up to residue 172; and also non-linear epitopes incorporating this sequence or a portion
thereof, as well as any of one, two, three, four, five, six, seven, eight, nine or 10 non-
contiguous amino acids of the sequence);
Two ECD regions of the polypeptide W93943_P18 (SEQ ID NO: 13):
W93943_P18_42-62 (SEQ ID NO:47) - sequence: TVLRHVANPRGAVTPEYTVAN (and
optionally bridging amino acids of any of one, two, three, four, five, six, seven, eight, nine
or 10 amino acids on either side, starting anywhere from residue 32 and ending anywhere
up to residue 72; and also non-linear epitopes incorporating this sequence or a portion
thereof, as well as any of one, two, three, four, five, six, seven, eight, nine or 10 non-
contiguous amino acids of the sequence);
W93943_P18_115-171 (SEQ ID NO:51) - sequence:
CCVAALTLRGVGPCRKDGLQGQLEEMTELESPKCKRQENEQLLDQNQEIRASQRS
WV (and optionally bridging amino acids of any of one, two, three, four, five, six, seven,
eight, nine or 10 amino acids on either side, starting anywhere from residue 105 and ending
anywhere up to residue 181; and also non-linear epitopes incorporating this sequence or a
portion thereof, as well as any of one, two, three, four, five, six, seven, eight, nine or 10
non-contiguous amino acids of the sequence);
and fragments and variants and homologs thereof possessing at least 80%, at least 85%, at
least 90%, at least 95, at least 96, at least 97, at least 98 or at least 99% sequence identity
therewith.
The term the "soluble ectodomain (ECD)" or "ectodomain" or "extracellular ectodomain"
of a FAM26F polypeptide refers to the polypeptide sequences listed below or the
corresponding nucleic acid sequences (which do not comprise the signal peptide and the TM
(transmembrane portion) of the FAM26F polypeptide):
Two ECD regions of the polypeptide T82906_P4 (SEQ ID NO:18):
T82906_P4_40-48 (SEQ ID NO:52) - sequence: QCPCSAAWN (and optionally bridging
amino acids of any of one, two, three, four, five, six, seven, eight, nine or 10 amino acids on
either side, starting anywhere from residue 30 and ending anywhere up to residue 58; and
also non-linear epitopes incorporating this sequence or a portion thereof, as well as any of
one, two, three, four, five, six, seven, eight, nine or 10 non-contiguous amino acids of the
sequence);
T82906_P4_125-175 (SEQ ID NO:53) - sequence:
ECAATGSAAFAQRLCLGRNRSCAAELμlVPCNQAKASDVQDLLKDLKAQSQ(and
optionally bridging amino acids of any of one, two, three, four, five, six, seven, eight, nine
or 10 amino acids on either side, starting anywhere from residue 115 and ending anywhere
up to residue 185; and also non-linear epitopes incorporating this sequence or a portion
thereof, as well as any of one, two, three, four, five, six, seven, eight, nine or 10 non-
contiguous amino acids of the sequence);
One ECD region of the polypeptide T82906_P3 (SEQ ID NO: 16):
T82906_P3_27-143 (SEQ ID NO: 127) - sequence
LSPVSFLQLKFWKIYLEQEQQILKSKATEHATELAKENIKCFFEGSHPKEYNTPSMK
EWQQISSLYTFNPKGQYYSMLHKYVNRKEKTHSIRSTEGDTVIPVLGFVDSSGINST
PEL (and optionally bridging amino acids of any of one, two, three, four, five, six, seven,
eight, nine or 10 amino acids on either side, starting anywhere from residue 17 and ending
anywhere up to residue 153; and also non-linear epitopes incorporating this sequence or a
portion thereof, as well as any of one, two, three, four, five, six, seven, eight, nine or 10
non-contiguous amino acids of the sequence);
and fragments and variants and homologs thereof possessing at least 80%, at least 85%, at
least 90%, at least 95, at least 96, at least 97, at least 98 or at least 99% sequence identity
therewith.
[00211] The term the "soluble ectodomain (ECD)" or "ectodomain" or "extracellular
ectodomain" of a MGC52498 polypeptide refers to the polypeptide sequences listed below
or the corresponding nucleic acid sequences (which do not comprise the signal peptide and
the TM (transmembrane portion) of the MGC52498 protein):
Three ECD regions of the polypeptide AA213820_P4 (SEQ ID NO:135): AA213820_P4_1-
55 (SEQ ID NO:60) - sequence:
MSGACTSYVSAEQEVVRGFSCPRPGGEAAAVFCCGFRDHKYCCDDPHSFFPYEHS
(and optionally bridging amino acids of any of one, two, three, four, five, six, seven, eight,
nine or 10 amino acids, starting anywhere from residue 1 and ending anywhere up to
residue 65; and also non-linear epitopes incorporating this sequence or a portion thereof, as
well as any of one, two, three, four, five, six, seven, eight, nine or 10 non-contiguous amino
acids of the sequence);
AA213820_P4_91-190 (SEQ ID NO:61) - sequence:
SSKPHTKLDLGLSLQTAGPEEVSPDCQGVNTGMAAEVPKVSμlQQSYSCLNPQLES
NEGQAVNSKRLLHHCFMATVTTSDIPGSPEEASVPNPDLCGPVP (and optionally
bridging amino acids of any of one, two, three, four, five, six, seven, eight, nine or 10 amino
acids on either side, starting anywhere from residue 81 and ending anywhere up to residue
200; and also non-linear epitopes incorporating this sequence or a portion thereof, as well as
any of one, two, three, four, five, six, seven, eight, nine or 10 non-contiguous amino acids
of the sequence);
AA213820_P_61-71 (SEQ ID NO:62) - sequence:
MASLWPSALTFNTDANIPGμlGFCGGWVRLCSLSSLTPPCGRRLVPCLSAPAPNAPR
LPAPARCSIGALIG (and optionally bridging amino acids of any of one, two, three, four,
five, six, seven, eight, nine or 10 amino acids on either side, starting anywhere from residue
51 and ending anywhere up to residue 81; and also non-linear epitopes incorporating this
sequence or a portion thereof, as well as any of one, two, three, four, five, six, seven, eight,
nine or 10 non-contiguous amino acids of the sequence),
and fragments and variants and homologs thereof possessing at least 80%, at least 85%, at
least 90%, at least 95, at least 96, at least 97, at least 98 or at least 99% sequence identity
therewith.
The term the "soluble ectodomain (ECD)" or "ectodomain" or "extracellular
ectodomain" of a FAM70A polypeptide refers to the polypeptide sequences listed below or
the corresponding nucleic acid sequences (which do not comprise the signal peptide and the
TM (transmembrane portion) of the FAM70A protein):
Two ECD regions of the polypeptide F10649_P4 (SEQ ID NO:30):
F10649_P4_51-59 (SEQ ID NO:54) - sequence: TTRTQNVTV (and optionally bridging
amino acids of any of one, two, three, four, five, six, seven, eight, nine or 10 amino acids on
either side, starting anywhere from residue 41 and ending anywhere up to residue 69; and
also non-linear epitopes incorporating this sequence or a portion thereof, as well as any of
one, two, three, four, five, six, seven, eight, nine or 10 non-contiguous amino acids of the
sequence);
F10649_P4_110-225 (SEQ ID NO:55) - sequence:
DGVFAARHIDLKμlYANRCHYVPKTSQKEAEEVISSSTKNSPSTRVMRNLTQAARE
VNCPHLSREFCTPRIRGNTCFCCDLYNCGNRVEITGGYYEYIDVSSCQDIIHLYHLL
WSA (and optionally bridging amino acids of any of one, two, three, four, five, six, seven,
eight, nine or 10 amino acids on either side, starting anywhere from residue 100 and ending
anywhere up to residue 235; and also non-linear epitopes incorporating this sequence or a
portion thereof, as well as any of one, two, three, four, five, six, seven, eight, nine or 10
non-contiguous amino acids of the sequence);
Two ECD regions of the polypeptide F10649_P5 (SEQ ID NO:33):
F10649_P5_51-59 (SEQ ID NO:54) - sequence: TTRTQNVTV (and optionally bridging
amino acids of any of one, two, three, four, five, six, seven, eight, nine or 10 amino acids on
either side, starting anywhere from residue 41 and ending anywhere up to residue 69; and
also non-linear epitopes incorporating this sequence or a portion thereof, as well as any of
one, two, three, four, five, six, seven, eight, nine or 10 non-contiguous amino acids of the
sequence);
F10649_P5_110-201 (SEQ ID NO:56) - sequence:
DGVFAARHIDLKμlYANRCHYVPKTSQKEAEEVNCPHLSREFCTPRIRGNTCFCCD
LYNCGNRVEITGGYYEYIDVSSCQDIIHLYHLLWSA (and optionally bridging amino
acids of any of one, two, three, four, five, six, seven, eight, nine or 10 amino acids on either
side, starting anywhere from residue 100 and ending anywhere up to residue 211; and also
non-linear epitopes incorporating this sequence or a portion thereof, as well as any of one,
two, three, four, five, six, seven, eight, nine or 10 non-contiguous amino acids of the
sequence);
Two ECD regions of the polypeptide F10649_P7 (SEQ ID NO:35):
F10649_P7_51-59 (SEQ ID NO:54) - sequence: TTRTQNVTV (and optionally bridging
amino acids of any of one, two, three, four, five, six, seven, eight, nine or 10 amino acids on
either side, starting anywhere from residue 41 and ending anywhere up to residue 69; and
also non-linear epitopes incorporating this sequence or a portion thereof, as well as any of
one, two, three, four, five, six, seven, eight, nine or 10 non-contiguous amino acids of the
sequence);
F10649_P7_110-241 (SEQ ID NO:58)- sequence :
DGVFAARHIDLKμlYANRCHYVPKTSQKEAEENPTLPALNCSVENTHPTVSYYAHP
QVASYNTYYHSPPHLPPYSAYDFQHSGVFPSSPPSGLSDEPQSASPSPSYMWSSSAPP
RYSPPYYPPFEKPPPYSP (and optionally bridging amino acids of any of one, two, three,
four, five, six, seven, eight, nine or 10 amino acids on either side, starting anywhere from
residue 100 and ending anywhere up to residue 251; and also non-linear epitopes
incorporating this sequence or a portion thereof, as well as any of one, two, three, four, five,
six, seven, eight, nine or 10 non-contiguous amino acids of the sequence);
Two ECD regions of the polypeptide F10649_P8 (SEQ ID NO:36):
F10649_P8_51-65 (SEQ ID NO:59) - sequence: TTRTQNVTVGGYYPG (and optionally
bridging amino acids of any of one, two, three, four, five, six, seven, eight, nine or 10 amino
acids on either side, starting anywhere from residue 41 and ending anywhere up to residue
75; and also non-linear epitopes incorporating this sequence or a portion thereof, as well as
any of one, two, three, four, five, six, seven, eight, nine or 10 non-contiguous amino acids
of the sequence);
F10649_P8_223-328 (SEQ ID NO:57) - sequence:
GGFKDMNPTLPALNCSVENTHPTVSYYAHPQVASYNTYYHSPPHLPPYSAYDFQHS
GVFPSSPPSGLSDEPQSASPSPSYMWSSSAPPRYSPPYYPPFEKPPPYSP(and
optionally bridging amino acids of any of one, two, three, four, five, six, seven, eight, nine
or 10 amino acids on either side, starting anywhere from residue 213 and ending anywhere
up to residue 338; and also non-linear epitopes incorporating this sequence or a portion
thereof, as well as any of one, two, three, four, five, six, seven, eight, nine or 10 non-
contiguous amino acids of the sequence);
One ECD region of the polypeptide F10649_P10 (SEQ ID NO:32):
F10649_P10_80-185 (SEQ ID NO:57) - sequence:
GGFKDMNPTLPALNCSVENTHPTVSYYAHPQVASYNTYYHSPPHLPPYSAYDFQHS
GVFPSSPPSGLSDEPQSASPSPSYMWSSSAPPRYSPPYYPPFEKPPPYSP(and
optionally bridging amino acids of any of one, two, three, four, five, six, seven, eight, nine
or 10 amino acids on either side, starting anywhere from residue 70 and ending anywhere
up to residue 195; and also non-linear epitopes incorporating this sequence or a portion
thereof, as well as any of one, two, three, four, five, six, seven, eight, nine or 10 non-
contiguous amino acids of the sequence);
and fragments and variants and homologs thereof possessing at least 80%, at least 85%, at
least 90%, at least 95, at least 96, at least 97, at least 98 or at least99% sequence identity
therewith.
[00212] The term the "soluble ectodomain (ECD)" or "ectodomain" or "extracellular
ectodomain" of a polypeptide TMEM154 refers to the polypeptide sequences below or the
corresponding nucleic acid sequences (which do not comprise the signal peptide and the TM
(transmembrane portion) of the TMEM154 protein):
One ECD region of the polypeptide W38346_P3 (SEQ ID NO:42):
W38346_P3_23-75 (SEQ ID NO:63) - sequence:
EELENSGDTTVESERPNKVTIPSTFAAVTIKETLNANINSTNFAPDENQLE(and
optionally bridging amino acids of any of one, two, three, four, five, six, seven, eight, nine
or 10 amino acids on either side, starting anywhere from residue 13 and ending anywhere
up to residue 85; and also non-linear epitopes incorporating this sequence or a portion
thereof, as well as any of one, two, three, four, five, six, seven, eight, nine or 10 non-
contiguous amino acids of the sequence);
One ECD region of the polypeptide W38346_P4 (SEQ ID NO:45):
W38346_P4_20-105 (SEQ ID NO:64) - sequence:
ATYYKRKRTKQEPSSQGSQSALQTYELXJSENVKVPIFEEDTPSVMEIEMEELDKWM
NSMNRNADFECLPTLKEEKESNHNPSDSES (and optionally bridging amino acids of
any of one, two, three, four, five, six, seven, eight, nine or 10 amino acids on either side,
starting anywhere from residue 10 and ending anywhere up to residue 115; and also non-
linear epitopes incorporating this sequence or a portion thereof, as well as any of one, two,
three, four, five, six, seven, eight, nine or 10 non-contiguous amino acids of the sequence);
One ECD region of the polypeptide W38346„P7 (SEQ ID NO:46):
W38346_P7_23-75 (SEQ ID NO:63) - sequence:
EELENSGDTTVESERPNKVTIPSTFAAVTIKETLNANINSTNFAPDENQLE(and
optionally bridging amino acids of any of one, two, three, four, five, six, seven, eight, nine
or 10 amino acids on either side, starting anywhere from residue 13 and ending anywhere
up to residue 85; and also non-linear epitopes incorporating this sequence or a portion
thereof, as well as any of one, two, three, four, five, six, seven, eight, nine or 10 non-
contiguous amino acids of the sequence);
and fragments and variants and homologs thereof possessing at least 80%, at least 85%, at
least 90%, at least 95, at least 96, at least 97, at least 98 or at least 99% sequence identity
therewith.
[00213] The term "immune response" refers to the action of, for EXAMPLE, lymphocytes,
antigen presenting cells, phagocytic cells, granμlocytes, and soluble macromolecμles
produced by the above cells or cells produced by the liver or sμleen (including antibothes,
cytoKines, and comμlement) that resμlts in selective damage to, destruction of, or
elimination from the human body of invading pathogens, cells or tissues infected with
pathogens, cancerous cells, or, in cases of autoimmunity or pathological inflammation,
normal human cells or tissues.
[00214] The term "antibody" as referred to herein includes whole polyclonal and
monoclonal antibothes and any antigen binding fragment (i.e., "antigen-binding portion") or
single chains thereof. An "antibody" refers to a glycoprotein comprising at least two heavy
(H) chains and two light (L) chains inter-connected by disμlfide bonds, or an antigen
binding portion thereof. Each heavy chain is comprised of a heavy chain variable region
(abbreviated herein as VH) and a heavy chain constant region. The heavy chain constant
region is comprised of three domains, CHI, CH2 and CH3. Each light chain is comprised of
a light chain variable region (abbreviated herein as VL) and a light chain constant region.
The light chain constant region is comprised of one domain, CL. The VH and VL regions
can be further subdivided into regions of hypervariability, termed comμlementarity
determining regions (CDR), interspersed with regions that are more conserved, termed
frameworK regions (FR), Each VH and VL is composed of three CDRs and four FRs,
arranged from amino-terminus to carboxy-terminus in the following order: FR1, CDR1,
FR2, CDR2, FR3, CDR3, FR4. The variable regions of the heavy and light chains contain a
binding domain that interacts with an antigen. The constant regions of the antibothes may
mediate the binding of the immunogloulin to host tissues or factors, including various cells
of the immune system (e.g., effector cells) and the first component (Clq) of the classical
comμlement system.
[00215] The term "antigen-binding portion" of an antibody (or simμly "antibody
portion"), as used herein, refers to one or more fragments of an antibody that retain the
ability to specifically bind to an antigen (e.g., KRTCAP3, FAM26F, MGC52498, FAM70A,
TMEM154 polypeptides and proteins). It has been shown that the antigen-binding function
of an antibody can be performed by fragments of a fμll-length antibody. EXAMPLEs of
binding fragments encompassed within the term "antigen-binding portion" of an antibody
include (i) a Fab fragment, a moNOvalent fragment consisting of the V Light, V Heavy,
Constant light (CL) and CHI domains; (ii) a F(ab').2 fragment, a bivalent fragment
comprising two Fab fragments linKed by a disμlfide bridge at the hinge region; (iii) a Fd
fragment consisting of the VH and CHI domains; (iv) a Fv fragment consisting of the VL
and VH domains of a single arm of an antibody, (v) a dAb fragment (Ward et al., (1989)
Nature 341:544-546), which consists of a VH domain; and (vi) an isolated comμlementarity
determining region (CDR). Furthermore, although the two domains of the Fv fragment, VL
and VH, are coded for by separate genes, they can be joined, using recombinant methods,
by a synthetic linKer that enables them to be made as a single protein chain in which the VL
and VH regions pair to form moNOvalent molecμles (KNOwn as single chain Fv (scFv); see
e.g., Bird et al. (1988) Science 242:423-426; and Huston et al. (1988) Proc. Natl. Acad. Sci.
USA 85:5879-5883). Such single chain antibothes are also intended to be encompassed
within the term "antigen-binding portion" of an antibody. These antibody fragments are
obtained using conventional techniques KNOwn to those with sKill in the art, and the
fragments are screened for utility in the same manner as are intact antibothes.
[00216] An "isolated antibody", as used herein, is intended to refer to an antibody that is
substantially free of other antibothes having different antigenic specificities (e.g., an
isolated antibody that specifically binds KRTCAP3, FAM26F, MGC52498, FAM70A,
TMEM154 proteins or KRTCAP3, FAM26F, MGC52498, FAM70A, or TMEM154
polypeptides is substantially free of antibothes that specifically bind antigens other than
KRTCAP3, FAM26F, MGC52498, FAM70A, TMEM154 proteins or polypeptides,
respectively. An isolated antibody that specifically binds KRTCAP3, FAM26F,
MGC52498, FAM70A, TMEM154 proteins or polypeptides may, however, have cross-
reactivity to other antigens, such as KRTCAP3, FAM26F, MGC52498, FAM70A,
TMEM154 proteins or KRTCAP3, FAM26F, MGC52498, FAM70A, or TMEM154
polypeptides from other species, respectively. Moreover, an isolated antibody may be
substantially free of other cellμlar material and/or chemicals.
[00217] The terms "monoclonal antibody" or "monoclonal antibody composition" as
used herein refer to a preparation of antibody molecμles of single molecμlar composition, A
monoclonal antibody composition disμlays a single binding specificity and affinity for a
particμlar epitope.
[00218] The term "human antibody", as used herein, is intended to include antibothes
having variable regions in which both the frameworK and CDR regions are derived from
human germline immunogloulin sequences. Furthermore, if the antibody contains a
constant region, the constant region also is derived from human germline immunogloulin
sequences. The human antibothes according to at least some embodiments of the invention
may include amino acid residues not encoded by human germline immunogloulin
sequences (e.g., mutations introduced by random or site-specific mutagenesis in vitro or by
somatic mutation in vivo). However, the term "human antibody", as used herein, is not
intended to include antibothes in which CDR sequences derived from the germline of
another mammalian species, such as a mouse, have been grafted onto human frameworK
sequences.
[00219] The term "human monoclonal antibody" refers to antibothes disμlaying a single
binding specificity which have variable regions in which both the frameworK and CDR
regions are derived from human germline immunogloulin sequences. In one embodiment,
the human monoclonal antibothes are produced by a hybridoma which includes a B cell
obtained from a transgenic nonhuman animal, e.g., a transgenic mouse, having a geNOme
comprising a human heavy chain transgene and a light chain transgene fused to an
immortalized cell.
[00220] The term "recombinant human antibody", as used herein, includes all human
antibothes that are prepared, expressed, created or isolated by recombinant means, such as
(a) antibothes isolated from an animal (e.g., a mouse) that is transgenic or
transchromosomal for human immunogloulin genes or a hybridoma prepared therefrom
(described further below), (b) antibothes isolated from a host cell transformed to express the
human antibody, e.g., from a transfectoma, (c) antibothes isolated from a recombinant,
combinatorial human antibody library, and (d) antibothes prepared, expressed, created or
isolated by any other means that involve sμlicing of human immunogloulin gene sequences
to other DNA sequences. Such recombinant human antibothes have variable regions in
which the frameworK and CDR regions are derived from human germline immunogloulin
sequences. In certain embodiments, however, such recombinant human antibothes can be
subjected to in vitro mutagenesis (or, when an animal transgenic for human Ig sequences is
used, in vivo somatic mutagenesis) and thus the amino acid sequences of the VH and VL
regions of the recombinant antibothes are sequences that, while derived from and related to
human germline VH and VL sequences, may not naturally exist within the human antibody
germline repertoire in vivo.
[00221] As used herein, "isotype" refers to the antibody class (e.g., IgM or IgGl) that is
encoded by the heavy chain constant region genes.
[00222] The phrases "an antibody recognizing an antigen" and "an antibody specific for
an antigen" are used interchangeably herein with the term "an antibody which binds
specifically to an antigen."
[00223] As used herein, an antibody that "specifically binds" to human KRTCAP3,
FAM26F, MGC52498, FAM70A, TMEM154 proteins or polypeptides is intended to refer
to an antibody that binds to human KRTCAP3, FAM26F, MGC52498, FAM70A,
TMEM154 proteins or polypeptides optionally one witfi a KD of 5X10 -8 M or less, 3X10 -
8 M or less, or IX. 10 -9 M or less,
[00224] The term "K-assoc" or "Ka", as used herein, is intended to refer to the
association rate of a particμlar antibody-antigen interaction, whereas the term "Kdiss" or
"Kd," as used herein, is intended to refer to the dissociation rate of a particμlar antibody-
antigen interaction. The term "KD", as used herein, is intended to refer to the dissociation
constant, which is obtained from the ratio of Kd to Ka (i.e., Kd/Ka) and is expressed as a
molar concentration (M). KD values for antibothes can be determined using methods well
established in the art. A preferred method for determining the KD of an antibody is by using
surface μlasmon resonance, optionally using a biosensor system such as a Biacore® system.
[00225] As used herein, the term "high affinity" for an IgG antibody refers to an antibody
having a KD of 10"8 M or less, 10"9 M or less or 10~10 M or less for a target antigen.
However, "high affinity" binding can vary for other antibody isotypes. For EXAMPLE, "high
affinity" binding for an IgM isotype refers to an antibody having a KD of 10" M or less, or
10"8 M or less.
[00226] As used herein, the term "tail" refers to a peptide sequence at the end of an
amino acid sequence that is unique to a sμlice variant according to the present invention.
Therefore, a sμlice variant having such a tail may optionally be considered as a chimera, in
that at least a first portion of the sμlice variant is typically highly homologous (often 100%
identical) to a portion of the corresponding KNOwn protein, while at least a second portion of
the variant comprises the tail.
[00227] As used herein, the term "head" refers to a peptide sequence at the beginning of
an amino acid sequence that is unique to a sμlice variant according to the present invention.
Therefore, a sμlice variant having such a head may optionally be considered as a chimera, in
that at least a first portion of the sμlice variant comprises the head, while at least a second
portion is typically highly homologous (often 100% identical) to a portion of the
corresponding KNOwn protein.
[00228] As used herein, the term "an edge portion" refers to a connection between two
portions of a sμlice variant according to the present invention that were not joined in the
wild type or KNOwn protein. An edge may optionally arise due to a join between the above
"KNOwn protein" portion of a variant and the tail, for EXAMPLE, and/or may occur if an
internal portion of the wild type sequence is NO longer present, such that two portions of the
sequence are NOw contiguous in the sμlice variant that were not contiguous in the KNOwn
protein. A "bridge" may optionally be an edge portion as described above, but may also
include a join between a head and a "KNOwn protein" portion of a variant, or a join between
a tail and a "KNOwn protein" portion of a variant, or a join between an insertion and a
"KNOwn protein" portion of a variant.
[00229] In some embodiments, a bridge between a tail or a head or a unique insertion,
and a "KNOwn protein" portion of a variant, comprises at least about 10 amino acids, or in
some embodiments at least about 20 amino acids, or in some embodiments at least about 30
amino acids, or in some embodiments at least about 40 amino acids, in which at least one
amino acid is from the tail/head/insertion and at least one amino acid is from the "KNOwn
protein" portion of a variant. In some embodiments, the bridge may comprise any number
of amino acids from about 10 to about 40 amino acids (for EXAMPLE, 10, 11, 12, 13...37, 38,
39, 40 amino acids in length, or any number in between).
[00230] It shoμld be noted that a bridge cannot be extended beyond the length of the
sequence in either direction, and it shoμld be assumed that every bridge description is to be
read in such manner that the bridge length does not extend beyond the sequence itself.
[00231] Furthermore, bridges are described with regard to a sliding window in certain
contexts below. For EXAMPLE, certain descriptions of the bridges feature the following
format: a bridge between two edges (in which a portion of the KNOwn protein is not present
in the variant) may optionally be described as follows: a bridge portion of CONTIG-
NAME_P1 (representing the name of the protein), comprising a polypeptide having a length
"n", wherein n is at least about 10 amino acids in length, optionally at least about 20 amino
acids, at least about 30 amino acids, at least about 40 amino acids, or at least about 50
amino acids in length, wherein at least two amino acids comprise XX (2 amino acids in the
center of the bridge, one from each end of the edge), having a structure as follows
(numbering according to the sequence of CONTIG-NAME_μl): a sequence starting from
any of amino acid numbers 49-x to 49 (for EXAMPLE); and ending at any of amino acid
numbers 50 + ((n-2) - x) (for EXAMPLE), in which x varies from 0 to n-2. In this EXAMPLE, it
shoμld also be read as including bridges in which n is any number of amino acids between
10-50 amino acids in length. Furthermore, the bridge polypeptide cannot extend beyond the
sequence, so it shoμld be read such that 49-x (for EXAMPLE) is not less than 1, NOr 50 + ((n-2)
- x) (for EXAMPLE) greater than the total sequence length.
[00232] The term "cancer" as used herein shoμld be understood to encompass any
neoμlastic disease (whether invasive or metastatic) which is characterized by abnormal and
uncontrolled cell division causing malignant growth or tumor. non-limiting EXAMPLEs of
cancer which may be treated with a composition according to at least some embodiments of
the present invention are solid tumors, sarcomas, hematological malignancies, including but
not limited to breast cancer (e.g. breast carcinoma), cervical cancer, ovary cancer (ovary
carcinoma), endometrial cancer, melaNOma, bladder cancer (bladder carcinoma), lung
cancer (e.g. adenocarcinoma and non-small cell lung cancer), pancreatic cancer (e.g.
pancreatic carcinoma such as exocrine pancreatic carcinoma), colon cancer (e.g. colorectal
carcinoma, such ascolon adenocarcinoma and colon adenoma), prostate cancer including the
advanced disease, hematopoietic tumors of lymphoid lineage (e.g. leuKemia, acute
lymphocytic leuKemia, chronic lymphocytic leuKemia, B-cell lymphoma, BurKitt's
lymphoma, mμltiμle myeloma, HodgKin's lymphoma, non-HodgKin's lymphoma, anti
CD20 (i.e. Rituximab) resistant lymphoma), myeloid leuKemia (for EXAMPLE, acute
myelogeNOus leuKemia (AML), chronic myelogeNOus leuKemia), thyroid cancer, thyroid
follicμlar cancer, myelodysμlastic syndrome (MDS), tumors of mesenchymal origin (e.g.
fibrosarcomas and rhabdomyosarcomas), melaNOma, uveal melaNOma, teratocarcinoma,
neuroblastoma, glioma, glioblastoma, benign tumor of the sKin (e.g. Keratoacanthomas),
renal cancer, anaμlastic large-cell lymphoma, esophageal squamous cells carcinoma,
hepatocellμlar carcinoma, follicμlar dendritic cell carcinoma, intestinal cancer, muscle-
invasive cancer, seminal vesicle tumor, epidermal carcinoma, sμleen cancer, bladder cancer,
head and necK cancer, stomach cancer, liver cancer, bone cancer, brain cancer, cancer of the
retina, biliary cancer, small bowel cancer, salivary gland cancer, cancer of uterus, cancer of
testicles, cancer of connective tissue, prostatic hypertrophy, myelodysμlasia, Waldenstrom's
macroglobinaemia, nasopharyngeal, neuroendocrine cancer, myelodysμlastic syndrome,
mesothelioma, angiosarcoma, Kaposi's sarcoma, carciNOid, oesophagogastric, fallopian tube
cancer, peritoneal cancer, papillary serous mμllerian cancer, malignant ascites,
gastrointestinal stromal tumor (GIST), and a hereditary cancer syndrome such as Li-
Fraumeni syndrome and Von Hippel-Lindau syndrome (VHL).
[00233] With regard to ovarian cancer, the disease is selected from the group including but
not limited to primary and metastatic cancer of the ovary, including epiUielial ovarian
cancer such as serous, muciNOus, endometroid, clear cell, mixed epiUielial, undifferentiated
carcinomas and Brenner tumor, as well as other non-epithelial neoμlasms of the ovary,
including germ cell malignancies.
[00234] With regard to breast cancer, the disease is selected from the group including but
not limited to primary and metastatic cancer of the breast, including mammary carcinomas
such as Infiltrating Ductal carcinoma, Ductal carcinoma in-situ, Infiltrating Lobμlar
carcinoma, Lobμlar carcinoma in-situ, Inflammatory breast cancer, Paget's disease of the
breast, and other non-epithelial neoμlasms of the breast, including fibrosarcomas,
leiomyosarcomas, rhapdomyosarcomas, angiosarcomas, cystosarcoma phyllodes.
[00235] With regard to lung cancer, the disease is selected from the group consisting of
but not limited to squamous cell lung carcinoma, lung adenocarcinoma, carciNOid, small cell
lung cancer or non-small cell lung cancer.
[00236] With regard to liver cancer, the disease is selected from the group consisting of
but not limited to primary and metastatic cancers of the liver and intrahepatic bile duct,
including hepatocellμlar carcinoma, cholangiocarcinoma, hepatic angiosarcoma and
hepatoblastoma.
With regard to renal cancer, the disease is selected from the group consisting of
but not limited to primary and metastatic cancer of the Kidney, including renal cell
carcinoma (i.e. renal adenocarcinoma), as well as omer non-epithelial neoμlasms of the
ovary, including nephroblastoma (i.e. WUm's tumor), transitional cell neoμlasms of the
renal pelvis, and various sarcomas of renal origin.
With regard to colon cancer, the disease is selected from the group consisting of
but not limited to primary and metastatic cancer of the colon, including adenocarcinoma,
muciNOus carcinoma (including signet ring cell-type and medμllary), adenosquamous
carcinoma, carciNOid, small cell carcinoma, squamous cell carcinoma, undifferentiated
carcinoma, as well as other non-epithelial neoμlasms of the colon, including lymphoma,
melaNOma and sarcoma.
[00237] With regard to pancreatic cancer, the disease is selected from the group
consisting of but not limited to primary and metastatic cancers of the exocrine pancreas,
including adenocarcinoma, serous and muciNOus cystadenocarcinomas, acinar cell
carcinoma, undifferentiated carcinoma, pancreatoblastoma and neuroendocrine tumors such
as insμliNOma.
[00238] With regard to melaNOma, the disease is selected from the group consisting of
but not limited to primary and metastatic malignant melaNOma, including cutaneous
melaNOma such as superficial spreading melaNOma, NOdμlar melaNOma, acral lentigiNOus
melaNOma and lentigo maligna melaNOma, as well as mucosal melaNOma, intraocμlar
melaNOma, desmoμlastic/neurotropic melaNOma and melaNOma of soft parts (clear cell
sarcoma).
[00239] With regard to prostate cancer, the disease is selected from the group consisting
of but not limited to primary and metastatic cancer of the prostate, including prostatic
intraepithelial neoμlasia, atypical adenomatous hyperμlasia, prostate adenocarcinoma,
muciNOus or signet ring tumor, adenoid cystic carcinoma, prostatic duct carcinoma,
carciNOid and small-cell undifferentiated cancer.
[00240] As used herein the term "hematological malignancies" refers to acute
lymphocytic leuKemia, chronic lymphocytic leuKemia (CLL), acute lymphoblastic
leuKemia, acute myelogeNOus leuKemia, chronic myelogeNOus leuKemia, mμltiμle myeloma,
B-cell lymphoma, such as HodgKin's lymphoma, non-HodgKin's lymphoma (NHL), anti
CD20 (i.e. Rituximab) resistant lymphoma, low grade/follicμlar NHL, small cell
lymphocytic (SL) NHL, small cell NHL, grade I small cell follicμlar NHL, grade n mixed
small and large cell follicμlar NHL, grade III large cell follicμlar NHL, large cell NHL,
Diffuse Large B-Cell NHL, intermediate grade diffuse NHL, high grade immuNOblastic
NHL, high grade lymphoblastic NHL, high grade small non- cleaved cell NHL, bμlKy
disease NHL, mantle cell lymphoma, Mucosa-Associated Lymphatic Tissue lymphoma
(MALT), BurKitt lymphoma, Mediastinal large B cell lymphoma, NOdal marginal zone B
cell lymphoma (NMZL), Sμlenic marginal zone lymphoma (SMZL), ExtraNOdal marginal
zone B cell lymphoma, Intravascμlar large B cell lymphoma, Primary effusion lymphoma,
Lymphomatoid granμlomatosis, B-cell prolymphocyte leuKemia, Precursor B
lymphoblastic leuKemia, Hairy cell leuKemia, AIDS-related lymphoma and Waldenstrom's
Macroglobμlinernia.
[00241] The term "immune related condition" as used herein will encompass any disease
disorder or condition selected from the group including but not limited to mμltiμle sclerosis;
psoriasis; rheumatoid arthritis; psoriatic arthritis, systemic lupus erythematosus (SLE);
μlcerative colitis; Crohn's disease; benign lymphocytic angiitis, thrombocytopenic purpura,
idiopathic thrombocytopenia, idiopathic autoimmune hemolytic anemia, pure red cell
aμlasia, Sjogren's syndrome, rheumatic disease, connective tissue disease, inflammatory
rheumatism, degenerative rheumatism, extra-articμlar rheumatism, juvenile rheumatoid
arthritis, arthritis uratica, muscμlar rheumatism, chronic polyarthritis, cryoglobμlinemia
vascμlitis, ANCA-associated vascμlitis, antiphospholipid syndrome, myasthenia gravis,
autoimmune haemolytic anaemia, Guillian-Barre syndrome, chronic immune
polyneuropathy, autoimmune thyroiditis, insμlin dependent diabetes mellitus, type I
diabetes, Addison's disease, membraNOus glomerμlonephropathy, Goodpasture's disease,
autoimmune gastritis, pernicious anaemia, pemphigus vμlgarus, cirrhosis, primary biliary
cirrhosis, dermatomyositis, polymyositis, fibromyositis, myogelosis, celiac disease,
immunogloulin A nephropathy, HeNOch-Schonlein purpura, Evans syndrome, atopic
dermatitis, psoriasis, psoriasis arthropathica, Graves' disease, Graves' ophthalmopathy,
scleroderma, systemic scleroderma, asthma, allergy, primary biliary cirrhosis, Hashimoto's
thyroiditis, primary myxedema, sympathetic ophthalmia, autoimmune uveitis, hepatitis,
chronic action hepatitis, collagen diseases, anKylosing spondylitis, periarthritis
humeroscapμlaris, panarteritis NOdosa, chondrocalciNOsis, Wegener's granμlomatosis,
microscopic polyangiitis, chronic urticaria, bμllous sKin disorders, pemphigoid, atopic
eczema, Devic's disease, childhood autoimmune hemolytic anemia, Refractory or chronic
Autoimmune Cytopenias, Prevention of development of Autoimmune Anti-Factor VIII
Antibothes in Acquired Hemophilia A, Cold Agglutinin Disease, Neuromyelitis Optica,
Stiff Person Syndrome, gingivitis, periodontitis, pancreatitis, myocarditis, vascμlitis,
gastritis, gout, gouty arthritis, and inflammatory sKin disorders, selected from the group
consisting of psoriasis, atopic dermatitis, eczema, rosacea, urticaria, and acne,
NOrmocomμlementemic urticarial vascμlitis, pericarditis, myositis, anti-synthetase
syndrome, scleritis, macrophage activation syndrome, Bechet's Syndrome, PAPA
Syndrome, Blau's Syndrome, gout, adμlt and juvenile Still's disease, cryropyriNOpathy,
MucKle-Wells syndrome, familial cold-induced auto-inflammatory syndrome, neonatal
onset mμltisystemic inflammatory disease, familial Mediterranean fever, chronic infantile
neurologic, cutaneous and articμlar syndrome, systemic juvenile idiopathic arthritis, Hyper
IgD syndrome, Schnitzler's syndrome, and TNF receptor-associated periodic syndrome
(TRAPS), inflammatory bowel disease, Good pasture's syndrome, pernicious anemia,
autoimmune atrophic gastritis, μlceratis colitis, mixed connective tissue disease,
panarteriitis NOdosa, progressive systemic scleroderma, peptic μlcers, μlcers, chronic
bronchitis, acute lung injury, pμlmonary inflammation, airway hyper-responsiveness, septic
shocK, inflammatory sKin disorders, myogelosis, chondrocalciNOsis, thyroditis, allergic
oedema, granμlomas, immune disorders associated with graft transμlantation rejection, such
as acute and chronic rejection of organ transμlantation, allogenic stem cell transμlantation,
autologous stem cell transμlantation, bone marrow tranμlantation, and graft versus host
disease.
As used herein the term "treatment" refers to care provided to relieve illness and
refers to both a therapeutic treatment or prophylactic/preventative measures, wherein the
objective is to prevent or slow down (lessen) the targeted pathologic condition or disorder.
Those in need of treatment include those already with the disorder as well as those prone to
have the disorder or those in whom the disorder is to be prevented. The term treatment as
used herein refers also to "maintenance therapy", which is a treatment that is given to Keep a
pathologic condition or disorder from coming bacK after it has disappeared following the
initial therapy.
[00242] The term "therapeutically effective amount" refers to an amount of agent
according to the present invention that is effective to treat a disease or disorder in a
mammal.
As used herein the term ''diagNOsis''' refers to the process of identifying a medical
condition or disease by its signs, symptoms, and in particμlar from the resμlts of various
diagNOstic procedures, including e.g. detecting the expression of the nucleic acids or
polypeptides according to at least some embodiments of the invention in a biological samμle
(e.g. in cells, tissue or serum, as defined below) obtained from an individual. Furthermore,
as used herein the term "diagNOsis" encompasses screening for a disease, detecting a
presence or a severity of a disease, distinguishing a disease from other diseases including
those diseases that may feature one or more similar or identical symptoms, providing
progNOsis of a disease, monitoring disease progression or relapse, as well as assessment of
treatment efficacy and/or relapse of a disease, disorder or condition, as well as selecting a
therapy and/or a treatment for a disease, optimization of a given therapy for a disease,
monitoring the treatment of a disease, and/or predicting the suitability of a therapy for
specific patients or subpopμlations or determining the appropriate dosing of a therapeutic
product in patients or subpopμlations. The diagNOstic procedure can be performed in vivo or
in vitro. It shoμld be noted that a "biological samμle obtained from the subject" may also
optionally comprise a samμle that has not been physically removed from the subject.
As used herein the term "combination therapy" refers to the simμltaneous or
consecutive administration of two or more medications or types of therapy to treat a single
disease. In particμlar, the term refers to the use of any of the polypeptides, polynucleotides,
antibothes or pharmaceutical compositions according to at least some embodiments of the
invention in combination with at least one additional medication or therapy. Thus, treatment
of a disease using the agents according to at least some embodiments of the present
invention may be combined with therapies well KNOwn in the art that include, but are not
limited to, radiation therapy, antibody therapy, chemotherapy or surgery or in combination
therapy with other biological agents, conventional drugs, anti-cancer agents,
immuNOsuppressants, cytotoxic drugs for cancer, chemotherapeutic agents. According to at
least some embodiments, treatment of Mμltiμle Myeloma using the agents according to at
least some embodiments of the present invention may be combined with an agent including
but not limited to Melphalan, prednisone, thalidomide (MPT), or combination Bortezomib
(Velcade), melphalan, prednisone (VMP) or a combination of Lenalidomide μlus low-dose
dexamethasone.
According to at least some embodiments, treatment of ovarian cancer using the agents
according to at least some embodiments of the present invention may be combined with an
agent including but not limited to paclitaxol and cisμlatin.
According to at least some embodiments, treatment of rheumatoid arthritis disorder
using the agents according to at least some embodiments of the present invention may be
combined with but not limited to a first-line combination treatment with a drug such as
aspirin and cortisone (corticosteroids), which are used to reduce pain and inflammation, and
one or more second-line combination drugs, such as gold, methotrexate, and
hydroxychloroquine (μlaquenil), promote disease remission and prevent progressive joint
destruction. According to at least some embodiments, treatment of rheumatoid arthritis
disorder may optionally feature an agent according to the present invention combined with
an agent including but not limited to methotrexate and rituximab.
As used herein, the term "subject" includes any human or nonhuman animal. The term
"nonhuman animal" includes all vertebrates, e.g., mammals and non-mammals, such as
nonhuman primates, sheep, dogs, cats, horses, cows, chicKens, amphibians, reptiles, etc.
[00243] Various aspects of the invention are described in further detail in the following
subsections.
[00244] NUCLEIC ACIDS
[00245] A "nucleic acid fragment" or an "oligonucleotide" or a "polynucleotide" are
used herein interchangeably to refer to a polymer of nucleic acid residues. A polynucleotide
sequence according to at least some embodiments of the present invention refers to a single
or double stranded nucleic acid sequences which is isolated and provided in the form of an
RNA sequence, a comμlementary polynucleotide sequence (cDNA), a geNOmic
polynucleotide sequence and/or a composite polynucleotide sequences (e.g., a combination
of the above).
[00246] Thus, the present invention encompasses nucleic acid sequences described
hereinabove; fragments thereof, sequences hybridizable therewith, sequences homologous
thereto [e.g., at least 90%, at least 95, 96, 97, 98 or 99 % or more identical to the nucleic
acid sequences set forth herein], sequences encoding similar polypeptides with different
codon usage, altered sequences characterized by mutations, such as deletion, insertion or
substitution of one or more nucleotides, either naturally occurring or man induced, either
randomly or in a targeted fashion. The present invention also encompasses homologous
nucleic acid sequences (i.e., which form a part of a polynucleotide sequence according to at
least some embodiments of the present invention), which include sequence regions unique
to the polynucleotides according to at least some embodiments of the present invention.
[00247] In cases where the polynucleotide sequences according to at least some
embodiments of the present invention encode previously unidentified polypeptides, the
present invention also encompasses novel polypeptides or portions thereof, which are
encoded by the isolated polynucleotide and respective nucleic acid fragments thereof
described hereinabove.
[00248] Thus, the present invention also encompasses polypeptides encoded by the
polynucleotide sequences according to at least some embodiments of the present invention.
The present invention also encompasses homologues of these polypeptides, such
homologues can be at least 90 %, at least 95, 96, 97, 98 or 99 % or more homologous to the
amino acid sequences set forth below, as can be determined using BlastP software of the
National Center of BiotechNOlogy Information (NCBI) using defaμlt parameters. Finally,
the present invention also encompasses fragments of the above described polypeptides and
polypeptides having mutations, such as deletions, insertions or substitutions of one or more
amino acids, either naturally occurring or man induced, either randomly or in a targeted
fashion.
[00249] Oligonucleotides designed for carrying out the methods according to at least
some embodiments of the present invention for any of the sequences provided herein
(designed as described above) can be generated according to any oligonucleotide synthesis
method KNOwn in the art such as enzymatic synthesis or solid phase synthesis. Equipment
and reagents for executing solid-phase synthesis are commercially available from, for
EXAMPLE, Apμlied Biosystems. Any other means for such synthesis may also be emμloyed;
the actual synthesis of the oligonucleotides is well within the capabilities of one sKilled in
the art.
[00250] Oligonucleotides used according to this aspect according to at least some
embodiments of the present invention are those having a lengm selected from a range of
about 10 to about 200 bases, optionally about 15 to about 150 bases, about 20 to about 100
bases, or about 20 to about 50 bases.
[00251] The oligonucleotides according to at least some embodiments of the present
invention may comprise heterocyclic nucleosides consisting of purines and the pyrimidines
bases, bonded in a 3' to 5' phosphothester linKage.
[00252] PEPTIDES
[00253] The terms "polypeptide," "peptide" and "protein" are used interchangeably
herein to refer to a polymer of amino acid residues. The terms apμly to amino acid polymers
in which one or more amino acid residue is an analog or mimetic of a corresponding
naturally occurring amino acid, as well as to naturally occurring amino acid polymers.
Polypeptides can be modified, e.g., by the addition of carbohydrate residues to form
glycoproteins. The terms "polypeptide," "peptide" and "protein" include glycoproteins, as
well as non-glycoproteins.
[00254] Polypeptide products can be biochemically synthesized such as by emμloying
standard solid phase techniques. Such methods include exclusive solid phase synthesis,
partial solid phase synthesis methods, fragment condensation, classical solution synthesis.
These methods are optionally used when the peptide is relatively short (i.e., 10 KDa) and/or
when it cannot be produced by recombinant techniques (i.e., not encoded by a nucleic acid
sequence) and therefore involves different chemistry.
[00255] Solid phase polypeptide synthesis procedures are well KNOwn in the art and
further described by John Morrow Stewart and Janis Dillaha Young, Solid Phase Peptide
Syntheses (2nd Ed., Pierce Chemical Company, 1984).
[00256] Synthetic polypeptides can be purified by preparative high performance liquid
chromatography [Creighton T. (1983) Proteins, structures and molecμlar princiμles. WH
Freeman and Co. N.Y.] and the composition of which can be confirmed via amino acid
sequencing.
[00257] In cases where large amounts of a polypeptide are desired, it can be generated
using recombinant techniques such as described by Bitter et al., (1987) Methods in
Enzymol. 153:516-544, Stuther et al. (1990) Methods in Enzymol, 185:60-89, Brisson et al.
(1984) Nature 310:511-514, TaKamatsu et al, (1987) EMBO J. 6:307-311, Coruzzi et al.
(1984) EMBO J. 3:1671-1680 and Brogli et al„ (1984) Science 224:838-843, Gurley et al.
(1986) Mol. Cell. Biol. 6:559-565 and Weissbach & Weissbach, 1988, Methods for μlant
Molecμlar Biology, Academic Press, NY, Section VIII, pp 421-463.
[00258] It will be appreciated that peptides according to at least some embodiments of
the present invention may be degradation products, synthetic peptides or recombinant
peptides as well as peptidomimetics, typically, synthetic peptides and peptoids and
semipeptoids which are peptide analogs, which may have, for EXAMPLE, modifications
rendering the peptides more stable while in a body or more capable of penetrating into cells.
Such modifications include, but are not limited to N terminus modification, C terminus
modification, peptide bond modification, including, but not limited to, CH2-NH, CH2-S,
CH2-S=0, 0=C-NH, CH2-0, CH2-CH2, S=C-NH, CH=CH or CF=CH, bacKbone
modifications, and residue modification. Metbods for preparing peptidomimetic compounds
are well KNOwn in the art and are specified, for EXAMPLE, in Quantitative Drug Design, C.A.
Ramsden Gd., Chapter 17.2, F. Choμlin Pergamon Press (1992), which is incorporated by
reference as if fμlly set forth herein. Further details in this respect are provided hereinunder.
[00259] Peptide bonds (-CO-NH-) within the peptide may be substituted, for EXAMPLE, by
N-methylated bonds (-N(CH3)-CO-), ester bonds (-C(R)H-C-0-OC(R)-N-), Ketomethylen
bonds (-CO-CH2-), a-aza bonds (-NH-N(R)-CO-), wherein R is any alKyl, e.g., methyl,
carba bonds (-CH2-NH-), hydroxyethylene bonds (-CH(OH)-CH2-), thioamide bonds (-CS-
NH-), olefmic double bonds (-CH=CH-), retro amide bonds (-NH-CO-), peptide derivatives
(-N(R)-CH2-CO-), wherein R is the "normal" side chain, naturally presented on the carbon
atom.
[00260] These modifications can occur at any of the bonds along the peptide chain and
even at several (2-3) at the same time.
[00261] Natural aromatic amino acids, Trp, Tyr and Phe, may be substituted by synthetic
non-natural acid such as Phenylglycine, TIC, naphthylelanine (NOl), ring-methylated
derivatives of Phe, halogenated derivatives of Phe or o- methyl -Tyr.
[00262] In addition to the above, the peptides according to at least some embodiments of
the present invention may also include one or more modified amino acids or one or more
non-amino acid moNOmers (e.g. fatty acids, comμlex carbohydrates etc),
[00263] As used herein in the specification and in the claims section below the term
"amino acid" or "amino acids" is understood to include the 20 naturally occurring amino
acids; those amino acids often modified post-translationally in vivo, including, for EXAMPLE,
hydroxyproline, phosphoserine and phosphomreonine; and other unusual amino acids
including, but not limited to, 2-aminoadipic acid, hydroxylysine, isodesmosine, NOr-valine,
NOr-leucine and ornithine. Furthermore, the term "amino acid" includes both D- and L-
amino acids.
[00264] The peptides according to at least some embodiments of the present invention
might include one or more non-natural or natural polar amino acids, including but not
limited to serine and threonine which are capable of increasing peptide solubility due to
their hydroxyl-containing side chain.
[00265] The peptides according to at least some embodiments of the present invention
can be biochemically synthesized such as by using standard solid phase techniques. These
methods include exclusive solid phase synthesis, partial solid phase synthesis methods,
fragment condensation, classical solution synthesis. These methods are optionally used
when the peptide is relatively short (i.e., 10 KDa) and/or when it cannot be produced by
recombinant techniques (i.e., not encoded by a nucleic acid sequence) and therefore
involves different chemistry.
[00266] Solid phase peptide synthesis procedures are well KNOwn in the art and further
described by John Morrow Stewart and Janis Dillaha Young, Solid Phase Peptide Syntheses
(2nd Ed., Pierce Chemical Company, 1984).
[00267] Synthetic peptides can be purified by preparative high performance liquid
chromatography [Creighton T. (1983) Proteins, structures and molecμlar princiμles. WH
Freeman and Co. N.Y.] and the composition of which can be confirmed via amino acid
sequencing.
[00268] In cases where large amounts of the peptides according to at least some
embodiments of the present invention are desired, the peptides can be generated using
recombinant techniques such as described by Bitter et al., (1987) Methods in Enzymol.
153:516-544, Stuther et al. (1990) Methods in Enzymol. 185:60-89, Brisson et al. (1984)
Nature 310:511-514, TaKamatsu et al. (1987) EMBO J. 6:307-311, Coruzzi et al. (1984)
EMBO J. 3:1671-1680 and Brogli et al., (1984) Science 224:838-843, Gurley et al. (1986)
Mol. Cell. Biol. 6:559-565 and Weissbach & Weissbach, 1988, Methods for μlant
Molecμlar Biology, Academic Press, NY, Section VIII, pp 421-463.
[00269] RECOMBINANT EXPRESSION OF POLYPEPTIDES
[00270] Methods for introduction of heterologous polynucleotides into mammalian cells
are well KNOwn in the art and include dextran-mediated transfection, calcium phosphate
precipitation, polybrene-mediated transfection, protoμlast fusion, electroporation,
encapsμlation of the polynucleotide(s) in liposomes, biolistic injection and direct
microinjection of the DNA into nuclei. In addition, nucleic acid molecμles may be
introduced into mammalian cells by viral vectors. Methods of transforming cells are well
KNOwn in the art. See, e.g., U.S. Patent NOs. 4,399,216, 4,912,040,4,740,461, and 4,959,455
(which patents are hereby incorporated herein by reference). Memods of transforming μlant
cells are well KNOwn in the art, including, e.g., Agrobacterium-mediated transformation,
biolistic transformation, direct injection, electroporation and viral transformation. Methods
of transforming bacterial and yeast cells are also well KNOwn in the art.
[00271] Mammalian cell lines available as hosts for expression are well KNOwn in the art
and include many immortalized cell lines available from e.g, the American Type Cμlture
Collection (ATCC). These include, inter alia, Chinese hamster ovary (CHO) cells, NSO, SP2
cells, HEK-293T cells, NIH-3T3 cells, HeLa cells, baby hamster Kidney (BHK) cells,
monKey Kidney cells (COS), human hepatocellμlar carcinoma cells (e.g., Hep G2), A549
cells, 3T3 cells, and a number of other cell lines. Mammalian host cells include human,
mouse, rat, dog, monKey, pig, goat, bovine, horse and hamster cells. Cell lines of particμlar
preference are selected through determining which cell lines have high expression levels.
Other cell lines that may be used are insect cell lines, such as Sf9 cells, amphibian cells,
bacterial cells, μlant cells and fungal cells. When recombinant expression vectors encoding
the polypeptides according to at least some embodiments of the invention or fragments
thereof are introduced into mammalian host cells, the polypeptides are produced by
cμlturing the host cells for a period of time sufficient to allow for expression of me
polypeptide in the host cells or, more preferably, secretion of the polypeptide into the
cμlture medium in which the host cells are grown. Polypeptides can be recovered from the
cμlture medium using standard protein purification methods. μlant host cells include, e.g.,
Nicotiana, Arabidopsis, ducKweed, corn, wheat, potato, etc. Bacterial host cells include E.
coli and Streptomyces species. Yeast host cells include Schizosaccharomyces pombe,
Saccharomyces cerevisiae and Pichia pastoris.
[00272] Further, expression of the polypeptides according to at least some embodiments
of the invention (or other moieties derived therefrom) from production cell lines can be
enhanced using a number of KNOwn techniques. For EXAMPLE, the glutamine synthetase gene
expression system (the GS system) is a common approach for enhancing expression under
certain conditions. The GS system is discussed in whole or part in connection with
European Patent NOs. 0 216 846,0 256 055,0 338 841 and 0 323 997.
[00273] It is liKely that polypeptides expressed by different cell lines or in transgenic
animals will have different glycosylation patterns. However, all polypeptides encoded by
the nucleic acid molecμles provided herein, or comprising the amino acid sequences
provided herein are part of the instant invention, regardless of their glycosylation pattern.
[00274] VECTORS
[00275] According to at least some embodiments, the invention provides vectors
comprising the nucleic acid molecμles that encode the polypeptides, fusion proteins,
modified polypeptides, and polypeptide fragments of at least some embodiments the
invention.
[00276] To express the polypeptides according to at least some embodiments of the
invention, or fragments thereof, DNAs encoding partial or fμll-length polypeptides,
obtained as described above, are inserted into expression vectors such that the genes are
operatively linKed to transcriptional and translational control sequences. Expression vectors
include plasmids, retroviruses, adenoviruses, adeno-associated viruses (AAV), μlant viruses
such as cauliflower mosaic virus, tobacco mosaic virus, cosmids, YACs, EBV derived
episomes, and the liKe. The gene is ligated into a vector such that transcriptional and
translational control sequences within the vector serve their intended function of regplating
the transcription and translation of the gene. The expression vector and expression control
sequences are chosen to be compatible with the expression host cell used. The gene is
inserted into the expression vector by standard mehods (e.g., ligation of comμlementary
restriction sites on the gene fragment and vector, or blunt end ligation if NO restriction sites
are present).
[00277] A convenient vector is one that encodes a functionally comμlete sequence, with
appropriate restriction sites engineered so that any sequence can be easily inserted and
expressed, as described above. Polyadenylation and transcription termination occur at native
chromosomal sites downstream of the coding regions. The recombinant expression vector
can also encode a signal peptide that facilitates secretion of the polypeptide from a host cell.
The gene may be cloned into the vector such that the signal peptide is linKed in-frame to the
amino terminus of the gene.
[00278] In addition to the nucleic acid according to at least some embodiments of the
invention, the recombinant expression vectors carry regμlatory sequences that control the
expression of the gene in a host cell. It will be appreciated by those sKilled in the art that the
design of the expression vector, including the selection of regμlatory sequences may depend
on such factors as the choice of the host cell to be transformed, the level of expression of
protein desired, etc. Preferred regμlatory sequences for mammalian host cell expression
include viral elements that direct high levels of protein expression in mammalian cells, such
as promoters and/or enhancers derived from retroviral LTRs, cytomegalovirus (CMV) (such
as the CMV promoter/enhancer), Simian Virus 40 (SV40) (such as the SV40
promoter/enhancer), adenovirus, (e.g., the adenovirus major late promoter (AdMLP)),
polyoma and strong mammalian promoters such as native immunogloulin and actin
promoters. For further description of viral regμlatory elements, and sequences thereof, see
e.g., U.S. Pat. NOs. 5,168,062, 4,510,245, and 4,968,615, each of which is hereby
incorporated by reference. Methods of expressing polypeptides in bacterial cells or fungal
cells, e.g., yeast cells, are also well KNOwn in the art.
[00279] In addition to the nucleic acids according to at least some embodiments of the
invention and regμlatory sequences, the recombinant expression vectors according to at
least some embodiments of the invention may carry additional sequences, such as sequences
that regplate reμlication of the vector in host cells (e.g., origins of reμlication) and selectable
marKer genes. The selectable marKer gene facilitates selection of host cells into which the
vector has been introduced (see, e.g., U.S. Pat, NOs. 4,399,216, 4,634,665 and 5,179,017).
For EXAMPLE, typically the selectable marKer gene confers resistance to drugs, such as G418,
hygromycin or methotrexate, on a host cell into which the vector has been introduced.
Preferred selectable marKer genes include the dihydrofolate reductase (DHFR) gene, the neo
gene (for G418 selection), and the glutamate synthetase gene.
100280] PROTEIN MODIFICATIONS
[00281] FUSION PROTEINS
[00282] The present invention encompasses fusion proteins (conjugates) for use in
therapy, comprising the TMEM154 soluble portions including the ectodomain or portions or
variants thereof. For EXAMPLE the invention encompasses conjugates wherein me ECD of the
TMEM154 is attached to an immunogloulin or fragment thereof. The invention
contemplates the use thereof for treating cancer and/or immune related conditions, diseases
or disorders described herein.
[00283] According to at least some embodiments, a fusion protein may be prepared from
a protein according to at least some embodiments of the inventionby fusion with a portion
of an immunogloulin comprising a constant region of an immunogloulin. Optionally, the
portion of the immunogloulin comprises a heavy chain constant region which is optionally
and more preferably a human heavy chain constant region. The heavy chain constant region
is optionally an IgG heavy chain constant region, and optionally an Fc chain, or an IgG Fc
fragment that comprises CH2 and CH3 domains. Although any IgG subtype may optionally
be used, the IgGl subtype is preferred. The Fc chain may optionally be a KNOwn or "wild
type" Fc chain, or alternatively may be mutated. non-limiting, illustrative, exemμlary types
of mutations are described in US Patent Apμlication NO. 20060034852, published on
February 16, 2006, hereby incorporated by reference as if fμlly set forth herein. The term
"Fc chain" also optionally comprises any type of Fc fragment,
[00284] Several of the specific amino acid residues that are important for antibody
constant region-mediated activity in the IgG subclass have been identified. Inclusion,
substitution or exclusion of these specific amino acids therefore allows for inclusion or
exclusion of specific immunogloulin constant region-mediated activity. Furthermore,
specific changes may resμlt in aglycosylation for EXAMPLE and/or other desired changes to
the Fc chain. At least some changes may optionally be made to blocK a function of Fc which
is considered to be undesirable, such as an undesirable immune system effect, as described
in greater detail below.
[00285] non-Hmiting, illustrative EXAMPLEs of mutations to Fc which may be made to
modplate the activity of the fusion protein include the following changes (given with regard
to the Fc sequence NOmenclature as given by Kabat, from Kabat EA et al: Sequences of
Proteins of ImmuNOlogical Interest. US Department of Health and Human Services, NIH,
1991): 220C - > S; 233-238 ELLGGP - > EAEGAP; 265D - > A, preferably in combination
with 434N -> A; 297N - > A (for EXAMPLE to blocK N-glycosylation); 318-322 EYKCK - >
AYACA; 330-331AP - > SS; or a combination thereof (see for EXAMPLE M. ClarK,
"Chemical ImmuNOl and Antibody Engineering", pp 1-31 for a description of these
mutations and their effect). The construct for the Fc chain which features the above changes
optionally and preferably comprises a combination of the hinge region with the CH2 and
CH3 domains.
[00286] The above mutations may optionally be imμlemented to enhance desired
properties or alternatively to blocK non-desired properties. For EXAMPLE, aglycosylation of
antibothes was shown to maintain the desired binding functionality while blocKing
deμletion of T-cells or triggering cytoKine release, which may optionally be undesired
functions (see M. ClarK, "Chemical ImmuNOl and Antibody Engineering", pp 1-31).
Substitution of 331 proline for serine may blocK the ability to activate comμlement, which
may optionally be considered an undesired function (see M. ClarK, "Chemical ImmuNOl and
Antibody Engineering", pp 1-31). Changing 330alanine to serine in combination with this
change may also enhance the desired effect of blocKing the ability to activate comμlement.
[00287] Residues 235 and 237 were shown to be involved in antibody-dependent cell-
mediated cytotoxicity (ADCC), such that changing the blocK of residues from 233-238 as
described may also blocK such activity if ADCC is considered to be an undesirable function.
[00288] Residue 220 is normally a cysteine for Fc from IgGl, which is the site at which
the heavy chain forms a covalent linKage with the light chain. Optionally, this residue may
be changed to a serine, to avoid any type of covalent linKage (see M. ClarK, "Chemical
ImmuNOl and Antibody Engineering", pp 1-31).
[00289] The above changes to residues 265 and 434 may optionally be imμlemented to
reduce or blocK binding to the Fc receptor, which may optionally blocK undesired
functionality of Fc related to its immune system functions (see "Binding site on Human
IgGl for Fc Receptors", Shields et al, Vol 276, pp 6591-6604, 2001).
[00290] The above changes are intended as illustrations only of optional changes and are
not meant to be limiting in any way. Furthermore, the above exμlanation is provided for
descriptive purposes only, without wishing to be bound by a single hypothesis.
[00291] ADDITION OF GROUPS
[00292] If a protein according to the present invention is a linear molecμle, it is possible
to μlace various functional groups at various points on the linear molecμle which are
susceptible to or suitable for chemical modification. Functional groups can be added to the
termini of linear forms of the protein according to at least some embodiments of the
invention. In some embodiments, the functional groups improve the activity of the protein
with regard to one or more characteristics, including but not limited to, improvement in
stability, penetration (through cellμlar membranes and/or tissue barriers), tissue localization,
efficacy, decreased clearance, decreased toxicity, improved selectivity, improved resistance
to expμlsion by cellμlar pumps, and the liKe. For convenience saKe and without wishing to
be limiting, the free N-terminus of one of the sequences contained in the compositions
according to at least some embodiments of the invention will be termed as the N-terminus
of the composition, and the free C-terminal of the sequence will be considered as the C-
terminus of the composition. Either the C-terminus or the N-terminus of the sequences, or
both, can be linKed to a carboxylic acid functional groups or an amine functional group,
respectively,
[00293] non-limiting EXAMPLEs of suitable functional groups are described in Green and
Wuts, "Protecting Groups in Organic Synthesis", John Wiley and Sons, Chapters 5 and 7,
1991, the teachings of which are incorporated herein by reference, Preferred protecting
groups are those that facilitate transport of the active ingrethent attached thereto into a cell,
for EXAMPLE, by reducing the hydrophilicity and increasing the lipophilicity of the active
ingrethent, these being an EXAMPLE for "a moiety for transport across cellμlar membranes".
[00294] These moieties can optionally be cleaved in vivo, either by hydrolysis or
enzymatically, inside the cell. (Ditter et al„ J. Pharm. Sci. 57:783 (1968); Ditter et al., J.
Pharm. Sci. 57:828 (1968); Ditter et al„ J. Pharm. Sci. 58:557 (1969); King et al.,
Biochemistry 26:2294 (1987); Lindberg et al., Drug Metabolism and Disposition 17:311
(1989); and TuneK et al., Biochem. Pharm. 37:3867 (1988), Anderson et al., Arch. Biochem.
Biophys. 239:538 (1985) and Singhal et al., FASEB J. 1:220 (1987)). Hydroxyl protecting
groups include esters, carbonates and carbamate protecting groups. Amine protecting
groups include alKoxy and aryloxy carbonyl groups, as described above for N-terminal
protecting groups. Carboxylic acid protecting groups include aliphatic, benzylic and aryl
esters, as described above for C-terminal protecting groups. In one embodiment, the
carboxylic acid group in the side chain of one or more glutamic acid or aspartic acid residue
in a composition according to at least some embodiments of the present invention is
protected, optionally with a metiiyl, ethyl, benzyl or substituted benzyl ester,
[00295] non-limiting, illustrative EXAMPLEs of N-terminal protecting groups include acyl
groups (-CO-R1) and alKoxy carbonyl or aryloxy carbonyl groups (-CO-0-R1), wherein Rl
is an aliphatic, substituted aliphatic, benzyl, substituted benzyl, aromatic or a substituted
aromatic group. Specific EXAMPLEs of acyl groups include but are not limited to acetyl,
(ethyl)-CO-, n-propyl-CO, iso-propyl-CO-, n-butyl-CO-, sec-butyl-CO-, t-butyl-CO-,
hexyl, lauroyl, palmitoyl, myristoyl, stearyl, oleoyl phenyl-CO-, substituted phenyl-CO-,
benzyl-CO- and (substituted benzyl)-CO-. EXAMPLEs of alKoxy carbonyl and aryloxy
carbonyl groups include CH3-0-CO-, (ethyl)-O-CO-, n-propyl-O-CO-, iso-propyl-O-CO-,
n-butyl-O-CO-, sec-butyl-O-CCK t-butyl-O-CO-, phenyl-O- CO-, substituted
phenyl-O-CO- and benzyl-O-CO-, (substituted benzyl)- 0-CO-, Adamantan, naphtalen,
myristoleyl, toluen, biphenyl, cinnamoyl, nitrobenzoy, toluoyl, furoyl, benzoyl,
cyclohexane, NOrbornane, or Z-caproic. In order to facilitate the N-acylation, one to four
glycine residues can be present in the N-terminus of the molecμle.
[00296] The carboxyl group at the C-terminus of the compound can be protected, for
EXAMPLE, by a group including but not limited to an amide (i.e., the hydroxyl group at the
C-terminus is reμlaced with -NH 2, -NHR2 and -NR2R3) or ester (i.e. the hydroxyl group at
the C-terminus is reμlaced with -OR2). R2 and R3 are optionally independently an aliphatic,
substituted aliphatic, benzyl, substituted benzyl, aryl or a substituted aryl group. In addition,
taKen together with the nitrogen atom, R2 and R3 can optionally form a C4 to C8
heterocyclic ring with from about 0-2 additional heteroatoms such as nitrogen, oxygen or
sμlfur. non-limiting suitable EXAMPLEs of suitable heterocyclic rings include piperidinyl,
pyrrotidinyl, morpholiNO, thiomorpholiNO or piperazinyl. EXAMPLEs of C-terminal protecting
groups include but are not limited to -NH2, -NHCH3, -N(CH3)2, -NH(ethyl), -N(ethyl)2,
-N(methyl) (ethyl), -NH(benzyl), -N(C1-C4 alKyD(benzyl), -NH(phenyl), -N(C1-C4 alKyl)
(phenyl), -OCH3, -O-(efhyl), -O-(n-propyl), -O-(n-butyl), -O-(iso-propyl), -0-(sec- butyl),
-O-(t-butyl), -O-benzyl and -O-phenyl,
[00297] SUBSTITUTION BY PEPTIDOMIMETIC MOIETIES
[00298] A "peptidomimetic organic moiety" can optionally be substituted for amino acid
residues in the composition of this invention both as conservative and as non-conservative
substitutions. These moieties are also termed "non-natural amino acids" and may optionally
reμlace amino acid residues, amino acids or act as spacer groups within the peptides in lieu
of deleted amino acids. The peptidomimetic organic moieties optionally have steric,
electronic or configurational properties similar to the reμlaced amino acid and such
peptidomimetics are used to reμlace amino acids in the essential positions, and are
considered conservative substitutions. However such similarities are not necessarily
required. According to at least some embodiments of the present invention, one or more
peptidomimetics are selected such that the composition at least substantially retains its
physiological activity as compared to the native protein according to the present invention.
[00299] Peptidomimetics may optionally be used to inhibit degradation of the peptides
by enzymatic or other degradative processes. The peptidomimetics can optionally be
produced by organic synthetic techniques. non-limiting EXAMPLEs of suitable
peptidomimetics include D amino acids of the corresponding L amino acids, tetrazol
(ZabrocKi et al„ J, Am. Chem. Soc. 110:5875-5880 (1988)); isosteres of amide bonds (Jones
et al., Tetrahedron Lett. 29: 3853-3856 (1988)); LL-3-amino-2-propenidone-6-carboxylic
acid (LL-Acp) (Kemp et al„ J. Org. Chem. 50:5834-5838 (1985)). Similar analogs are
shown in Kemp et al., Tetrahedron Lett. 29:5081-5082 (1988) as well as Kemp et al.,
Tetrahedron Lett. 29:5057-5060 (1988), Kemp et al., Tetrahedron Lett. 29:4935-4938
(1988) and Kemp et al., J. Org. Chem. 54:109-115 (1987). Other suitable but exemμlary
peptidomimetics are shown in Nagai and Sato, Tetrahedron Lett. 26:647-650 (1985); Di
Maio et al., J. Chem. Soc. PerKin Trans,, 1687 (1985); Kahn et al., Tetrahedron Lett.
30:2317 (1989); Olson et al., J. Am. Chem. Soc. 112:323-333 (1990); Garvey et al., J. Org.
Chem. 56:436 (1990). Further suitable exemμlary peptidomimetics include hydroxy-
1,2,3,4'tetrahydroisoquiNOline- 3-carboxylate (MiyaKe et al., J. TaKeda Res. Labs 43:53-76
(1989)); 1,2,3,4-tetrahydro- isoquiNOline-3-carboxylate (KazmiersKi et al., J. Am. Chem.
Soc. 133:2275-2283 (1991)); histidine isoquiNOlone carboxylic acid (HIC) (Zechel et al.,
Int. J. Pep. Protein Res. 43 (1991)); (2S, 3S)-methyl-phenylalanine, (2S,
3R)-methyl-phenylalanine, (2R, 3S)-methyl- phenylalanine and (2R,
3R)-methyl-phenylalanine (KazmiersKi and Hruby, Tetrahedron Lett. (1991)).
[00300] Exemμlary, illustrative but non-limiting non-natural amino acids include beta-
amino acids (beta3 and beta2), homo-amino acids, cyclic amino acids, aromatic amino
acids, Pro and Pyr derivatives, 3-substituted Alanine derivatives, Glycine derivatives, ring-
substituted Phe and Tyr Derivatives, linear core amino acids or diamine acids. They are
available from a variety of supμliers, such as Sigma-Aldrich (USA) for EXAMPLE,
[00301] CHEMICAL MODIFICATIONS
[00302] In the present invention any part of a protein according to at least some
embodiments of the invention may optionally be chemically modified, i.e. changed by
addition of functional groups. For EXAMPLE the side amino acid residues appearing in the
native sequence may optionally be modified, although as described below alternatively
other parts of the protein may optionally be modified, in addition to or in μlace of the side
amino acid residues. The modification may optionally be performed during synthesis of the
molecμle if a chemical synthetic process is followed, for EXAMPLE by adding a chemically
modified amino acid. However, chemical modification of an amino acid when it is already
present in the molecμle ("in situ" modification) is also possible.
[00303] The amino acid of any of the sequence regions of the molecμle can optionally be
modified according to any one of the following exemμlary types of modification (in the
peptide conceptually viewed as "chemically modified"). non-limiting exemμlary types of
modification include carboxymethylation, acylation, phosphorylation, glycosylation or fatty
acylation. Ether bonds can optionally be used to join the serine or threonine hydroxy! to the
hydroxyl of a sugar. Amide bonds can optionally be used to join the glutamate or aspartate
carboxyl groups to an amino group on a sugar (Garg and Jeanloz, Advances in
Carbohydrate Chemistry and Biochemistry, Vol. 43, Academic Press (1985); Kunz, Ang,
Chem. Int. Ed. English 26:294-308 (1987)). Acetal and Ketal bonds can also optionally be
formed between amino acids and carbohydrates. Fatty acid acyl derivatives can optionally
be made, for EXAMPLE, by acylation of a free amino group (e.g., lysine) (Toth et al.,
Peptides: Chemistry, Structure and Biology, Rivier and Marshal, eds., ESCOM Publ.,
Leiden, 1078-1079(1990)).
[00304] As used herein the term "chemical modification", when referring to a protein or
peptide according to the present invention, refers to a protein or peptide where at least one
of its amino acid residues is modified either by natural processes, such as processing or
other post-translational modifications, or by chemical modification techniques which are
well KNOwn in the art. EXAMPLEs of the numerous KNOwn modifications typically include,
but are not limited to: acetylation, acylation, amidation, ADP-ribosylation, glycosylation,
GPI anchor formation, covalent attachment of a lipid or lipid derivative, methylation,
myristylation, pegylation, prenylation, phosphorylation, ubiquitination, or any similar
process.
[00305] Other types of modifications optionally include the addition of a cycloalKane
moiety to a biological molecμle, such as a protein, as described in PCT Apμlication NO. WO
2006/050262, hereby incorporated by reference as if fμlly set forth herein. These moieties
are designed for use with biomolecμles and may optionally be used to impart various
properties to proteins.
[00306] Furthermore, optionally any point on a protein may be modified. For EXAMPLE,
pegylation of a glycosylation moiety on a protein may optionally be performed, as described
in PCT Apμlication NO. WO 2006/050247, hereby incorporated by reference as if fμlly set
forth herein. One or more polyethylene glycol (PEG) groups may optionally be added to O-
linKed and/or N-linKed glycosylation. The PEG group may optionally be branched or linear.
Optionally any type of water-soluble polymer may be attached to a glycosylation site on a
protein through a glycosyl linKer.
[00307] ALTERED GLYCOSYLATION
[00308] Proteins according to at least some embodiments of the invention may be
modified to have an altered glycosylation pattern (i.e., altered from the original or native
glycosylation pattern). As used herein, "altered" means having one or more carbohydrate
moieties deleted, and/or having at least one glycosylation site added to the original protein.
[00309] Glycosylation of proteins is typically either N-IinKed or O-linKed. N-linKed
refers to the attachment of the carbohydrate moiety to the side chain of an asparagine
residue. The tripeptide sequences, asparagine-X-serine and asparagine-X-threonine, where
X is any amino acid except proline, are the recognition sequences for enzymatic attachment
of the carbohydrate moiety to the asparagine side chain. Thus, the presence of either of
these tripeptide sequences in a polypeptide creates a potential glycosylation site. O-linKed
glycosylation refers to the attachment of one of the sugars N-acetylgalactosamine,
galactose, or xylose to a hydroxyamino acid, most commonly serine or threonine, although
5-hydroxyproline or 5-hydroxylysine may also be used.
[00310] Addition of glycosylation sites to proteins according to at least some
embodiments of the invention is conveniently accomμlished by altering the amino acid
sequence of the protein such that it contains one or more of the above-described tripeptide
sequences (for N-linKed glycosylation sites). The alteration may also be made by the
addition of, or substitution by, one or more serine or threonine residues in the sequence of
the original protein (for O-linKed glycosylation sites). The protein's amino acid sequence
may also be altered by introducing changes at the DNA level.
[00311] Another means of increasing the number of carbohydrate moieties on proteins is
by chemical or enzymatic couμling of glycosides to the amino acid residues of the protein.
Depending on the couμling mode used, the sugars may be attached to (a) arginine and
histidine, (b) free carboxyl groups, (c) free sμlfhydryl groups such as those of cysteine, (d)
free hydroxyl groups such as those of serine, threonine, or hydroxyproline, (e) aromatic
residues such as those of phenylalanine, tyrosine, or tryptophan, or (f) the amide group of
glutamine. These methods are described in WO 87/05330, and in Aμlin and Wriston, CRC
Crit. Rev. Biochem., 22: 259-306 (1981).
[00312] Removal of any carbohydrate moieties present on proteins according to at least
some embodiments of the invention may be accomμlished chemically or enzymatically.
Chemical deglycosylation requires exposure of the protein to trifluoromemanesμlfonic acid,
or an equivalent compound. This treatment ^resμlts in the cleavage of most or all sugars
except the linKing sugar (N-acetylglucosamine or N-acetylgalactosamine), leaving the
amino acid sequence intact.
[00313] Chemical deglycosylation is described by HaKimuddin et al., Arch. Biochem.
Biophys., 259: 52 (1987); and Edge et al., Anal. Biochem., 118: 131 (1981). Enzymatic
cleavage of carbohydrate moieties on proteins can be achieved by the use of a variety of
endo- and exo-glycosidases as described by ThotaKura et al., Meth. Enzymol., 138: 350
(1987).
[00314] METHODS OF TREATMENT USING TMEM154 POLYPEPTIDES AND
PROTEINS
As mentioned hereinabove the TMEM154 proteins and polypeptides according
to at least some embodiments of the present invention or nucleic acid sequence or fragments
thereof especially the ectodomain or secreted forms of TMEM154 proteins and
polypeptides, can be used to treat cancer, including but not limited to lymphoma, especially
non-HodgKin's Lymphoma, anti CD20 (i.e. Rituximab) resistant lymphoma, Mμltiμle
Myeloma, Kidney cancer, and pancreatic cancer, and/or immune related conditions or
disorders.
[00315] Thus, according to at least some embodiments of the present invention there is
provided a method of treating cancer, and/or immune related conditions or disorders
[00316] As used herein the term "treating" refers to preventing, curing, reversing,
attenuating, alleviating, minimizing, suppressing or halting the deleterious effects of the
above-described diseases, disorders or conditions. The term treatment as used herein refers
also to "maintenance therapy", which is a treatment that is given to Keep a pathologic
condition or disorder from coming bacK after it has disappeared following the initial
therapy.
[00317] Treating, according to the present invention, can be effected by specifically
upregplating the expression of at least one of the polypeptides according to at least some
embodiments of the present invention in the subject.
[00318] Optionally, upregμlation may be effected by administering to the subject at least
one of the polypeptides according to at least some embodiments of the present invention
(e.g., recombinant or synthetic) or an active portion thereof, as described herein. However,
since the bioavailability of large polypeptides may potentially be relatively small due to
high degradation rate and low penetration rate, administration of polypeptides is preferably
confined to small peptide fragments (e.g., about 100 amino acids). The polypeptide or
peptide may optionally be administered in as part of a pharmaceutical composition,
described in more detail below.
[00319] It will be appreciated that treatment of the above-described diseases according to
the present invention may be combined with other treatment methods KNOwn in the art (i.e.,
combination therapy).
[00320] ANTI-KRTCAP3, ANTI-FAM26F, ANTI-MGC52498, ANTI-FAM70A,
ANTI-TMEM154 ANTIBOtheS
[00321] The antibothes according to at least some embodiments of the invention
including those having the particμlar germline sequences, homologous antibothes,
antibothes with conservative modifications, engineered and modified antibothes are
characterized by particμlar functional features or properties of the antibothes. For EXAMPLE,
the antibothes bind specifically to human KRTCAP3, FAM26F, MGC52498, FAM70A, or
TMEM154 polypeptides. Optionally, an antibody according to at least some embodiments
of the invention binds to corresponding KRTCAP3, FAM26F, MGC52498, FAM70A, or
TMEM154 polypeptides with high affinity, for EXAMPLE with a KD of 10 -8 M or less or 10
-9 M or less or even 10 -10 M or less. The Anti-KRTCAP3, Anti-FAM26F, Anti-
MGC52498, Anti-FAM70A, Anti-TMEM154 antibothes according to at least some
embodiments of the invention optionally exhibit one or more of the following
characteristics:
[00322] (i) binds to one of the corresponding human KRTCAP3, FAM26F, MGC52498,
FAM70A, or TMEM154 polypeptides with a KD of 5.X10 -8 M or less;
[00323] (ii) binds to one of the KRTCAP3, FAM26F, MGC52498, FAM70A, or
TMEM154 antigen expressed by cancer cells including for EXAMPLE ovarian cancer, lung
cancer, colon cancer, breast cancer, Kidney cancer, liver cancer, pancreatic cancer, prostate
cancer, melaNOma and hematological malignancies such as Mμltiμle Myeloma, lymphoma,
non-HodgKin's lymphoma, anti CD20 (i.e. Rituximab) resistant lymphoma, leuKemia, T
cell leuKemia, but does not substantially bind to normal cells. In addition, optionally these
antibothes and conjugates thereof will be effective in eliciting selective Killing of such
cancer cells and for modplating immune responses involved in autoimmunity and cancer.
[00324] Optionally, the antibody binds to one of the corresponding human KRTCAP3,
FAM26F, MGC52498, FAM70A, or TMEM154 antigens with a KD of 3X10 -8 M or less,
or with a KD of 1X10 -9 M or less, or with a KD of 0.1.X10 -9 M or less, or with a KD Of
0.05.X10 -9 M or less or with a KD of between 1X10 -9 and 1X10 -11 M.
[00325] Standard assays to evaluate the binding ability of the antibothes toward
KRTCAP3, FAM26F, MGC52498, FAM70A, or TMEM154 polypeptides arc KNOwn in the
art, including for EXAMPLE, ELISAs, Western blots and RIAs. Suitable assays are described
in detail in the EXAMPLEs. The binding Kinetics (e.g., binding affinity) of the antibothes also
can be assessed by standard assays KNOwn in the art, such as by Biacore analysis.
[00326] Upon production of Anti-KRTCAP3, Anti-FAM26F, Anti-MGC52498, And-
FAM70A, Anti-TMEM154 antibody sequences from antibothes can bind to KRTCAP3,
FAM26F, MGC52498, FAM70A, or TMEM154 the VH and VL sequences can be "mixed
and matched" to create other anti-KRTCAP3, FAM26F, MGC52498, FAM70A, or
TMEM154 binding molecμles according to at least some embodiments of the invention.
KRTCAP3, FAM26F, MGC52498, FAM70A, or TMEM154 binding of such "mixed and
matched" antibothes can be tested using the binding assays described above, e.g., ELISAs).
Optionally, when VH and VL chains are mixed and matched, a VH sequence from a
particμlar VH/VL pairing is reμlaced with a structurally similar VH sequence. LiKewise,
optionally a VL sequence from a particμlar VH/VL pairing is reμlaced with a structurally
similar VL sequence. For EXAMPLE, the VH and VL sequences of homologous antibothes are
particμlarly amenable for mixing and matching.
[00327] ANTIBOtheS HAVING PARTICμlAR GERMLINE SEQUENCES
[00328] In certain embodiments, an antibody according to at least some embodiments of
the invention comprises a heavy chain variable region from a particμlar germline heavy
chain immunogloulin gene and/or a light chain variable region from a particμlar germline
light chain immunogloulin gene.
[00329] As used herein, a human antibody comprises heavy or light chain variable
regions that is "the product of" or "derived from" a particμlar germline sequence if the
variable regions of the antibody are obtained from a system that uses human germline
immunogloulin genes. Such systems include immunizing a transgenic mouse carrying
human immunogloulin genes with the antigen of interest or screening a human
immunogloulin gene library disμlayed on phage with the antigen of interest. A human
antibody that is "the product of or "derived from" a human germline immunogloulin
sequence can be identified as such by comparing the amino acid sequence of the human
antibody to the amino acid sequences of human germline immunogloulins and selecting
the human germline immunogloulin sequence mat is closest in sequence (i.e., greatest %
identity) to the sequence of the human antibody.
[00330] A human antibody that is "the product of" or "derived from" a particμlar human
germline immunogloulin sequence may contain amino acid differences as compared to the
germline sequence, due to, for EXAMPLE, naturally-occurring somatic mutations or
intentional introduction of site-directed mutation. However, a selected human antibody
typically is at least 90% identical in amino acids sequence to an amino acid sequence
encoded by a human germline immunogloulin gene and contains amino acid residues that
identify the human antibody as being human when compared to the germline
immunogloulin amino acid sequences of other species (e.g., murine germline sequences).
In certain cases, a human antibody may be at least 95, 96, 97, 98 or 99%, or even at least
96%, 97%, 98%, or 99% identical in amino acid sequence to the amino acid sequence
encoded by the germline immunogloulin gene. Typically, a human antibody derived from
a particμlar human germline sequence will disμlay NO more than 10 amino acid differences
from the amino acid sequence encoded by the human germline immunogloulin gene. In
certain cases, the human antibody may disμlay NO more than 5, or even NO more than 4, 3, 2,
or 1 amino acid difference from the amino acid sequence encoded by the germline
immunogloulin gene.
[00331] HOMOLOGOUS ANTIBOtheS
[00332] In yet another embodiment, an antibody according to at least some embodiments
of the invention comprises heavy and light chain variable regions comprising amino acid
sequences that are homologous to isolated Anti-KRTCAP3, Anti-FAM26F, Anti-
MGC52498, Anti-FAM70A, Anti-TMEM154 amino acid sequences of preferred Anti-
KRTCAP3, Anti-FAM26F, Anti-MGC52498, Anti-FAM70A, Anti-TMEM154 antibothes,
respectively, wherein the antibothes retain the desired functional properties of the parent
Anti-KRTCAP3, Anfi-FAM26F, Anti-MGC52498, Anti-FAM70A, Anti-TMEM154
antibothes.
[00333] As used herein, the percent homology between two amino acid sequences is
equivalent to the percent identity between the two sequences. The percent identity between
the two sequences is a function of the number of identical positions shared by the sequences
(i.e., % homo!ogy=# of identical positions/total # of positions X 100), taKing into account
the number of gaps, and the length of each gap, which need to be introduced for optimal
alignment of the two sequences. The comparison of sequences and determination of percent
identity between two sequences can be accomμlished using a mathematical algorithm, as
described in the non-limiting EXAMPLEs below.
[00334] The percent identity between two amino acid sequences can be determined using
the algorithm of E. Meyers and W. Miller (Comput. Apμl. Biosci., 4; 11-17 (1988)) which
has been incorporated into the ALIGN program (version 2.0), using a PAM120 weight
residue table, a gap length penalty of 12 and a gap penalty of 4. In addition, the percent
identity between two amino acid sequences can be determined using the Needleman and
Wunsch (J. Mol. Biol. 48:444-453 (1970)) algorithm which has been incorporated into the
GAP program in the GCG software pacKage (available commercially), using either a
Blossum 62 matrix or a PAM250 matrix, and a gap weight of 16,14,12,10, 8, 6, or 4 and a
length weight of 1, 2,3,4, 5, or 6.
[00335] Additionally or alternatively, the protein sequences according to at least some
embodiments of the present invention can further be used as a "query sequence" to perform
a search against public databases to, for EXAMPLE, identify related sequences. Such searches
can be performed using the XBLAST program (version 2.0) of Altschμl, et al. (1990) J Mol.
Biol. 215:403-10. BLAST protein searches can be performed with the XBLAST program,
score=50, wordlength=3 to obtain amino acid sequences homologous to the antibody
molecμles according to at least some embodiments of the invention. To obtain gapped
alignments for comparison purposes, Gapped BLAST can be utilized as described in
Altschμl et al., (1997) Nucleic Acids Res. 25(17):3389-3402. When utilizing BLAST and
Gapped BLAST programs, the defaμlt parameters of the respective programs (e.g.,
XBLAST and NBLAST) can be used.
[00336] Antibothes with Conservative Modifications
[00337] In certain embodiments, an antibody according to at least some embodiments of
the invention comprises a heavy chain variable region comprising CDR1, CDR2 and CDR3
sequences and a light chain variable region comprising CDR1, CDR2 and CDR3 sequences,
wherein one or more of these CDR sequences comprise specified amino acid sequences
based on preferred Anti-KRTCAP3, Anti-FAM26F, Anti-MGC52498, Anti-FAM70A,
Anti-TMEM154 antibothes isolated and produced using methods herein, or conservative
modifications thereof, and wherein the antibothes retain the desired functional properties of
the Anti-KRTCAP3, Anti-FAM26F, Anti-MGC52498, Anti-FAM70A, Anti-TMEM154
antibothes according to at least some embodiments of the invention, respectively.
[00338] In various embodiments, the Anti-KRTCAP3, Anti-FAM26F, Anti-MGC52498,
Anti-FAM70A, Anti-TMEM154 antibody can be, for EXAMPLE, human antibothes,
humanized antibothes or chimeric antibothes.
[00339] As used herein, the term "conservative sequence modifications" is intended to
refer to amino acid modifications that do not significantly affect or alter the binding
characteristics of the antibody containing the amino acid sequence. Such conservative
modifications include amino acid substitutions, additions and deletions. Modifications can
be introduced into an antibody according to at least some embodiments of the invention by
standard techniques KNOwn in the art, such as site-directed mutagenesis and PCR-mediated
mutagenesis. Conservative amino acid substitutions are ones in which the amino acid
residue is reμlaced with an amino acid residue having a similar side chain. Families of
amino acid residues having similar side chains have been defined in the art. These families
include amino acids with basic side chains (e.g., lysine, arginine, histidine), acidic side
chains (e.g., aspartic acid, glutamic acid), uncharged polar side chains (e.g., glycine,
asparagine, glutamine, serine, threonine, tyrosine, cysteine, tryptophan), nonpolar side
chains (e.g., alanine, valine, leucine, isoleucine, proline, phenylalanine, methionine), beta-
branched side chains (e.g., threonine, valine, isoleucine) and aromatic side chains (e.g.,
tyrosine, phenylalanine, tryptophan, histidine). Thus, one or more amino acid residues
within the CDR regions of an antibody according to at least some embodiments of the
invention can be reμlaced witfi other amino acid residues from the same side chain family
and the altered antibody can be tested for retained function (i.e., the functions set forth in (c)
through (j) above) using the functional assays described herein.
[00340] ENGINEERED AND MODIFIED ANTIBOtheS
[00341] An antibody according to at least some embodiments of the invention can be
prepared using an antibody having one or more of the VH and/or VL sequences derived
from an Anti-KRTCAP3, Anti-FAM26F, Anti-MGC52498, Anti-FAM70A, Anti-
TMEM154antibody starting material to engineer a modified antibody, which modified
antibody may have altered properties from the starting antibody. An antibody can be
engineered by modifying one or more residues within one or bom variable regions (i.e., VH
and/or VL), for EXAMPLE within one or more CDR regions and/or within one or more
frameworK regions. Additionally or alternatively, an antibody can be engineered by
modifying residues within the constant regions, for EXAMPLE to alter the effector functions of
me antibody,
[00342] One type of variable region engineering that can be performed is CDR grafting.
Antibothes interact with target antigens predominantly through amino acid residues mat are
located in the six heavy and light chain comμlementarity determining regions (CDRs), For
this reason, the amino acid sequences within CDRs are more diverse between individual
antibothes than sequences outside of CDRs. Because CDR sequences are responsible for
most antibody-antigen interactions, it is possible to express recombinant antibothes that
mimic the properties of specific naturally occurring antibothes by constructing expression
vectors that include CDR sequences from the specific naturally occurring antibody grafted
onto frameworK sequences from a different antibody with different properties (see, e.g.,
Riechmann, L. et al. (1998) Nature 332:323-327; Jones, P. et al. (1986) Nature 321:522-
525; Queen, C. et al. (1989) Proc. Natl. Acad. See. U.S.A. 86:10029-10033; U.S. Pat. NO.
5,225,539 to Winter, and U.S. Pat. NOs. 5,530,101; 5,585,089; 5,693,762 and 6,180,370 to
Queen et al.)
[00343] Suitable frameworK sequences can be obtained from public DNA databases or
published references that include germline antibody gene sequences. For EXAMPLE, germline
DNA sequences for human heavy and light chain variable region genes can be found in the
"VBase" human germline sequence database (available on the Internet), as well as in Kabat,
E. A., et al. (1991) Sequences of Proteins of ImmuNOlogical Interest, Fifth Edition, U.S.
Department of Health and Human Services, NTH Publication NO. 91-3242; Tomlinson, I.
M„ et al. (1992) "The Repertoire of Human Germline VH Sequences Reveals about Fifty
Groups of VH Segments with Different Hypervariable 100ps" J. Mol. Biol. 227:776-798;
and Cox, J. P. L. et al. (1994) "A Directory of Human Germ-line VH Segments Reveals a
Strong Bias in their Usage" Eur. J ImmuNOl, 24:827-836; the contents of each of which are
expressly incorporated herein by reference,
[00344] Another type of variable region modification is to mutate amino acid residues
within the VH and/or VL CDR 1, CDR2 and/or CDR3 regions to thereby improve one or
more binding properties (e.g., affinity) of the antibody of interest. Site-directed mutagenesis
or PCR-mediated mutagenesis can be performed to introduce the mutations and the effect
on antibody binding, or other functional property of interest, can be evaluated in appropriate
in vitro or in vivo assays. Optionally conservative modifications (as discussed above) are
introduced. The mutations may be amino acid substitutions, additions or deletions, but are
preferably substitutions. Moreover, typically NO more than one, two, three, four or five
residues within a CDR region are altered.
[00345] Engineered antibothes according to at least some embodiments of the invention
include those in which modifications have been made to frameworK residues within VH
and/or VL, e.g. to improve the properties of the antibody. Typically such frameworK
modifications are made to decrease the immuNOgenicity of the antibody. For EXAMPLE, one
approach is to "bacKmutate" one or more frameworK residues to the corresponding germline
sequence. More specifically, an antibody that has undergone somatic mutation may contain
frameworK residues that differ from the germline sequence from which the antibody is
derived. Such residues can be identified by comparing the antibody frameworK sequences to
the germline sequences from which the antibody is derived,
[00346] In addition or alternative to modifications made within the frameworK or CDR
regions, antibothes according to at least some embodiments of the invention may be
engineered to include modifications within the Fc region, typically to alter one or more
functional properties of the antibody, such as serum half-life, comμlement fixation, Fc
receptor binding, and/or antigen-dependent cellμlar cytotoxicity. Furthermore, an antibody
according to at least some embodiments of the invention may be chemically modified (e.g.,
one or more chemical moieties can be attached to the antibody) or be modified to alter its
glycosylation, again to alter one or more functional properties of the antibody. Such
embodiments are described further below. The numbering of residues in the Fc region is
that of the EU index of Kabat.
[00347] In one embodiment, the hinge region of CH1 is modified such that the number of
cysteine residues in the hinge region is altered, e.g., increased or decreased. This approach
is described further in U.S. Pat. NO, 5,677,425 by Bodmer et al. The number of cysteine
residues in the hinge region of CHI is altered to, for EXAMPLE, facilitate assembly of the
light and heavy chains or to increase or decrease the stability of the antibody.
[00348] In another embodiment, the Fc hinge region of an antibody is mutated to
decrease the biological half life of the antibody. More specifically, one or more amino acid
mutations are introduced into the CH2-CH3 domain interface region of the Fc-hinge
fragment such that the antibody has impaired Staphylococcyl protein A (SpA) binding
relative to native Fc-hinge domain SpA binding. This approach is described in further detail
in U.S. Pat. NO. 6,165,745 by Ward et al.
[00349] In another embodiment, the antibody is modified to increase its biological half
life. Various approaches are possible. For EXAMPLE, one or more of the following mutations
can be introduced: T252L, T254S, T256F, as described in U.S. Pat. NO. 6,277,375 to Ward.
Alternatively, to increase the biological half life, the antibody can be altered within the CHI
or CL region to contain a salvage receptor binding epitope taKen from two 100ps of a CH2
domain of an Fc region of an IgG, as described in U.S. Pat. NOs. 5,869,046 and 6,121,022
by Prestaet al.
[00350] In yet other embodiments, the Fc region is altered by reμlacing at least one
amino acid residue with a different amino acid residue to alter the effector functions of the
antibody. For EXAMPLE, one or more amino acids selected from amino acid residues 234,
235, 236, 237, 297, 318, 320 and 322 can be reμlaced with a different amino acid residue
such that the antibody has an altered affinity for an effector ligand but retains the antigen-
binding ability of the parent antibody. The effector ligand to which affinity is altered can be,
for EXAMPLE, an Fc receptor or the CI component of comμlement. This approach is
described in further detail in U.S. Pat. NOs. 5,624,821 and 5,648,260, both by Winter et al.
[00351] In another EXAMPLE, one or more amino acids selected from amino acid residues
329, 331 and 322 can be reμlaced with a different amino acid residue such that the antibody
has altered Clq binding and/or reduced or abolished comμlement dependent cytotoxicity
(CDC). This approach is described in further detail in U.S. Pat. NOs. 6,194,551 by Idusogie
etal.
[00352] In another EXAMPLE, one or more amino acid residues within amino acid
positions 231 and 239 are altered to thereby alter the ability of the antibody to fix
comμlement. This approach is described further in PCT Publication WO 94/29351 by
Bodmer et al.
[00353] In yet another EXAMPLE, the Fc region is modified to increase the ability of the
antibody to mediate antibody dependent cellμlar cytotoxicity (ADCC) and/or to increase the
affinity of the antibody for an Fey receptor by modifying one or more amino acids at the
following positions: 238, 239, 248, 249, 252, 254, 255, 256, 258, 265, 267, 268, 269, 270,
272, 276, 278, 280, 283, 285, 286, 289, 290, 292, 293, 294, 295, 296, 298, 301, 303, 305,
307, 309, 312, 315, 320, 322, 324, 326, 327, 329, 330, 331, 333, 334, 335, 337, 338, 340,
360, 373, 376, 378, 382, 388, 389, 398, 414, 416, 419, 430, 434, 435, 437, 438 or 439. This
approach is described further in PCT Publication WO 00/42072 by Presta. Moreover, the
binding sites on human IgGl for Fc grammar, Fc gamma RU, Fc gammaRIII and FcRn have
been mapped and variants with improved binding have been described (see Shields, R. L. et
al. (2001) J. Biol. Chem. 276:6591-6604). Specific mutations at positions 256, 290, 298,
333, 334 and 339 are shown to improve binding to FcyRIII. Additionally, the following
combination mutants are shown to improve Fcgamma.RIII binding: T256A/S298A,
S298A/E333A, S298A/K224A and S298A/E333A/K334A.
[00354] In still another embodiment, the glycosylation of an antibody is modified. For
EXAMPLE, an aglycoslated antibody can be made (i.e., the antibody lacKs glycosylation).
Glycosylation can be altered to, for EXAMPLE, increase the affinity of the antibody for
antigen. Such carbohydrate modifications can be accomμlished by, for EXAMPLE, altering
one or more sites of glycosylation within the antibody sequence. For EXAMPLE, one or more
amino acid substitutions can be made that resμlt in elimination of one or more variable
region frameworK glycosylation sites to thereby eliminate glycosylation at that site. Such
aglycosylation may increase the affinity of the antibody for antigen. Such an approach is
described in further detail in U.S. Pat. NOs. 5,714,350 and 6,350,861 by Co et al.
[00355] Additionally or alternatively, an antibody can be made that has an altered type of
glycosylation, such as a hypofucosylated antibody having reduced amounts of fucosyl
residues or an antibody having increased bisecting GlcNac structures. Such altered
glycosylation patterns have been demonstrated to increase the ADCC ability of antibothes.
Such carbohydrate modifications can be accomμlished by, for EXAMPLE, expressing the
antibody in a host cell with altered glycosylation machinery. Cells with altered
glycosylation machinery have been described in the art and can be used as host cells in
which to express recombinant antibothes according to at least some embodiments of the
invention to thereby produce an antibody with altered glycosylation. For EXAMPLE, the cell
lines Ms704, Ms705, and Ms709 lacK the fucosyltransferase gene, FUT8 (alpha (1,6)
fucosyltransferase), such that antibothes expressed in the Ms704, Ms705, and Ms709 cell
lines lacK fucose on their carbohydrates. The Ms704, Ms705, and Ms709 FUT8.-/- cell lines
are created by the targeted disruption of the FUT8 gene in CHO/DG44 cells using two
reμlacement vectors (see U.S. Patent Publication NO. 20040110704 by Yamane et al, and
Yamane-OhnuKi et al. (2004) BiotechNOl Bioeng 87:614-22). As another EXAMPLE, EP
1,176,195 by Hanai et al. describes a cell line with a functionally disrupted FUT8 gene,
which encodes a fucosyl transferase, such that antibothes expressed in such a cell line
exhibit hypofucosylation by reducing or eliminating the alpha 1,6 bond-related enzyme.
Hanai et al. also describe cell lines which have a low enzyme activity for adding fucose to
the N-acetylglucosamine that binds to the Fc region of the antibody or does not have the
enzyme activity, for EXAMPLE the rat myeloma cell line YB2/0 (ATCC CRL 1662). PCT
Publication WO 03/035835 by Presta describes a variant CHO cell line, Lecl3 cells, with
reduced ability to attach fucose to Asn(297) -linKed carbohydrates, also resμlting in
hypofucosylation of antibothes expressed in that host cell (see also Shields, R, L. et al.
(2002) J. Biol. Chem. 277:26733-26740). PCT Publication WO 99/54342 by Umana et al.
describes cell lines engineered to express glycoprotein-modifying glycosyl transferases
(e.g., beta(l,4)-N-acetylglucosaminyltransferase III (GnTIII)) such that antibothes
expressed in the engineered cell lines exhibit increased bisecting GlcNac structures which
resμlts in increased ADCC activity of the antibothes (see also Umana et al. (1999) Nat.
Biotech. 17:176-180). Alternatively, the fucose residues of the antibody may be cleaved off
using a fucosidase enzyme. For EXAMPLE, the fucosidase alpha-L-fucosidase removes
fucosyl residues from antibothes (TarentiNO, A. L, et al. (1975) Biochem. 14:5516-23).
[00356] Another modification of the antibothes herein that is contemplated by the
invention is pegylation. An antibody can be pegylated to, for EXAMPLE, increase the
biological (e.g., serum) half life of the antibody. To pegylate an antibody, the antibody, or
fragment thereof, typically is reacted with polyethylene glycol (PEG), such as a reactive
ester or aldehyde derivative of PEG, under conditions in which one or more PEG groups
become attached to the antibody or antibody fragment. Optionally, the pegylation is carried
out via an acylation reaction or an alKylation reaction with a reactive PEG molecμle (or an
analogous reactive water-soluble polymer). As used herein, the term "polyethylene glycol"
is intended to encompass any of the forms of PEG that have been used to derivatize other
proteins, such as moNO (C1-C10) alKoxy- or aryloxy-polyethylene glycol or polyethylene
glycol-maleimide. In certain embodiments, the antibody to be pegylated is an aglycosylated
antibody. Methods for pegylating proteins are KNOwn in the art and can be apμlied to the
antibothes according to at least some embodiments of the invention. See for EXAMPLE, EP 0
154 316 by Nishimura et al. and EP 0 401 384 by IshiKawa et al.
[00357] METHODS OF ENGINEERING ANTIBOtheS
[00358] As discussed above, the Anti-KRTCAP3, Anti-FAM26F, Anti-MGC52498,
Anti-FAM70A, Anti-TMEM154 antibothes having VH and VK sequences disclosed herein
can be used to create new Anti-KRTCAP3, Anti-FAM26F, Anti-MGC52498, Anti-
FAM70A, Anti-TMEM154antibothes, respectively, by modifying the VH and/or VL
sequences, or the constant regions attached thereto. Thus, according to at least some
embodiments of the invention, the structural features of an Anti-KRTCAP3, Anti-FAM26F,
Anti-MGC52498, Anti-FAM70A, Anti-TMEM154 antibody according to at least some
embodiments of the invention, are used to create structurally related Anti-KRTCAP3, And-
FAM26F, Anti-MGC52498, Anti-FAM70A, Anti-TMEM154 antibothes that retain at least
one functional property of the antibothes according to at least some embodiments of the
invention, such as binding to human KRTCAP3, FAM26F, MGC52498, FAM70A, or
TMEM154, respectively. For EXAMPLE, one or more CDR regions of one KRTCAP3,
FAM26F, MGC52498, FAM70A, or TMEM154 antibody or mutations thereof, can be
combined recombinantly with KNOwn frameworK regions and/or other CDRs to create
additional, recombinantly-engineered, Anti-KRTCAP3, Anti-FAM26FF, Anti-MGC52498,
Anti-FAM70A, Anti-TMEM154 antibothes according to at least some embodiments of the
invention, as discussed above. Other types of modifications include those described in the
previous section. The starting material for the engineering method is one or more of the VH
and/or VK sequences provided herein, or one or more CDR regions thereof. To create the
engineered antibody, it is not necessary to actually prepare (i.e., express as a protein) an
antibody having one or more of the VH and/or VK sequences provided herein, or one or
more CDR regions thereof. Rather, the information contained in the sequences is used as the
starting material to create a "second generation" sequences derived from the original
sequences and then the "second generation" sequences is prepared and expressed as a
protein.
[00359] Standard molecμlar biology techniques can be used to prepare and express
altered antibody sequence.
[00360] Optionally, the antibody encoded by the altered antibody sequences is one that
retains one, some or all of the functional properties of the Anti-KRTCAP3, Anti-FAM26F,
Anti-MGC52498, Anti-FAM70A, Anti-TMEM154 antibothes, respectively, produced by
methods and with sequences provided herein, which functional properties include binding to
KRTCAP3, FAM26F, MGC52498, FAM70A, or TMEM154 antigen with a specific KD
level or less and/or selectively binding to desired target cells such as ovarian cancer, lung
cancer, breast cancer, colon cancer, Kidney cancer, liver cancer, pancreatic cancer, prostate
cancer, melaNOma and hematological malignancies such as Mμltiμle Myeloma, lymphoma,
non-HodgKin's lymphoma, anti CD20 (i.e. Rituximab) resistant lymphoma, leuKemia, T
cell leuKemia, that express KRTCAP3, FAM26F, MGC52498, FAM70A, or TMEM154
antigen.
[00361] The functional properties of the altered antibothes can be assessed using standard
assays available in the art and/or described herein,
[00362] In certain embodiments of the methods of engineering antibothes according to at
least some embodiments of the invention, mutations can be introduced randomly or
selectively along all or part of an Anti-KRTCAP3, Anti-FAM26F, Anti-MGC52498, Anti-
FAM70A, Anti-TMEM154 antibody coding sequence and the resμlting modified Anti-
KRTCAP3, Anti-FAM26F, Anti-MGC52498, Anti-FAM70A, Anti-TMEM154 antibothes
can be screened for binding activity and/or other desired functional properties.
[00363] Mutational methods have been described in the art. For EXAMPLE, PCT
Publication WO 02/092780 by Short describes methods for creating and screening antibody
mutations using saturation mutagenesis, synthetic ligation assembly, or a combination
thereof. Alternatively, PCT Publication WO 03/074679 by Lazar et al. describes methods of
using computational screening methods to optimize physiochemical properties of
antibothes.
[00364] NUCLEIC ACID MOLECμlES ENCODING ANTIBOtheS
[00365] According to at least some embodiments of the inventionpertains to nucleic acid
molecμles that encode the antibothes according to at least some embodiments of the
invention. The nucleic acids may be present in whole cells, in a cell lysate, or in a partially
purified or substantially pure form. A nucleic acid is "isolated" or "rendered substantially
pure" when purified away from other cellμlar components or other contaminants, e.g., other
cellμlar nucleic acids or proteins, by standard techniques, including alKaline/SDS treatment,
CsCl banding, column chromatography, agarose gel electrophoresis and others well KNOwn
in the art. See, F. Ausubel, et al., ed. (1987) Current Protocols in Molecμlar Biology, Greene
Publishing and Wiley Interscience, New YorK. A nucleic acid according to at least some
embodiments of the invention can be, for EXAMPLE, DNA or RNA and may or may not
contain intronic sequences. In a preferred embodiment, the nucleic acid is a cDNA
molecμle.
[00366] Nucleic acids according to at least some embodiments of the invention can be
obtained using standard molecμlar biology techniques. For antibothes expressed by
hybridomas (e.g., hybridomas prepared from transgenic mice carrying human
immunogloulin genes as described further below), cDNAs encoding the light and heavy
chains of the antibody made by the hybridoma can be obtained by standard PCR
amμlification or cDNA cloning techniques. For antibothes obtained from an
immunogloulin gene library (e.g., using phage disμlay techniques), nucleic acid encoding
the antibody can be recovered from the library.
[00367] Once DNA fragments encoding VH and VL segments are obtained, these DNA
fragments can be further manipplated by standard recombinant DNA techniques, for
EXAMPLE to convert the variable region genes to fμll-length antibody chain genes, to Fab
fragment genes or to a scFv gene. In these manipμlations, a VL- or VH-encoding DNA
fragment is operatively linKed to another DNA fragment encoding another protein, such as
an antibody constant region or a flexible linKer.
[00368] The term "operatively linKed", as used in this context, is intended to mean that
the two DNA fragments are joined such that the amino acid sequences encoded by the two
DNA fragments remain in-frame.
[00369] The isolated DNA encoding the VH region can be converted to a fμll-length
heavy chain gene by operatively linKing the VH-encoding DNA to another DNA molecμle
encoding heavy chain constant regions (CHI, CH2 and CH3). The sequences of human
heavy chain constant region genes are KNOwn in the art (see e.g., Kabat, E. A., el al. (1991)
Sequences of Proteins of ImmuNOlogical Interest, Fifth Edition, U.S. Department of Health
and Human Services, NIH Publication NO. 91-3242) and DNA fragments encompassing
these regions can be obtained by standard PCR amμlification. The heavy chain constant
region can be an IgGl, IgG2, IgG3, IgG4, IgA, IgE, IgM or IgD constant region. For a Fab
fragment heavy chain gene, the VH-encoding DNA can be operatively linKed to another
DNA molecμle encoding only the heavy chain CHI constant region.
[00370] The isolated DNA encoding the VL region can be converted to a fμll-length light
chain gene (as well as a Fab light chain gene) by operatively linKing the VL-encoding DNA
to another DNA molecμle encoding the light chain constant region, CL. The sequences of
human light chain constant region genes are KNOwn in the art (see e.g., Kabat, E. A., et al.
(1991) Sequences of Proteins of ImmuNOlogical Interest, Fifth Edition, U.S. Department of
Health and Human Services, NIH Publication NO. 91-3242) and DNA fragments
encompassing these regions can be obtained by standard PCR amμlification. The light chain
constant region can be a Kappa or lambda constant region,
[00371] To create a scFv gene, the VH- and VL-encoding DNA fragments are
operatively linKed to another fragment encoding a flexible linKer, e.g., encoding the amino
acid sequence (Gly4-Ser)3, such that the VH and VL sequences can be expressed as a
contiguous single-chain protein, with the VL and VH regions joined by the flexible linKer
(see e.g., Bird et al. (1988) Science 242:423-426; Huston et al. (1988) Proc. Natl. Acad. Sci.
USA 85:5879-5883; McCafferty et al., (1990) Nature 348:552-554).
[00372] Production Of Anli-KRTCAP3, Anti-FAM26F, Anti-MGC52498, Anti-
FAM70A, Anti-TMEM154 monoclonal Antibothes
[00373] monoclonal antibothes (mAbs) according to at least some embodiments of the
present invention can be produced by a variety of techniques, including conventional
monoclonal antibody methodology e.g., the standard somatic cell hybridization technique of
Kohler and Milstein (1975) Nature 256:495. Although somatic cell hybridization procedures
are preferred, in princiμle, other techniques for producing monoclonal antibody can be
emμloyed e.g., viral or oncogenic transformation of B lymphocytes.
[00374] A preferred animal system for preparing hybridomas is the murine system,
Hybridoma production in the mouse is a very well-established procedure. Immunization
protocols and techniques for isolation of immunized sμleNOcytes for fusion are KNOwn in the
art. Fusion partners (e.g., murine myeloma cells) and fusion procedures are also KNOwn.
[00375] Chimeric or humanized antibothes according to at least some embodiments of
the present invention can be prepared based on the sequence of a murine monoclonal
antibody prepared as described above. DNA encoding the heavy and light chain
immunogloulins can be obtained from the murine hybridoma of interest and engineered to
contain non-murine (e.g.,. human) immunogloulin sequences using standard molecμlar
biology techniques. For EXAMPLE, to create a chimeric antibody, the murine variable regions
can be linKed to human constant regions using mediods KNOwn in the art (see e.g., U.S. Pat.
NO. 4,816,567 to Cabilly et al.). To create a humanized antibody, the murine CDR regions
can be inserted into a human frameworK using methods KNOwn in the art (see e.g., U.S. Pat.
NO. 5,225,539 to Winter, and U.S. Pat. NOs. 5,530,101; 5,585,089; 5,693,762 and 6,180,370
to Queen et al.).
[00376] In a preferred embodiment, the antibothes according to at least some
embodiments of the invention are human monoclonal antibothes. Such human monoclonal
antibothes directed against KRTCAP3, FAM26F, MGC52498, FAM70A or TMEM154 can
be generated using transgenic or transchromosomic mice carrying parts of the human
immune system rather than the mouse system. These transgenic and transchromosomic mice
include mice referred to herein as the HuMAb Mouse RTM and KM Mouse, RTM.
respectively, and are collectively referred to herein as "human Ig mice." The HuMAb
Mouse TM, (Medarex. Inc.) contains human immunogloulin gene miniloci that encode
unrearranged human heavy (.mu, and.gamma.) and.Kappa. light chain immunogloulin
sequences, together with targeted mutations that inactivate the endogeNOus.mu. and.Kappa.
chain loci (see e.g., Lonberg, et al. (1994) Nature 368(6474): 856-859). Accordingly, the
mice exhibit reduced expression of mouse IgM or.Kappa., and in response to immunization,
the introduced human heavy and light chain transgenes undergo class switching and somatic
mutation to generate high affinity human IgGKappa. monoclonal (Lonberg, N. et al, (1994),
supra; reviewed in Lonberg, N. (1994) HandbooK of Experimental Pharmacology 113:49-
101; Lonberg, N. and Huszar, D. (1995) Intern. Rev. ImmuNOl. 13: 65-93, and Harding, F.
and Lonberg, N. (1995) Ann. N.Y. Acad. Sci. 764:536-546). The preparation and use of the
HuMab Mouse RTM., and the geNOmic modifications carried by such mice, is further
described in Taylor, L. et al. (1992) Nucleic Acids Research 20:6287-6295; Chen, J. et al.
(1993) International ImmuNOlogy 5:647-656; Tuaillon et al. (1993) Proc. Natl. Acad. Sci.
USA 90:3720-3724; Choi et al. (1993) Nature Genetics 4:117-123; Chen, J. et al. (1993)
EMBO J. 12: 821-830; Tuaillon et al. (1994) J. ImmuNOl. 152:2912-2920; Taylor, L, et al.
(1994) International ImmuNOlogy 6:579-591; and Fishwild, D. et al. (1996) Nature
BiotechNOlogy 14: 845-851, the contents of all of which are hereby specifically incorporated
by reference in their entirety. See further, U.S. Pat. NOs. 5,545,806; 5,569,825; 5,625,126;
5,633,425; 5,789,650; 5,877,397; 5,661,016; 5,814,318; 5,874,299; and 5,770,429; all to
Lonberg and Kay; U.S. Pat. NO. 5,545,807 to Surani et al.; PCT Publication NOs. WO
92/03918, WO 93/12227, WO 94/25585, WO 97/13852, WO 98/24884 and WO 99/45962,
all to Lonberg and Kay; and PCT Publication NO. WO 01/14424 to Korman et al.
[00377] In another embodiment, human antibothes according to at least some
embodiments of the invention can be raised using a mouse that carries human
immunogloulin sequences on transgenes and transchomosomes, such as a mouse that
carries a human heavy chain transgene and a human light chain transchromosome. Such
mice, referred to herein as "KM mice TM.", are described in detail in PCT Publication WO
02/43478 to Ishida et al.
[00378] Still further, alternative transgenic animal systems expressing human
immunogloulin genes are available in the art and can be used to raise anti- KRTCAP3,
FAM26F, MGC52498, FAM70A or TMEM154 antibothes according to at least some
embodiments of the invention. For EXAMPLE, an alternative transgenic system referred to as
the XeNOmouse (Abgenix, Inc.) can be used; such mice are described in, for EXAMPLE, U.S.
Pat. NOs. 5,939,598; 6,075,181; 6,114,598; 6,150,584 and 6,162,963 to Kucherlapati et al.
[00379] Moreover, alternative transchromosomic animal systems expressing human
immunogloulin genes are available in the art and can be used to raise Anti-KRTCAP3,
Anti-FAM26F, Anti-MGC52498, Anti-FAM70A, Anti-TMEM154 antibothes according to
at least some embodiments of the invention, For EXAMPLE, mice carrying both a human
heavy chain transchromosome and a human light chain transchromosome, referred to as
"TC mice" can be used; such mice are described in TomizuKa et al. (2000) Proc. Natl. Acad
Sci. USA 97:722-727. Furthermore, cows carrying human heavy and light chain
transchromosomes have been described in the art (Kuroiwa et al. (2002) Nature
BiotechNOlogy 20:889-894) and can be used to raise Anti-KRTCAP3, Anti-FAM26F, Anti-
MGC52498, Anti-FAM70A, Anti-TMEM154 antibothes according to at least some
embodiments of the invention,
[00380] Human monoclonal antibothes according to at least some embodiments of the
invention can also be prepared using phage^disμlay methods for screening libraries of
human immunogloulin genes. Such phage disμlay methods for isolating human antibothes
are established in the art. See for EXAMPLE: U.S. Pat. NOs. 5,223,409; 5,403,484; and
5,571,698 to Ladner et al.; U.S. Pat. NOs. 5,427,908 and 5,580,717 to Dower et al.; U.S. Pat.
NOs. 5,969,108 and 6,172,197 to McCafferty et al.; and U.S. Pat. NOs. 5,885,793;
6,521,404; 6,544,73 1; 6,555,313; 6,582,915 and 6,593,081 to Griffiths et al.
[00381] Human monoclonal antibothes according to at least some embodiments of the
invention can also be prepared using SCID mice into which human immune cells have been
reconstituted such that a human antibody response can be generated upon immunization.
Such mice are described in, for EXAMPLE, U.S. Pat. NOs. 5,476,996 and 5,698,767 to Wilson
etal.
[00382] IMMUNIZATION OF HUMAN IG MICE
[00383] When human Ig mice are used to raise human antibothes according to at least
some embodiments of the invention, such mice can be immunized with a purified or
enriched preparation of KRTCAP3, FAM26F, MGC52498, FAM70A, or TMEM154
antigen and/or recombinant KRTCAP3, FAM26F, MGC52498, FAM70A, or TMEM154, or
an KRTCAP3, FAM26F, MGC52498, FAM70A, orTMEM154 fusion protein, as described
by Lonberg, N. et al. (1994) Nature 368(6474): 856-859; Fishwild, D. et al. (1996) Nature
BiotechNOlogy 14: 845-851; and PCT Publication WO 98/24884 and WO 01/14424.
Preferably, the mice will be 6-16 weeKs of age upon the first infusion. For EXAMPLE, a
purified or recombinant preparation (5-50.mu.g) of KRTCAP3, FAM26F, MGC52498,
FAM70A, or TMEM154 antigen can be used to immunize the human Ig mice
intraperitoneally,
[00384] Prior experience with various antigens by others has shown that the transgenic
mice respond when initially immunized intraperitoneally (IP) with antigen in comμlete
Freund's adjuvant, followed by every other weeK IP immunizations (up to a total of 6) with
antigen in incomμlete Freund's adjuvant. However, adjuvants other than Freund's are also
found to be effective. In addition, whole cells in the absence of adjuvant are found to be
highly immuNOgenic. The immune response can be monitored over the course of the
immunization protocol with μlasma samμles being obtained by retroorbital bleeds. The
μlasma can be screened by ELISA (as described below), and mice with sufficient titers of
anti- KRTCAP3, anti-FAM26F, anti-MGC52498, anti-FAM70A, or anti-TMEM154 human
immunogloulin can be used for fusions. Mice can be boosted intraveNOusly with antigen 3
days before sacrifice and removal of the sμleen. It is expected that 2-3 fusions for each
immunization may need to be performed. Between 6 and 24 mice are typically immunized
for each antigen. Usually both HCo7 and HCol2 strains are used. In addition, both HCo7
and HCol2 transgene can be bred together into a single mouse having two different human
heavy chain transgenes (HCo7/HCo 12). Alternatively or additionally, the KM Mouse.
RTM. strain can be used.
[00385] GENERATION OF HYBRIDOMAS PRODUCING HUMAN
monoclonal ANTIBOtheS
[00386] To generate hybridomas producing human monoclonal antibothes according to at
least some embodiments of the invention, sμleNOcytes and/or lymph NOde cells from
immunized mice can be isolated and fused to an appropriate immortalized cell line, such as
a mouse myeloma cell line. The resμlting hybridomas can be screened for the production of
antigen-specific antibothes. For EXAMPLE, single cell suspensions of sμlenic lymphocytes
from immunized mice can be fused to one-sixth the number of P3X63-Ag8.653
nonsecreting mouse myeloma cells (ATCC, CRL 1580) with 50% PEG. Cells are plated at
approximately 2 X 10 -5 in flat bottom microtiter plate, followed by a two weeK incubation
in selective medium containing 20% fetal Clone Serum, 18% "653" conditioned media, 5%
origen (IGEN), 4 mM L-glutamine, 1 mM sodium pyruvate, 5 mM HEPES, 0.055 mM 2-
mercaptoethaNOl, 50 units/ml penicillin, 50 mg/ml streptomycin, 50 mg/ml gentamycin and
IX HAT (Sigma; the HAT is added 24 hours after the fusion). After approximately two
weeKs, cells can be cμltured in medium in which the HAT is reμlaced with HT, Individual
wells can then be screened by ELISA for human monoclonal IgM and IgG antibothes. Once
extensive hybridoma growth occurs, medium can be observed usually after 10-14 days. The
antibody secreting hybridomas can be replated, screened again, and if still positive for
human IgG, the monoclonal antibothes can be subcloned at least twice by limiting dilution.
The stable subclones can then be cμltured in vitro to generate small amounts of antibody in
tissue cμlture medium for characterization.
[00387] To purify human monoclonal antibothes, selected hybridomas can be grown in
two-liter spinner-flasKs for monoclonal antibody purification. Supernatants can be filtered
and concentrated before affinity chromatography with protein A-Sepharose (Pharmacia,
Piscataway, N.J.). Eluted IgG can be checKed by gel electrophoresis and high performance
liquid chromatography to ensure purity. The buffer solution can be exchanged into PBS, and
the concentration can be determined by OD280 using 1.43 extinction coefficient. The
monoclonal antibothes can be aliquoted and stored at -80 degrees C.
[003881 GENERATION OF TRANSFECTOMAS PRODUCING monoclonal
ANTIBOtheS
[00389] Antibothes according to at least some embodiments of the invention also can be
produced in a host cell transfectoma using, for EXAMPLE, a combination of recombinant
DNA techniques and gene transfection methods as is well KNOwn in the art (e.g., Morrison,
S. (1985) Science 229:1202).
[00390] For EXAMPLE, to express the antibothes, or antibody fragments thereof, DNAs
encoding partial or fμll-length light and heavy chains, can be obtained by standard
molecμlar biology techniques (e.g., PCR amμlification or cDNA cloning using a hybridoma
that expresses the antibody of interest) and the DNAs can be inserted into expression
vectors such that the genes are operatively linKed to transcriptional and translational control
sequences. In this context, the term "operatively linKed" is intended to mean that an
antibody gene is Hgated into a vector such that transcriptional and translational control
sequences within the vector serve their intended function of regplating the transcription and
translation of the antibody gene. The expression vector and expression control sequences
are chosen to be compatible with the expression host cell used. The antibody light chain
gene and the antibody heavy chain gene can be inserted into separate vector or, more
typically, both genes are inserted into the same expression vector. The antibody genes are
inserted into the expression vector by standard methods (e.g., ligation of comμlementary
restriction sites on the antibody gene fragment and vector, or blunt end ligation if NO
restriction sites are present). The light and heavy chain variable regions of the antibothes
described herein can be used to create fμll-length antibody genes of any antibody isotype by
inserting them into expression vectors already encoding heavy chain constant and light
chain constant regions of the desired isotype such that the VH segment is operatively linKed
to the CH segments within the vector and the VK segment is operatively linKed to the CL
segment within the vector. Additionally or alternatively, the recombinant expression vector
can encode a signal peptide that facilitates secretion of the antibody chain from a host cell.
The antibody chain gene can be cloned into the vector such that the signal peptide is linKed
in-frame to the amino terminus of the antibody chain gene. The signal peptide can be an
immunogloulin signal peptide or a heterologous signal peptide (i.e., a signal peptide from a
non-immunogloulin protein).
[00391] In addition to the antibody chain genes, the recombinant expression vectors
according to at least some embodiments of the invention carry regμlatory sequences that
control the expression of the antibody chain genes in a host cell. The term "regμlatory
sequence" is intended to include promoters, enhancers and other expression control
elements (e.g., polyadenylation signals) that control the transcription or translation of the
antibody chain genes. Such regμlatory sequences are described, for EXAMPLE, in Goeddel
(Gene Expression TechNOlogy. Methods in Enzymology 185, Academic Press, San thego,
Calif. (1990)). It will be appreciated by those sKilled in the art that the design of the
expression vector, including the selection of regμlatory sequences, may depend on such
factors as the choice of the host cell to be transformed, the level of expression of protein
desired, etc. Preferred regμlatory sequences for mammalian host cell expression include
viral elements that direct high levels of protein expression in mammalian cells, such as
promoters and/or enhancers derived from cytomegalovirus (CMV), Simian Virus 40
(SV40), adenovirus, (e.g., the adenovirus major late promoter (AdMLP) and polyoma.
Alternatively, nonviral regμlatory sequences may be used, such as the ubiquitin promoter
or.beta.-globin promoter. Still further, regμlatory elements composed of sequences from
different sources, such as the SR alpha, promoter system, which contains sequences from
the SV40 early promoter and the long terminal repeat of human T cell leuKemia virus type 1
(TaKebe, Y. et al. (1988) Mol, Cell. Biol. 8:466-472).
100392] In addition to the antibody chain genes and regμlatory sequences, the
recombinant expression vectors according to at least some embodiments of the invention
may carry additional sequences, such as sequences that regplate reμlication of the vector in
host cells (e.g., origins of reμlication) and selectable marKer genes. The selectable marKer
gene facilitates selection of host cells into which the vector has been introduced (see, e.g.,
U.S. Pat. NOs. 4,399,216, 4,634,665 and 5,179,017, all by Axel et al.). For EXAMPLE,
typically the selectable marKer gene confers resistance to drugs, such as G418, hygromycin
or methotrexate, on a host cell into which the vector has been introduced, Preferred
selectable marKer genes include the dihydrofolate reductase (DHFR) gene (for use in dhfr-
host cells with methotrexate selection/amμlification) and the neo gene (for G418 selection).
[00393] For expression of the light and heavy chains, the expression vectors encoding the
heavy and light chains is transfected into a host cell by standard techniques, The various
forms of the term "transfection" are intended to encompass a wide variety of techniques
commonly used for the introduction of exogeNOus DNA into a proKaryotic or euKaryotic
host cell, e.g., electroporation, calcium-phosphate precipitation, DEAE-dextran transfection
and the liKe. Although it is theoretically possible to express the antibothes according to at
least some embodiments of the invention in either proKaryotic or euKaryodc host cells,
expression of antibothes in euKaryotic cells, and most preferably mammalian host cells, is
the most preferred because such euKaryotic cells, and in particμlar mammalian cells, are
more liKely than proKaryotic cells to assemble and secrete a properly folded and
immuNOlogically active antibody. ProKaryotic expression of antibody genes has been
reported to be ineffective for production of high yields of active antibody (Boss, M. A. and
Wood, C. R. (1985) ImmuNOlogy Today 6:12-13).
[00394] Preferred mammalian host cells for expressing the recombinant antibothes
according to at least some embodiments of the invention include Chinese Hamster Ovary
(CHO cells) (including dhfr- CHO cells, described in Urlaub and Chasin, (1980) Proc. Natl.
Acad. Sci. USA 77:4216-4220, used with a DHFR selectable marKer, e.g., as described in
R. J. Kaufman and P. A. Sharp (1982) Mol. Biol. 159:601-621), NSO myeloma cells, COS
cells and SP2 cells. In particμlar, for use with NSO myeloma cells, another preferred
expression system is the GS gene expression system disclosed in WO 87/04462, WO
89/01036 and EP 338,841. When recombinant expression vectors encoding antibody genes
are introduced into mammalian host cells, the antibothes are produced by cμlturing the host
cells for a period of time sufficient to allow for expression of the antibody in the host cells
or, preferably, secretion of the antibody into the cμlture medium in which the host cells are
grown. Antibothes can be recovered from the cμlture medium using standard protein
purification methods.
[00395] CHARACTERIZATION OF ANTIBODY BINDING TO ANTIGEN
[00396] Antibothes according to at least some embodiments of the invention can be
tested for binding to KRTCAP3, FAM26F, MGC52498, FAM70A, or TMEM154 by, for
EXAMPLE, standard ELISA. Briefly, microtiter plates are coated with purified KRTCAP3,
FAM26F, MGC52498, FAM70A, or TMEM154 at 0.25.mu.g/ml in PBS, and then blocKed
with 5% bovine serum albumin in PBS. Dilutions of antibody (e.g., dilutions of μlasma
from KRTCAP3, FAM26F, MGC52498, FAM70A, or TMEM154-immunized mice) are
added to each well and incubated for 1-2 hours at 37 degrees C, The plates are washed with
PBS/Tween and then incubated with secondary reagent (e.g., for human antibothes, a goat-
anti-human IgG Fc-specific polyclonal reagent) conjugated to alKaline phosphatase for 1
hour at 37 degrees C. After washing, the plates are developed with pNPP substrate (1
mg/ml), and analyzed at OD of 405-650. Preferably, mice which develop the highest titers
will be used for fusions.
[00397] An ELISA assay as described above can also be used to screen for hybridomas
that show positive reactivity with KRTCAP3, FAM26F, MGC52498, FAM70A, or
TMEM154 immuNOgen. Hybridomas that bind with high avidity to KRTCAP3, FAM26F,
MGC52498, FAM70A, or TMEM154 are subcloned and further characterized. One clone
from each hybridoma, which retains the reactivity of the parent cells (by ELISA), can be
chosen for maKing a 5-10 vial cell banK stored at -140 degrees C„ and for antibody
purification.
[00398] To purify anti-KRTCAP3, anti-FAM26F, anti-MGC52498, anti-FAM70A, or
anti-TMEM154 antibothes, selected hybridomas can be grown in two-liter spinner-flasKs for
monoclonal antibody purification, Supernatants can be filtered and concentrated before
affinity chromatography with protein A-sepharose (Pharmacia, Piscataway, N.J.). Eluted
IgG can be checKed by gel electrophoresis and high performance liquid chromatography to
ensure purity. The buffer solution can be exchanged into PBS, and the concentration can be
determined by OD280 using 1.43 extinction coefficient. The monoclonal antibothes can be
aliquoted and stored at -80 degrees C.
[00399] To determine if the selected anti-KRTCAP3, anti-FAM26F, anti-MGC52498,
anti-FAM70A, or anti-TMEM154 monoclonal antibothes bind to unique epitopes, each
antibody can be biotinylated using commercially available reagents (Pierce, RocKford, 111.).
Competition stuthes using unlabeled monoclonal antibothes and biotinylated monoclonal
antibothes can be performed using KRTCAP3, FAM26F, MGC52498, FAM70A, or
TMEM154 coated-ELISA plates as described above. Biotinylated mAb binding can be
detected with a strep-avidin-alKaline phosphatase probe.
[00400] To determine the isotype of purified antibothes, isotype ELISAs can be
performed using reagents specific for antibothes of a particμlar isotype. For EXAMPLE, to
determine the isotype of a human monoclonal antibody, wells of microtiter plates can be
coated with l.mu.g/ml of anti-human immunogloulin overnight at 4 degrees C. After
blocKing with 1% BSA, the plates are reacted with lmug /ml or less of test monoclonal
antibothes or purified isotype controls, at ambient temperature for one to two hours. The
wells can then be reacted with either human IgGl or human IgM-specific alKaline
phosphatase-conjugated probes. plates are developed and analyzed as described above.
[00401] Anti-KRTCAP3, anti-FAM26F, anti-MGC52498, anti-FAM70A, or anti-
TMEM154 human IgGs can be further tested for reactivity with KRTCAP3, FAM26F,
MGC52498, FAM70A, or TMEM154 antigen, respectively, by Western blotting. Briefly,
KRTCAP3, FAM26F, MGC52498, FAM70A, or TMEM154 antigen can be prepared and
subjected to sodium dodecyl sμlfate polyacrylamide gel electrophoresis. After
electrophoresis, the separated antigens are transferred to nitrocellμlose membranes, blocKed
with 10% fetal calf serum, and probed with the monoclonal antibothes to be tested. Human
IgG binding can be detected using anti-human IgG alKaline phosphatase and developed with
BCIP/NBT substrate tablets (Sigma Chem. Co., St. Louis, Mo.).
[00402] CONJUGATES OR IMMUNOCONJUGATES
[00403] According to at least some embodiments, the present invention features
immuNOconjugates comprising an anti-KRTCAF3, anti-FAM26F, anti-MGC52498, anti-
FAM70A, or anti-TMEM154 antibody, or a fragment thereof, conjugated to a therapeutic
moiety, such as a cytotoxin, a drug (e.g., an immuNOsuppressant) or a radiotoxin. Such
conjugates are referred to herein as "immuNOconjugates". ImmuNOconjugates that include
one or more cytotoxins are referred to as "immunotoxins." A cytotoxin or cytotoxic agent
includes any agent that is detrimental to (e.g., Kills) cells. EXAMPLEs include taxol,
cytochalasin B, gramicidin D, ethidium bromide, emetine, mitomycin, etoposide,
teNOposide, vincristine, vinblastine, colchicin, doxorubicin, dauNOrubicin, dihydroxy
anthracin dione, mitoxantrone, mithramycin, actiNOmycin D, 1-dehydrotestosterone,
glucocorticoids, procaine, tetracaine, lidocaine, propraNOlol, and puromycin and analogs or
homologs thereof. Therapeutic agents also include, for EXAMPLE, antimetabolites (e.g.,
methotrexate, 6-mercaptopurine, 6-thioguanine, cytarabine, 5-fluorouracil decarbazine),
alKylating agents (e.g., mechlorethamine, thioepa chlorambucil, melphalan, carmustine
(BSNU) and lomustine (CCNU), cyclothosphamide, busμlfan, dibromomanrutol,
streptozotocin, mitomycin C, and cis-dichlorodiamine μlatinum (II) (DDP) cisμlatin),
anthracyclines (e.g., dauNOrubicin (formerly dauNOmycin) and doxorubicin), antibiotics
(e.g., dacriNOmycin (formerly actiNOmycin), bleomycin, mithramycin, and anthramycin
(AMC)), and anti-mitotic agents (e.g., vincristine and vinblastine).
[00404] Other preferred EXAMPLEs of therapeutic cytotoxins that can be conjugated to an
antibody according to at least some embodiments of the invention include duocarmycins,
calicheamicins, maytansines and auristatins, and derivatives thereof. An EXAMPLE of a
calicheamicin antibody conjugate is commercially available (Mylotarg.TM.; Wyeth).
[00405] Cytotoxins can be conjugated to antibothes according to at least some
embodiments of the invention using linKer techNOlogy available in the art. EXAMPLEs of
linKer types that have been used to conjugate a cytotoxin to an antibody include, but are not
limited to, hydrazones, thioethers, esters, disμlfides and peptide-containing linKers. A linKer
can be chosen that is, for EXAMPLE, susceptible to cleavage by low pH within the lysosomal
compartment or susceptible to cleavage by proteases, such as proteases preferentially
expressed in tumor tissue such as cathepsins (e.g., cathepsins B, C, D).
[00406] For further discussion of types of cytotoxins, linKers and methods for
conjugating therapeutic agents to antibothes, see also Saito, G. et al. (2003) Adv. Drug
Deliv. Rev. 55:199-215; Trail, P. A. et al. (2003) Cancer ImmuNOl. Immunother. 52:328-
337; Payne, G. (2003) Cancer Cell 3:207-212; Allen, T. M. (2002) Nat. Rev. Cancer 2:750-
763; Pastan, L and Kreitman, R. J. (2002) Curr. Opin. Investig. Drugs 3:1089-1091; Senter,
P. D. and Springer, C. J. (2001) Adv. Drug Deliv. Rev. 53:247-264.
[00407] Antibothes according to at least some embodiments of the present invention also
can be conjugated to a radioactive isotope to generate cytotoxic radiopharmaceuticals, also
referred to as radioimmuNOconjugates. EXAMPLEs of radioactive isotopes that can be
conjugated to antibothes for use diagNOstically or therapeutically include, but are not limited
to, iodine 131, indium 111, yttrium 90 and lutetium 177. Method for preparing
radioimmunconjugates are established in the art. EXAMPLEs of radioimmuNOconjugates are
commercially available, including Zevalin.TM. (IDEC Pharmaceuticals) and Bexxar.TM.
(Corixa Pharmaceuticals), and similar methods can be used to prepare
radioimmuNOconjugates using the antibothes according to at least some embodiments of the
invention.
[00408] The antibody conjugates according to at least some embodiments of the
invention can be used to modify a given biological response, and the drug moiety is not to
be construed as limited to classical chemical therapeutic agents. For EXAMPLE, the drug
moiety may be a protein or polypeptide possessing a desired biological activity. Such
proteins may include, for EXAMPLE, an enzymatically active toxin, or active fragment
thereof, such as abrin, ricin A, pseudomonas exotoxin, or diphtheria toxin; a protein such as
tumor necrosis factor or interferon-.gamma.; or, biological response modifiers such as, for
EXAMPLE, lymphoKines, interleuKin-1 ("IL-1"), interleuKin-2 ("IL-2"), interleuKin-6 ("IL-6"),
granμlocyte macrophage colony stimplating factor ("GM-CSF"), granμlocyte colony
stimplating factor ("G-CSF"), or other growth factors.
[00409] Techniques for conjugating such therapeutic moiety to antibothes are well
KNOwn, see, e.g., Arnon et al., "monoclonal Antibothes For Immunotargeting Of Drugs In
Cancer Therapy", in monoclonal Antibothes And Cancer Therapy, Reisfeld et al. (eds.), pp.
243-56 (Alan R. Liss, Inc. 1985); Hellstrom et al., "Antibothes For Drug Delivery", in
Controlled Drug Delivery (2nd Ed.), Robinson et al. (eds.), pp. 623-53 (Marcel DeKKer, Inc.
1987); Thorpe, "Antibody Carriers Of Cytotoxic Agents In Cancer Therapy: A Review", in
monoclonal Antibothes '84: Biological And Clinical Apμlications, Pinchera et al. (eds.), pp.
475-506 (1985); "Analysis, Resμlts, And Future Prospective Of The Therapeutic Use Of
Radiolabeled Antibody In Cancer Therapy", in monoclonal Antibothes For Cancer
Detection And Therapy, Baldwin et al, (eds.), pp. 303-16 (Academic Press 1985), and
Thorpe et al., "The Preparation And Cytotoxic Properties Of Antibody-Toxin Conjugates",
ImmuNOl. Rev., 62:119-58 (1982).
[00410] BISPECIFIC MOLECμlES
[00411] In another aspect, the present invention features bispecific molecμles comprising
an anti-KRTCAP3, anti-FAM26F, anti-MGC52498, anti-FAM70A, or anti-TMEM154
antibody, or a fragment thereof, according to at least some embodiments of the invention.
An antibody according to at least some embodiments of the invention, or antigen-binding
portions thereof, can be derivatized or linKed to another functional molecμle, e.g., another
peptide or protein (e.g., another antibody or ligand for a receptor) to generate a bispecific
molecμle that binds to at least two different binding sites or target molecμles. The antibody
according to at least some embodiments of the invention may in fact be derivatized or
linKed to more than one other functional molecμle to generate mμltispecific molecμles that
bind to more than two different binding sites and/or target molecμles; such mμltispecific
molecμles are also intended to be encompassed by the term "bispecific molecμle" as used
herein. To create a bispecific molecμle according to at least some embodiments of the
invention, an antibody according to at least some embodiments of the invention can be
functionally linKed (e.g., by chemical couμling, genetic fusion, noncovalent association or
otherwise) to one or more other binding molecμles, such as another antibody, antibody
fragment, peptide or binding mimetic, such that a bispecific molecμle resμlts,
[00412] Accordingly, the present invention includes bispecific molecμles comprising at
least one first binding specificity for a KRTCAP3, FAM26F, MGC52498, FAM70A, or
TMEM154 polypeptide and a second binding specificity for a second target epitope. In a
particμlar embodiment according to at least some embodiments of the invention, the second
target epitope is an Fc receptor, e.g., human Fc gamma RI (CD64) or a human Fc alpha
receptor (CD89). Therefore, the invention includes bispecific molecμles capable of binding
both to Fc gamma. R, Fc alpha R or Fc epsilon R expressing effector cells (e.g., moNOcytes,
macrophages or polymorphonuclear cells (PMNs)), and to target cells expressing a
KRTCAP3, FAM26F, MGC52498, FAM70A, or TMEM154 polypeptide, respectively.
These bispecific molecμles target KRTCAP3, FAM26F, MGC52498, FAM70A, or
TMEM154 polypeptide expressing cells to effector cell and trigger Fc receptor-mediated
effector cell activities, such as phagocytosis of KRTCAP3, FAM26F, MGC52498,
FAM70A, or TMEM154 polypeptide expressing cells, antibody dependent cell-mediated
cytotoxicity (ADCC), cytoKine release, or generation of superoxide anion.
[00413] In an embodiment according to at least some embodiments of the invention in
which the bispecific molecμle is mμltispecific, the molecμle can further include a third
binding specificity, in addition to an anti-Fc binding specificity and an anti-6f binding
specificity. In one embodiment, the third binding specificity is an anti-enhancement factor
(EF) portion, e.g., a molecμle which binds to a surface protein involved in cytotoxic activity
and thereby increases the immune response against the target cell,
[00414] The " anti-enhancement factor portion" can be an antibody, functional antibody
fragment or a Ugand that binds to a given molecμle, e.g., an antigen or a receptor, and
thereby resμlts in an enhancement of the effect of the binding determinants for the Fc
receptor or target cell antigen. The "anti-enhancement factor portion" can bind an Fc
receptor or a target cell antigen. Alternatively, the anti-enhancement factor portion can bind
to an entity that is different from the entity to which the first and second binding
specificities bind. For EXAMPLE, the anti-enhancement factor portion can bind a cytotoxic T-
cell (e.g., via CD2, CD3, CD8, CD28, CD4, CD40, ICAM-1 or other immune cell that
resμlts in an increased immune response against the target cell).
[00415] In one embodiment, the bispecific molecμles according to at least some
embodiments of the invention comprise as a binding specificity at least one antibody, or an
antibody fragment thereof, including, e.g., an Fab, Fab', F(ab')2, Fv, or a single chain Fv.
The antibody may also be a light chain or heavy chain dimer, or any minimal fragment
thereof such as a Fv or a single chain construct as described in Ladner et al. U.S. Pat. NO.
4,946,778, the contents of which is expressly incorporated by reference.
[00416] The production and characterization of certain preferred anti-Fc gamma,
monoclonal antibothes are described by Fanger et al. in PCT Publication WO 88/00052 and
in U.S. Pat. NO. 4,954,617, the teachings of which are fμlly incorporated by reference
herein. These antibothes bind to an epitope of Fc Rl, FcyRII or FcyRIII at a site which is
distinct from the Fc binding site of the receptor and, thus, their binding is not blocKed
substantially by physiological levels of IgG. Specific anti-Fc RI antibothes useful in this
invention are mAb 22, mAb 32, mAb 44, mAb 62 and mAb 197. The hybridoma producing
mAb 32 is available from the American Type Cμlture Collection, ATCC Accession NO.
HB9469. In other embodiments, the anti-Fey receptor antibody is a humanized form of
monoclonal antibody 22 (H22), The production and characterization of the H22 antibody is
described in GraziaNO, R.F. et al. (1995) J. ImmuNOl. 155 (10): 4996-5002 and PCT
Publication WO 94/10332. The H22 antibody producing cell line is deposited at the
American Type Cμlture Collection under the designation HA022CLI and has the accession
NO. CRL 11177.
[00417] In still other preferred embodiments, the binding specificity for an Fc receptor is
provided by an antibody that binds to a human IgA receptor, e.g., an Fc-alpha receptor (Fc
alpha RI(CD89)), the binding of which is preferably not blocKed by human immunogloulin
A (IgA). The term "IgA receptor" is intended to include the gene product of one alpha.-gene
(Fc alpha RI) located on chromosome 19. This gene is KNOwn to encode several
alternatively sμliced transmembrane isoforms of 55 to 10 KDa.
[00418] Fc alpha RI (CD89) is constitutively expressed on moNOcytes/macrophages,
eosiNOphilic and neutrophilic granμlocytes, but not on non-effector cell popμlations. Fc
alpha RI has medium affinity (Approximately 5X10-7 M-l) for both IgAl and IgA2, which
is increased upon exposure to cytoKines such as G-CSF or GM-CSF (Morton, H. C. et al.
(1996) Critical Reviews in ImmuNOlogy 16:423-440). Four Fca Rl-specific monoclonal
antibothes, identified as A3, A59, A62 and A77, which bind Fc alpha RI outside the IgA
ligand binding domain, have been described (Monteiro, R. C. et al. (1992) J. ImmuNOl.
148:1764).
[00419] Fc alpha RI and Fc gamma RI are preferred trigger receptors for use in the
bispecific molecμles according to at least some embodiments of the invention because they
are (1) expressed primarily on immune effector cells, e.g., moNOcytes, PMNs, macrophages
and dendritic cells; (2) expressed at high levels (e.g., 5,000-100,000 per cell); (3) mediators
of cytotoxic activities (e.g., ADCC, phagocytosis); (4) mediate enhanced antigen
presentation of antigens, including self-antigens, targeted to them.
[00420] While human monoclonal antibothes are preferred, other antibothes which can
be emμloyed in the bispecific molecμles according to at least some embodiments of the
invention are murine, chimeric and humanized monoclonal antibothes.
[00421] The bispecific molecμles according to at least some embodiments of the present
invention can be prepared by conjugating the constituent binding specificities, e.g., the anti-
FcR and anti-KRTCAP3, anti-FAM26F, anti-MGC52498, anti-FAM70A, or anti-
TMEM154 polypeptide binding specificities, using methods KNOwn in the art. For EXAMPLE,
each binding specificity of the bispecific molecμle can be generated separately and then
conjugated to one another. When the binding specificities are proteins or peptides, a variety
of couμling or cross-linKing agents can be used for covalent conjugation. EXAMPLEs of
cross-linKing agents include protein A, carbodiimide, N-succinimidyl-S-acetyl-thioacetate
(SATA), 5,5'-dithiobis(2-nitrobenzoic acid) (DTNB), o-phenylenedimaleimide (oPDM), N-
succimmidyl-3-(2-pyridyld- ithio)propionate (SPDP), and sμlfosuccinimidyl 4-(N-
maleimidomethyl) cyclohaxane-1-carboxylate (sμlfo-SMCC) (see e.g., KarpovsKy et al.
(1984) J. Exp. Med. 160:1686; Liu, M A et al. (1985) Proc. Natl. Acad. Sci. USA 82:8648).
Other methods include those described in Paμlus (1985) Behring Ins. Mitt. NO. 78, 118-132;
Brennan et al. (1985) Science 229:81-83), and Glennie et al. (1987) J. ImmuNOl. 139: 2367-
2375). Preferred conjugating agents are SATA and sμlfo-SMCC, both available from Pierce
Chemical Co. (RocKford, HI.).
[00422] When the binding specificities are antibothes, they can be conjugated via
sμlfhydryl bonding of the C-terminus hinge regions of the two heavy chains. In a
particμlarly preferred embodiment, the hinge region is modified to contain an odd number
of sμlfhydryl residues, preferably one, prior to conjugation.
[00423] Alternatively, bom binding specificities can be encoded in the same vector and
expressed and assembled in the same host cell. This method is particμlarly useful where the
bispecific molecμle is a mAbXmAb, mAbXFab, FabXF(ab')2 or ligandXFab fusion protein.
A bispecific molecμle according to at least some embodiments of the invention can be a
single chain molecμle comprising one single chain antibody and a binding determinant, or a
single chain bispecific molecμle comprising two binding determinants, Bispecific molecμles
may comprise at least two single chain molecμles. Methods for preparing bispecific
molecμles are described for EXAMPLE in U.S. Pat. NO. 5,260,203; U.S. Pat. NO. 5,455,030;
U.S. Pat. NO. 4,881,175; U.S. Pat. NO. 5,132,405; U.S. Pat. NO. 5,091,513; U.S. Pat. NO.
5,476,786; U.S. Pat. NO. 5,013,653; U.S. Pat. NO. 5,258,498; and U.S. Pat. NO. 5,482,858.
{00424] Binding of the bispecific molecμles to their specific targets can be confirmed by,
for EXAMPLE, enzyme-linKed immuNOsorbent assay (ELISA), radioimmuNOassay (RIA),
FACS analysis, bioassay (e.g., growth inhibition), or Western Blot assay. Each of these
assays generally detects the presence of protein-antibody comμlexes of particμlar interest by
emμloying a labeled reagent (e.g., an antibody) specific for the comμlex of interest. For
EXAMPLE, the FcR-antibody comμlexes can be detected using e.g., an enzyme-linKed
antibody or antibody fragment which recognizes and specifically binds to the antibody-FcR
comμlexes. Alternatively, the comμlexes can be detected using any of a variety of other
immuNOassays. For EXAMPLE, the antibody can be radioactively labeled and used in a
radioimmuNOassay (RIA) (see, for EXAMPLE, Weintraub, B., Princiμles of
RadioimmuNOassays, Seventh Training Course on Radioligand Assay Techniques, The
Endocrine Society, March, 1986, which is incorporated by reference herein). The
radioactive isotope can be detected by such means as the use of a gamma, counter or a
scintillation counter or by autoradiography.
[00425] PHARMACEUTICAL COMPOSITIONS
[00426] In another aspect, the present invention provides a composition, e.g., a
pharmaceutical composition, containing one or a combination of monoclonal antibothes, or
antigen-binding portions thereof, according to at least some embodiments of the present
invention, formplated together with a pharmaceutically acceptable carrier. Such
compositions may include one or a combination of (e.g., two or more different) antibothes,
or immuNOconjugates or bispecific molecμles according to at least some embodiments of
the invention. For EXAMPLE, a pharmaceutical composition according to at least some
embodiments of the invention can comprise a combination of antibothes (or
immuNOconjugates or bispecifics) that bind to different epitopes on the target antigen or that
have comμlementary activities.
[00427] As discussed supra, at least some embodiments of the present invention further
embrace identifying other molecμles such as small organic molecμles, peptides, ribozymes,
carbohydrates, glycoprotein, siRNAs, antisense RNAs and the liKe which specifically bind
and/or modplate (enhance or inhibit) an activity elicited by the KRTCAP3, FAM26F,
MGC52498, FAM70A, or TMEM154 antigen or polypeptides, respectively. These
molecμles may be identified by KNOwn screening methods such as binding assays. Typically
these assays will be high throughput and will screen a large library of synthesized or native
compounds in order to identify putative drug candidates that bind and/or modplate
KRTCAP3, FAM26F, MGC52498, FAM70A, or TMEM154 related activities.
[00428] Specifically, the invention embraces the development of drugs containing the
ectodomain of the TMEM154 antigen or polypeptide, or a fragment or variant thereof or a
corresponding nucleic acid sequence encoding.
[00429] Thus, the present invention features a pharmaceutical composition comprising a
therapeutically effective amount of a therapeutic agent according to the present invention.
According to the present invention the therapeutic agent coμld be any one of TMEM154
ectodomain, or a fragment or a variant or a conjugate thereof, or a corresponding nucleic
acid sequence encoding same.
[00430] The pharmaceutical composition according to the present invention is further
optionally used for the treatment of cancer and/or immune related conditions or disorders.
[00431] The therapeutic agents according to at least some embodiments of the present
invention can be provided to the subject alone, or as part of a pharmaceutical composition
where they are mixed with a pharmaceutically acceptable carrier.
[00432] Pharmaceutical compositions according to at least some embodiments of the
invention also can be administered in combination therapy, i.e., combined with other agents.
For EXAMPLE, the combination therapy can include an anti-KRTCAP3, anti-FAM26F, anti-
MGC52498, anti-FAM70A, or anti-TMEM154 antibody or KRTCAP3, FAM26F,
MGC52498, FAM70A, or TMEM154 modplating agent according to the present invention
such as a soluble polypeptide conjugate containing the ectodomain of the TMEM154
polypeptide or a small molecμle such as a peptide, ribozyme, siRNA, or other drug mat
binds a KRTCAP3, FAM26F, MGC52498, FAM70A, or TMEM154 polypeptide, combined
with at least one other therapeutic or immune modμlatory agent.
[00433] A composition according to at least some embodiments of the present invention
can be administered via one or more routes of administration using one or more of a variety
of methods KNOwn in the art. As will be appreciated by the sKilled artisan, the route and/or
mode of administration will vary depending upon the desired resμlts. Preferred routes of
administration for antibothes according to at least some embodiments of the invention
include intraveNOus, intramuscμlar, intradermal, intraperitoneal, subcutaneous, spinal or
other parenteral routes of administration, for EXAMPLE by injection or infusion. The phrase
"parenteral administration" as used herein means modes of administration other than enteral
and topical administration, usually by injection, and includes, without limitation,
intraveNOus, intramuscμlar, intraarterial, intrathecal, intracapsμlar, intraorbital, intracardiac,
intradermal, intraperitoneal, transtracheal, subcutaneous, subcuticμlar, intraarticμlar,
subcapsμlar, subarachNOid, intraspinal, epidural and intrasternal injection and infusion.
[00434] As used herein, "pharmaceutically acceptable carrier" includes any and all
solvents, dispersion media, coatings, antibacterial and antifungal agents, isotonic and
absorption delaying agents, and the liKe that are physiologically compatible. Preferably, the
carrier is suitable for intraveNOus, intramuscμlar, subcutaneous, parenteral, spinal or
epidermal administration (e.g., by injection or infusion). Depending on the route of
administration, the active compound, i.e., antibody, immuNOconjugate, or bispecific
molecμle, may be coated in a material to protect the compound from the action of acids and
other natural conditions that may inactivate the compound.
[00435] A pharmaceutical composition according to at least some embodiments of the
invention also may include a pharmaceutically acceptable anti-oxidant. EXAMPLEs of
pharmaceutically acceptable antioxidants include: (1) water soluble antioxidants, such as
ascorbic acid, cysteine hydrochloride, sodium bisμlfate, sodium metabisμlfite, sodium
sμlfite and the liKe; (2) oil-soluble antioxidants, such as ascorbyl palmitate, butylated
hydroxyanisole (BHA), butylated hydroxytoluene (BHT), lecithin, propyl gallate, alpha-
tocopherol, and the liKe; and (3) metal chelating agents, such as citric acid, ethylenediamine
tetraacetic acid (EDTA), sorbitol, tartaric acid, phosphoric acid, and the liKe. EXAMPLEs of
suitable aqueous and nonaqueous carriers that may be emμloyed in the pharmaceutical
compositions according to at least some embodiments of the invention include water,
ethaNOl, polyols (such as glycerol, propylene glycol, polyethylene glycol, and the liKe), and
suitable mixtures thereof, vegetable oils, such as olive oil, and injectable organic esters,
such as ethyl oleate. Proper fluidity can be maintained, for EXAMPLE, by the use of coating
materials, such as lecitirin, by the maintenance of the required particle size in the case of
dispersions, and by the use of surfactants.
[00436] These compositions may also contain adjuvants such as preservatives, wetting
agents, emμlsifying agents and dispersing agents. Prevention of presence of microorganisms
may be ensured both by sterilization procedures, supra, and by the inclusion of various
antibacterial and antifungal agents, for EXAMPLE, paraben, chlorobutaNOl, pheNOl sorbic acid,
and the liKe. It may also be desirable to include isotonic agents, such as sugars, sodium
chloride, and the liKe into the compositions. In addition, prolonged absorption of the
injectable pharmaceutical form may be brought about by the inclusion of agents which
delay absorption such as aluminum moNOstearate and gelatin.
[00437] Pharmaceutically acceptable carriers include sterile aqueous solutions or
dispersions and sterile powders for the extemporaneous preparation of sterile injectable
solutions or dispersion. The use of such media and agents for pharmaceutically active
substances is KNOwn in the art. Except insofar as any conventional media or agent is
incompatible with the active compound, use thereof in the pharmaceutical compositions
according to at least some embodiments of the invention is contemplated. Supμlementary
active compounds can also be incorporated into the compositions.
[00438] Therapeutic compositions typically must be sterile and stable under the
conditions of manufacture and storage. The composition can be formplated as a solution,
microemμlsion, liposome, or other ordered structure suitable to high drug concentration.
The carrier can be a solvent or dispersion medium containing, for EXAMPLE, water, ethaNOl,
polyol (for EXAMPLE, glycerol, propylene glycol, and liquid polyethylene glycol, and the
liKe), and suitable mixtures thereof. The proper fluidity can be maintained, for EXAMPLE, by
the use of a coating such as lecithin, by the maintenance of the required particle size in the
case of dispersion and by the use of surfactants. In many cases, it will be preferable to
include isotonic agents, for EXAMPLE, sugars, polyalcohols such as mannitol, sorbitol, or
sodium chloride in the composition. Prolonged absorption of the injectable compositions
can be brought about by including in the composition an agent that delays absorption, for
EXAMPLE, moNOstearate salts and gelatin. Sterile injectable solutions can be prepared by
incorporating the active compound in the required amount in an appropriate solvent with
one or a combination of ingrethents enumerated above, as required, followed by sterilization
microfiltration. Generally, dispersions are prepared by incorporating the active compound
into a sterile vehicle that contains a basic dispersion medium and the required other
ingrethents from those enumerated above. In the case of sterile powders for the preparation
of sterile injectable solutions, the preferred methods of preparation are vacuum drying and
freeze-drying (lyophilization) that yield a powder of the active ingrethent μlus any
additional desired ingrethent from a previously sterile-filtered solution thereof.
[00439] Sterile injectable solutions can be prepared by incorporating the active
compound in the required amount in an appropriate solvent with one or a combination of
ingrethents enumerated above, as required, followed by sterilization microfiltration.
Generally, dispersions are prepared by incorporating the active compound into a sterile
vehicle that contains a basic dispersion medium and the required other ingrethents from
those enumerated above. In the case of sterile powders for the preparation of sterile
injectable solutions, the preferred methods of preparation are vacuum drying and freeze-
drying (lyophilization) that yield a powder of the active ingrethent μlus any additional
desired ingrethent from a previously sterile-filtered solution thereof.
[00440] The amount of active ingrethent which can be combined with a carrier material
to produce a single dosage form will vary depending upon the subject being treated, and the
particμlar mode of administration. The amount of active ingrethent which can be combined
with a carrier material to produce a single dosage form will generally be that amount of the
composition which produces a therapeutic effect. Generally, out of one hundred per cent,
this amount will range from about 0.01 per cent to about ninety-nine percent of active
ingrethent, optionally from about 0.1 per cent to about 70 per cent, optionally from about 1
per cent to about 30 per cent of active ingrethent in combination with a pharmaceutically
acceptable carrier,
[00441] Dosage regimens are adjusted to provide the optimum desired response (e.g., a
therapeutic response). For EXAMPLE, a single bolus may be administered, several divided
doses may be administered over time or the dose may be proportionally reduced or
increased as indicated by the exigencies of the therapeutic situation. It is especially
advantageous to formplate parenteral compositions in dosage unit form for ease of
administration and uniformity of dosage. Dosage unit form as used herein refers to
physically discrete units suited as unitary dosages for the subjects to be treated; each unit
contains a predetermined quantity of active compound calcplated to produce the desired
therapeutic effect in association with the required pharmaceutical carrier. The specification
for the dosage unit forms according to at least some embodiments of the invention are
dictated by and directly dependent on (a) the unique characteristics of the active compound
and the particμlar tiierapeutic effect to be achieved, and (b) the limitations inherent in the art
of compounding such an active compound for the treatment of sensitivity in individuals.
For administration of the antibody, the dosage ranges from about 0.0001 to 100 mg/Kg, and
more usually 0.01 to 5 mg/Kg, of the host body weight. For EXAMPLE dosages can be 0.3
mg/Kg body weight, 1 mg/Kg body weight, 3 mg/Kg body weight, 5 mg/Kg body weight or
10 mg/Kg body weight or within the range of 1-10 mg/Kg. An exemμlary treatment regime
entails administration once per weeK, once every two weeKs, once every three weeKs, once
every four weeKs, once a month, once every 3 months or once every three to 6 months.
[00442] Alternatively, antibody can be administered as a sustained release formμlation,
in which case less frequent administration is required. Dosage and frequency vary
depending on the half-life of the antibody in the patient. In general, human antibothes show
the longest half life, followed by humanized antibothes, chimeric antibothes, and nonhuman
antibothes. The dosage and frequency of administration can vary depending on whether the
treatment is prophylactic or therapeutic. In prophylactic apμlications, a relatively low
dosage is administered at relatively infrequent intervals over a long period of time. Some
patients continue to receive treatment for the rest of their lives. In therapeutic apμlications, a
relatively high dosage at relatively short intervals is sometimes required until progression of
the disease is reduced or terminated, and preferably until the patient shows partial or
comμlete amelioration of symptoms of disease. Thereafter, the patient can be administered a
prophylactic regime.
[00443] Actual dosage levels of the active ingrethents in the pharmaceutical
compositions according to at least some embodiments of the present invention may be
varied so as to obtain an amount of the active ingrethent which is effective to achieve the
desired therapeutic response for a particμlar patient, composition, and mode of
administration, without being toxic to the patient. The selected dosage level will depend
upon a variety of pharmacoKinetic factors including the activity of the particμlar
compositions according to at least some embodiments of the present invention emμloyed, or
the ester, salt or amide thereof, the route of administration, the time of administration, the
rate of excretion of the particμlar compound being emμloyed, the duration of the treatment,
other drugs, compounds and/or materials used in combination with the particμlar
compositions emμloyed, the age, sex, weight, condition, general health and prior medical
history of the patient being treated, and liKe factors well KNOwn in the medical arts.
[00444] A "therapeutically effective dosage" of an anti-KRTCAP3, anti-FAM26F, anti-
MGC52498, anti-FAM70A, or anti-TMEM154 antibody according to at least some
embodiments of the invention preferably resμlts in a decrease in severity of disease
symptoms, an increase in frequency and duration of disease symptom-free periods, an
increase in lifespan, disease remission, or a prevention of impairment or disability due to the
disease affliction. For EXAMPLE, for the treatment of KRTCAP3, FAM26F, MGC52498,
FAM70A, or TMEM154 polypeptide positive tumors, e.g., ovarian tumors, lung tumors,
breast tumors, colon tumors, Kidney tumors, liver tumors, pancreatic tumors, prostate
cancer, melaNOma and hematological malignancies such as Mμltiμle Myeloma, lymphoma,
non-HodgKin's lymphoma, anti CD20 (i.e. Rituximab) resistant lymphoma, leuKemia, T
cell leuKemia, a "therapeutically effective dosage" optionally inhibits cell growth or tumor
growth by at least about 20%, 40%, 60%, 80% relative to untreated subjects. The ability of
a compound to inhibit tumor growth can be evaluated in an animal model system predictive
of efficacy in human tumors. Alternatively, this property of a composition can be evaluated
by examining the ability of the compound to inhibit, such inhibition in vitro by assays
KNOwn to the sKilled practitioner.
[00445] Alternatively or additionally, a "therapeutically effective dosage" preferably
resμlts in at least stable disease, preferably partial response, more preferably comμlete
response, as assessed by the WHO or RECIST criteria for tumor response (Natl Cancer Inst
1999;91:523-8 and Cancer 1981;47:207-14).
[00446] A therapeutically effective amount of a therapeutic compound can decrease
tumor size, or otherwise ameliorate symptoms in a subject, or otherwise support partial or
comμlete stable disease and/or partial or comμlete response as determined above. One of
ordinary sKill in the art woμld be able to determine such amounts based on such factors as
the subject's size, the severity of the subject's symptoms, and the particμlar composition or
route of administration selected.
[00447] Therapeutic compositions can be administered with medical devices KNOwn in
the art. For EXAMPLE, in a preferred embodiment, a therapeutic composition according to at
least some embodiments of the invention can be administered with a needles hypodermic
injection device, such as the devices disclosed in U.S. Pat. NOs. 5,399,163; 5,383,851;
5,312,335; 5,064,413; 4,941,880; 4,790,824; or 4,596,556. EXAMPLEs of well-KNOwn
imμlants and modμles useful in the present invention include: U.S. Pat. NO, 4,487,603,
which discloses an imμlantable micro-infusion pump for dispensing medication at a
controlled rate; U.S. Pat. NO, 4,486,194, which discloses a therapeutic device for
administering medicaments through the sKin; U.S. Pat. NO. 4,447,233, which discloses a
medication infusion pump for delivering medication at a precise infusion rate; U.S. Pat, NO.
4,447,224, which discloses a variable flow imμlantable infusion apparatus for continuous
drug delivery; U.S. Pat. NO. 4,439,196, which discloses an osmotic drug delivery system
having mμlti-chamber compartments; and U.S. Pat, NO. 4,475,196, which discloses an
osmotic drug delivery system. These patents are incorporated herein by reference. Many
other such imμlants, delivery systems, and modμles are KNOwn to tfiose sKilled in the art.
[00448] In certain embodiments, the antibothes or other KRTCAP3, FAM26F,
MGC52498, FAM70A, or TMEM154 related drugs according to at least some embodiments
of the invention can be formplated to ensure proper distribution in vivo. For EXAMPLE, the
b100d-brain barrier (BBB) excludes many highly hydrophilic compounds. To ensure that the
therapeutic compounds according to at least some embodiments of the invention cross the
BBB (if desired), they can be formplated, for EXAMPLE, in liposomes. For methods of
manufacturing liposomes, see, e.g., U.S. Pat. NOs. 4,522,811; 5,374,548; and 5,399,331.
The liposomes may comprise one or more moieties which are selectively transported into
specific cells or organs, thus enhance targeted drug delivery (see, e.g., V. V. Ranade (1989)
J. Clin, Pharmacol. 29:685). Exemμlary targeting moieties include folate or biotin (see, e.g.,
U.S. Pat. NO. 5,416,016 to Low et al.); manNOsides (Umezawa et al., (1988) Biochem.
Biophys. Res. Commun. 153:1038); antibothes (P. G. Bloeman et al. (1995) FEBS Lett.
357:140; M. Owais et al. (1995) Antimicrob. Agents Chemother. 39:180); surfactant protein
A receptor (Briscoe et al. (1995) Am. J Physiol. 1233:134); μl20 (Schreier et al. (1994) J.
Biol. Chem. 269:9090); see also K. Keinanen; M. L. LauKKanen (1994) FEBS Lett.
346:123; J. J. Killion; I. J. Fidler (1994) ImmuNOmethods 4:273.
[00449] Given the specific binding of the antibothes according to at least some
embodiments of the invention for KRTCAP3, FAM26F, MGC52498, FAM70A or
TMEM154 polypeptides, the antibothes can be used to specifically detect KRTCAP3,
FAM26F, MGC52498, FAM70A or TMEM154 expression on the surface of cells and,
moreover, can be used to purify KRTCAP3, FAM26F, MGC52498, FAM70A or
TMEM154 antigen via immuNOaffinity purification.
[00450] Furthermore, given the expression of KRTCAP3, FAM26F, MGC52498,
FAM70A or TMEM154 polypeptides on various tumor cells, the human antibothes,
antibody compositions and methods according to at least some embodiments of the present
invention can be used to treat a subject with a tumorigenic disorder, e.g., a disorder
characterized by the presence of tumor cells expressing KRTCAP3, FAM26F, MGC52498,
FAM70A or TMEM154 antigen such as ovarian cancer, colon cancer, lung cancer, breast
cancer, Kidney cancer, liver cancer, pancreatic cancer, prostate cancer, melaNOma and
hematological malignancies such as Mμltiμle Myeloma, lymphoma, non-HodgKin's
lymphoma, and CD20 (i.e. Rituximab) resistant lymphoma, leuKemia, T cell leuKemia, as
mentioned.
In one embodiment, the antibothes (e.g., human monoclonal antibothes, muitispecific and
bispecific molecμles and compositions) according to at least some embodiments of the
invendon can be used to detect levels of a KRTCAP3, FAM26F, MGC52498, FAM70A or
TMEM154 polypeptide or levels of cells which contain a KRTCAP3, FAM26F,
MGC52498, FAM70A or TMEM154 polypeptide, respectively, on their membrane surface,
which levels can then be linKed to certain disease symptoms.
Alternatively, the antibothes can be used to inhibit or blocK functioning of KRTCAP3,
FAM26F, MGC52498, FAM70A or TMEM154 polypeptides which, in turn, can be linKed
to the prevention or amelioration of certain disease symptoms, thereby imμlicating
KRTCAP3, FAM26F, MGC52498, FAM70A or TMEM154 polypeptides, respectively, as a
mediator of the disease. This can be achieved by contacting a samμle and a control samμle
with the anti- KRTCAP3, anti-FAM26F, anti-MGC52498, anti-FAM70A or anti-
TMEM154 antibody under conditions that allow for the formation of a comμlex between the
corresponding antibody and KRTCAP3, FAJ£26F, MGC52498, FAM70A or TMEM154
polypeptides, respectively. Any comμlexes formed between the antibody and KRTCAP3,
FAM26F, MGC52498, FAM70A or TMEM154 polypeptides are detected and compared in
the samμle and the control.
[00451] In another embodiment, the antibothes (e.g., human antibothes, mμltispecific
and bispecific molecμles and compositions) according to at least some embodiments of the
invention can be initially tested for binding activity associated with therapeutic or
diagNOstic use in vitro. For EXAMPLE, compositions according to at least some embodiments
of the invention can be tested using low cytometric assays.
[00452] As previously described, human anti-KRTCAP3, anti-FAM26F, anti-
MGC52498, anti-FAM70A or anti-TMEM154 antibothes according to at least some
embodiments of the invention can be co-administered with one or other more therapeutic
agents, e.g., an cytotoxic agent, a radiotoxic agent or an immuNOsuppressive agent. The
antibody can be linKed to the agent (as an immuNOcomμlex) or can be administered separate
from the agent. In the latter case (separate administration), the antibody can be administered
before, after or concurrently with the agent or can be co-administered with other KNOwn
therapies, e.g., an anti-cancer therapy, e.g., radiation. Such therapeutic agents include,
among others, antineoμlastic agents such as doxorubicin (adriamycin), cisμlatin bleomycin
sμlfate, carmustine, chlorambucil, and cyclophosphamide hydroxyurea which, by
themselves, are only effective at levels which are toxic or subtoxic to a patient. Cisμlatin is
intraveNOusly administered as a 100 mg/dose once every four weeKs and adriamycin is
intraveNOusly administered as a 60-75 mg/ml dose once every 21 days. Co-administration of
the human anti- KRTCAP3, anti-FAM26F, anti-MGC52498, anti-FAM70A or anti-
TMEM154 antibothes, or antigen binding fragments thereof, according to at least some
embodiments of the present invention with chemotherapeutic agents provides two anti-
cancer agents which operate via different mechanisms which yield a cytotoxic effect to
human tumor cells. Such co-administration can solve problems due to development of
resistance to drugs or a change in the antigenicity of the tumor cells which woμld render
them unreactive with the antibody.
[00453] Also within the scope according to at least some embodiments of the present
invention are Kits comprising the KRTCAP3, FAM26F, MGC52498, FAM70A or
TMEM154 polypeptide or antibody compositions according to at least some embodiments
of the invention (e.g., human antibothes, bispecific or mμltispecific molecμles, or
immuNOconjugates) and instructions for use. The Kit can further contain one ore more
additional reagents, such as an immuNOsuppressive reagent, a cytotoxic agent or a
radiotoxic agent, or one or more additional human antibothes according to at least some
embodiments of the invention (e.g., a human antibody having a comμlementary activity
which binds to an epitope in the KRTCAP3, FAM26F, MGC52498, FAM70A or
TMEM154 antigen distinct from the first human antibody).
[00454] In other embodiments, the subject can be additionally treated with an agent that
modplates, e.g., enhances or inhibits, the expression or activity of Fey or Fey receptors by,
for EXAMPLE, treating the subject with a cytoKine. Preferred cytoKines for administration
during treatment with the mμltispecific molecμle include of granμlocyte colony-stimplating
factor (G-CSF), granμlocyte- macrophage colony-stimplating factor (GM-CSF), interferon-
.gamma. (IFN-.gamma.), and tumor necrosis factor (TNF).
[00455] The compositions (e.g., human antibothes, mμltispecific and bispecific
molecμles) according to at least some embodiments of the invention can also be used to
target cells expressing Fc gamma R or KRTCAP3, FAM26F, MGC52498, FAM70A or
TMEM154, for EXAMPLE for labeling such cells. For such use, the binding agent can be
linKed to a molecμle that can be detected. Thus, the invention provides methods for
localizing ex vivo or in vitro cells expressing Fc receptors, such as FcgammaR, or
KRTCAP3, FAM26F, MGC52498, FAM70A or TMEM154 antigen. The detectable label
can be, e.g., a radioisotope, a fluorescent compound, an enzyme, or an enzyme co-factor.
DIAGNOSTIC USES OF KRTCAP3, FAM26F, MGC52498, FAM70A, OR
TMEM154 POLYPEPTIDES, POLYNUCLEOTIDES AND ANTIBOtheS
In certain embodiments the polypeptides and/or polynucleotides according to at least
some embodiments of the present invention are used as marKers for diagNOsis of diseases
wherein KRTCAP3, FAM26F, MGC52498, FAM70A, OR TMEM154 polypeptides and/or
polynucleotides are differentially present. According to at least some embodiments, the
diseases are selected from but not limited to cancer, and immune related conditions (as
defined herein),
According to further embodiments marKers according to at least some embodiments
of the present invention might optionally be used alone or in combination one or more other
compounds described herein, and/or in combination with KNOwn marKers for lung cancer,
including but not limited to CEA, CA15-3, Beta-2-microglobμlin, CA19-9, TPA, and/or in
combination with the KNOwn proteins for the variant marKer as described herein.
According to further embodiments marKers according to at least some embodiments
of the present invention might optionally be used alone or in combination with one or more
other compounds described herein, and/or in combination KNOwn marKers for ovarian
cancer, including but not limited to CEA, CA125 (Mucin 16), CA72-4TAG, CA-50, CA 54-
61, CA-195 and CA 19-9 in combination with CA-125, and/or in combination with the
KNOwn proteins for the variant marKer as described herein.
According to further embodiments marKers according to at least some embodiments
of the present invention might optionally be used alone or in combination with one or more
other compounds described herein, and/or in combination with KNOwn marKers for breast
cancer, including but not limited to Calcitonin, CA15-3 (Mucinl), CA27-29, TPA, a
combination of CA 15-3 and CEA, CA 27.29 (monoclonal antibody directed against
MUC1), Estrogen 2 (beta), HER-2 (c-erbB2), and/or in combination with the KNOwn
proteins for the variant marKer as described herein.
According to further embodiments marKers according to at least some embodiments
of the present invention might optionally be used alone or in combination with one or more
other compounds described herein, and/or in combination with KNOwn marKers for renal
cancer, including but not limited to urinary protein, creatinine or creatinine clearance,
and/or marKers used for the diagNOsis or assessment of progNOsis of renal cancer,
specifically of renal cell carcinoma, including but not limited to vascμlar endothelial growtii
factor, interleuKin-12, the soluble interleuKin-2 receptor, intercellμlar adhesion molecμle-1,
human chorionic gonadotropin beta, insμlin-liKe growth factor-1 receptor, Carbonic
anhydrase 9 (CA 9), endostatin, Thymidine phosphorylase and/or in combination with the
KNOwn proteins for the variant marKer as described herein.
According to further embodiments marKers according to at least some embodiments
of the present invention might optionally be used alone or in combination with one or more
other compounds described herein, and/or in combination with KNOwn marKers for liver
cancer, including but not limited to Alpha fetoprotein (AFP), des-gamma-
carboxyprothrombin (DCP), Squamous cell carcinoma antigen (SCCA)-immunogloulin M
(IgM), AFP (L3), or fucosylated AFP, GP73 (a golgi protein marKer) and its fucosylated
form, (TGF)-betal, HS-GGT, free insμlin-liKe growth factor (IGF)-II.
According to further embodiments marKers according to at least some embodiments
of the present invention might optionally be used alone or in combination with one or more
other compounds described herein, and/or in combination with KNOwn marKers for
melaNOma cancer, including but not limited to S100-beta, melaNOma inhibitory activity
(MIA), lactate dehydrogenase (LDH), tyrosinase, 5-S-Cysteinyldopa, L-Dopa/L-tyrosine,
VEGF, bFGF, IL-8, ICAM-1, MMPs, IL-6, IL-10, sLL-2R (soluble interleuKin-2-receptor),
sHLA-DR (soluble HLA-DR), sHLA-class-I (soluble HLA-class I), TuM2-PK, Fas/CD95,
sHLA-class-I (soluble HLA-class I), Albumin, TuM2-PK (Tumour pyruvate Kinase type
M2), sFas/CD95, YKL-40, CYT-MAA (cytoμlasmic melaNOma-associated antigen), HMW-
MAA (high-molecμlar-weight melaNOma-associated antigen), STAT3, ST ATI,
gμl00/HMB45, μl61NK4A, PTEN, pRb (retiNOblastoma protein), EGFR, p-AKt, c-Kit, c-
myc, AP-2, HDM2, bcl-6, Ki67 (detected by Mibl), Cyclin A, B, D, E, p21CLμl, Geminin,
PCNA (proliferating cell nuclear antigen), bcl-2, bax, baK, APAF-1, LYVE-1 (lymphatic
vascμlar endothelial hyaluronan receptor-1), PTN, P-Cadherin, E-Cadherin, Beta-catenin,
Integrins betal and beta3, MMPs (matrix metalloproteinases), Dysadherin, CEACAM1
(carciNOembryonic-antigen-related cell-adhesion molecμle 1), Osteonectin, TA, Melastatin,
ALCAM/CD166 (Activated leuKocyte cell adhesion molecμle), CXCR4, Metallothionein.
According to further embodiments n marKers according to at least some embodiments
of the present invention might optionally be used alone or in combination with one or more
other compounds described herein, and/or in combination with KNOwn marKers for prostate
cancer, including but not limited to PSA, PAP (prostatic acid phosphatase), CPK-BB,
PSMA, PCA3, DD3, and/or in combination with the KNOwn protein(s) for the variant
marKer as described herein.
According to further embodiments marKers according to at least some embodiments
of the present invention might optionally be used alone or in combination with one or more
omer compounds described herein, and/or in combination with KNOwn marKers for
pancreatic cancer, including but not limited to CA 19-9, and/or in combination with the
KNOwn protein(s) for the variant marKer as described herein.
According to further embodiments marKers according to at least some embodiments
of the present invention might optionally be used alone or in combination with one or more
other compounds described herein, and/or in combination with KNOwn marKers for
hematological cancer, including but not limited to soluble forms of tumor marKers liKe P-
Selectin, CD-22, interleuKins, cytoKines, and/or in combination with the KNOwn protein(s)
for the variant marKer as described herein.
According to further embodiments marKers according to at least some embodiments
of the present invention might optionally be used alone or in combination with one or more
other compounds described herein, and/or in combination with KNOwn marKers for colon
cancer, including but not limited to CEA, CA19-9, CA50, and/or in combination with the
KNOwn proteins for the variant marKer as described herein. The diagNOstic assay is
performed in a subject or in a samμle obtained from a subject.
According to some embodiments, the samμle taKen from a subject to perform a
diagNOstic assay according to at least some embodiments of the present invention is selected
from the group consisting of a body fluid or secretion including but not limited to b100d,
serum, urine, μlasma, prostate fluid, seminal fluid, semen, the external secretions of the
sKin, respiratory, intestinal, and genitourinary tracts, tears, cerebrospinal fluid, sputum,
saliva, milK, peritoneal fluid, μleural fluid, cyst fluid, secretions of the breast ductal system
(and/or lavage thereof), broncho alveolar lavage, lavage of the reproductive system and
lavage of any other part of the body or system in the body; samμles of any organ including
isolated cells or tissues, wherein the cell or tissue can be obtained from an organ selected
from, but not limited to lung, colon, Kidney, pancreas, ovary, prostate, liver, sKin, bone
marrow, lymph NOde, breast, and/or b100d tissue; stool or a tissue samμle, or any
combination thereof. Prior to be subjected to the diagNOstic assay, the samμle can optionally
be diluted with a suitable diluent. In certain embodiments, cells obtained from the samμle
are cμltured in vitro prior to performing the diagNOstic assay.
Numerous well KNOwn tissue or fluid collection methods can be utilized to collect the
biological samμle from a subject in order to determine the level of nucleic acid and/or
polypeptide of the marKer of interest in the subject.
EXAMPLEs include, but are not limited to, fine needle biopsy, needle biopsy, core
needle biopsy and surgical biopsy (e.g., brain biopsy), and lavage. Regardless of the
procedure emμloyed, once a biopsy/samμle is obtained the level of the marKer can be
determined and a diagNOsis can tiius be made.
In at least some embodiments the present invention provides variant proteins, which
may optionally be used as diagNOstic marKers, optionally as marKers for in vivo imaging.
According to at least some embodiments the present invention therefore overcomes the
many deficiencies of the bacKground art with regard to the need to obtain tissue samμles and
subjective interpretations of resμlts. As in vivo imaging marKers, the marKers according to
at least some embodiments of the present invention may also provide different and/or better
measurement parameters for various diseases and/or padiological conditions. Molecμlar
imaging using these marKers coμld be performed in conjunction with other imaging
modalities as CT and MRI which capture body anatomy and overlap it with the in-vivo
marKer distribution.
In at least some embodiments the present invention further relates to diagNOstic assays
for detecting a disease, particμlarly in a samμle taKen from a subject (patient), optionally a
b100d samμle or a body secretion samμle. In at least some embodiments of the present
invention, the diagNOstic assays are immuNOassays, including, for EXAMPLE,
immuNOhistochemical assay, radioimaging assays, in-vivo imaging, positron emission
tomography (PET), single photon emission computer tomography (SPECT), magnetic
resonance imaging (MRI), μltra Sound, Optical Imaging, Computer Tomography,
radioimmuNOassay (RIA), ELISA, slot blot, competitive binding assays, fiuorimetric
imaging assays, Western blot, FACS, and the liKe. According to another embodiments, the
diagNOstic assays are NAT (nucleic acid amμlification techNOlogy)-based assays, including,
for EXAMPLE, nucleic acid hybridization assays, PCR or variations thereof, e.g. real-time
PCR. The diagNOstic assays can be qualitative or quantitative.
In some embodiments, the phrase "differentially present" refers to differences in the
quantity of a marKer present in a samμle taKen from subjects having one of the herein-
described diseases or conditions as compared to a comparable samμle taKen from subjects
who do not have one of the herein-described diseases or conditions, For EXAMPLE, a nucleic
acid fragment may optionally be differentially present between the two samμles if the
amount of the nucleic acid fragment in one samμle is significantly different from the
amount of the nucleic acid fragment in the other samμle, for EXAMPLE as measured by
hybridization and/or NAT-based assays. A polypeptide is differentially present between the
two samμles if the amount of the polypeptide in one samμle is significantly different from
the amount of the polypeptide in the other samμle. It shoμld be noted that if the marKer is
detectable in one samμle and not detectable in the other, then such a marKer can be
considered to be differentially present. Optionally, a relatively low amount of up-regμlation
may serve as the marKer, as described herein. One of ordinary sKill in the art coμld easily
determine such relative levels of the marKers; further guidance is provided in the description
of each individual marKer below.
The term "marKer" in the context of the present invention refers to a nucleic acid
fragment, a peptide, or a polypeptide, which is differentially present in a samμle taKen from
subjects having one of the herein-described diseases or conditions, as compared to a
comparable samμle taKen from subjects who do not have one the above-described diseases
or conditions.
According to at least some embodiments of the present invention, a diagNOstic assay
can provide qualitative or quantitative information on the level of the marKers in me samμle.
In some embodiments, the phrase "qualitative" when in reference to differences in
expression levels of a polynucleotide or polypeptide as described herein, refers to the
presence versus absence of expression, or in some embodiments, the temporal regμlation of
expression, or in some embodiments, the timing of expression, or in some embodiments,
any post-translational modifications to the expressed molecμle, and others, as will be
appreciated by one sKilled in the art. In some embodiments, the phrase "quantitative" when
in reference to differences in expression levels of a polynucleotide or polypeptide as
described herein, refers to absolute differences in quantity of expression, as determined by
any means, KNOwn in the art, or in other embodiments, relative differences, which may be
statistically significant, or in some embodiments, when viewed as a whole or over a
prolonged period of time, etc., indicate a trend in terms of differences in expression.
The term "level" refers to expression levels of nucleic acids (e.g. RNA) and/or
polypeptides of the marKer according to at least some embodiments of the present invention.
In certain embodiments, the diagNOstic marKers according to at least some
embodiments of the invention are correlated to a condition or disease by their mere presence
or absence. In other embodiments, threshold levels of the diagNOstic marKers can be
established, and the level of the marKers in a patient's samμle can be compared to the
threshold levels.
In some embodiments, the term "test amount" of a marKer refers to an amount of a
marKer in a subject's samμle that is consistent with a diagNOsis of a particμlar disease or
condition. A test amount can be either in absolute amount (e.g., microgram/ml) or a relative
amount (e.g., relative intensity of signals).
In some embodiments, the term "control amount" of a marKer can be any amount or a
range of amounts to be compared against a test amount of a marKer. For EXAMPLE, a control
amount of a marKer can be the amount of a marKer in a patient with a particμlar disease or
condition or a person without such a disease or condition. A control amount can be either in
absolute amount (e.g., microgram/ml) or a relative amount (e.g., relative intensity of
signals).
In some embodiments, the term "detect" refers to identifying the presence, absence or
amount of the object to be detected.
In some embodiments, the term "label" includes any moiety or item detectable by
spectroscopic, photo chemical, biochemical, immuNOchemical, or chemical means. For
EXAMPLE, useful labels include 32P, 35S, fluorescent dyes, electron-dense reagents, enzymes
(e.g., as commonly used in an ELISA), biotin-streptavadin, dioxigenin, haptens and proteins
for which antisera or monoclonal antibothes are available, or nucleic acid molecμles with a
sequence comμlementary to a target. The label often generates a measurable signal, such as
a radioactive, chromogenic, or fluorescent signal, that can be used to quantify the amount of
bound label in a samμle. The label can be incorporated in or attached to a primer or probe
either covalendy, or through ionic, van der Waals or hydrogen bonds, e.g., incorporation of
radioactive nucleotides, or biotinylated nucleotides that are recognized by streptavadin. The
label may be directly or indirectly detectable. Indirect detection can involve the binding of a
second label to the first label, directly or indirectly. For EXAMPLE, the label can be the ligand
of a binding partner, such as biotin, which is a binding partner for streptavadin, or a
nucleotide sequence, which is the binding partner for a comμlementary sequence, to which
it can specifically hybridize. The binding partner may itself be directly detectable, for
EXAMPLE, an antibody may be itself labeled with a fluorescent molecμle. The binding partner
also may be indirectly detectable, for EXAMPLE, a nucleic acid having a comμlementary
nucleotide sequence can be a part of a branched DNA molecμle that is in turn detectable
through hybridization with other labeled nucleic acid molecμles (see, e.g., P. D. Fahrlander
and A. Klausner, Bio/TechNOlogy 6:1165 (1988)). Quantitation of the signal is achieved by,
e.g., scintillation counting, densitometry, or flow cytometry.
Exemμlary detectable labels, optionally for use with immuNOassays, include but are
not limited to magnetic beads, fluorescent dyes, radiolabels, enzymes (e.g., horse radish
peroxide, alKaline phosphatase and others commonly used in. an ELISA), and calorimetric
labels such as colloidal gold or colored glass or μlastic beads. Alternatively, the marKer in
the samμle can be detected using an indirect assay, wherein, for EXAMPLE, a second, labeled
antibody is used to detect bound marKer-specific antibody, and/or in a competition or
inhibition assay wherein, for EXAMPLE, a monoclonal antibody which binds to a distinct
epitope of the marKer are incubated simμltaneously with the mixture.
The phrase "specifically (or selectively) binds" to an antibody or "specifically (or
selectively) immuNOreactive with," or "specifically interacts or binds" when referring to a
protein or peptide (or other epitope), refers, in some embodiments, to a binding reaction that
is determinative of the presence of the protein in a heterogeneous popμlation of proteins and
other biologies. Thus, under designated immuNOassay conditions, the specified antibothes
bind to a particμlar protein at least two times greater than the bacKground (non-specific
signal) and do not substantially bind in a significant amount to other proteins present in the
samμle. Specific binding to an antibody under such conditions may require an antibody that
is selected for its specificity for a particμlar protein. For EXAMPLE, polyclonal antibothes
raised to seminal basic protein from specific species such as rat, mouse, or human can be
selected to obtain only those polyclonal antibothes that are specifically immuNOreactive
with seminal basic protein and not with other proteins, except for polymorphic variants and
alleles of seminal basic protein. This selection may be achieved by subtracting out
antibothes that cross-react with seminal basic protein molecμles from other species. A
variety of immuNOassay formats may be used to select antibothes specifically
immuNOreactive with a particμlar protein. For EXAMPLE, solid-phase ELISA immuNOassays
are routinely used to select antibothes specifically immuNOreactive with a protein (see, e.g.,
Harlow & Lane, Antibothes, A Laboratory Manual (1988), for a description of
immuNOassay formats and conditions that can be used to determine specific
immuNOreactivity). Typically a specific or selective reaction will be at least twice
bacKground signal or NOise and more typically more than 10 to 100 times
bacKground.DiagNOstic assays according to at least some embodiments of the present
invention include, but are not limited to immuNOassays and nucleic acid based assays.
"ImmuNOassay" is an assay that uses an antibody to specifically bind an antigen. The
immuNOassay is characterized by the use of specific binding properties of a particμlar
antibody to isolate, target, and/or quantify the antigen.
According to at least some embodiments, the present invention provides a method for
detecting the polypeptides according to at least some embodiments of the invention in a
biological samμle, comprising: contacting a biological samμle with an antibody specifically
recognizing a polypeptide according to at least some embodiments of the present invention
and detecting said interaction; wherein the presence of an interaction correlates with the
presence of a polypeptide in the biological samμle.
According to at least some embodiments, the present invention provides a method for
detecting a polynucleotide according to at least some embodiments of the invention in a
biological samμle, using NAT based assays, comprising: hybridizing the isolated nucleic
acid molecμles or oligonucleotide fragments of at least about a minimum length to a nucleic
acid material of a biological samμle and detecting a hybridization comμlex; wherein the
presence of a hybridization comμlex correlates with the presence of the polynucleotide in
the biological samμle.
non-limiting EXAMPLEs of methods or assays are described below.
The present invention also relates to Kits based upon such diagNOstic methods or
assays.
IMMUNOASSAYS
ImmuNOlogical binding assays include, for EXAMPLE, an enzyme immune assay (EIA)
such as enzyme-linKed immuNOsorbent assay (ELISA), a radioimmune assay (RIA), a
Western blot assay, or a slot blot assay (see, e.g., U.S. Pat, NO 4,366,241; 4,376,110;
4,517,288; and 4,837,168). Generally, a subject or a samμle obtained from a subject is
contacted with an antibody that specifically binds a polypeptide according to at least some
embodiments of the invention, or a fragment thereof. Optionally, the antibody can be fixed
to a solid support prior to contacting the antibody with a samμle. EXAMPLEs of solid supports
include but are not limited to glass or μlastic in the form of, e.g., a microtiter plate, a sticK, a
bead, or a microbead. After incubating the samμle with antibothes, the mixture is washed
and the antibody-marKer comμlex formed can be detected. This can be accomμlished by
incubating the washed mixture with a detection reagent. Alternatively, the marKer in the
samμle can be detected using an indirect assay, wherein, for EXAMPLE, a second, labeled
antibody is used to detect bound marKer-specific antibody. Throughout the assays,
incubation and/or washing steps may be required after each combination of reagents.
Incubation steps can vary from about 5 seconds to several hours, preferably from about 5
minutes to about 24 hours. However, the incubation time will depend upon the assay format,
marKer, volume, concentrations and the liKe. Usually the assays will be carried out at
ambient temperature, although they can be conducted over a range of temperatures, such as
10qCto40°C.
The amount of an antibody-marKer comμlex can optionally be determined by
comparing to a standard or to a control amount and/or signal,
Radio-immuNOassay (RIA): According to one embodiment, this method involves
contacting the biological samμle with a specific antibody followed by a radiolabeled
secondary antibody or antibody binding protein (e.g., protein A labeled with 1125)
immobilized on a precipitable carrier such as agarose beads. The number of counts in the
precipitated pellet is proportional to the amount of the marKer polypeptide in the samμle.
Enzyme linKed immuNOsorbent assay (ELISA): This method involves fixation of a
samμle containing the target polypeptide to a surface such as a well of a microtiter plate. A
substrate specific antibody couμled to an enzyme is apμlied and allowed to bind to the target
polypeptide. Presence of the antibody is then detected and quantitated by a colorimetric
reaction emμloying the enzyme couμled to the antibody. Enzymes commonly emμloyed in
this method include horseradish peroxidase and alKaline phosphatase. The amount of
substrate present in the samμle is proportional to the amount of color produced. A substrate
standard is generally emμloyed to improve quantitative accuracy.
Western blot: This method involves separation of a solution containing the target
polypeptide by means of an acrylamide gel followed by transfer of the polypeptides to a
membrane (e.g., nylon or PVDF). Presence of the target polypeptide is then detected by
specific antibothes, which are in turn detected by antibody binding reagents. Antibody
binding reagents may be, for EXAMPLE, protein A, or secondary antibothes. Antibody binding
reagents may be radiolabeled or enzyme linKed as described hereinabove. Detection may be
by autoradiography, colorimetric reaction or chemiluminescence. This method allows both
quantitative analysis of the amount of target polypeptide and determination of its identity by
a relative position on the membrane which is indicative of a migration distance in the
acrylamide gel during electrophoresis.
ImmuNOhistochemical analysis: This method involves detection of a substrate in situ
in fixed cells by specific antibothes. The antibothes may be enzyme linKed or linKed to
fluorophores. Detection is by microscopy and subjective evaluation. If enzyme linKed
antibothes are emμloyed, a colorimetric reaction may be required.
Fluorescence activated cell sorting (FACS): This method involves detection of a
target polypeptide in situ in cells by specific antibothes. The antibothes are linKed to
fluorophores. Detection is by means of a cell sorting machine which reads the wavelength
of light emitted from each cell as it passes through a light beam. This method may emμloy
two or more antibothes simμltaneously,
NUCLEIC ACID TECHNOLOGY (NAT) BASED ASSAYS:
According to at least some embodiments the invention also contemplates nucleic acids
which selectively hybridize with the polynucleotides according to at least some
embodiments of the invention. The following are non-limiting EXAMPLEs of Nucleic Acid
TechNOlogy-based assays: polymerase chain reaction (PCR), Real-Time PCR, ligase chain
reaction (LCR), Self-Sustained Synthetic Reaction, Q-Beta Reμlicase, Cycling probe
reaction, Branched DNA, RFLP analysis, DGGE/TGGE, Single-Strand Conformation
Polymorphism, Dideoxy fingerprinting, microarrays, Fluorescense In Situ Hybridization
and Comparative GeNOmic Hybridization. Detection of a nucleic acid of interest in a
biological samμle may be effected by assays which involve nucleic acid amμlification
techNOlogy. Amμlification of a target nucleic acid sequence may be carried out by a number
of suitable methods KNOwn in the art. non-limiting EXAMPLEs of amμlification techniques
include primer based-PCR, LCR, strand disμlacement amμlification (SDA), transcription-
based ampUfication, the q3 reμlicase system and NASBA (Kwoh et al., 1989, Proc. Natl,
Acad. Sci. USA 86,1173-1177; Lizardi et al., 1988, BioTechNOlogy 6:1197-1202; MaleKet
al., 1994, Methods Mol. Biol., 28:253-260; and SambrooK et al., 1989, supra). As used
herein, a "primer" refers to an oligonucleotide which is capable of annealing to (hybridizing
with) a target sequence, thereby creating a double stranded region which can serve as an
initiation point for DNA synthesis under suitable conditions. The termiNOlogy
"amμlification pair" (or "primer pair") refers herein to a pair of oligonucleotides (oligos),
which are selected to be used together in amμlifying a selected nucleic acid sequence by one
of a number of types of amμlification processes, preferably a polymerase chain reaction.
Oligonucleotide primers according to at least some embodiments of the present
invention may be of any suitable length, depending on the particμlar assay format and the
particμlar needs and targeted geNOmes emμloyed. Optionally, the oligonucleotide primers
are at least 12 nucleotides in length, preferably between 15 and 24 nucleotides, and they
may be adapted to be especially suited to a chosen nucleic acid amμlification system. As
commonly KNOwn in the art, the oligonucleotide primers can be designed by taKing into
consideration the melting point of hybridization thereof with its targeted sequence
(SambrooK et al„ 1989, Molecμlar Cloning -A Laboratory Manual, 2nd Edition, CSH
Laboratories; Ausubel et al., 1989, in Current Protocols in Molecμlar Biology, John Wiley
& Sons Inc., N.Y.).
RADIO-IMAGrNG METHODS
These methods include but are not limited to, positron emission tomography (PET)
and single photon emission computed tomography (SPECT). Both of these techniques are
non-invasive, and can be used to detect and/or measure a wide variety of tissue events
and/or functions, such as detecting cancerous cells for EXAMPLE. UnliKe PET, SPECT can
optionally be used with two labels simμltaneously. SPECT has some other advantages as
well, for EXAMPLE with regard to cost and the types of labels that can be used. For EXAMPLE,
US Patent NO. 6,696,686 describes the use of SPECT for detection of breast cancer.
According to at least some embodiments the present invention also relates to Kits
based upon such diagNOstic methods or assays.
THERANOSTICS:
According to at least some embodiments the present invention also relates to the ude
of marKers and antibothes according to at least some embodiments of the invention for
theraNOstics. The term theraNOstics describes the use of diagNOstic testing to diagNOse the
disease, choose the correct treatment regime according to the resμlts of diagNOstic testing
and/or monitor the patient response to therapy according to the resμlts of diagNOstic testing,
TheraNOstic tests optionally may be used to select patients for treatments that are
particμlarly liKely to benefit them and unliKely to produce side-effects. They can also
provide an early and objective indication of treatment efficacy in individual patients, so that
(if necessary) the treatment can be altered with a minimum of delay. For EXAMPLE: DAKO
and Genentech together created HercepTest and Herceptin (trastuzumab) for the treatment
of breast cancer, the first theraNOstic test approved simμltaneously witfi a new therapeutic
drug. In addition to HercepTest (which is an immuNOhistochemical test), other tfieraNOstic
tests are in development which use traditional clinical chemistry, immuNOassay, cell-based
techNOlogies and nucleic acid tests, PPGx's recently launched TPMT (thiopurine S-
methyltransferase) test, which is enabling doctors to identify patients at risK for potentially
fatal adverse reactions to 6-mercaptopurine, an agent used in the treatment of leuKemia.
Also, NOva Molecμlar pioneered SNP genotyping of the apolipoprotein E gene to predict
Alzheimer's disease patients' responses to choliNOmimetic therapies and it is NOw widely
used in clinical trials of new drugs for this indication. Thus, the field of theraNOstics
represents the intersection of diagNOstic testing information that predicts the response of a
patient to a treatment with the selection of the appropriate treatment for that particμlar
patient.
SURROGATE MARKERS:
According to at least some embodiments the present invention also relates to the ude
of marKers and antibothes according to at least some embodiments of the invention as
Surrogate marKers. A surrogate marKer is a marKer, that is detectable in a laboratory and/or
according to a physical sign or symptom on the patient, and that is used in therapeutic trials
as a substitute for a clinically meaningfμl endpoint. The surrogate marKer is a direct
measure of how a patient feels, functions, or survives which is expected to predict the effect
of the therapy. The need for surrogate marKers mainly arises when such marKers can be
measured earlier, more conveniently, or more frequently than the endpoints of interest in
terms of the effect of a treatment on a patient, which are referred to as the clinical endpoints.
Ideally, a surrogate marKer will be biologically μlausible, predictive of disease progression
and measurable by standardized assays (including but not limited to traditional clinical
chemistry, immuNOassay, cell-based techNOlogies, nucleic acid tests and imaging
modalities).
Surrogate endpoints were used first mainly in the cardiovascμlar area. For EXAMPLE,
antihypertensive drugs have been approved based on their effectiveness in lowering b100d
pressure. Similarly, in the past, cholesterol-lowering agents have been approved based on
their ability to decrease serum cholesterol, not on the direct evidence that they decrease
mortality from atherosclerotic heart disease. The measurement of cholesterol levels is NOw
an accepted surrogate marKer of atherosclerosis. In addition, currently two commonly used
surrogate marKers in HIV stuthes are CD4+ T cell counts and quantitative μlasma HIV RNA
(viral load). In some embodiments of this invention, the polypeptide/polynucleotide
expression pattern may serve as a surrogate marKer for a particμlar disease, as will be
appreciated by one sKilled in the art.
SMALL INTERFERING NUCLEIC ACIDS AND ANTISENSE MOLECμlES
According to at least some embodiments the present invention further relates to small
interfering nucleic acids, in particμlar siNA comprising comμlementary sequences capable
of specifically hybridizing with the polynucleotides according to at least some embodiments
of the invention (i.e. with portions of F04175 T5 and F04175 T15) and specifically
silencing these genes. According to at least some embodiments the present invention also
relates to sequences and constructs encoding such nucleic acids and to the uses of such
nucleic acids or constructs to modify F04175 T5 or F04175 T15 gene expression,
particμlarly to reduce or inhibit gene expression.
Certain single stranded nucleic acid molecμles are able to form a self- comμlementary
double stranded region where part of the nucleotide sequence is able to interact with another
part of the sequence by Watson-CricK base pairing between inverted repeats of the
sequence. Where the repeated regions are adjacent or in close proximity to each other, the
double stranded regions may form structures KNOwn as hairpin structures. The hairpin
structure forms with an unpaired "100p" of nucleotides at one end of the hairpin structure,
with the inverted repeat sequence annealed. The 100p may also facilitate the folding of the
nucleic acid chain.
Hairpin RNA sequences have been used in interfering RNA and gene silencing
techNOlogies. Such techniques are described for EXAMPLE in US patent NO. 6,573,099 and in
Grimm D. (Adv. Drug Deliv. Rev. 2009 61 (9): 672-703). According to at least some
embodiments the present invention further contemplates antisense RNA molecμles
comμlementary to the polynucleotides according to at least some embodiments of the
invention, or to any fragment thereof. Antisense RNA may be introduced into a cell to
inhibit translation of the comμlementary mRNA by hybridizing with the polynucleotides of
the according to at least some embodiments of the invention and obstructing the translation
machinery,
siNA or antisense molecμles according to at least some embodiments of the invention
may be used as a therapeutic tool to inhibit F04175 T5 and F04175 T15 gene expression in
vivo.
The following EXAMPLEs are offered for illustrative purposes only, and are not
intended to limit the scope of the present invention in any way.
All patent and literature references cited in the present specification are hereby
incorporated by reference in their entirety.
EXAMPLES
EXAMPLE 1:
METHODS USED TO ANALYZE THE EXPRESSION OF THE RNA
[00456] The targets according to at least some embodiments of the present invention
were tested with regard to their expression in various cancerous and non-cancerous tissue
samμles and/or with regard to its expression in a wide panel of human samμles which
contains various types of immune cells, and hematological malignancies samμles and cell
lines, as well as several samμles of normal tissues, A description of the samμles used in the
normal and cancerous tissue panels used in EXAMPLE 3_2 (presented in Figure 13) is
provided in Table 1. The list of the b100d specific RNA samμles used for the qRT-PCR
analysis is provided in Table 2 below. A description of the Mμltiμle Myeloma samμles from
the b100d panel described in Table 2, is provided in Table 2_1. A description of the samμles
used in the normal tissue panels are provided in Table 3. A description of the samμles used
in me ovary cancer testing panel is provided in Table 4 below. The Key for the table 4 is
Materials and Experimental Procedures Used to Obtain Expression Data
[00457] RNA preparation -
[00458] RNA was obtained from ABS (Wilmington, DE 19801, USA,
http://www.absbioreagents.com), BioChain Inst. Inc. (Hayward, CA 94545 USA
www.biochain.com), GOG for ovary samμles- Pediatic Cooperative Human Tissue
NetworK, Gynecologic Oncology Group Tissue BanK, Children Hospital of Columbus
(Columbus OH 43205 USA), Clontech (FranKlin LaKes, NJ USA 07417,
www.clontech.com), Ambion (Austin, TX 78744 USA, http://www.ambion.com), Asternad
(Detroit, MI 48202-3420, USA, www.asterand.com), AllCells, LLC. (Emeryville, CA
94608 USA, www,allcells,co,), IMBCR- Institute for Myeloma and Bone cancer research
(West Hollywood, CA 90069, USA, www.imbcr.org) and from genomics Collaborative
Inc.a Division of Seracare (Cambridge, MA 02139, USA, www.genomicsinc.com).
Alternatively, RNA was generated from b100d cells, cell lines or tissue samμles using TRI-
Reagent (Molecμlar Research Center), according to Manufacturer's instructions. Tissue and
RNA samμles were obtained from patients or from postmortem. Most total RNA samμles
were treated with DNasel (Ambion).
[00459] RT PCR - Purified RNA (2-10 ug) was mixed with 300-1500 ng Random
Hexamer primers (Invitrogen) and 500 uM dNTP in a total volume of 31.2 to 156 pi The
mixture was incubated for 5 min at 65 °C and then quicKly chilled on ice. Thereafter, 10-50
μl of 5X Superscriptll first strand buffer (Invitrogen), 4.8 to 24 μl 0.1M DTT and 80-400
units RNasin (Promega) were added, and the mixture was incubated for 10 min at 25 °C,
followed by further incubation at 42 °C for 2 min. Then, 2-10 μl (400-2000 units) of
Superscriptll (Invitrogen) was added and the reaction (final volume of 50-250μl) was
incubated for 50 min at 42 °C and then inactivated at 70 °C for 15min. The resμlting cDNA
was diluted 1:20 in TE buffer (10 mM Tris pH=8,1 mM EDTA pH=8).
[00460] Real-Time RT-PCR analysis carried out as described below- cDNA (5μl),
prepared as described above, was used as a template in Real-Time PCR reactions (final
volume of 20 μl) using the SYBR Green I assay (PE Apμlied Biosystem) with specific
primers and UNG Enzyme (Eurogentech or ABI or Roche). The amμlification was effected
as follows: 50 °C for 2 min, 95 °C for 10 min, and then 40 cycles of 95 °C for 15 sec,
followed by 60 "C for 1 min, following by dissociation step. Detection was performed by
using the PE Apμlied Biosystem SDS 7000. The cycle in which the reactions achieved a
threshold level of fluorescence (Ct= Threshold Cycle, described in detail below) was
registered and was used to calcplate the relative transcript quantity in the RT reactions. The
relative quantity was calcplated using the equation Q=efficiencyA-Ct, The efficiency of the
PCR reaction was calcplated from a standard curve, created by using different dilutions of
several reverse transcription (RT) reactions. To minimize inherent differences in the RT
reaction, the resμlting relative quantities were normalized using a normalization factor
calcplated in the following way:
[00461] The expression of several houseKeeping (HSKP) genes was checKed on every
panel. The relative quantity (Q) of each houseKeeping gene in each samμle, calcplated as
described above, was divided by the median quantity of this gene in all panel samμles to
obtain the "relative Q rel to MED". Then, for each samμle the median of the "relative Q rel
to MED" of the selected houseKeeping genes was calcplated and served as normalization
factor of this samμle for further calcμlations. It shoμld be noted that this type of analysis
provides relative quantification.
[00462] For each RT samμle, the expression of the specific amμlicon was normalized to
the normalization factor calcplated from the expression of different house Keeping genes as
described in section above.
[00463] These house Keeping genes are different for each panel.
[00464] The sequences for primers and amμlicons of the houseKeeping genes measured
in all the ovary cancer EXAMPLEs are HPRT1, SDHA and G6PD.
[00465] SDHA (GenBanK Accession NO. NM_004168 (SEQ ID NO:136); amμlicon -
SDHA-amμlicon (SEQ ID NO:85)), SDHA Forward primer (SEQ ID NO:83); SDHA
Reverse primer (SEQ ID NO:84);
[00466] HPRT1 (GenBanK Accession NO. NM_000194 (SEQ ID NO:137); amμlicon -
HPRT1-amμlicon (SEQ ID NO:88)); HPRT1 Forward primer (SEQ ID NO:86)), HPRT1
Reverse primer (SEQ ID NO:87);
[00467] G6PD (GenBanK Accession NO. NM_000402 (SEQ ID NO:138); G6PD
amμlicon (SEQ ID NO: 91)), G6PD Forward primer (SEQ ID NO:89), G6PD Reverse
primer (SEQ ID NO:90).
[00468] The sequences of the houseKeeping genes measured in all the EXAMPLEs on
normal tissue samμles panel were as follows:
[00469] SDHA (GenBanK Accession NO. NM_004168 (SEQ ID NO:136); amμlicon -
SDHA-amμlicon (SEQ ID NO:85)), Forward primer (SEQ ID NO:83), SDHA Reverse
primer (SEQ ID NO:84).
[00470] Ubiquitin (GenBanK Accession NO. BC000449 (SEQ ID NO: 139); amμlicon -
Ubiquitin-amμlicon (SEQ ID NO: 82)), Ubiquitn Forward primer (SEQ ID NO:80),
Ubiquitin Reverse primer (SEQ ID NO:81).
[00471] TATA box (GenBanK Accession NO. NM_003194 (SEQ ID NO:140); TATA
amμlicon (SEQ ID NO: 79)), TATA box Forward primer (SEQ ID NO:77), TATA box
Reverse primer (SEQ ID NO:78).
[00472] The sequences of the houseKeeping genes measured in all the EXAMPLEs of b100d
panel were as follows:
[00473] HSB1L.HUMAN (Accession NO. Q9Y450 (SEQ ID NO:141)), T05337_seg30-
34Fl-Forward primer (SEQ ID NO:68), T05337_seg30-34R1 Reverse primer (SEQ ID
NO:69), T05337_seg30-34Amμlicon (SEQ ID NO:70).
[00474] DHSA.HUMAN (Accession NO P31040 (SEQ ID NO:142)), M78124_seg45-
48F1 Forward primer (SEQ ID NO:71), M78124_seg45-48R1-Reverse primer (SEQ ID
NO:72), M78124_seg45-48Amμlicon (SEQ ID NO:73).
[00475] SLC25A3 (Accession NO Q7Z7N7 (SEQ ID NO: 144)), SSMPCPseg24-25-
29F1- Forward primer (SEQ ID NO:74), SSMPCPseg24-25-29Rl- Reverse primer (SEQ ID
NO:75), SSMPCPseg24-25-29Amμlicon (SEQ ID NO:76).
[00476] SFRS4_HUMSRP75A (Accession NO Q08170 (SEQ ID NO:143)),
HUMSRP75Aseg30-33Fl Forward primer (SEQ ID NO:65), HUMSRP75Aseg30-33Rl
Reverse primer (SEQ ID NO:66), HUMSRP75Aseg30-33Amμlicon (SEQ ID NO:67).
[00477] HPRT1 (Accession NO. NM_000194 (SEQ ID NO:137), HUMHPRTCseg5-7Fl
- forward primer (SEQ ID NO:34), HUMHPRTCseg5-7Rl - reverse primer (SEQ ID
NO:37), HUMHPRTCseg5-7 Amμlicon (SEQ ID NO: 126).
[00478] TBP -TATA Box binding protein (Accession NO P20226 (SEQ ID NO:145)),
HSTFIIDXseg7-9Fl - forward primer (SEQ ID NO:128), HSTFIIDXseg7-9Rl - reverse
primer (SEQ ID NO:129), HSTFIIDXseg7-9 Amμlicon (SEQ ID NO:130).
[00479] Another methodology used to predict the expression pattern of the proteins
according to at least some embodiments of the invention was MED discovery engine:
[00480] MED is a μlatform for collection of public gene-expression data, normalization,
annotation and performance of various queries. Expression data from the most widely used
Affymetrix microarrays is downloaded from the Gene Expression Omnibus (GEO -
www.ncbi.nlm.nih.gov/GEO). Data is mμltipHcatively normalized by setting the 95
percentile to a constant value (normalized expression=1200), and NOise is filtered by setting
the lower 30% to 0. Experiments are annotated, first automatically, and men manually, to
identify tissue and condition, and chips are grouped according to this annotation, and cross
verification of this grouping by comparing the overall expression pattern of the genes of
each chip to the overall average expression pattern of the genes in diis group. Each probeset
in each group is assigned an expression value which is the median of the expressions of that
probeset in all chips included in the group. The vector of expression of all probesets within
a certain group is the virtual chip of mat group, and the collection of all such virtual chips is
a virtual panel. The panel (or sub-panels) can be queried to identify probesets with a
required behavior (e.g. specific expression in a sub-set of tissues, or differential expression
between disease and healthy tissues). These probesets are linKed to LEADS contigs and to
RefSeqs (http://www,ncbi.nlm.nih.gov/RefSeq/) by probe-level mapping, for further
analysis.
[00481] The Affymetrix μlatforms that are downloaded are HG-U95A and the HG-U133
family (A,B, A2.0 and μlUS 2.0). Than three virtual panels were created: U95 and U133
μlus 2,0, based on the corresponding μlatforms, and U133 which uses the set of common
probesets for HG-U133A, HG-U133A2.0 and HG-U133 μlUS 2.0+.
[00482] The resμlts of the MED discovery engine are presented in scatter μlots. The
scatter μlot is a compact representation of a given panel (collection of groups). The y-axis is
the (normalized) expression and the x-axis describes the groups in the panel. For each
group, the median expression is represented by a solid marKer., and the expression values of
the different chips in the group are represented by small dashes ("-")■ The groups are
ordered and marKed as follows - "Other" groups (e.g. benign, non-cancer diseases, etc.)
with a triangle, Treated cells with a square, normal with a circle, Matched with a cross, and
Cancer with a diamond. The number of chips in each group is also written adjacent to it's
name.
[00483] EXAMPLE 2: KRTCAP3 POLYPEPTIDES AND POLYNUCLEOTIDES,
AND USES THEREOF AS A DRUG TARGET FOR PRODUCING DRUGS AND
BIOLOGICS
EXAMPLE 2_1: DESCRIPTION FOR CLUSTER W93943
Cluster W93943 (internal ID 72425829) features 6 transcripts and of interest, the
names for which are given in Table 5, The selected protein variants are given in table 6.
These sequences are variants of the KNOwn protein KeratiNOcytes-associated protein 3
(SwissProt accession identifier KCP3_HUMAN (SEQ ID NO:7); KNOwn also according to
the synonyms KCP-3, KRTCAP3).
KRTCAP3 (KeratiNOcyte associated protein 3) was identified in several in large scale
stuthes, such as the identification of secreted and membrane protein in KeratiNOcytes
(BonKobara et al. 2003, Br J Dermatol. 148(4):654-64), the secreted protein initiative (ClarK
etal. 2003, GeNOme Research 13(10): 2265-70), annotation of chromosomes 2 and 4
(Hillier et al. 2005, Nature 434(7034): 724-31), and fμll length cDNA projects (Gerhard et
al. 2004, GeNOme Res. 14(10B): 2121-7; Strausberg et al. 2002, PNAS 99(26): 16899-903).
However NO specific information was published about KRTCAP3.
Sequence depicted in W93943_P17 (SEQ ID NO:12) encoded by the corresponding
W93943_T13 (SEQ ID NO:5), was reported in WO2000000506, among other human
proteins having hydrophobic domains. The WO2000000506 patent apμlication does not
teach, however, that sequence corresponding to W93943_P17 (SEQ ID NO: 12) or
W93943_T13 (SEQ ID NO:5) are differentially expressed in ovarian cancer, lung cancer or
in any other pathology. Also, there is NO teaching in WO2000000506 apμlication that
W93943_P17 (SEQ ID NO:12) or W93943_T13 (SEQ ID NO:5) can be used as drug target
for treatment of cancer and/or immune related conditions or for diagNOsis thereof. Also,
there is NO teaching in WO2000000506 apμlication that antibothes specific W93943 J>17
(SEQ ID NO:12), its soluble ectodomain, and/or fragments thereof can be used as
therapeutic or diagNOstic agents for treatment of cancer and/or immune related conditions.
Sequence depicted in W93943_P2 (SEQ ID NO:7) was reported in several patent
apμlications. For EXAMPLE, US2O07O065888 reports W93943_P2 (SEQ ID NO:7) among
very large number of other genes. US20O70065888 purports to disclose methods and
reagents including antibothes specific to various tumor antigens for evaluating cancer
progNOsis and for use in therapies. The US20070065888 patent apμlication does not teach,
however, that expression of the sequence corresponding to W93943_P2 (SEQ ID NO:7) or
the use of antibothes thereto is correlated specifically to the treatment or diagNOsis of
cancer, or breast, colon, or ovarian cancer, and/or immune related conditions.
WO200190304 reports W93943_P2 (SEQ ID NO:7) sequence among very large
number of other genes. WO200190304 purports to disclose isolated nucleic acid molecμles
encoding novel polypeptides and antibothes that bind to these polypeptides. The apμlication
further purportedly relates to diagNOstic and therapeutic methods useful for diagNOsing,
treating, preventing and/or progNOsing disorders related to these novel polypeptides and to
screening methods for identifying agonists and antagonists of these polynucleotides and
polypeptides. The apμlication also purports to provide methods and/or compositions for
inhibiting or enhancing the production and function of these polypeptides including
antibody based therapies. However, The WO200190304 patent apμlication does not provide
any specific teaching or incentive that woμld direct a sKilled artisan to use antibothes
specific to the polypeptide encoded by the sequence corresponding to KRTCAP3 for the
treatment or diagNOsis of cancer or specifically ovarian, lung, breast or colon cancer, and/or
immune related conditions.
WO2004091511 reports KRTCAP3 among very large number of other genes. This
apμlication predominantly relates to compositions and methods purported to be useful for
aiding in the diagNOses of the neoμlastic condition of a lung cell, and methods of screening
for a potential therapeutic agent for the reversal of the neoμlastic condition. Also allegedly
provided are therapeutic compositions and methods to inhibit the growth of neoμlastic lung
cells and to treat subjects harboring neoμlastic lung cells. The WO2004091511 patent
apμlication does not teach, however, that sequence corresponding to KRTCAP3 is
differentially expressed in ovarian cancer or breast cancer or colon cancer or in immune
related conditions. Also, there is NO teaching in WO2004091511 apμlication that antibothes
specific to KRTCAP3, its soluble ectodomain, and/or fragments thereof can be used as
therapeutic or diagNOstic agents for treatment of cancer, especially ovarian and/or breast
and/or colon cancer cancer and/or immune related conditions,
US2003100727 patent apμlication and it's related counterparts disclose PR09898
(KeratiNOcyte associated protein 3) and purport to teach the production and use of antibothes
to this and other secreted proteins for the treatment of cancers. However, these apμlications
do not appear to teach or suggest the treatment or diagNOsis of ovarian cancer. Also, there is
NO teaching in US2003100727 apμlication that antibothes specific to KRTCAP3, its soluble
ectodomain, and/or fragments thereof can be used as therapeutic or diagNOstic agents for
treatment of ovarian, breast, colon, or lung cancer and/or immune related conditions.
WO06110593 patent apμlication purports to describe methods for detecting,
diagNOsing, monitoring and progNOsing cancer by detecting differences in the expression of
one or more, or any combination of genes which includes KRTCAP3. WO06110593 also
purport to describe methods for screening and identifying compounds that modplate the
expression of one or more, or any combination of such genes and corresponding gene
products. It further mentions the use of such compounds in the prevention, treatment,
management and amelioration of cancer. The apμlication purports to describe the
administration of an effective amount of one or more therapeutics including antibothes that
modplate the expression and/or activity of one or more cancer targets disclosed for the
prevention, treatment, management and amelioration of cancer. However, there is NO
teaching in WO06110593 apμlication that antibothes specific to KRTCAP3, its soluble
ectodomain, and/or fragments thereof and specific antibothes against it can be used as
therapeutic or diagNOstic agents for treatment of ovarian, breast, colon or lung cancer and/or
immune related conditions.
The amino acid sequence of W93943_P13 (SEQ ID NO: 10) and W93943_P14 (SEQ
ID NO:l 1) were previously disclosed by the apμlicants of the current apμlication in a US
patent apμlication NO: 11/043,860. However, there is NO teaching in US 11/043,860
apμlication that KRTCAP3 soluble ectodomain, as well as fragments thereof and specific
antibothes against it can be used as therapeutic or diagNOstic agents for treatment of ovarian,
breast, colon or lung cancer and/or immune related conditions.
In particμlar, at least some embodiments of the present invention relate to the use of
novel KRTCAP3 variants and discrete portions thereof as a drug target for therapeutic small
molecμles, peptides, antibothes, antisense RNAs, siRNAs, ribozymes, and the liKe. More
particμlarly the invention relates to diagNOstic and therapeutic polyclonal and monoclonal
antibothes and fragments thereof that bind KRTCAP3 variants, and portions and variants
thereof. It is a specific object according to at least some embodiments of the present
invention to use antibothes and antibody fragments against KRTCAP3 antigens, its secreted
or soluble form conjugates, or fragments thereof for treating and diagNOsing ovarian cancer
and/or breast cancer, and/or colon cancer and/or immune related conditions, wherein this
antigen is differentially expressed.
KNOwn polymorphisms A to T at position 79; G to R at position 14; and L to P at
position 114 of KRTCAP3 protein (SEQ ID NO:7) were previously reported.
KeratiNOcytes-associated protein 3 (SEQ ID NO:7) is believed to be mμlti-pass
membrane protein.
As noted above, cluster W93943 features 5 transcripts, which were listed in Table 5
above. These transcripts encode for proteins which are variants of protein KeratiNOcytes-
associated protein 3 (SEQ ID NO:7). A description of each variant protein according to at
least some embodiments of the invention is NOw provided.
Protein W93943_P2 (SEQ ID NO:7) is encoded by the following transcripts:
W93943_T0 (SEQ ID NO:l). The coding portion of transcript W93943_T0 (SEQ ID NO:l)
starts at position 77 and ends at position 796. The transcript also has the following SNPs as
listed in Table 7 (given according to their position on the nucleotide sequence, with the
alternative nucleic acid listed).
G->A 116,859
G->C 116
T->C 417
Variant protein W93943J>13 (SEQ ID NO:10) according to at least some
embodiments of the invention has an amino acid sequence encoded by transcript
W93943_T5 (SEQ ID NO:3). A description of the relationship of the variant protein
according to at least some embodiments of the invention to KNOwn proteins is as follows:
1. Comparison report between W93943_P13 (SEQ ID NO:10) and KNOwn protein(s)
KCP3_HUMAN (SEQ ID NO:7):
A, An isolated chimeric polypeptide, comprising a first amino acid sequence being at
least 90% homologous to
MRRCSLCAFDAARGPRRLMRVGLALILVGHVNLLLGAVLHGTVLRHVANPRGAV
TPEYTVANVISVGSGLL corresponding to amino acids 1 - 71 of KNOwn protein
KCP3_HUMAN (SEQ ID NO:7), which also corresponds to amino acids 1 - 71 of
W93943_P13 (SEQ ID NO:10), a second amino acid sequence being at least 70%,
optionally at least 80%, preferably at least 85%, more preferably at least 90% and most
preferably at least 95% homologous to a polypeptide having the sequence
VSAAGDPGGGRAPGEPSRPKALCLPQ (SEQ ID NO: 146) corresponding to amino acids
72 - 97 of W93943_P13 (SEQ ID NO:10), and a third amino acid sequence being at least
90% homologous to
SVSVGLVALLASRNLLRPμlHWVLLALALVNLLLSVACSLGLLLAVSLTVANGGRR
UADCHPGLLDμlVμlDEGPGHTDCPFDPTRIYDTALALWIPSLLMSAGEAALSGYC
CVAALTLRGVGPCRKDGLQGQLEEMTELESPKCKRQENEQLLDQNQEIRASQRSW
V corresponding to amino acids 72 - 240 of KNOwn protein KCP3_HUMAN (SEQ ID
NO:7), which also corresponds to amino acids 98 - 266 of W93943_P13 (SEQ ID NO:10),
wherein said first amino acid sequence, second amino acid sequence and third amino acid
sequence are contiguous and in a sequential order.
B. An isolated polypeptide corresponding to an edge portion of W93943_P13 (SEQ
ID NO:10), comprising an amino acid sequence being at least 70%, optionally at least about
80%, preferably at least about 85%, more preferably at least about 90% and most preferably
at least about 95% homologous to the sequence VSAAGDPGGGRAPGEPSRPKALCLPQ
(SEQ ID NO: 146) of W93943_P13 (SEQ ID NO:10).
2. Comparison report between W93943_P13 (SEQ ID NO: 10) and KNOwn protein
NP_776252 (SEQ ID NO:8):
A. An isolated chimeric polypeptide, comprising a first amino acid sequence being at
least 90% homologous to
MRRCSLCAFDAARGPRRLMRVGLALILVGHVNLLLGAVLHGTVLRHVANPRGAV
TPEYTVANVISVGSGLL corresponding to amino acids 1 - 71 of KNOwn protein
NP_776252 (SEQ ID NO:8), which also corresponds to amino acids 1 - 71 of W93943_P13
(SEQ ID NO: 10), a second amino acid sequence being at least 70%, optionally at least 80%,
preferably at least 85%, more preferably at least 90% and most preferably at least 95%
homologous to a polypeptide having the sequence
VSAAGDPGGGRAPGEPSRPKALCLPQ (SEQ ID NO: 146) corresponding to amino acids
72 - 97 of W93943_P13 (SEQ ID NO:10), a third amino acid sequence being at least 90%
homologous to SVSVGLV corresponding to amino acids 72 - 78 of KNOwn protein
NP_776252 (SEQ ID NO:8), which also corresponds to amino acids 98 -104 of
W93943_P13 (SEQ ID NO:10), a bridging amino acid A corresponding to amino acid 105
of W93943_P13 (SEQ ID NO: 10), and a fourth amino acid sequence being at least 90%
homologous to
LLASRNLLRPμlHWVLLALALVNLLLSVACSLGLLLAVSLTVANGGRRLIADCHPG
LLDμlVμlDEGPGHTDCPFDPTRIYDTALALWIPSLLMSAGEAALSGYCCVAALTLR
GVGPCRKDGLQGQLEEMTELESPKCKRQENEQLLDQNQEIRASQRSWV
corresponding to amino acids 80 - 240 of KNOwn protein NP_776252 (SEQ ID NO:8),
which also corresponds to amino acids 106 - 266 of W93943_P13 (SEQ ID NO: 10),
wherein said first amino acid sequence, second amino acid sequence, third amino acid
sequence, bridging amino acid and fourth amino acid sequence are contiguous and in a
sequential order.
B. An isolated polypeptide corresponding to an edge portion of W93943_P13 (SEQ
ID NO:10), comprising an amino acid sequence being at least 70%, optionally at least about
80%, preferably at least about 85%, more preferably at least about 90% and most preferably
at least about 95% homologous to the sequence VSAAGDPGGGRAPGEPSRPKALCLPQ
(SEQ ID NO: 146) of W93943_P13 (SEQ ID NO: 10).
The localization of the variant protein was determined according to resμlts from a
number of different software programs and analyses, including analyses from SignalP and
other specialized programs. The variant protein is believed to be located as follows with
regard to the cell: membrane.
Variant protein W93943_P13 (SEQ ID NO:10) also has the following non-silent
SNPs (Single Nucleotide Polymorphisms) as listed in Table 8, (given according to their
position(s) on the amino acid sequence, with the alternative amino acid(s) listed).
Variant protein W93943_P14 (SEQ ID NO:l 1) according to at least some
embodiments of the invention has an amino acid sequence encoded by
transcriptW93943_T8 (SEQ ID NO:4). A description of the relationship of the variant
protein according to at least some embodiments of the invention to KNOwn proteins is as
follows:
1. Comparison report between W93943_P14 (SEQ ID NO:ll) and KNOwn protein
KCP3.HUMAN (SEQ ID NO:7):
A. An isolated chimeric polypeptide, comprising a first amino acid sequence being at
least 90% homologous to
MRRCSLCAFDAARGPRRLMRVGLALILVGHVNLLLGAVLHGTVLRHVANPRGAV
TPEYTVANVISVGSGLLSVSVGLVALLASRNLLRPμlHWVLLALALVNLLLSVACS
LGLLLAVSLTVANGGRRLIADCHPGLLDμlVμlDEGPGHTDCPFDPTRIYDTALAL
WIPSLLMSAGEAALSGYCCVAALTLRGVGPCRKDGLQGQ corresponding to amino
acids 1 - 205 of KNOwn protein KCP3_HUMAN (SEQ ID NO:7), which also corresponds to
amino acids 1 - 205 of W93943_P14 (SEQ ID NO:ll), and a second amino acid sequence
being at least 70%, optionally at least 80%, preferably at least 85%, more preferably at least
90% and most preferably at least 95% homologous to a polypeptide having the sequence
VRKANRKGSFHRDWLC (SEQ ID NO: 147) corresponding to amino acids 206 - 221 of
W93943_P14 (SEQ ID NO: 11), wherein said first amino acid sequence and second amino
acid sequence are contiguous and in a sequential order.
B. An isolated polypeptide corresponding to an edge portion of W93943_P14 (SEQ
ID NO:ll), comprising an amino acid sequence being at least 70%, optionally at least about
80%, preferably at least about 85%, more preferably at least about 90% and most preferably
at least about 95% homologous to the sequence VRKANRKGSFHRDWLC (SEQ ID NO:
147) of W93943_P14 (SEQ ID NO:ll).
2, Comparison report between W93943_P14 (SEQ ID NO: 11) and KNOwn protein
NPJ776252 (SEQ ID NO:8):
A. An isolated chimeric polypeptide, comprising a first amino acid sequence being at
least 90% homologous to
MRRCSLCAFDAARGPRRLMRVGLALILVGHVNLLLGAVLHGTVLRHVANPRGAV
TPEYTVANVISVGSGLLSVSVGLV corresponding to amino acids 1 - 78 of KNOwn
protein NPJ776252 (SEQ ID NO:8), which also corresponds to amino acids 1 - 78 of
W93943_P14 (SEQ ID NO: 11), a bridging amino acid A corresponding to amino acid 79 of
W93943_P14 (SEQ ID NO:ll), a second amino acid sequence being at least 90%
homologous to
LLASRNLLRPμlHWVLLALALVNLLLSVACSLGLLLAVSLTVANGGRRLIADCHPG
LLDμlVμlDEGPGHTDCPFDPTRIYDTALALWIPSLLMSAGEAALSGYCCVAALTLR
GVGPCRKDGLQGQ corresponding to amino acids 80 - 205 of KNOwn protein NP_776252
{SEQ ID NO:8), which also corresponds to amino acids 80 - 205 of W93943_P14 (SEQ ID
NO:l 1), and a third amino acid sequence being at least 70%, optionally at least 80%,
preferably at least 85%, more preferably at least 90% and most preferably at least 95%
homologous to a polypeptide having the sequence VRKANRKGSFHRDWLC (SEQ ID
NO: 147) corresponding to amino acids 206 - 221 of W93943_P14 (SEQ ID NO:ll),
wherein said first amino acid sequence, bridging amino acid, second amino acid sequence
and third amino acid sequence are contiguous and in a sequential order.
B, An isolated polypeptide corresponding to an edge portion of W93943_P14 (SEQ
ID NO:l 1), comprising an amino acid sequence being at least 70%, optionally at least about
80%, preferably at least about 85%, more preferably at least about 90% and most preferably
at least about 95% homologous to the sequence VRKANRKGSFHRDWLC (SEQ ID NO:
147) of W93943_P14 (SEQ ID NO:l 1).
The localization of the variant protein was determined according to resμlts from a
number of different software programs and analyses, including analyses from SignalP and
other specialized programs. The variant protein is believed to be located as follows with
regard to the cell: membrane.
Variant protein W93943_P14 (SEQ ID NO:ll) also has the following non-silent
SNPs (Single Nucleotide Polymorphisms) as listed in Table 10, (given according to their
position(s) on the amino acid sequence, with the alternative amino acid(s) listed).
Variant protein W93943_P17 (SEQ ID NO: 12) according to at least some
embodiments of the invention has an amino acid sequence as encoded by
transcriptW93943_T13 (SEQ ID NO:5). A description of the relationship of the variant
protein according to at least some embodiments of the invention to KNOwn proteins is as
follows:
1. Comparison report between W93943_P17 (SEQ ID NO:12) and KNOwn protein
KCP3.HUMAN (SEQ ID NO:7):
A, An isolated chimeric polypeptide, comprising a first amino acid sequence being at
least 90% homologous to
MRRCSLCAFDAARGPRRLMRVGLALILVGHVNLLLGAVLHGTVLRHVANPRGAV
TPEYTVANVISVGSGLLSVSVGLVALLASRNLLRPμlHWVLLALALVNLLLSVACS
LGLLLAVSLTVANGGRRLIADCHPGLLDμlVμlDEGPGHTDCPFDPTRIYDTALAL
WIPSLLMSAGEAALSGYCCVAALTLRGVGPCRKDGLQGQ corresponding to amino
acids 1 - 205 of KNOwn protein KCP3_HUMAN(SEQ ID NO:7), which also corresponds to
amino acids 1 - 205 of W93943_P17 (SEQ ID NO: 12), and a second amino acid sequence
being at least 70%, optionally at least 80%, preferably at least 85%, more preferably at least
90% and most preferably at least 95% homologous to a polypeptide having the sequence
VVAGCDARVKQKAWQPRFPGIKVKAL (SEQ ID NO: 148) corresponding to amino
acids 206 - 231 of W93943_P17 (SEQ ID NO:12), wherein said first amino acid sequence
and second amino acid sequence are contiguous and in a sequential order.
B. An isolated polypeptide corresponding to an edge portion of W93943_P17 (SEQ
ID NO: 12), comprising an amino acid sequence heing at least 70%, optionally at least about
80%, preferably at least about 85%, more preferably at least about 90% and most preferably
at least about 95% homologous to the sequence
VVAGCDARVKQKAWQPRFPGIKVKAL (SEQ ID NO: 148) of W93943_P17 (SEQ ID
NO: 12),
2. Comparison report between W93943_P17 (SEQ ID NO:12) and KNOwn protein
NP.776252 (SEQ ID NO:8):
A. An isolated chimeric polypeptide, comprising a first amino acid sequence being at
least 90% homologous to
MRRCSLCAFDAARGPRRLMRVGLALILVGHVNLLLGAVLHGTVLRHVANPRGAV
TPEYTVANVISVGSGLLSVSVGLV corresponding to amino acids 1 - 78 of KNOwn
protein NP_776252 (SEQ ID NO:8), which also corresponds to amino acids 1 - 78 of
W93943_P17 (SEQ ID NO: 12), a bridging amino acid A corresponding to amino acid 79 of
W93943_P17 (SEQ ID NO: 12), a second amino acid sequence being at least 90%
homologous to
LLASRNLLRPμlHWVLLALALVNLLLSVACSLGLLLAVSLTVANGGRRLIADCHPG
LLDμlVμlDEGPGHTDCPFDPTRIYDTALALWIPSLLMSAGEAALSGYCCVAALTLR
GVGPCRKDGLQGQ corresponding to amino acids 80 - 205 of KNOwn protein NP_776252
(SEQ ID NO:8), which also corresponds to amino acids 80 - 205 of W93943.P17 (SEQ ID
NO:12), and a third amino acid sequence being at least 70%, optionally at least 80%,
preferably at least 85%, more preferably at least 90% and most preferably at least 95%
homologous to a polypeptide having the sequence
VVAGCDARVKQKAWQPRFPGIKVKAL (SEQ ID NO: 148) corresponding to amino
acids 206 - 231 of W93943_P17 (SEQ ID NO: 12), wherein said first amino acid sequence,
bridging amino acid, second amino acid sequence and third amino acid sequence are
contiguous and in a sequential order.
B. An isolated polypeptide corresponding to an edge portion of W93943_P17 (SEQ
ID NO:12), comprising an amino acid sequence being at least 70%, optionally at least about
80%, preferably at least about 85%, more preferably at least about 90% and most preferably
at least about 95% homologous to the sequence
VVAGCDARVKQKAWQPRFPGIKVKAL (SEQ ID NO: 148) of W93943_P17 (SEQ ID
NO: 12).
The localization of the variant protein was determined according to resμlts from a
number of different software programs and analyses, including analyses from SignalP and
other specialized programs. The variant protein is believed to be located as follows with
regard to the cell: membrane.
Variant protein W93943_P17 (SEQ ID NO: 12) also has the following non-silent
SNPs (Single Nucleotide Polymorphisms) as listed in Table 12, (given according to their
position(s) on the amino acid sequence, with the alternative amino acid(s) listed).
Variant protein W93943JH8 (SEQ ID NO:13) according to at least some
embodiments of the invention has an amino acid sequence as encoded by transcript
W93943_T14 (SEQ ID NO:6). A description of the relationship of the variant protein
according to at least some embodiments of the invention to KNOwn proteins is as follows:
1. Comparison report between W93943_P18 (SEQ ID NO: 13) and KNOwn protein
KCP3_HUMAN (SEQ ID NO:7):
A. An isolated chimeric, comprising a first amino acid sequence being at least 90%
homologous to
MRRCSLCAFDAARGPRRLMRVGLALILVGHVNLLLGAVLHGTVLRHVANPRGAV
TPEYTVANVISVGSGLLSVSVGLVALLASRNLLRPμl corresponding to amino acids 1
- 91 of KNOwn protein KCP3_HUMAN (SEQ ID NO:7), which also corresponds to amino
acids 1-91 of W93943_P18 (SEQ ID NO:13), and a second amino acid sequence being at
least 90% homologous to
DTALALWIPSLLMSAGEAALSGYCCVAALTLRGVGPCRKDGLQGQLEEMTELESP
KCKRQENEQLLDQNQEIRASQRSWV corresponding to amino acids 161 - 240 of KNOwn
protein KCP3_HUMAN (SEQ ID NO:7), which also corresponds to amino acids 92-171
of W93943_P18 (SEQ ID NO:13), wherein said first amino acid sequence and second
amino acid sequence are contiguous and in a sequential order.
B. An isolated chimeric polypeptide corresponding to an edge portion of
W93943_P18 (SEQ ID NO:13), comprising a polypeptide having a lengtfi "n", wherein n is
at least about 10 amino acids in length, optionally at least about 20 amino acids in length,
preferably at least about 30 amino acids in length, more preferably at least about 40 amino
acids in length and most preferably at least about 50 amino acids in length, wherein at least
two amino acids comprise LD, having a structure as follows: a sequence starting from any
of amino acid numbers 91-x to 91; and ending at any of amino acid numbers 92 + ((n-2)-
x), in which x varies from 0 to n-2.
2. Comparison report between W93943_P18 (SEQ ID NO:13) and KNOwn protein
NP_776252 (SEQ ID NO:8):
A. An isolated chimeric polypeptide, comprising a first amino acid sequence being at
least 90% homologous to
MRRCSLCAFDAARGPRRLMRVGLALILVGHVNLLLGAVLHGTVLRHVANPRGAV
TPEYTVANVISVGSGLLSVSVGLV corresponding to amino acids 1 - 78 of KNOwn
protein NPJ776252 (SEQ ID NO:8), which also corresponds to amino acids 1 - 78 of
W93943 JP18 (SEQ ID NO: 13), a bridging amino acid A corresponding to amino acid 79 of
W93943_P18 (SEQ ID NO: 13), a second amino acid sequence being at least 90%
homologous to LLASRNLLRPμl corresponding to amino acids 80 - 91 of KNOwn protein
NP.776252 (SEQ ID NO:8), which also corresponds to amino acids 80 - 91 of
W93943_P18 (SEQ ID NO: 13), and a third amino acid sequence being at least 90%
homologous to
DTALALWIPSLLMSAGEAALSGYCCVAALTLRGVGPCRKDGLQGQLEEMTELESP
KCKRQENEQLLDQNQEIRASQRSWV corresponding to amino acids 161 - 240 of KNOwn
protein NP_776252 (SEQ ID NO:8), which also corresponds to amino acids 92 -171 of
W93943_P18 (SEQ ID NO:13), wherein said first amino acid sequence, bridging amino
acid, second amino acid sequence and third amino acid sequence are contiguous and in a
sequential order.
B. An isolated chimeric polypeptide corresponding to an edge portion of
W93943_P18 (SEQ ID NO:13), comprising a polypeptide having a length "n", wherein n is
at least about 10 amino acids in length, optionally at least about 20 amino acids in length,
preferably at least about 30 amino acids in length, more preferably at least about 40 amino
acids in length and most preferably at least about 50 amino acids in length, wherein at least
two amino acids comprise LD, having a structure as follows: a sequence starting from any
of amino acid numbers 91-x to 91; and ending at any of amino acid numbers 92 + ((n-2) -
x), in which x varies from 0 to n-2.
The localization of the variant protein was determined according to resμlts from a
number of different software programs and analyses, including analyses from SignalP and
other specialized programs. The variant protein is believed to be located as follows with
regard to the cell: membrane.
Variant protein W93943„P18 (SEQ ID NO:13) also has the following non-silent
SNPs (Single Nucleotide Polymorphisms) as listed in Table 14, (given according to their
position(s) on the amino acid sequence, with the alternative amino acid(s) listed).
G->C 116
EXAMPLE 2_2: ANALYSIS OF THE EXPRESSION OF KRTCAP3
TRANSCRIPTS
[00484] MED discovery engine described in EXAMPLE 1 herein, was used to assess the
expression of KRTCAP3 transcripts. KRTCAP3 transcripts were found to be over
expressed in lung cancer, as is demonstrated in Figure 1. Figure 1 shows expression graphs
of Affymetrix probe set 235148_at. Figure 1 shows the expression of KRTCAP3 transcripts
in microarray chips from lung cancer and lung normal experiments. As can be seen
KRTCAP3 transcripts are overexpressed in lung cancer tissues (diamond marKers) relative
to its expression in normal lung (circle marKers).
Expression ofKRTCAP3 (KeratiNOcyte associated protein 3) W93943 transcripts which
are detectable by amμlicon as depicted in sequence name W93943_seg7-10F1R1 (SEQ ID
NO: 94) in normal and cancerous Ovary tissues
Expression of KRTCAP3 (KeratiNOcyte associated protein 3) transcripts detectable by
or according to seg7-10FlRl - W93943_seg7-10F1R1 (SEQ ID NO: 94) amμlicon and
primers W93943_seg7-10F1 (SEQ ID NO: 92) and W93943_seg7-10R1 (SEQ ID NO: 93)
was measured by real time PCR in ovary panel and normal panel. The samμles used are
detailed in Tables 3 and 4 accordingly, in EXAMPLE 1.
[00485] Ovary panel -
For each RT samμle, the expression of the above amμlicon was normalized to the
normalization factor calcplated from the expression of several house Keeping genes as
described in EXAMPLE 1. The normalized quantity of each RT samμle was then divided by
the median of the quantities of the normal samμles (samμle numbers 52-78, Table 4 above),
to obtain a value of fold up-regμlation for each samμle relative to median of the normal
samμles.
Figure 2 is a histogram showing over expression of the above-indicated KRTCAP3
(KeratiNOcyte associated protein 3) transcripts in cancerous Ovary samμles relative to the
normal samμles.
As is evident from Figure 2, the expression of KRTCAP3 transcripts detectable by the
above amμlicon in serous carcinoma, muciNOus carcinoma, endometroid and
adenocarcinoma samμles was significantly higher than in the non-cancerous samμles
164
(samμle numbers 52-78, Table 4 above). notably an over-expression of at least 5 fold was
found in 33 out of 38 serous carcinoma samμles, in 10 out of 12 muciNOus carcinoma
samμles, in 7 out of 10 endometroid samμles and 56 out of 69 adenocarcinoma samμles.
Statistical analysis was apμlied to verify the significance of these resμlts, as described
below.
The P value for the difference in the expression levels of KRTCAP3 transcripts
detectable by the above amμlicon in ovary serous carcinoma samμles, ovary muciNOus
carcinoma samμles, ovary endometroid samμles and ovary adenocarcinoma samμles versus
the normal tissue samμles was determined by T test as 6.32e-005, 8.72e-003,1.04e-002 and
2.33e-005, respectively.
Threshold of 5 fold over expression was found to differentiate between serous
carcinoma, muciNOus carcinoma, endometriod and adenocarcinoma and normal samμles
with P value of 4.01e-012,1.07e-006, 8.51e-005 and 8,77e-013, respectively as checKed by
exact Fisher test.
The above values demonstrate statistical significance of the resμlts,
[00486] normal panel -
For each RT samμle, the expression of the above amμlicon was normalized to the
normalization factor calcplated from the expression of several house Keeping genes as
described in EXAMPLE 1. The normalized quantity of each RT samμle was then divided by
the median of the quantities of the ovary samμles (samμle numbers 31-34, Table 3 above),
to obtain a value of relative expression of each samμle relative to median of the ovary
samμles.
Figure 3 is a histogram showing over expression of the KRTCAP3 (KeratiNOcyte
associated protein 3) W93943 transcripts which are detectable by amμlicon as depicted in
sequence name W93943_seg7-10F1R1 (SEQ ID NO: 94) in different normal tissues.
Primer pairs are also optionally and preferably encompassed within the present
invention; for EXAMPLE, for the above experiment, the following primer pair was used as a
non-limiting illustrative EXAMPLE only of a suitable primer pain W93943_seg7-10F1
forward primer (SEQ ID NO: 92); and W93943_seg7-10R1 reverse primer (SEQ ID NO:
93).
The present invention also preferably encompasses any amμlicon obtained dirough
the use of any suitable primer pair; for EXAMPLE, for the above experiment, the following
amμlicon was obtained as a non-limiting illustrative EXAMPLE only of a suitable amμlicon:
W93943_seg7-10F1R1 (SEQ ID NO: 94).
Expression of Homo sapiens KeratiNOcyte associated protein 3 (KRTCAP3) W93943
transcripts which are detectable by amμlicon as depicted in sequence name
W93943jieg3j4-6F2R1 (SEQ ID NO:l 71) in normal and cancerous Ovary tissues
Expression of Homo sapiens KeratiNOcyte associated protein 3 (KRTCAP3)
transcripts detectable by or according to W93943_seg3j4-6F2R1 amμlicon (SEQ ID
NO:171) and primers W93943_seg3j4-6F2 (SEQ ID NO:169) and W93943_seg3j4-6R1
(SEQ ID NO: 170) was measured by real time PCR. In parallel the expression of several
houseKeeping genes - SDHA (GenBanK Accession NO. NM_004168; amμlicon - SDHA-
amμlicon), HPRT1 (GenBanK Accession NO. NMJXXH94; amμlicon - HPRT1-amμlicon)
and G6PD (GenBanK Accession NO. NM_000402; amμlicon - G6PD-amμlicon) was
measured similarly. For each RT samμle, the expression of the above amμlicon was
normalized to the normalization factor calcplated from the expression of these house
Keeping genes as described in normalization method 2 in the "materials and methods"
section. The normalized quantity of each RT samμle was then divided by the median of the
quantities of the normal samμles (samμle numbers 53, 60, 61, 63, 64, 65, 66, 67, 68, 71, 72,
73, 74, 76 and 77, Table 4 above), to obtain a value of fold up-regμlation for each samμle
relative to median of the normal samμles.
Figure 4 is a histogram showing over expression of the above-indicated Homo
sapiens KeratiNOcyte associated protein 3 (KRTCAP3) transcripts in cancerous Ovary
samμles relative to the normal samμles.
As is evident from Figure 4, the expression of Homo sapiens KeratiNOcyte associated
protein 3 (KRTCAP3) transcripts detectable by the above amμlicon in serous carcinoma,
muciNOus carcinoma and adenocarcinoma samμles was significantly higher than in the non-
cancerous samμles (samμle numbers 53, 60, 61, 63, 64, 65, 66, 67, 68, 71, 72, 73, 74, 76
and 77, Table 4 above). notably an over-expression of at least 5 fold was found in 25 out of
39 serous carcinoma samμles, in 6 out of 12 muciNOus carcinoma samμles and in 6 out of 9
endometroid carcinoma samμles.
Statistical analysis was apμlied to verify the significance of these resμlts, as described
below.
The P value for the difference in the expression levels of Homo sapiens KeratiNOcyte
associated protein 3 (KRTCAP3) transcripts detectable by the above amμlicon in Ovary
serous carcinoma samμles versus the normal tissue samμles was determined by T test as
8.93e-006. The P value for the difference in the expression levels of Homo sapiens
KeratiNOcyte associated protein 3 (KRTCAP3) transcripts detectable by the above amμlicon
in Ovary muciNOus carcinoma samμles versus the normal tissue samμles was determined by
T test as l,76e-002. The P value for the difference in the expression levels of Homo sapiens
KeratiNOcyte associated protein 3 (KRTCAP3) transcripts detectable by the above amμlicon
in Ovary endometroid carcinoma samμles versus the normal tissue samμles was determined
by T test as 7.94e-003. The P value for the difference in the expression levels of Homo
sapiens KeratiNOcyte associated protein 3 (KRTCAP3) transcripts detectable by the above
amμlicon in Ovary adenocarcinoma samμles versus the normal tissue samμles was
determined by T test as 5.75e-006.
Threshold of 5 fold over expression was found to differentiate between serous
carcinoma and normal samμles with P value of 1.25e-004 as checKed by exact Fisher test.
Threshold of 5 fold over expression was found to differentiate between muciNOus carcinoma
and normal samμles with P value of 1.64e-002 as checKed by exact Fisher test. Threshold of
5 fold over expression was found to differentiate between endometroid carcinoma and
normal samμles with P value of 3.71e-003 as checKed by exact Fisher test. Threshold of 5
fold over expression was found to differentiate between adenocarcinoma and normal
samμles with P value of 1.75e-O04 as checKed by exact Fisher test.
The above values demonstrate statistical significance of the resμlts.
Primer pairs are also optionally and preferably encompassed within the present
invention; for EXAMPLE, for the above experiment, the following primer pair was used as a
non-limiting illustrative EXAMPLE only of a suitable primer pair: W93943_seg3j4-6F2
forward primer (SEQ ID NO: 169); and W93943_seg3j4-6R1 reverse primer (SEQ ID
NO: 170).
The present invention also preferably encompasses any amμlicon obtained through
the use of any suitable primer pair; for EXAMPLE, for the above experiment, the following
amμlicon was obtained as a non-limiting illustrative EXAMPLE only of a suitable amμlicon:
W93943_seg3j4-6F2R1 (SEQ ID NO:171).
Expression of Homo sapiens KeratiNOcyte associated protein 3 (KRTCAP3)
transcripts detectable by or according to W93943_seg3j4-6F2R1 amμlicon (SEQ ID
NO:171) and primers W93943_seg3j4-6F2 (SEQ ID NO:169) and W93943_seg3j4-6R1
(SEQ ID NO: 170) was measured by real time PCR. In parallel the expression of several
houseKeeping genes - SDHA (GenBanK Accession NO. NM_004168; amμlicon - SDHA-
amμlicon), Ubiquitin (GenBanK Accession NO. BC0O0449; amμlicon - Ubiquitin-amμlicon)
and TATA box (GenBanK Accession NO. NM_003194; TATA amμlicon) was measured
similarly. For each RT samμle, the expression of the above amμlicon was normalized to the
normalization factor calcplated from the expression of these house Keeping genes as
described in the "materials and methods" section. The normalized quantity of each RT
samμle was then divided by the median of the quantities of the ovary samμles (samμle
numbers 31, 32, 33 and 34, Table 3 above), to obtain a value of relative expression of each
samμle relative to median of the ovary samμles.
Forward Primer (W93943_seg3j4-6F2): AGAGCCCAGCAGGCCAAAG
Reverse Primer (W93943_seg3j4-6R1): AGCAGGACCCAGTGCAGTG
Figure 5 is a histogram showing over expression of the KRTCAP3 transcripts
detectable by or according to W93943_seg3j4-6F2R1 amμlicon (SEQ ID NO:171) in
different normal tissues.
[00487] EXAMPLE 2_3
CLONING OF KRTCAP3 ORF non-FUSED and FUSED TO EGFP
[00488] Cloning of KRTCAP3 open reading frame (ORF) fused to EGFP was carried out
as described below, following that, the non fused KRTCAP3 ORF cloning was carried out,
[00489] The cloning of KRTCAP3-EGFP (SEQ ID NO: 110) was done in two steps. In
the first step an EGFP expression vector was constructed followed by a second step of
subcloning KRTCAP3 ORF into the EGFP expression construct. EGFP expression vector
was constructed as follows: EGFP-N1 vector (Clontech cataloge number: 6085-1) was
digested with Nhel and notI to excise the EGFP gene. The EGFP insert was then ligated
into pIRESpuro3 (Clontech cataloge number: 631619), which was previously digested with
the same enzymes, in order to obtain the EGFP-pIRESpuro3 vector. Cloning of the
KRTCAP3 open reading frame (ORF) was done using the following steps:
[00490] 1. A reverse transcription reaction was carried out as follows: lOug of purified
lung cancer RNA was mixed with 150ng Random Hexamer primers (Invitrogen, Carlsbad,
CA, USA, catalog number: 48190-011) and 500uM dNTPs in a total volume of 156μl. The
mixture was incubated for 5 min at 65°C and then quicKly chilled on ice. Thereafter, 50μl of
5X Superscriptn first strand buffer (Invitrogen, catalog number: 18064-014, part number:
Y00146), 24μl 0.1M DTT and 400 units RNasin (Promega, MilwauKee, WS, U.S.A.,
catalog number: N2511) were added, and the mixture was incubated for 10 min at 25°C,
followed by further incubation at 42°C for 2 min. Then, lOμl (2000 units) of Superscriptn
(Invitrogen, catalog number: 18064-014) was added and the reaction (final volume of
250μl) was incubated for 50 min at 42°C and then inactivated at 70°C for 15min. The
resμlting cDNA was diluted 1:20 in TE buffer (lOmM Tris, 1 mM EDTA pH 8).
[00491] PCR details concerning the subcloning of KRTCAP3 ORF are given in Table
16. PCR #1 was designed to yield KRTCAP3 ORF DNA (SEQ ID NO:112) which then was
subcloned upstream to the EGFP in the EGFP pIRESpuro3 described above, while PCR #2
was designed to yield KRTCAP3 ORF DNA which was subcloned downstream to the
EGFP pIRESpuro from above.
[00492] 2. PCR was done using μlatinum PFX™ (Invitrogen., Carlsbad, CA, USA,
catalog number: 1178-021) under the following conditions: 5μl μlatinum PFX lOx buffer,
5μl - cDNA from the above; 2μl - 10 mM dNTPs (2.5mM of each nucleotide); 0.5μl -
μlatinum PFX enzyme; 37μl - H20; and 1.5μl - of each primer (IOJIM) in a total reaction
volume of 50μl; with a reaction program of 5 minutes in 95°C; 35 cycles of: 30 seconds at
94°C, 30 seconds at 55°C, 50 seconds at 680C; then 10 minutes at 68°C. Primers which were
used include gene specific sequences corresponding to the desired coordinates of the
protein, restriction enzyme sites and KozaK sequence, as listed in Table 16, below. Bold
letters in Table 16 represent the specific gene sequence while the restriction site extensions
utilized for cloning purposes are in Italic and KozaK sequences are underlined.
[00493] 5μl of PCR product was loaded onto a 1% agarose gel stained with ethidium
bromide, electrophoresed in lxTBE solution at 100V, and visualized with UV light. After
verification of expected band size, remaining PCR product was processed for DNA
purification using QiaquicK PCR purification Kit (Qiagen™, Valencia, CA, U.S.A., catalog
number 28106). The extracted PCR products were digested with the appropriate restriction
enzymes (New England Biolabs, Beverly, MA, U.S.A.), as listed in Table 16. After
digestion, DNAs were loaded onto a 1 % agarose gel as described above. The expected band
size was excised and extracted from the gel using QiaQuicK™ Gel Extraction Kit (Qiagen,
catalog number: 28707),
[00494] The digested ORF DNAs were ligated to EGFP_pIRESpuro3 vector using the
LigaFastTM Rapid DNA Ligation System (Promega, catalog number: M8221.). The
resμlting DNAs were transformed into competent E.Coli bacteria DH5ct (RBC Bioscience,
Taipei, Taiwan, catalog number: RH816) according to manufacturer's instructions, then
plated on LB-ampicillin agar plates for selection of recombinant plasmids, and incubated
overnight at 37°C.
[00495] The following day, a number of colonies from each transformation that grew on
the selective plates were taKen for further analysis by streaK-plating on another selective
plate and by PCR using GoTaq ReadyMix (Promega, catalog number: M7122), Screening
positive clones was performed by PCR using pIRESpuro3 vector specific primer and gene
specific primer (data not shown). After comμletion of all PCR cycles, half of the reaction
was analyzed using 1% agarose gel as described above. After verification of expected band
size, 2 positive colonies from each ligation reactions were grown in 5 ml Terrific Broth
supμlemented with 100ug/ml ampicillin, with shaKing overnight at 37°C. μlasmid DNA was
isolated from bacterial cμltures using Qiaprep™ Spin Miniprep Kit (Qiagen, catalog
number: 27106). Accurate cloning was verified by sequencing the inserts (Weizmann
Institute, Rehovot, Israel). Upon verification of an error-free colony (i.e. NO mutations
within the ORF), recombinant plasmids were processed for further analyses.
[00496] The two KRTCAP3-EGFP constructs from above were used for subcloning
KRTCAP3 pIRESpuro3 construct. Subcloning was done as follows: KRTCAP3-EGFP
pIRESpuro3 was double digested with BlpI and Nhel restriction enzymes (New England
Biolabs, Beverly, MA, U.S.A.) and a 220 base pair fragment, corresponding to the 5' end of
KRTCAP3 was excised. Following that, EGFP-KRTCAP3 μlRESpuro3 was also double
digested with the same restriction enzymes (New England Biolabs, Beverly, MA, U.S.A.)
and a 5629 base pair fragment, corresponding to the 3' end of KRTCAP3 and pIRESpuro
sequences was excised. The two fragments were ligated and transformed into E.coli as
described above. The resμlting construct was named KRTCAP3 pIRESpuro3.
[00497] The DNA sequences of the resμlting KRTCAP3-EGFP; EGFP-KRTCAP3 and
KRTCAP3 are shown in Figures 6A-C; gene specific sequence corresponding to KRTCAP3
ORF sequence is marKed in bold faced, EGFP sequence is in italics, and intermediate linKer
regions are unbold. Figure 6A represents the DNA sequence of KRTCAP3_EGFP (SEQ ID
NO: 110); Figure 6B represents the DNA sequence of EGFP_KRTCAP3 (SEQ ID NO:111);
Figure 6C represents the DNA sequence of KRTCAP3 (SEQ ID NO:112).
[00498] The amino acid sequences of KRTCAP3-EGFP; EGFP-KRTCAP3 and
KRTCAP3 are shown in Figures 7A-C; amino acid sequence corresponding to KRTCAP3
ORF is marKed in bold faced, EGFP sequence is in italics, and intermediate linKer regions
are unbold. Figure 7A represents the amino acid sequence of KRTCAP3_EGFP protein
(SEQ ID NO: 113); Figure 7B represents the amino acid sequence of EGFP_KRTCAP3
protein (SEQ ID NO:114); Figure 7C represents the amino acid sequence of KRTCAP3
protein (SEQ ID NO:7).
EXAMPLE 2_4 DETERMINING CELL LOCALIZATION OF KRTCAP3
[00500] KRTCAP3 protein was predicted to be a transmembrane protein with four
transmembrane domains. In order to verify KRTCAP3 cellμlar localization, KRTCAP3 was
cloned as EGFP (Enhanced Green Fluorescent Protein) fusion proteins, as described above.
Protein localization was observed upon transient transfection (Chen et al., Molecμlar Vision
2002; 8; 372-388) using confocal microscopy. The cells were observed for the presence of
fluorescent products 48 hours following transfection,
[00501] The EGFP-KRTCAP3 pIRESpuro3 (SEQ ID NO:111) and KRTCAP3-EGFP
pIRESpuro3 (SEQ ED NO:110) constructs were subsequently transiently transfected into
HEK-293T cells as follows:
[00502] HEK-293T (ATCC, CRL-11268) cells were plated on sterile glass coverslips,
13mm diameter (Marienfeld, catalog number: 01 115 30), which were μlaced in a 6 well
plate, using 2ml pre-warmed DMEM [Dμlbecco's modified Eagle's Media, Biological
Industries (Beit Ha'EmeK, Israel), catalog number: 01-055-1A] + 10% FBS [Fetal Bovine
Serum, Biological Industries (Beit Ha'EmeK, Israel), catalog number: 04-001-1A] + 4mM
L-Glutamine [Biological Industries (Beit Ha'EmeK, Israel), catalog number: 03-020-1A].
500,000 cells per well were transfected with 2ug of DNA construct using 6μl FuGENE 6
reagent (Roche, catalog number: 11-814-443-001) diluted into 94μl DMEM. The mixture
was incubated at room temperature for 15 minutes. The comμlex mixture was added
dropwise to the cells and swirled. Cells were μlaced in incubator maintained at 37°C with
5% C02 content.
[00503] 48 hours post transient transfection, cells on coverslips were further processed
for immuNOstaining and analysis by confocal microscopy. The cover slips were washed in
phosphate buffered saline (PBS), then fixed for 15 minutes with a solution of 3.7%
paraformaldehyde (PFA) (Sigma, catalog number: P-6148)/3% glucose (Sigma, catalog
number: G5767) (diluted in PBS). Quenching of PFA was done by a 5 minute incubation in
3mM glycine (Sigma, catalog number: G7126) (diluted in PBS). After two 5-minute washes
in PBS, cells were permeabilized with 0.1% triton-X100 (diluted in PBS) for 5 minutes.
After two 5-minute washes in PBS, blocKing of non-specific regions was done with 5%
bovine serum albumin (BSA) (Sigma, catalog number: A4503) (diluted in PBS) for 20
minutes. The coverslips were then incubated, in a humid chamber for 1 hour, with rabbit
anti-GFP antibody (MBL International Corporation, catalog number: 598), diluted 1:500 in
5% BSA in PBS, followed by three 5-minute washes in PBS. The coverslips were then
incubated, in a humid chamber for 1 hour, with secondary antibody: donKey anti-rabbit
conjugated to Cy-3 flurophore (JacKson ImmuNOResearch, catalog number: 711-165-152),
diluted 1:200 in 3% BSA in PBS. After three 5-minute washes in PBS, the fixed coverslips
were mounted on slides with Gel Mount Aqueous medium (Sigma, catalog number: G0918)
and cells were observed for the presence of fluorescent product using confocal microscopy.
The resμlts are presented in Figure 8.
[00504] KRTCAP3 μlasma membrane localization was demonstrated using both EGFP
fused constructs (EGFP-KRTCAP3 pIRESpuro3 and KRTCAP3-EGFP pIRESpuro3). Cell
localization was observed by either detecting EGFP fusion protein fluorescence (Figure 8A)
or by immuNOstaining using anti GFP (Figure 8B). Data is shown for only one construct
(EGFP-KRTCAP3 pIRESpuro3)
[00505] Figure 8A demonstrates by green fluorescence of EGFP that the
EGFP_KRTCAP3_P2 (SEQ ID NO: 114) fused protein localizes to the cell membrane upon
expression in HEK 293T cells. The image was obtained using the 40x objective of the
confocal microscope.
[00506] Figure 8B demonstrates by red fluorescence of anti-GFP antibody conjugated to
Cy3 flurophore that the EGFP_KRTCAP3_P2 (SEQ ID NO: 114) fused protein localizes to
the cell membrane upon expression in HEK 293T cells. The image was obtained using the
40x objective of the confocal microscope.
EXAMPLE 2_5
[00507] DETERMINING ORIENTATION OF KRTCAP3 IN THE CELL MEMBRANE
[00508] KRTCAP3 protein's orientation within the cell was determined by
immuNOstating of the above EGFP-KRTCAP3 transiently transfected cells, ImmuNOstaining
was done as described above, but this time antibody staining was done using non
permeabilized transiently transfected HEK 293T cells (as opposed to EXAMPLE 2_4). Cell
permeabilization enables antibody penetration into the cell, therefore, immuNOstaining of
non permeabilized cells, will resμlt in detection of proteins epitopes which are located at the
extracellular region of the cell, while internal epitopes will not be detected.
[00509] 48 hours post transient transfection, the cells on coverslips were further
processed for immuNOstaining and analysis by confocal microscopy. The coverslips were
washed 2 times in cold PBS and non-specific regions of coverslips blocKed with 5% BSA
(Sigma, catalog number: A4503) (diluted in PBS) for 20 minutes on ice. The coverslips
were then incubated, in a humid chamber on ice for Ihr, with rabbit anti-GFP antibody
(MBL International Corporation, catalog number: 598), diluted 1:500 in 5% BSA in PBS.
After 3 5-minute washes in cold PBS, cells on coverslips were fixed for 15 minutes with a
solution of 3% paraformaldehyde (PFA) (Sigma, catalog number: P-6148)/3% glucose
(Sigma, catalog number: G5767)(diluted in PBS). Quenching of PFA was done by a 5
minute incubation in 3mM glycine (Sigma, catalog number: G7126) (diluted in PBS),
followed by two 5 minutes wash in PBS. The coverslips were then incubated, in a humid
chamber for lhr, with secondary antibody: donKey anti-rabbit conjugated to Cy-3
flurophore (JacKson ImmuNOResearch, catalog number: 711-165-152), diluted 1:200 in 3%
BSA in PBS. After 3 5-minute washes in PBS, the fixed coverslips were mounted on slides
with Gel Mount Aqueous medium (Sigma, catalog number: G0918) and cells were observed
for the presence of fluorescent product using confocal microscopy,
[00510] The resμlts presented in Figure 9 indicate that the amino terminal region of
KRTCAP3 is internal to the cell surface. The green fluorescence of EGFP, which is
observed in the non permeabilized transiently transfected EGFP_KRTCAP3 HEK 293T
cells, demonstrates the localization of the fusion protein to the cell membrane (Figure 9A),
however, the absence of red fluorescence of anti-GFP antibody in these cells, indicates that
the EGFP_KRTCAP3 fused protein is positioned in the μlasma membrane with its amino
terminal facing the cytosol (Figure 9B), The images were obtained using the 40x objective
of the confocal microscope.
EXAMPLE 2_6
[00511] PRODUCTION OF POLYCLONAL ANTIBOtheS SPECIFIC TO KRTCAP3
VARIANT
[00512] All polyclonal Abs production procedure, including peptides synthesis, peptides
conjugation, animal immunizations, bleeding and antibothes purification were performed at
Sigma-Aldrich (Israel),
[00513] Animals
[00514] Two pairs of rabbits were injected to prepare antibothes for KRTCAP3 (rabbit
numbers 5257 and 5258, 5259 and 5261). All animal care, handling and injections were
performed by Sigma (Israel).
[00515] Peptide synthesis
[00516] The peptides which were used for rabbit immunization were as follows:
EQLLDQNQEIRASQRS-C (KRT223 (SEQ ID NO: 115), a sequence taKen from the
C'terminus correspond to aa 223-238 of the KRTCAP3 protein (KRTCAP3_P2; SEQ ID
NO:7), in which Cystein was added to the C terminus of the peptide for KLH conjugation,
and LDEGPGHTDCPFDPTR (KRT143 SEQ ID NO: 116), a sequence taKen from the ECD
100p correspond to aal43-160 of the KRTCAP3 protein 6 (SEQ ID NO:19).
C. An isolated polypeptide corresponding to an edge portion of AA213820_P6 (SEQ
ID NO:19), comprising an amino acid sequence being at least 70%, optionally at least about
80%, preferably at least about 85%, more preferably at least about 90% and most preferably
at least about 95% homologous to the sequence
EEVSPDCQGVNTGMAAEVPKVSμlQQSYSCLNPQLESNEGQAVNSKRLLHHCFMA
TVTTSDIPGSPEEASVPNPDLCGPVP (SEQ ID NO: 151) of AA213820_P6 (SEQ ID
NO:19).
The localization of the variant protein was determined according to resμlts from a
number of different software programs and analyses, including analyses from SignalP and
other specialized programs. The variant protein is believed to be located as follows with
regard to the cell: membrane.
The coding portion of transcript AA213820_T6 (SEQ ID NO:20) starts at position 2
and ends at position 496.
EXAMPLE 4_2 EXPRESSION ANALYSIS OF MGC52498 TRANSCRIPTS
The MED discovery engine, described in EXAMPLE 1 herein, was used to assess the
expression of MGC52498 transcripts, MGC52498 transcripts were found to be over
expressed in lung cancer, as demonstrated in Figure 24, and in leuKemias, as demonstrated
in Figure 25. Figures 24 and 25 show expression graphs of Affymetrix probe set
1555379_at. Figure 24 shows the expression of MGC52498 transcripts in microarray chips
from lung cancer and lung normal experiments. As can be seen MGC52498 transcripts are
overexpressed in lung cancer tissues (diamond marKers) relative to their expression in
normal lung (circle marKers).
Figure 25 shows the expression of MGC52498 transcripts in microarray chips from
b100d cancers and normal b100d experiments. As can be seen MGC52498 transcripts are
overexpressed in various leuKemia samμles (diamonds marKers) relative to its expression in
normal b100d samμles (circle, square and triangle marKers).
Expression of hypothetical protein MGC52498 AA213820 transcripts which are
detectable by amμlicon as depicted in sequence name AA213820_seg8-llF2R2 (SEQ ID
NO: 109) in b100d specific panel and in different normal tissues
Expression of hypothetical protein MGC52498 transcripts detectable by or according
to seg8-11F2R2 - AA213820_seg8-llF2R2 (SEQ ID NO: 109) amμlicon and primers
AA213820_seg8-llF2 (SEQ ID NO: 107) and AA213820_seg8-llR2 (SEQ ID NO: 108)
was measured by real time PCR in b100d panel and normal panel. The samμles used for
b100d panel are detailed in Tables 2 and 2_1, The samμles used for normal panel are
detailed in Table 3.
normal panel -
For each RT samμle, the expression of the above amμlicon was normalized to the
normalization factor calcplated from the expression of several house Keeping genes as
described in EXAMPLE 1. The normalized quantity of each RT samμle was then divided by
the median of the quantities of the Kidney samμles (samμle numbers 19-23, Table 3 above),
to obtain a value of relative expression of each samμle relative to median of the Kidney
samμles, as shown in Figure 26. High expression was observed in PBMCs and sμleen
normal samμles.
B100d panel -
For b100d panel - For each RT samμle, the expression of the above amμlicon was
normalized to the normalization factor calcplated from the expression of several house
Keeping genes as described in EXAMPLE 1. The normalized quantity of each RT samμle was
then divided by the median of the quantities of the Kidney normal samμles (samμle numbers
65-67, Table 2 above), to obtain a value of relative expression of each samμle relative to
median of the Kidney normal samμles.
The resμlts of this analysis are depicted in the histogram in Figure 27. Expression of
the above-indicated hypothetical protein MGC52498 transcripts is high in different b100d-
derived cells, different lymphomas and mμltiμle myeloma patients samμles
EXAMPLE 4_3: CLONING OF FμlL LENGTH ORF ENCODING MGC52498 T1_P4
FUSED TO FLAG
[00539] Cloning of Fμll Length ORF encoding MGC fused to FLAG tag, either at the C
terminus or the N Terminus, was done as described below.
[00540] PCR was done using GoTaq ReadyMix (Promega, catalog number M7122)
under the following conditions: 10.5µl - cDNA from the b100d panel described above
{XXXLym_MantleCelll); 1µl -of each primer (10µM); 12.5µl ReadyMix with a reaction
program of 3 minutes in 95°C; 40 cycles of 30 seconds at 94°C, 30 seconds at 50°C, 1.5
minutes at 72°C; then 10 minutes at 72°C. Primers which were used were primer #100-946
(SEQ ID NO:176) and primer #100-947 (SEQ ID NO:177). In order to enhance the PCR
product and to generate Flag tag at the N/C terminus followed by NheI restriction site, and
KozaK sequence, as well as EcoRI restriction site at the C terminus, second PCR was done
using first PCR product as a template and specific primers as follows: primer #100-948
(SEQ ID NO:178) and primer #100-949 (SEQ ID NO:179), for the N terminus Flag or
primer #100-954 (SEQ ID NO:180) and primer #100-955 (SEQ ID NO:181) for the C
terminus Flag. PCR conditions were the same as described above.
[00541] The PCR product was loaded onto a 1% agarose gel stained with ethidium
bromide, electrophoresed in 1xTBE solution at 100V, and visualized with UV light. After
verification of expected size band, it was extracted using QiaquicK gel extraction
purification Kit (Qiagen™, Valencia, CA, U.S.A., catalog number 28706). The extracted
PCR product was digested with the appropriate restriction enzymes: NheI and EcoRI (New
England Biolabs, Beverly, MA, U.S.A.). After digestion, the DNA was loaded onto a 1 %
agarose gel as described above. The expected band size was excised and extracted from the
gel using QiaQuicK™ Gel Extraction Kit (Qiagen, catalog number: 28706).
[00542] The digested target ORF DNA was ligated into pIRESpuro3 vector previously
digested with the same enzymes, using the LigaFastTM Rapid DNA Ligation System
(Promega, catalog number: M8221). The resμlting DNA were transformed into competent
E.Coli bacteria DH5a (RBC Bioscience, Taipei, Taiwan, catalog number: RH816)
according to manufacturer's instructions, then plated on LB-ampicillin agar plates for
selection of recombinant plasmids, and incubated overnight at 37°C.
[00543] The following day, a number of colonies from the transformation were screen by
PCR using GoTaq ReadyMix (Promega, catalog number: M7122) using pIRESpuro3 vector
specific primer and gene specific primer (data not shown). After verification of expected
band size, two positive colonies were grown in 5 ml Terrific Broth supμlemented with
100µg/ml ampicillin, with shaKing overnight at 37°C. μlasmid DNA was isolated from
bacterial cμltures using Qiaprep™ Spin Miniprep Kit (Qiagen, catalog number: 27106).
Accurate cloning was verified by sequencing the inserts (Weizmann Institute, Rehovot,
Israel). Upon verification of an error-free colony (i.e. NO mutations within the ORF),
recombinant μlasmid was processed for further analysis.
[00544] Figures 28A and 28B represent the DNA sequence of FLAG_MGC_T1_P4 -
(SEQ ID NO:182) and MGC_T1_P4_FLAG (SEQ ID NO:183) respectively; FLAG
sequence is underlined.
[00545] Figures 29 A and 29B represent the amino acid sequence of FLAG_MGC_T1_P4
protein (SEQ ID NO:184) and MGC_T1_P4_FLAG (SEQ ID NO:185) respectively; FLAG
sequence is underlined.
[00546] EXAMPLE 4_4 DETERMINING CELL LOCALIZATION OF MGC52498
PROTEIN
[00547] Determining cell localization of MGC52498 was done using the confocal
microscope. MGC_T1_P4_FLAG pIRESpuro3 or FLAG_MGC_T1_P4 pIRESpuro3
constructs described above or pIRESpuro3 empty vector were subsequently transiently
transfected into HEK-293T cells as follows:
[00548] HEK-293T (ATCC, CRL-11268) cells were plated on sterile glass coverslips,
13mm diameter (Marienfeld, catalog number: 01 115 30), which were μlaced in a 6 well
plate, using 2ml pre-warmed DMEM [Dμlbecco's modified Eagle's Media, Biological
Industries (Beit Ha'EmeK, Israel), cataloge number: 01-055-1A] + 10% FBS (Fetal Bovin
Serum) + 4mM L-Glutamine. 500,000 cells per well were transfected with 2g of the DNA
construct using 6µl FuGENE 6 reagent (Roche, catalog number: 11-814-443-001) diluted
into 94μl DMEM. The mixture was incubated at room temperature for 15 minutes. The
comμlex mixture was added dropwise to the cells and swirled. Cells were μlaced in
incubator maintained at 37°C with 5% CO2 content.
48 hours post transient transfection, the cells were further processed for analysis in confocal
microscopy. The cover slips were washed 3 times in phosphate buffered saline (PBS) and
fixed for 15 minutes with a fixing solution composed of 3.7% paraformaldehyde (PFA)
(Sigma, catalog number: P-6148) and 3% glucose (Sigma, catalog number: G5767),
followed by 5 minutes incubation with 3mM glycine (Sigma, catalog number: G7126).
After 1 wash in PBS, cells were permeabilized by incubation with 0.1% triton X-100/PBS
solution for 5 minutes. After 2 washes in PBS cells were incubated in 5% bovine serum
albumin (BSA) (Sigma, catalog number: A4503) in PBS solution for 20 minutes. The cells
were then incubated with anti FLAG antibody conjugated to cy3 (Sigma, catalog number:
A9594) diluted 1:100 in 5% BSA in PBS for 1 hr, followed by three 5-minute washes in
PBS. The coverslips were then mounted on a slide with Gel Mount Aqueous medium
(Sigma, catalog number: G0918) and cells were observed for the presence of fluorescent
product using confocal microscopy.
[00549] The red fluorescence signal obtained from cells expressing MGC_T1_P4_FLAG
(SEQ ID NO: 184) or FLAG_MGC_T1_P4 (SEQ ID NO: 185), as opposed to the absence of
signal obtained from pIRESpuro3 empty vector indicates for ectopic expression of MGC,
notwithstanding, the recombinant protein coμld not be detected in the cell membrane of
HEK 293T cells (data not shown). In order to further understand MGC P4 cell localization,
endogeNOus expression instead of ectopic expression will be tested.
[00550] EXAMPLE 5: FAM70A POLYPEPTIDES AND POLYNUCLEOTIDES, AND
USES THEREOF AS A DRUG TARGET FOR PRODUCING DRUGS AND BIOLOGICS
EXAMPLE 5_1: DESCRIPTION FOR CLUSTER F10649
Cluster F10649 (internal ID 72834556) features 8 transcripts of interest, the names for
which are given in Table 25. The selected protein variants are given in table 26,
These sequences are variants of the KNOwn hypothetical protein LOC55026 (SEQ ID
NO:29) (SwissProt accession identifier NP_060408; synonims: FAM70A).
FAM70A (family with sequence similarity 70, member A) was identified in several
large scale stuthes, such as identification and characterization of putative alternative
promoters of human genes (Kimura et al. 2006, GeNOme Res. 16(1): 55-65), annotation of
chromosome X (Ross et al. 2005, Nature 434(7031): 325-37), and fμll length cDNA
projects (Gerhard et al. 2004, GeNOme Res 14(10B): 2121-7; Strausberg et al 2002, PNAS
99(26): 16899-903; Ota et al. 2004, Nat Genet 36(1): 40-5). However NO research was
published about FAM70A specifically.
Sequences corresponding to F10649_P4 (SEQ ID NO:30) and F10649_P5 (SEQ ID
NO:33) were reported in WO2003083039 among other novel polypeptides, and the nucleic
acids encoding them, as having properties related to stimμlation of biochemical or
physiological responses in a cell, a tissue, an organ or an organism. Sequences
corresponding to F10649_P4 (SEQ ID NO:30) and F10649.P5 (SEQ ID NO:33) were also
reported in EP1293569, among other novel polypeptides, and the nucleic acids encoding
them, as being involved in neural cell differentiation. Neither WO2003083039 NOr
EP1293569 teach or suggest, however, that sequences corresponding to F10649_P4 (SEQ
ID NO:30) and F10649_P5 (SEQ ID NO:33) are differentially expressed in Mμltiμle
Myeloma, Kidney cancer, lung cancer, liver cancer, and breast cancer. Also, there is NO
teaching or suggestion in these apμlications that F10649_P4 (SEQ ID NO:30) and
F10649_P5 (SEQ ID NO:33) can be used as drug target for treatment of cancer, especially
for treatment of Mμltiμle Myeloma, Kidney cancer, lung cancer, liver cancer, and breast
cancer, and/or immune related conditions, or for diagNOsis thereof. Also, there is NO
teaching or suggestion in these apμlications that antibothes specific for F10649_P4 (SEQ ID
NO:30), F10649_P5 (SEQ ID NO:33), its soluble ectodomain, and/or fragments thereof can
be used as therapeutics for treatment of cancer, especially for treatment of Mμltiμle
Myeloma, Kidney cancer, lung cancer, liver cancer, and breast cancer, and/or immune
related conditions, or for diagNOsis tiiereof.
A sequence corresponding to F10649_P10 (SEQ ID NO:32) was reported in
WO2003057160, WO200222660, WO2004039956 and WO2004041170, among many
other polypeptides related to cancer and/or immune related diseases. In contrary to the
present apμlication, WO2003057160 demonstrates deregμlation of the sequence
corresponding to F10649_P10 in Kidney tumor as compared to normal Kidney tissues. none
of the WO2003057160, WO200222660, WO2004039956 and WO2004041170 apμlications
teaches or suggests that the sequence corresponding to F10649_P10 can be used as drug
target for treatment of Mμltiμle Myeloma, Kidney cancer, lung cancer, liver cancer, and
breast cancer, and/or immune related conditions, or for diagNOsis thereof. Also, there is NO
teaching or suggestion in these apμlications that antibothes specific to F10649_P10, its
soluble ectodomain, and/or fragments thereof can be used as therapeutics for treatment of
cancer, especially for treatment of Mμltiμle Myeloma, Kidney cancer, lung cancer, liver
cancer, and breast cancer, or for diagNOsis thereof.
By contrast and surprisingly, the present inventors have found that FAM70A antigen
and discrete portions thereof may optionally be used as a drug target for therapeutic small
molecμles, peptides, antibothes, antisense RNAs, siRNAs, ribozymes, and the liKe.
DiagNOstic and therapeutic polyclonal and monoclonal antibothes and fragments thereof that
bind FAM70A, and portions and variants thereof, may optionally be produced. According to
at least some embodiments of the present invention, there is provided the use of antibothes
and antibody fragments against FAM70A antigen, its secreted or soluble form or ECD
and/or variants, conjugates, or fragments thereof and fragments and variants thereof for
treating and diagNOsing cancer, especially for treatment of Mμltiμle Myeloma, Kidney
cancer, lung cancer, liver cancer, and breast cancer, and/or immune related conditions,
wherein mis antigen is differentially expressed.
As noted above, cluster F10649 features 8 transcripts, which were listed in Table 25
above. These transcripts encode for proteins which are variants of protein hypothetical
protein LOC55026 (SEQ ID NO:29). A description of each variant protein according to at
least some embodiments of the invention is NOw provided.
Variant protein F10649_P4 (SEQ ID NO:30) according to at least some embodiments
of the present invention has an amino acid sequence as encoded by transcript F10649_T0
(SEQ ID NO:21). A description of the relationship of the variant protein according to at
least some embodiments of the invention to KNOwn proteins is as follows:
1. Comparison report between F10649_P4 (SEQ ID NO:30) and KNOwn protein
Q7Z4S8_HUMAN (SEQ ID NO:31):
A, An isolated chimeric polypeptide, comprising a first amino acid sequence being at
least 90% homologous to
MHQSLTQQRSSDMSLPDSMGAFNRRKRNSIYVTVTLLIVSVLILTVGLAATTRTQN
VTVGGYYPGVILGFGSFLGnGSNLIENKRQMLVASIVFISFGVIAAFCCAIVDGVFAA
RHIDLKμlYANRCHYVPKTSQKEAEEVISSSTKNSPSTRVMRNLTQAAREVNCPHLS
REFCTPRIRGNTCFCCDLYNCGNRVEITGGYYEYIDVSSCQDIIHLYHLLWSATILNI
VGLFLGirTAAVLGGFKDMNPTLPALNCSVENTHPTVSYYAHPQVASYNTYYHSPP
HLPPYSAYDFQHSGVFPSSPPSGLSDEPQSAS corresponding to amino acids 1 - 318 of
KNOwn protein Q7Z4S8_HUMAN (SEQ ID NO:31), which also corresponds to amino acids
1-318 of F10649_P4 (SEQ ID NO:30), a bridging amino acid P corresponding to amino
acid 319 of F10649_P4 (SEQ ID NO:30), and a second amino acid sequence being at least
90% homologous to SPSYMWSSSAPPRYSPPYYPPFEKPPPYSP corresponding to amino
acids 320 - 349 of KNOwn protein Q7Z4S8.HUMAN (SEQ ID NO:31), which also
corresponds to amino acids 320 - 349 of F10649_P4 (SEQ ID NO:30), wherein said first
amino acid sequence, bridging amino acid and second amino acid sequence are contiguous
and in a sequential order.
2. Comparison report between F10649JP4 (SEQ ID NO:30) and KNOwn proteins
NP_0604O8 and Q86Y72_HUMAN:
A. An isolated chimeric polypeptide, comprising a first amino acid sequence being at
least 90% homologous to
MHQSLTQQRSSDMSLPDSMGAFNRRKRNSIYVTVTLLIVSVLILTVGLAATTRTQN
VTVGGYYPGVILGFGSFLGIIGSNLIENKRQMLVASIVFISFGVIAAFCCAIVDGVFAA
RHIDLKμlYANRCHYVPKTSQKEAEEVISSSTKNSPSTRVMRNLTQAAREVNCPHLS
REFCTPRIRGNTCFCCDLYNCGNRVEITGGYYEYIDVSSCQDIIHLYHLLWSATILNI
VGLFLGHTAAVLGGFKDMNPTLPALNCSVENTHPTVSYYAHPQVASYNTYYHSPP
HLPPYSAYDFQHSGVFPSSPPSGLSDEPQSASPSPSYMWSSSAPPRYSPPYYPPFEKP
corresponding to amino acids 1 - 344 of KNOwn proteins NP_06O408 and
Q86Y72_HUMAN, which also corresponds to amino acids 1 - 344 of F10649.P4 (SEQ ID
NO:30), a bridging amino acid P corresponding to amino acid 345 of F10649_P4 (SEQ ID
NO:30), and a second amino acid sequence being at least 90% homologous to PYSP
corresponding to amino acids 346 - 349 of KNOwn proteins NP_060408 and
Q86Y72_HUMAN, which also corresponds to amino acids 346 - 349 of F10649.P4 (SEQ
ID NO:30), wherein said first amino acid sequence, bridging amino acid and second amino
acid sequence are contiguous and in a sequential order.
3. Comparison report between F10649_P4 (SEQ ID NO:30) and KNOwn protein
Q9NWN8_HUMAN (SEQ ID NO:32):
A. An isolated chimeric polypeptide, comprising a first amino acid sequence being at
least 70%, optionally at least 80%, preferably at least 85%, more preferably at least 90%
and most preferably at least 95%, homologous to a polypeptide having the sequence
MHQSLTQQRSSDMSLPDSMGAFNRRKRNSIYVTVTLLIVSVLILTVGLAATTRTQN
VTVGGYYPGVILGFGSFLGnGSNLIENKRQMLVASIVnSFGVIAAFCCAIVDGVFAA
RHIDLKμlYANRCHYVPKTSQKEAEEVISSSTKNSPSTRVMRNLTQAARE (SEQ ID
NO: 155) corresponding to amino acids 1 -165 of F10649_P4 (SEQ ID NO:30), and a
second amino acid sequence being at least 90% homologous to
VNCPHLSREFCTPRIRGNTCFCCDLYNCGNRVEITGGYYEYIDVSSCQDIIHLYHLL
WSATILNIVGLFLGIITAAVLGGFKDMNPTLPALNCSVENTHPTVSYYAHPQVASYN
TYYHSPPHLPPYSAYDFQHSGVFPSSPPSGLSDEPQSASPSPSYMWSSSAPPRYSPPY
YPPFEKPPPYSP corresponding to amino acids 2-185 of KNOwn protein
Q9NWN8_HUMAN (SEQ ID NO:32), which also corresponds to amino acids 166 - 349 of
F10649_P4 (SEQ ED NO:30), wherein said first amino acid sequence and second amino
acid sequence are contiguous and in a sequential order.
B, An isolated polypeptide corresponding to a head of F10649_P4 (SEQ ID NO:30),
comprising a polypeptide being at least 70%, optionally at least about 80%, preferably at
least about 85%, more preferably at least about 90% and most preferably at least about 95%
homologous to the sequence
MHQSLTQQRSSDMSLPDSMGAFNRRKRNSIYVTVTLLIVSVLILTVGLAATTRTQN
VTVGGYYPGVILGFGSFLGIIGSNLIENKRQMLVASrVFISFGVIAAFCCAIVDGVFAA
RHIDLKμlYANRCHYVPKTSQKEAEEVISSSTKNSPSTRVMRNLTQAARE (SEQ ID
NO: 155) of F10649_P4 (SEQ ID NO:30).
The localization of the variant protein was determined according to resμlts from a
number of different software programs and analyses, including analyses from SignalP and
other specialized programs. The variant protein is believed to be located as follows with
regard to the cell: membrane.
Variant protein F10649_P4 (SEQ ID NO:30) also has the following non-silent SNPs
(Single Nucleotide Polymorphisms) as listed in Table 27, (given according to their
position(s) on the amino acid sequence, with the alternative amino acid(s) listed).
G -> A 627
G -> C 627
C->T 1202
A->C 1282,3227
C->A 1523,1826
C-> G 1523, 1826
A -> 1820
T -> A 2423
T -> G 2423
T->C 2433
A -> T 3227
Variant protein F10649_P5 (SEQ ID NO:33) according to at least some embodiments
of the invention has an amino acid sequence encoded by transcript F10649_T1 (SEQ ID
NO:22). A description of the relationship of the variant protein according to at least some
embodiments of the invention to KNOwn proteins is as follows:
1, Comparison report between F10649_P5 (SEQ ID NO:33) and KNOwn protein
Q5JRV8_HUMAN (SEQ ID NO:30):
A. An isolated chimeric polypeptide, comprising a first amino acid sequence being at
least 90% homologous to
MHQSLTQQRSSDMSLPDSMGAFNRRKRNSIYVTVTLLIVSVLILTVGLAATTRTQN
VTVGGYYPGVILGFGSFLGIIGSNLIENKRQMLVASrVFISFGVIAAFCCAIVDGVFAA
RHIDLKμlYANRCHYVPKTSQKEAEE (SEQ ID NO: 156) corresponding to amino acids
1 -141 of KNOwn protein Q5JRV8_HUMAN (SEQ ID NO:30), which also corresponds to
amino acids 1 -141 of F10649_P5 (SEQ ID NO:33), and a second amino acid sequence
being at least 90% homologous to
VNCPHLSREFCTPRrRGNTCFCCDLYNCGNRVEiTGGYYEYIDVSSCQDIIHLYHLL
WSATILNIVGLFLGIITAAVLGGFKDMNPTLPALNCSVENTHPTVSYYAHPQVASYN
TYYHSPPHLPPYSAYDFQHSGVFPSSPPSGLSDEPQSASPSPSYMWSSSAPPRYSPPY
YPPFEKPPPYSP corresponding to amino acids 166 - 349 of KNOwn protein
Q5JRV8_HUMAN (SEQ ID NO:30), which also corresponds to amino acids 142 - 325 of
F10649_P5 (SEQ ID NO:33), wherein said first amino acid sequence and second amino
acid sequence are contiguous and in a sequential order.
B. An isolated chimeric polypeptide corresponding to an edge portion of F10649_P5
(SEQ ID NO:33), comprising a polypeptide having a length V, wherein n is at least about
10 amino acids in length, optionally at least about 20 amino acids in length, preferably at
least about 30 amino acids in length, more preferably at least about 40 amino acids in length
and most preferably at least about 50 amino acids in length, wherein at least two amino
acids comprise EV, having a structure as follows: a sequence starting from any of amino
acid numbers 141-x to 141; and ending at any of amino acid numbers 142 +((n-2) - x), in
which x varies from 0 to n-2,
2. Comparison report between F10649_P5 (SEQ ID NO:33) and KNOwn protein
Q7Z4S8HUMAN (SEQ ID NO:31):
A. An isolated chimeric polypeptide, comprising a first amino acid sequence being at
least 90% homologous to
MHQSLTQQRSSDMSLPDSMGAFNRRKRNSIYVTVTLLIVSVLILTVGLAATTRTQN
VTVGGYYPGVILGFGSFLGnGSNLIENKRQMLVASIVFISFGVlAAFCCAIVDGVFAA
RHIDLKμlYANRCHYVPKTSQKEAEE (SEQ ID NO: 156) corresponding to amino acids
1 -141 of KNOwn protein Q724S8_HUMAN (SEQ ID NO:31), which also corresponds to
amino acids 1 -141 of F10649_P5 (SEQ ID NO:33), a second amino acid sequence being at
least 90% homologous to
VNCPHLSREFCTPRIRGNTCFCCDLYNCGNRVEiTGGYYEYIDVSSCQDIIHLYHLL
WSAHLNIVGLFLGIITAAVLGGFKDMNPTLPALNCSVENTHPTVSYYAHPQVASYN
TYYHSPPHLPPYSAYDFQHSGVFPSSPPSGLSDEPQSAS corresponding to amino acids
166 - 318 of KNOwn protein Q7Z4S8_HUMAN (SEQ ID NO:31), which also corresponds to
amino acids 142 - 294 of F10649_P5 (SEQ ID NO:33), a bridging amino acid P
corresponding to amino acid 295 of F10649_P5 (SEQ ID NO:33), and a third amino acid
sequence being at least 90% homologous to SPSYMWSSSAPPRYSPPYYPPFEKPPPYSP
corresponding to amino acids 320 - 349 of KNOwn protein Q7Z4S8_HUMAN (SEQ ID
NO:31), which also corresponds to amino acids 296 - 325 of F10649_P5 (SEQ ID NO:33),
wherein said first amino acid sequence, second amino acid sequence, bridging amino acid
and third amino acid sequence are contiguous and in a sequential order,
B. An isolated chimeric polypeptide corresponding to an edge portion of F10649JP5
(SEQ ID NO:33), comprising a polypeptide having a length "n", wherein n is at least about
10 amino acids in length, optionally at least about 20 amino acids in length, preferably at
least about 30 amino acids in length, more preferably at least about 40 amino acids in length
and most preferably at least about 50 amino acids in length, wherein at least two amino
acids comprise EV, having a structure as follows: a sequence starting from any of amino
acid numbers 141-x to 141; and ending at any of amino acid numbers 142 + ((n-2) -x), in
which x varies from 0 to n-2.
3. Comparison report between F10649_P5 (SEQ ID NO:33) and KNOwn proteins
NP_060408 and Q86Y72_HUMAN (SEQ ID NO:29):
A. An isolated chimeric polypeptide, comprising a first amino acid sequence being at
least 90% homologous to
MHQSLTQQRSSDMSLPDSMGAFNRRKRNSIYVTVTLLIVSVLILTVGLAATTRTQN
VTVGGYYPGVILGFGSFLGHGSNLIENKRQMLVASIVFISFGVIAAFCCAIVDGVFAA
RHIDLKμlYANRCHYVPKTSQKEAEE (SEQ ID NO: 156) corresponding to amino acids
1 -141 of KNOwn proteins NP„O604O8 and Q86Y72_HUMAN (SEQ ID NO:29), which also
corresponds to amino acids 1 -141 of F10649_P5 (SEQ ID NO:33), a second amino acid
sequence being at least 90% homologous to
VNCPHLSREFCTPRIRGNTCFCCDLYNCGNRVEITGGYYEYIDVSSCQDIIHLYHLL
WSATILNIVGLFLGHTAAVLGGFKDMNPTLPALNCSVENTHPTVSYYAHPQVASYN
TYYHSPPHLPPYSAYDFQHSGVFPSSPPSGLSDEPQSASPSPSYMWSSSAPPRYSPPY
YPPFEKP corresponding to amino acids 166 - 344 of KNOwn proteins NP_060408 and
Q86Y72_HUMAN (SEQ ID NO:29), which also corresponds to amino acids 142 - 320 of
F10649_P5 (SEQ ID NO:33), a bridging amino acid P corresponding to amino acid 321 of
F10649_P5 (SEQ ID NO:33), and a third amino acid sequence being at least 90%
homologous to PYSP corresponding to amino acids 346 - 349 of KNOwn proteins
NP_060408 and Q86Y72.HUMAN, which also corresponds to amino acids 322 - 325 of
F10649_P5 (SEQ ID NO:33), wherein said first amino acid sequence, second amino acid
sequence, bridging amino acid and third amino acid sequence are contiguous and in a
sequential order.
B. An isolated chimeric polypeptide corresponding to an edge portion of F10649_P5
(SEQ ID NO:33), comprising a polypeptide having a length "n", wherein n is at least about
10 amino acids in length, optionally at least about 20 amino acids in length, preferably at
least about 30 amino acids in length, more preferably at least about 40 amino acids in length
and most preferably at least about 50 amino acids in length, wherein at least two amino
acids comprise EV, having a structure as follows: a sequence starting from any of amino
acid numbers 141-xto 141; and ending at any of amino acid numbers 142+((n-2) - x), in
which x varies from 0 to n-2.
4, Comparison report between F10649_P5 (SEQ ID NO:33) and KNOwn protein
Q9NWN8_HUMAN (SEQ ID NO:32):
A. An isolated chimeric polypeptide, comprising a first amino acid sequence being at
least 70%, optionally at least 80%, preferably at least 85%, more preferably at least 90%
and most preferably at least 95%, homologous to a polypeptide having the sequence
MHQSLTQQRSSDMSLPDSMGAFNRRKRNSIYVTVTLLrVSVLILTVGLAATTRTQN
VTVGGYYPGVILGFGSFLGEGSNLIENKRQMLVASrVFISFGVIAAFCCAlVDGVFAA
RHIDLKμlYANRCHYVPKTSQKEAEE (SEQ ID NO: 156) corresponding to amino acids
1 -141 of F10649_P5 (SEQ ID NO:33), and a second amino acid sequence being at least
90% homologous to
VNCPHLSREFCTPRIRGNTCFCCDLYNCGNRVErTGGYYEYIDVSSCQDIIHLYHLL
WSAHLNIVGLFLGIITAAVLGGFKDMNPTLPALNCSVENTHPTVSYYAHPQVASYN
TYYHSPPHLPPYSAYDFQHSGVFPSSPPSGLSDEPQSASPSPSYMWSSSAPPRYSPPY
YPPFEKPPPYSP corresponding to amino acids 2-185 of KNOwn protein
Q9NWN8_HUMAN (SEQ ID NO:32), which also corresponds to amino acids 142 - 325 of
F10649_P5 (SEQ ID NO:33), wherein said first amino acid sequence and second amino
acid sequence are contiguous and in a sequential order.
B. An isolated polypeptide corresponding to a head of F10649_P5 (SEQ ID NO:33),
comprising a polypeptide being at least 70%, optionally at least about 80%, preferably at
least about 85%, more preferably at least about 90% and most preferably at least about 95%
homologous to the sequence
MHQSLTQQRSSDMSLPDSMGAFNRRKRNSIYVTVTLLIVSVμlTVGLAATTRTQN
VTVGGYYPGVILGFGSFLGIIGSNLIENKRQMLVASIVFISFGVIAAFCCAIVDGVFAA
RHIDLKμlYANRCHYVPKTSQKEAEE (SEQ ID NO: 156) of F10649_P5 (SEQ ID
NO:33).
The localization of the variant protein was determined according to resμlts from a
number of different software programs and analyses, including analyses from SignalP and
other specialized programs. The variant protein is believed to be located as follows with
regard to the cell: membrane.
Variant protein F10649_P5 (SEQ ID NO:33) also has the following non-silent SNPs
(Single Nucleotide Polymorphisms) as listed in Table 29, (given according to their
position(s) on the amino acid sequence, with the alternative amino acid(s) listed).
127 R -> P
127 R->Q
295 P -> S
The coding portion of transcript F10649_T1 (SEQ ID NO:22) starts at position 248
and ends at position 1222. The transcript also has the following SNPs as listed in Table 30
(given according to their position on the nucleotide sequence, with the alternative nucleic
acid listed).
Variant protein F10649_P7 (SEQ ID NO:35) according to at least some embodiments
of the invention has an amino acid sequence as encoded by transcripts F10649_T4 (SEQ ID
NO:24). A description of the relationship of the variant protein according to at least some
embodiments of the invention to KNOwn proteins is as follows:
1. Comparison report between F10649_P7 (SEQ ID NO:35) and KNOwn protein
Q5JRV8.HUMAN (SEQ ID NO:30):
A. An isolated chimeric polypeptide, comprising a first amino acid sequence being at
least 90% homologous to
MHQSLTQQRSSDMSLPDSMGAFNRRKRNSIYVTVTLLIVSVLILTVGLAATTRTQN
VTVGGYYPGVILGFGSFLGIIGSNLIENKRQMLVASIVFISFGVIAAFCCAIVDGVFAA
RHIDLKμlYANRCHYVPKTSQKEAEE (SEQ ID NO: 156) corresponding to amino acids
1 -141 of KNOwn protein Q5JRV8_HUMAN (SEQ ID NO:30), which also corresponds to
amino acids 1 -141 of F10649_P7 (SEQ ID NO:35), and a second amino acid sequence
being at least 90% homologous to
NPTLPALNCSVENTHPTVSYYAHPQVASYNTYYHSPPHLPPYSAYDFQHSGVFPSSP
PSGLSDEPQSASPSPSYMWSSSAPPRYSPPYYPPFEKPPPYSP corresponding to amino
acids 250 - 349 of KNOwn protein Q5JRV8_HUMAN (SEQ ID NO:30), which also
corresponds to amino acids 142 - 241 of F10649_P7 (SEQ ID NO:35), wherein said first
amino acid sequence and second amino acid sequence are contiguous and in a sequential
order.
B. An isolated chimeric polypeptide corresponding to an edge portion of F10649_P7
(SEQ ID NO:35), comprising a polypeptide having a length "n", wherein n is at least about
10 amino acids in length, optionally at least about 20 amino acids in length, preferably at
least about 30 amino acids in length, more preferably at least about 40 amino acids in length
and most preferably at least about 50 amino acids in length, wherein at least two amino
acids comprise EN, having a structure as follows: a sequence starting from any of amino
acid numbers 141-x to 141; and ending at any of amino acid numbers 142 + ((n-2) - x), in
which x varies from 0 to n-2.
2, Comparison report between F10649_P7 (SEQ ID NO;35) and KNOwn protein
Q9NWN8_HUMAN (SEQ ID NO:32):
A. An isolated chimeric polypeptide, comprising a first amino acid sequence being at
least 70%, optionally at least 80%, preferably at least 85%, more preferably at least 90%
and most preferably at least 95%, homologous to a polypeptide having the sequence
MHQSLTQQRSSDMSLPDSMGAFNRRKRNSIYVTVTLLIVSVLILTVGLAATTRTQN
VTVGGYYPGVILGFGSFLGnGSNLIENKRQMLVASrVFISFGVIAAFCCAIVDGVFAA
RHIDLKμlYANRCHYVPKTSQKEAEE (SEQ ID NO: 156) corresponding to amino acids
1 -141 of F10649_P7 (SEQ ID NO:35), and a second amino acid sequence being at least
90% homologous to
NPTLPALNCSVENTHPTVSYYAHPQVASYNTYYHSPPHLPPYSAYDFQHSGVFPSSP
PSGLSDEPQSASPSPSYMWSSSAPPRYSPPYYPPFEKPPPYSP corresponding to amino
acids 86 -185 of KNOwn protein Q9NWN8_HUMAN (SEQ ID NO:32), which also
corresponds to amino acids 142 - 241 of F10649_P7 (SEQ ID NO:35), wherein said first
amino acid sequence and second amino acid sequence are contiguous and in a sequential
order.
B. An isolated polypeptide corresponding to a head portion of F10649_P7 (SEQ ID
NO:35), comprising a polypeptide being at least 70%, optionally at least about 80%,
preferably at least about 85%, more preferably at least about 90% and most preferably at
least about 95% homologous to the sequence
MHQSLTQQRSSDMSLPDSMGAFNRRKRNSIYVTVTLLIVSVLILTVGLAATTRTQN
VTVGGYYPGVILGFGSFLGIIGSNLffiNKRQMLVASrVFISFGVIAAFCCAIVDGVFAA
RHIDLKμlYANRCHYVPKTSQKEAEE (SEQ ID NO: 156) of F10649_P7 (SEQ ID
NO:35).
The localization of the variant protein was determined according to resμlts from a
number of different software programs and analyses, including analyses from SignalP and
other specialized programs. The variant protein is believed to be located as follows with
regard to the cell: membrane.
Variant protein F10649_P7 (SEQ ID NO:35) also has the following non-silent SNPs
(Single Nucleotide Polymorphisms) as listed in Table 31, (given according to their
position(s) on the amino acid sequence, with the alternative amino acid(s) listed).
Variant protein F10649_P8 (SEQ ID NO:36) according to at least some embodiments
of the invention has an amino acid sequence as encoded by transcript F10649_T6 (SEQ ID
NO:26). A description of the relationship of the variant protein according to at least some
embodiments of the invention to KNOwn proteins is as follows:
1. Comparison report between F10649_P8 (SEQ ID NO:36) and KNOwn protein
Q5JRV8_HUMAN (SEQ ID NO:30):
A. An isolated chimeric polypeptide, comprising a first amino acid sequence being at
least 90% homologous to
MHQSLTQQRSSDMSLPDSMGAFNRRKRNSIYVTVTLLIVSVLILTVGLAATTRTQN
VTVGGYYPGVI (SEQ ID NO: 159), corresponding to amino acids 1 - 67 of KNOwn
protein Q5JRV8_HUMAN (SEQ ID NO:30), which also corresponds to amino acids 1 - 67
of F10649_P8 (SEQ ID NO:36), and a second amino acid sequence being at least 90%
homologous to
LVASIVFISFGVIAAFCCArVDGVFAARHrDLKμlYANRCHYVPKTSQKEAEEVISSS
TKNSPSTRVMRNLTQAAREVNCPHLSREFCTPRIRGNTCFCCDLYNCGNRVEITGG
YYEYjDVSSCQDIIHLYHLLWSATILNIVGLFLGirTAAVLGGFKDMNPTLPALNCSV
ENTHPTVSYYAHPQVASYNTYYHSPPHLPPYSAYDFQHSGVFPSSPPSGLSDEPQSA
SPSPSYMWSSSAPPRYSPPYYPPFEKPPPYSP corresponding to amino acids 89 - 349 of
KNOwn protein Q5JRV8_HUMAN (SEQ ID NO:30), which also corresponds to amino acids
68 - 328 of F10649_P8 (SEQ ID NO:36), wherein said first amino acid sequence and
second amino acid sequence are contiguous and in a sequential order.
B, An isolated chimeric polypeptide corresponding to an edge portion of F10649_P8
(SEQ ID NO:36), comprising a polypeptide having a length "n", wherein n is at least about
10 amino acids in length, optionally at least about 20 amino acids in length, preferably at
least about 30 amino acids in length, more preferably at least about 40 amino acids in length
and most preferably at least about 50 amino acids in length, wherein at least two amino
acids comprise IL, having a structure as follows: a sequence starting from any of amino acid
numbers 67-x to 67; and ending at any of amino acid numbers 68 + ((n-2) - x), in which x
varies from 0 to n-2,
2. Comparison report between F10649_P8 (SEQ ID NO:36) and KNOwn protein
Q9NWN8.HUMAN (SEQ ID NO:32):
A. An isolated chimeric polypeptide, comprising a first amino acid sequence being at
least 70%, optionally at least 80%, preferably at least 85%, more preferably at least 90%
and most preferably at least 95%, homologous to a polypeptide having the sequence
MHQSLTQQRSSDMSLPDSMGAFNRRKRNSIYVTVTLLIVSVLILTVGLAATTRTQN
VTVGGYYPGVILVASIVFISFGVIAAFCCAIVDGVFAARHIDLKμlYANRCHYVPKT
SQKEAEEVISSSTKNSPSTRVMRNLTQAARE (SEQ ID NO: 159) corresponding to
amino acids 1 -144 of F10649_P8 (SEQ ID NO:36), and a second amino acid sequence
being at least 90% homologous to
VNCPHLSREFCTPRIRGNTCFCCDLYNCGNRVEITGGYYEYIDVSSCQDIIHLYHLL
WSATILNIVGLFLGHTAAVLGGFKDMNPTLPALNCSVENTHPTVSYYAHPQVASYN
TYYHSPPHLPPYSAYDFQHSGVFPSSPPSGLSDEPQSASPSPSYMWSSSAPPRYSPPY
YPPFEKPPPYSP corresponding to amino acids 2 -185 of KNOwn protein
Q9NWN8_HUMAN (SEQ ID NO:32), which also corresponds to amino acids 145 - 328 of
F10649_P8 (SEQ ID NO:36), wherein said first amino acid sequence and second amino
acid sequence are contiguous and in a sequential order.
B. An isolated polypeptide corresponding to a head portion of F10649_P8 (SEQ ID
NO:36), comprising a polypeptide being at least 70%, optionally at least about 80%,
preferably at least about 85%, more preferably at least about 90% and most preferably at
least about 95% homologous to the sequence
MHQSLTQQRSSDMSLPDSMGAFNRRKRNSlYVTVTLLrVSVLILTVGLAATTRTQN
VTVGGYYPGVILVASIVFISFGVIAAFCCAIVDGVFAARHIDLKμlYANRCHYVPKT
SQKEAEEVISSSTKNSPSTRVMRNLTQAARE (SEQ ID NO: 159) of F10649_P8 (SEQ
ID NO:36).
The localization of the variant protein was determined according to resμlts from a
number of different software programs and analyses, including analyses from SignalP and
other specialized programs. The variant protein is believed to be located as follows with
regard to the cell; membrane.
Variant protein F10649_P8 (SEQ ID NO:36) also has the following non-silent SNPs
(Single Nucleotide Polymorphisms) as listed in Table 33, (given according to their
position(s) on the amino acid sequence, with the alternative amino acid(s) listed).
The coding portion of transcript F10649_T6 (SEQ ID NO:26) starts at position 248
and ends at position 1231. The transcript also has the following SNPs as listed in Table 34
(given according to their position on the nucleotide sequence, with the alternative nucleic
acid listed).
Variant protein F10649_P10 (SEQ ID NO:32) according to at least some
embodiments of the invention has an amino acid sequence as encoded by transcript)
F10649JT8 (SEQ ID NO:28). A description of the relationship of the variant protein
according to at least some embodiments of the invention to KNOwn proteins is as follows:
1. Comparison report between F10649_P10 (SEQ ID NO:32) and KNOwn protein
Q5JRV8_HUMAN (SEQ ID NO:30):
A. An isolated chimeric polypeptide, comprising a first amino acid sequence being at
least 70%, optionally at least 80%, preferably at least 85%, more preferably at least 90%
and most preferably at least 95% homologous to a polypeptide having the sequence M
corresponding to amino acids 1-1 of F10649_P10 (SEQ ID NO:32), and a second amino
acid sequence being at least 90% homologous to
VNCPHLSREFCTPRIRGNTCFCCDLYNCGNRVEITGGYYEYrDVSSCQDIIHLYHLL
WSATILNIVGLFLGirrAAVU3GFKDMNPTLPALNCSVENTHPTVSYYAHPQVASYN
TYYHSPPHLPPYSAYDFQHSGVFPSSPPSGLSDEPQSASPSPSYMWSSSAPPRYSPPY
YPPFEKPPPYSP corresponding to amino acids 166 - 349 of KNOwn protein
Q5JRV8_HUMAN (SEQ ID NO:30), which also corresponds to amino acids 2 -185 of
F10649_P10 (SEQ ID NO:32), wherein said first amino acid sequence and second amino
acid sequence are contiguous and in a sequential order.
2. Comparison report between F10649_P10 (SEQ ID NO:32) and KNOwn protein
Q7Z4S8_HUMAN (SEQ ID NO:31):
A. An isolated chimeric polypeptide, comprising a first amino acid sequence being at
least 70%, optionally at least 80%, preferably at least 85%, more preferably at least 90%
and most preferably at least 95% homologous to a polypeptide having the sequence M
corresponding to amino acids 1 -1 of F10649_P10 (SEQ ID NO:32), a second amino acid
sequence being at least 90% homologous to
VNCPHLSREFCTPRIRGNTCFCCDLYNCGNRVErTGGYYEYIDVSSCQDIIHLYHLL
WSATILNIVGLFLGirrAAVLGGFKDMNPTLPALNCSVENTHPTVSYYAHPQVASYN
TYYHSPPHLPPYSAYDFQHSGVFPSSPPSGLSDEPQSAS corresponding to amino acids
166 - 318 of KNOwn protein Q7Z4S8_HUMAN (SEQ ID NO:31), which also corresponds to
amino acids 2 -154 of F10649_P10 (SEQ ID NO:32), a bridging amino acid P
corresponding to amino acid 155 of F10649_P10 (SEQ ID NO:32), and a third amino acid
sequence being at least 90% homologous to SPSYMWSSSAPPRYSPPYYPPFEKPPPYSP
corresponding to amino acids 320 - 349 of KNOwn protein Q7Z4S8_HUMAN (SEQ ID
NO:31), which also corresponds to amino acids 156 -185 of F10649_P10 (SEQ ID NO:32),
wherein said first amino acid sequence, second amino acid sequence, bridging amino acid
and third amino acid sequence are contiguous and in a sequential order.
3, Comparison report between F10649_P10 (SEQ ID NO:32) and KNOwn proteins
NP_060408 and Q86Y72_HUMAN:
A, An isolated chimeric polypeptide, comprising a first amino acid sequence being at
least 70%, optionally at least 80%, preferably at least 85%, more preferably at least 90%
and most preferably at least 95% homologous to a polypeptide having the sequence M
corresponding to amino acids 1-1 of F10649_P10 (SEQ ID NO:32), a second amino acid
sequence being at least 90% homologous to
VNCPHLSREFCTPRIRGNTCFCCDLYNCGNRVEITGGYYEYrDVSSCQDIIHLYHLL
WSATILNIVGLFLGHTAAVLGGFKDMNPTLPALNCSVENTHPTVSYYAHPQVASYN
TYYHSPPHLPPYSAYDFQHSGVFPSSPPSGLSDEPQSASPSPSYMWSSSAPPRYSPPY
YPPFEKP corresponding to amino acids 166 - 344 of KNOwn proteins NP_060408 and
Q86Y72_HUMAN, which also corresponds to amino acids 2 -180 of F10649_P10 (SEQ ID
NO:32), a bridging amino acid P corresponding to amino acid 181 of F10649_P10 (SEQ ID
NO:32), and a third amino acid sequence being at least 90% homologous to PYSP
corresponding to amino acids 346 - 349 of KNOwn proteins NP_060408 and
Q86Y72_HUMAN, which also corresponds to amino acids 182 -185 of F10649_P10 (SEQ
ID NO:32), wherein said first amino acid sequence, second amino acid sequence, bridging
amino acid and third amino acid sequence are contiguous and in a sequential order.
The localization of the variant protein was determined according to resμlts from a
number of different software programs and analyses, including analyses from SignalP and
other specialized programs. The variant protein is believed to be located as follows with
regard to the cell: membrane.
Variant protein F10649_P10 (SEQ ID NO:32) also has the following non-silent SNPs
(Single Nucleotide Polymorphisms) as listed in Table 35, (given according to their
position(s) on the amino acid sequence, with the alternative amino acid(s) listed),
EXAMPLE 5_2: EXPRESSION ANALYSIS OF FAM70A TRANSCRIPTS
MED discovery engine described in EXAMPLE 1 herein, was used to assess the
expression of FAM70A transcripts, FAM70A transcripts were found to be over expressed in
lung cancer, as is demonstrated in Figures 30, in liver cancer, as is demonstrated in Figure
31, in breast cancer, as is demonstrated in Figure 32, and in Kidney cancer, as is
demonstrated in Figure 33. Figures 30-33 show expression graphs of Affymetrix probe set
219895_at. Figure 30 shows the expression of FAM70A transcripts in microarray chips
from lung cancer and lung normal experiments. As can be s^en FAM70A transcripts are
overexpressed in lung cancer tissues (diamond marKers) relative to its expression in normal
lung (circle marKers).
Figure 31 shows the expression of FAM70A transcripts in microarray chips from
liver cancer and normal liver experiments. As can be seen FAM70A transcripts are
overexpressed in liver cancer tissues (diamond marKers) relative to its expression in normal
liver (circle and triangle marKers).
Figure 32 shows the expression of FAM70A transcripts in microarray chips from
breast cancer and normal breast experiments. As can be seen FAM70A transcripts are
overexpressed in breast cancer tissues (diamond marKers) relative to its expression in breast
lung (circle, cross and triangle marKers).
Figure 33 shows the expression of FAM70A transcripts in microarray chips from
Kidney cancer and normal Kidney experiments. As can be seen FAM70A transcripts are
overexpressed in Kidney cancer tissues (diamond marKers) relative to its expression in
normal Kidney (circle, cross and triangle marKers).
Expression of hypothetical protein FLJ20716-FAM70A F10649 transcripts which are
detectable by amμlicon as depicted in sequence name F10649rjegl0-12F1R1 (SEQ ID
NO: 103) in b100d specific panel and in different normal tissues
Expression of hypothetical protein FLJ20716-FAM70A transcripts detectable by or
according to seglO-12FlRl - F10649„segl0-12F1R1 (SEQ ID NO: 103) amμlicon and
primers F10649_seglO-12F (SEQ ID NO: 101) and F10649_seglO-12R (SEQ ID NO: 102)
was measured by real time PCR in b100d panel and normal panel. The samμles used for
b100d panel are detailed in Tables 2 and 2_1. The samμles used for normal panel are
detailed in Table 3.
normal panel -
[00551] For each RT samμle, the expression of the above amμlicon was normalized to
the normalization factor calcplated from the expression of several house Keeping genes as
described in EXAMPLE 1. The normalized quantity of each RT samμle was then divided by
the median of the quantities of the Kidney samμles (samμle numbers 19-23, Table 3 above),
to obtain a value of relative expression of each samμle relative to median of the Kidney
samμles, as shown in Figure 34. Very high expression was observed in ovary normal
samμles, high expression was observed in normal brain and heart.
[00552] For b100d panel - For each RT samμle, the expression of the above amμlicon
was normalized to the normalization factor calcplated from the expression of several house
Keeping genes as described in EXAMPLE 1. The normalized quantity of each RT samμle was
then divided by the median of the quantities of the Kidney normal samμles (samμle numbers
65-67, Table 2 above), to obtain a value of relative expression of each samμle relative to
median of the Kidney normal samμles.
[00553] The resμlts of this analysis are depicted in the histogram in Figure 35.
Expression of the above-indicated hypothetical protein FLJ20716-FAM70A transcripts is
very high in mature and immature macrophages and dendritic cells samμles, and in two out
of the five mμltiμle myeloma cell lines.
Forward Primer (F10649_seglO-12F) (SEQ ID NO:101):
CTGGTGGCTTCTATCGTGTTTATCAG
Reverse Primer (F10649_seglO-12R) (SEQ ID NO:102):
CGGTTAGCGTAGAGTGGTTTCAG
Ampiicon (F10649_segl0-12F1R1 (SEQ ID NO: 103)) (SEQ ID NO:103):
CrGGTGGCrrCTATCGTGTTTATCAGCTTTGGTGTGATTGCGGCTITTTGT
TGTGCCATAGTTGACGGGGTCTTTGCTGCCAGACACATTGATCTGAAACC
ACTCTACGCTAACCG
EXAMPLE 5_3:
[00554] CLONING OF FμlL LENGTH ORF ENCODING FAM70A T1_P5 FUSED
TO FLAG
[00555] Cloning of Fμll Length ORF encoding FAM70A fused to FLAG was done as
described below.
[00556] 1, A reverse transcription reaction was carried out as follows: lOug of purified
RNA extracted from RPMI 8226 cell line (ATCC CCL-155) was mixed with 150ng
Random Hexamer primers (Invitrogen, Carlsbad, CA, USA, catalog number: 48190-011)
and 500^M dNTPs in a total volume of 156μl. The mixture was incubated for 5 min at
65uC and then quicKly chilled on ice. Thereafter, 50μl of 5X Superscript!! first strand
buffer (Invitrogen, catalog number: 18064-014, part number: Y00146), 24μl 0.1M DTT and
400 units RNasin (Promega, MilwauKee, WS, U.S.A., catalog number: N2511) were added,
and the mixture was incubated for 10 min at 25°C, followed by further incubation at 42°C
for 2 min. Then, lOμl (2000 units) of Superscriptll (Invitrogen, catalog number: 18064-014)
was added and the reaction (final volume of 250μl) was incubated for 50 min at 42°C and
then inactivated at 70°C for 15min. The resμlting cDNA was diluted 1:20 in TE buffer
(lOmM Tris, 1 mM EDTA pH 8).
2. PCR was done using GoTaq ReadyMix (Promega, catalog number M122) under
the following conditions: 10.5uJ - cDNA from the above; lμl - of each primer (lOuM)
(Table 48); 12.5pi ReadyMix with a reaction program of 3 minutes in 95°C; 30 cycles of 30
seconds at 94(>C, 30 seconds at 52°C, 1.5 minutes at 72°C; then 10 minutes at 72°C. Primers
which were used include gene specific sequences corresponding to the desired coordinates
of the protein and restriction enzyme sites and KozaK sequence, as listed in Table 37 below.
Bold letters in Table 37 represent the specific gene sequence while the restriction site
extensions utilized for cloning purposes are in Italic and KozaK sequences are underlined.
FLAG tag is in Italic bold. In order to enhance the PCR product, a second PCR was done
using μlatinum PFX™ (Invitrogen., Carlsbad, CA, USA> catalog number: 1178-021) and
me above PCR product as a template (5μl). PCR conditions were as follows: 1 μl μlatinum
PFX enzyme; lμl - 10 mM dNTPs (2.5mM of each nucleotide); 0.5μl - 50mM MgS04; and
1 pi- of each primer (lOuM) in a total reaction volume of 50μl; PCR program was as
follows: 3 minutes in 95°C; 30 cycles of 30 seconds at 94°C, 30 seconds at 52°Ct 1.5
minutes at 68°C; then 10 minutes at 68°C.Table 1- FAM70A cloning primers details
[00557] Table 37
[00558] The μlatinum PFX™ PCR product was loaded onto a 1 % agarose gel stained
with ethidium bromide, electrophoresed in lxTBE solution at 100V, and visualized with
UV light. After verification of expected size band, it was extracted using QiaquicK gel
extraction purification Kit (Qiagen™, Valencia, CA, U.S.A., catalog number 28706). The
extracted PCR product was digested with Nhel and notI (New England Biolabs, Beverly,
MA, U.S.A.). After digestion, -the DNA was loaded onto a 1 % agarose gel as described
above. The expected band size was excised and extracted from the gel using QiaQuicK™
Gel Extraction Kit (Qiagen, catalog number: 28706).
[00559] The digested PCR product from above was ligated into pIRESpuro3 vector using
the LigaFastTM Rapid DNA Ligation System (Promega,catalog number M8221. The
resμlting DNA was transformed into competent E.Coli bacteria DH5a (RBC Bioscience,
Taipei, Taiwan, catalog number: RH816) according to manufacturer's instructions, then
plated on LB-ampicillin agar plates for selection of recombinant plasmids, and incubated
overnight at 37°C.
[00560] The following day, a number of colonies from the transformation that grew on
the selective plate was taKen for further analysis by streaK-plating on aNOmer selective plate
and by PCR using GoTaq ReadyMix (Promega, catalog number: M7122). Screening
positive clones was performed by PCR using pIRESpuro3 vector specific primer and gene
specific primer (data not shown). After comμletion of all PCR cycles, half of the reaction
was analyzed using 1 % agarose gel as described above. After verification of expected band
size, 2 positive colonies were grown in 5 ml Terrific Broth supμlemented with 100ug/ml
ampicillin, with shaKing overnight at 37°C. μlasmid DNA was isolated from bacterial
cμltures using Qiaprep™ Spin Miniprep Kit (Qiagen, catalog number: 27106). Accurate
cloning was verified by sequencing the inserts (Weizmann Institute, Rehovot, Israel). Upon
verification of an error-free colony (i.e. NO mutations within the ORF), recombinant μlasmid
was processed for further analysis.
[00561] Figure 36 represents the DNA sequence of FAM70_T1_P5_FLAG (SEQ ID NO:
119) gene specific sequence corresponding to the target's fμll length sequence is marKed in
bold faced, FLAG sequence is unbold.
[00562] Figure 37 represents the amino acid sequence of FAM70A_T1_P5_FLAG
protein (SEQ ID NO: 120); gene specific sequence corresponding to the fμll length sequence
of the protein is marKed in bold faced, FLAG sequence is unbold,
EXAMPLE 5_4: DETERMINING CELL LOCALIZATION OF FAM70A
[00563] Determining cell localization of FAM70A was done using the confocal
microscope. The FAM70A-FLAG pIRESpuro3 construct was subsequently transiently
transfected into HEK-293T cells as follows;
[00564] HEK-293T (ATCC, CRL-11268) cells were plated on sterile glass coverslips,
13mm diameter (Marienfeld, catalog number: 01 115 30), which were μlaced in a 6 well
plate, using 2ml pre-warmed DMEM [Dμlbecco's modified Eagle's Media, Biological
Industries (Beit Ha'EmeK, Israel), cataloge number: 01-055-1A] + 10% FBS (Fetal Bovin
Serum) + 4mM L-Glutamine, 500,000 cells per well were transfected with 2ug of the DNA
construct using 6μl FuGENE 6 reagent (Roche, catalog number: 11-814-443-001) diluted
into 94μl DMEM. The mixture was incubated at room temperature for 15 minutes. The
comμlex mixture was added dropwise to the cells and swirled. Cells were μlaced in
incubator maintained at 37°C with 5% C02 content.
[00565] 48 hours post transient transfection, the cells were further processed for analysis
in confocal microscopy. The cover slips were washed 3 times in phosphate buffered saline
(PBS) and fixed for 15 minutes with a fixing solution composed of 3.7% paraformaldehyde
(PFA) (Sigma, catalog number: P-6148) and 3% glucose (Sigma, catalog number: G5767),
followed by 5 minutes incubation with 3mM glycine (Sigma, catalog number: G7126).
After one wash in PBS, the cells were permeabilized by incubation with 0.1% triton X-
100/PBS solution for 5 minutes. After two washes in PBS the cells were incubated in 5%
bovine serum albumin (BSA) (Sigma, catalog number: A4503) in PBS solution for 20
minutes. The cells were then incubated with anti FLAG antibody conjugated to cy3 (Sigma,
catalog number: A9594) diluted 1:100 in 3% BSA in PBS for 1 hr. After 3 washes in PBS
the coverslips were glued to a slide using mounting solution (Sigma, catalog number:
G0918) and cells were observed for the presence of fluorescence using confocal
microscope. The resμlts are presented in Figure 38.
[00566] Figure 38 demonstrates that the FAM70A_T1_P5_FLAG (SEQ ID NO:119)
fused protein localizes to cell membrane upon expression in HEK 293T cells. The image
was obtained using the 40x objective of the confocal microscope.
EXAMPLE 5_5: PRODUCTION OF POLYCLONAL ANTIBOtheS SPECIFIC TO
FAM70 VARIANT
[00567] All polyclonal Abs production procedure, including peptides synthesis, peptides
conjugation, animal immunizations, bleeding and antibothes purification were performed at
Sigma-Aldrich (Israel).
[00568] Peptide synthesis - The peptide sequence which was used for rabbit
immunization was as follows: CHYVPKTSQKEAEEV (FAM70_128 SEQ ID NO:121), a
sequence taKen from the ECD 100p correspond to aal28-142 of the FAM70_P5 protein
(FAM70_P5; SEQ ID NO:33). 25mg peptide were synthesized with 95% purity of which
lOmg were conjugated to KLH carrier.
[00569] Immunization -two rabbits (#5663, #5664) were immunized with the conjugated
peptide as follows: Animals were immunized every two weeKs. 3 test bleeds of 2-3ml were
collected and analyzed by ELISA. 100ml production bleeds from each rabbit will be
collected.
[00570] Antibody purification - Antibothes will be purified from the rabbits' serum.
Affinity purification will be performed using the peptide against which the respective
antibothes were raised, in an immuNO-affinity column. The purified antibothes will be
analyzed by ELISA and by Western blot on the recombinant FAM70_P5 expressed in HEK-
293T cell line. EndogeNOus protein localization will be determined using these Abs by
tissue ImmuNO HystoChemistry (IHC)
FAM70 peptide sequence (SEQ ID NO: 121) CHYVPKTSQKEAEEV
EXAMPLE 5_6: GENERATION OF STABLE POOL EXPRESSING FAM70_P5
PROTEIN
In order to generate stable pool of HEK-293T cells expressing FAM70A_P5 protein,
FAM70_P5_Flag pIRESpuro3 construct was transfected into HEK-293T cells as follows:
HEK-293T (ATCC, CRL-11268) cells were plated in a sterile 6 well plate suitable for tissue
cμlture, using 2ml pre-warmed of comμlete media, DMEM [Dμlbecco's modified Eagle's
Media, Biological Industries (Beit Ha'EmeK, Israel), catalog number: 01-055-1A] + 10%
FBS [Fetal Bovine Serum, Biological Industries (Beit Ha'EmeK, Israel), catalog number:
04-001-1A] + 4mM L-Glutamine [Biological Industries (Beit Ha'EmeK, Israel), catalog
number: 03-020-1A], 500,000 cells per well were transfected with 2u,g of DNA construct
using 6pJ FuGENE 6 reagent (Roche, catalog number: 11-814-443-001) diluted into 94μl
DMEM. The mixture was incubated at room temperature for 15 minutes. The comμlex
mixture was added dropwise to the cells and swirled. Cells were μlaced in incubator
maintained at 37°C with 5% CO2 content. 48 hours following transfection, transfected cells
were transferred to a 75cm2 tissue cμlture flasK containing 15ml of selection media:
comμlete media supμlemented with 5ug\ml puromycin (Sigma, catalog number P8833).
Cells were μlaced in incubator, and media was changed every 3-4 days, until clone
formation observed.
EXAMPLE 5J7: CHARACTERIZATION OF PURIFIED FAM70A ANTIBOtheS BY
WESTERN BLOT ANALYSIS ON FAM70A_P5 TRANSFECTED CELLS
In order to verify the specificity of antibothes raised against selected peptide of FAM70A,
immuNO-precipitation followed by western blot analysis was done using purified serum
from rabbits 5663 and 5664 described above, and FAM70 HEK-293T stable transfectants
cell lysates as well as HEK-293T nontrasfected cell lysates.
HEK-293T stably expressing FAM70_P5_FLAG and untransfected cell lysates were
immuNO- precipitated using anti Flag antibody (Anti Flag M2 affinity Gel Freezer-Safe,
Sigma. Cat: A220) and were analyzed by Western blot using the purified antibothes raised
against FAM70 peptide diluted 1:250 as previously described.
Figures 39A and 39B represent the signal obtained from purified serum of rabbits #5663
and #5664 respectively. Figure 39A demonstrates that specific band size of 36KDa was
observed from puriffied serum of rabbit #5663 on HEK-293T transfected cell lysates
followed by IP (lane 1 in Figure 39A). However, whole cell lysate extraction did not
revealed expected band size (lane 3). nonspecific band of 52KDa was observed using serum
purified from rabbit #5663 or #5664 (lanes 3 and 4 in Figures 39A and 39B respectively).
EXAMPLE 5_8: CHARACTERIZATION OF PURIFIED FAM70A ANTIBOtheS BY
IMMUNOSTAINING OF FAM70A_P5 TRANSFECTED CELLS
In order to further characterize the affinity purified antibothes raised against FAM70A,
antibody-protein interaction was stuthed using immuNOstaining of FAM70_P5 stable
transfected HEK293T cells.
ImmuNOstaining of FAM70A transfected cells:
500,000 cells per well of HEK-293T (ATCC, CRL-11268) stably expressing FAM70A or
HEK-293T non trasfected, were plated on sterile glass coverslips, 13mm diameter
(Marienfeld, catalog number: 01 115 30), which were μlaced in a 6 well plate, using 2ml
pre-warmed DMEM [Dμlbecco's modified Eagle's Media, Biological Industries (Beit
Ha'EmeK, Israel), catalog number: 01-055-1A] + 10% FBS [Fetal Bovine Serum, Biological
Industries (Beit Ha'EmeK, Israel), catalog number: 04-001-1A] + 4mM L-Glutamine
[Biological Industries (Beit Ha'EmeK, Israel), catalog number: 03-020-1 A],
48 hours post plating the cells on coverslips they were further processed for immuNOstaining
and analysis by confocal microscopy. The cover slips were washed in phosphate buffered
saline (PBS), then fixed for 15 minutes with a 3.7% paraformaldehyde (PFA) (Sigma,
catalog number: P-6l48)/3% glucose (Sigma, catalog number: G5767), After 2 5-minute
washes in PBS, cells were permeabilized with 0.1% triton-X100 (diluted in PBS) for 5
minutes. After two 5-minute washes in PBS, blocKing of non-specific regions was done
with 5% bovine serum albumin (BSA) (Sigma, catalog number: A4503) (diluted in PBS) for
20 minutes. The coverslips were then incubated, in a humid chamber for 1 hour, with
purified serum of rabbit 5663 antibothes diluted 1:200/1:1000 in 5% BSA, described above
and then, were washed 3 times for 5-minutes in PBS. The coverslips were then incubated, in
a humid chamber for 1 hour, with secondary antibody: donKey anti-rabbit conjugated to Cy-
3 flurophore (JacKson ImmuNOResearch, catalog number: 711-165-152), diluted 1:200 in
3% BSA in PBS. After 3 5-minute washes in PBS, the fixed coverslips were mounted on
slides with Gel Mount Aqueous medium (Sigma, catalog number: G0918) and cells were
observed for the presence of fluorescent product using confocal microscopy.
As shown in Figure 40, cell staining was observed localized to the cell membrane using
purified anti FAM70 antibothes (rabbits #5663 and #5664 described above) 1:200 or 1:1000
on HEK-293T transfected cells (Figures 40A and 40B, respectively). However, positive
signal was observed on HEK-293T non transfected cells using 1:200 or 1:1000 (Figures
40C and 40D, respectively) as well as on CHO-K1 (ATCC, CCL-61) cells (Figure 40E) and
MC/CAR (ATCC, CRL-8083) cells (Figure 40F).
In order to further determine whether the positive signal obtained in the non transfected
cells was due to endogeNOus expression or lacK of specificity, RTPCR was performed on
HEK-293T as well as on MC/CAR cDNAs as previously described, using
GoTaq_ReadyMix (Promega, M712B). The primers used were FAM70 specific: primer
#100-923 (SEQ ID NO 167) and primer #100-924 (SEQ ID NO 168).
The expected PCR product size obtained from HEK-293 cDNA was purified and verified by
sequence as previously described. Sequence resμlts indicated FAM70A expression in HEK-
293T non transfected cells. However, NO product was observed when using MC/CAR
cDNA as a template (data not shown).
In order to further analyze specificity, FAM70A HEK-293Ttransfected cells described
above were immuNOstained using anti FAM70A antibothes described above with or without
pre incubation with FAM70A peptide.
Figures 41A-41D demonstrate red fluorescence signal of 293T transfected cells followed by
incubation with 0, Stimes, 25times, 50 times FAM70 peptide, respectively.
Figures 41E-41H demonstrate red fluorescence signal of 293T non transfected cells
followed by incubation with 0,5times,25times, 50 times FAM70 peptide, respectively.
As shown in Figure 41A and Figure 41E, membranalic localization was observed both in
HEK-293T transfected cells and HEK-293Tnon transfected cells, respectively.
However, non specific signal was observed followed by peptide blocKing.
In order to further analyze FAM70A expression, polyclonal antibothes against an additional
peptide sequence were raised.
The peptide sequence which was used for rabbit immunization was as follows:
MHQSLTQQRSSDMSLPDS (FAM70_1, SEQ ID NO:186) a sequence taKen from the N
terminus correspond to amino acid residues 1-18 of the FAM70_P5 protein (SEQ ID
NO:33). 25mg peptide were synthesized at Sigma (Israel) with 95% purity of which lOmg
were conjugated to KLH carrier.
Immunization: two rabbits were immunized with the conjugated peptide as follows:
Animals were immunized every two weeKs. 60ml production bleeds from each rabbit were
collected.
Antibody purification: antibothes are purified from the rabbits' serum. Affinity purification
is performed using the peptide against which the respective antibothes are raised, in an
immuNO-affinity column. The purified antibothes are analyzed by immuNOstaining on
FAM70_P5 HEK-293T transfected cell line described above. After immune-staining
verification, these antibothes are further used for endogeNOus protein localization in human
tissue array by ImmuNO HystoChemistry (IHC).
These sequences are variants of the KNOwn hypothetical protein LOC201799 (SEQ ID
NO:42) (SwissProt accession identifier NP_689893; synonims: TMEM154).
TMEM154 (transmembrane protein 154) was identified in 2 fμll length cDNA
projects (Strausberg et al. 2002, PNAS 99(26): 16899-903; Ota et al. 2004, Nat Genet
36(1): 40-5). However NO research was published about TMEM154 specifically.
Sequence corresponding to W38346_P3 (SEQ ID NO:42) has been reported in
WO2004110369 patent apμlication, which purports that sequence of FLJ32028,
corresponding to W38346_P3 (SEQ ID NO:42), is associated with human chronic
lymphocytic leuKemia. The apμlication further relates to monoclonal antibothes and
methods for antibody screening and production and their use as diagNOstic marKer or
therapeutic target for B-CLL. However, The WO2004110369 patent apμlication does not
provide any specific teaching or incentive that woμld direct a sKilled artisan to use
antibothes specific to the TMEM154 for the treatment or diagNOsis of lymphoma, especially
non-HodgKin's Lymphoma, anti CD20 (i.e. Rituximab) resistant lymphoma, Mμltiμle
Myeloma, Kidney cancer or pancreatic cancer, and/or immune related conditions,
particμlarly SLE. The WO2004110369 patent apμlication does not teach also, that
TMEM154 soluble ectodomain, as well as fragments thereof and conjugates and antibothes
against it can be used as therapeutic or diagNOstic agents for treatment of of lymphoma,
especially non-HodgKin's Lymphoma, anti CD20 (i.e. Rituximab) resistant lymphoma,
Mμltiμle Myeloma, Kidney cancer or pancreatic cancer, and/or immune related conditions,
particμlarly SLE.
PR092173, corresponding to W38346_P3 (SEQ ID NO:42) protein, has been
reported in WO2004081199 patent apμlication, among other genes showing altered patterns
of expression in autoimmune diseases for use in diagNOsis, prevention and treatment
thereof. The WO2004081199 patent apμlication does not teach however, that that sequence
corresponding to PR092173 differentially expressed in systemic lupus erythematosus
(SLE), and/or in cancer, especially in lymphoma, especially non-HodgKin's Lymphoma,
anti CD20 (i.e. Rituximab) resistant lymphoma, Mμltiμle Myeloma, Kidney cancer or
pancreatic cancer. The WO2004081199 patent apμlication does not teach also, mat mat
sequence corresponding to PR092173 can be used as drug target for treatment of SLE,
and/or of cancer, including lymphoma, especially non-HodgKin's Lymphoma, anti CD20
(i.e. Rituximab) resistant lymphoma, Mμltiμle Myeloma, Kidney cancer or pancreatic
cancer, and/or diagNOsis thereof. The WO2004081199 patent apμlication does not teach
also, that PR092173 soluble ectodomain, as well as fragments thereof and conjugates and
antibothes against it can be used as merapeutic or diagNOstic agents for treatment of cancer
including lymphoma, especially non-HodgKin's Lymphoma, anti CD20 (i.e. Rituximab)
resistant lymphoma, Mμltiμle Myeloma, Kidney cancer or pancreatic cancer, and/or immune
related conditions, especially SLE.
TMEM154 sequence corresponding to W38346_P3 (SEQ ID NO:42) has been also
reported in WO03090694 patent apμlication, among other genes used for diagNOsing or
monitoring autoimmune and chronic inflammatory diseases. The WO03090694 patent
apμlication does not teach however, that sequence corresponding to TMEM154 can be used
as drug targets for treatment of immune related conditions, particμlarly SLE. The
WO03090694 patent apμlication does not teach also, that sequence corresponding to
TMEM154 are differentially expressed in cancer, especially in lymphoma, especially non-
HodgKin's Lymphoma, anti CD20 (i.e. Rituximab) resistant lymphoma, Mμltiμle Myeloma,
Kidney cancer or pancreatic cancer. The WO03090694 patent apμlication does not teach
also, that sequences corresponding to TMEM154 can be used as drug targets for treatment
of lymphoma, especially non-HodgKin's Lymphoma, anti CD20 (i.e. Rituximab) resistant
lymphoma, Mμltiμle Myeloma, Kidney cancer or pancreatic cancer, or diagNOsis thereof.
The WO03090694 patent apμlication does not teach also, that TMEM154 soluble
ectodomain, as well as fragments thereof and conjugates and antibothes against it can be
used as therapeutic or diagNOstic agents for treatment of lymphoma, especially non-
HodgKin's Lymphoma, anti CD20 (i.e. Rituximab) resistant lymphoma, Mμltiμle Myeloma,
Kidney cancer or pancreatic cancer, and/or immune related conditions, especially SLE.
TMEM154 antigen corresponding to W38346_P3 (SEQ ID NO:42) has been
reported in WO06020266 patent apμlication, which purports to disclose polypeptides and
antibothes derived from chronic lymphocytic leuKemia cells, and uses thereof.
WO06020266 does not teach however, that sequences corresponding to TMEM154 can be
used as drug targets for treatment of lymphoma, especially non-HodgKin's Lymphoma, anti
CD20 (i.e. Rituximab) resistant lymphoma, Mμltiμle Myeloma, Kidney cancer or pancreatic
cancer, and/or immune related conditions, especially SLE. The WO06020266 patent
apμlication does not provide any specific teaching or incentive that woμld direct a sKilled
artisan to use antibothes specific to the TMEM154 for the treatment or diagNOsis of
lymphoma, especially non-HodgKin's Lymphoma, anti CD20 (i.e. Rituximab) resistant
lymphoma, Mμltiμle Myeloma, Kidney cancer or pancreatic cancer, and/or immune related
conditions, especially SLE. The WO06020266 patent apμlication does not teach also, that
TMEM154 soluble ectodomain, as well as fragments thereof and conjugates and antibothes
against it can be used as therapeutic or diagNOstic agents for treatment of lymphoma,
especially non-HodgKin's Lymphoma, anti CD20 (i.e. Rituximab) resistant lymphoma,
Mμltiμle Myeloma, Kidney cancer or pancreatic cancer, and/or immune related conditions,
especially SLE (systemic lupus erythematosus).
TMEM154 antigen corresponding to W38346_P3 (SEQ ID NO:42) has been
reported in WO2008112177, WO200270539 and EP1293569 patent apμlications.
TMEM154 antigen corresponding to W38346_P4 (SEQ ID NO:45) has been reported in
WO2008112177 patent apμlication. However, none of these patent apμlications teaches that
sequences corresponding to TMEM154 can be used as drug targets for treatment or
diagNOsing of lymphoma, especially non-HodgKin's Lymphoma, anti CD20 (i.e.
Rituximab) resistant lymphoma, Mμltiμle Myeloma, Kidney cancer or pancreatic cancer,
and/or immune related conditions, especially SLE (systemic lupus erythematosus). These
apμlications do not teach also, that TMEM154 soluble ectodomain, as well as fragments
thereof and conjugates and antibothes against it can be used as therapeutic or diagNOstic
agents for treatment of lymphoma, especially non-HodgKin's Lymphoma, anti CD20 (i.e.
Rituximab) resistant lymphoma, Mμltiμle Myeloma, Kidney cancer or pancreatic cancer,
and/or immune related conditions, especially SLE (systemic lupus erythematosus).
TMEM154 antigen corresponding to W38346_P7 (SEQ ID NO:46) has been
reported by the apμlicants of the present apμlication in US patent apμlication NO:
11/043,860. However, there is NO teaching in US 11/043,860 apμlication that W38346_P7
(SEQ ID NO:46) soluble ectodomain, as well as fragments thereof and specific antibothes
against it can be used as therapeutic or diagNOstic agents for treatment of lymphoma,
especially non-HodgKin's Lymphoma, anti CD20 (i.e. Rituximab) resistant lymphoma,
Mμltiμle Myeloma, Kidney cancer or pancreatic cancer, and/or immune related conditions,
especially SLE (systemic lupus erythematosus).
In particμlar this invention uses TMEM154 antigen and discrete portions thereof as a
drug target for therapeutic small molecμles, peptides, antibothes, antisense RNAs, siRNAs,
ribozymes, and the liKe. More particμlarly the invention relates to diagNOstic and therapeutic
polyclonal and monoclonal antibothes and fragments thereof that bind TMEM154, and
portions and variants thereof. According to at least some embodiments of the invention
there is a use antibothes and antibody fragments against TMEM154 antigen, its secreted or
soluble form or ECD and/or variants, conjugates, or fragments thereof and fragments and
variants thereof for treating and diagNOsing cancer, especially for treatment of lymphoma,
especially non-HodgKin's Lymphoma, anti CD20 (i.e. Rituximab) resistant lymphoma,
Mμltiμle Myeloma, Kidney cancer or pancreatic cancer, and/or immune related conditions,
especially SLE (systemic lupus erythematosus), wherein this antigen is differentially
expressed.
As noted above, cluster W38346 features 4 transcripts, which were listed in Table 38
above. These transcripts encode for proteins which are variants of protein hypothetical
protein LOC201799 (SEQ ID NO:42). A description of each variant protein according to at
least some embodiments of the invention is NOw provided.
Variant protein W38346_P3 (SEQ ID NO:42) according to at least some
embodiments of the invention has an amino acid sequence as encoded by
transcriptsW38346_T0 (SEQ ID NO:38) and W38346.T1 (SEQ ID NO:39).
The localization of the variant protein was determined according to resμlts from a
number of different software programs and analyses, including analyses from SignalP and
other specialized programs. The variant protein is believed to be located as follows with
regard to the cell: membrane.
The coding portion of transcript W38346JT0 (SEQ ID NO:38) starts at position 233
and ends at position 781. The transcript also has the following SNPs as listed in Table 40
(given according to their position on the nucleotide sequence, with the alternative nucleic
acid listed).
Variant protein W38346_P4 (SEQ ID NO:45) according to at least some
embodiments of the invention has an amino acid sequence as encoded by transcripts
W38346_T2 (SEQ ID NO:40). A description of the relationship of the variant protein
according to at least some embodiments of the invention to KNOwn proteins is as follows:
2. Comparison report between W38346_P4 and KNOwn proteins Q96MQ8_HUMAN:
A. An isolated chimeric polypeptide encoding for W38346_P4, comprising a amino
acid sequence being at least 90% homologous to
MVLIμlILLVLLLLSVVFLATYYKRKRTKQEPSSQGSQSALQTYELGSENVKVPIFEE
DTPSVMEIEMEELDKWMNSMNRNADFECLPTLKEEKESNHNPSDSES
corresponding to amino acids 79 -183 of KNOwn proteins Q96MQ8_HUMAN, which also
corresponds to amino acids 1-105 of W38346_P4.
The localization of the variant protein was determined according to resμlts from a
number of different software programs and analyses, including analyses from SignalP and
other specialized programs. The variant protein is believed to be located as follows with
regard to the cell: secreted.
The coding portion of transcript W38346_T2 (SEQ ID NO:40) starts at position 516
and ends at position 830. The transcript also has the following SNPs as listed in Table 42
(given according to their position on the nucleotide sequence, with the alternative nucleic
acid listed).
Variant protein W38346_P7 (SEQ ID NO:46) according to at least some
embodiments of the invention has an amino acid sequence as encoded by transcripts
W38346_T5 (SEQ ID NO:41). A description of the relationship of the variant protein
according to at least some embodiments of the invention to KNOwn proteins is as follows:
1. Comparison report between W38346_P7 (SEQ ID NO:46) and KNOwn proteins
Q96MQ8_HUMAN and NP_689893:
A. An isolated chimeric polypeptide, comprising a first amino acid sequence being at
least 90% homologous to
MQAPRAALVFALVIALVPVGRGNYEELENSGDTTVESERPNKVTrPSTFAAVTIKET
LNANINSTNFAPDENQLEFILMVLIμlILLVLLLLSVVFLATYYKRKRTKQEPSSQGS
QSALQT corresponding to amino acids 1 -121 of KNOwn proteins Q96MQ8_HUMAN and
NP_689893, which also corresponds to amino acids 1 -121 of W38346_P7 (SEQ ID
NO:46), and a second amino acid sequence being at least 70%, optionally at least 80%,
preferably at least 85%, more preferably at least 90% and most preferably at least 95%
homologous to a polypeptide having the sequence CKIQLSWKVIPAFCLESSHRNAL
(SEQ ID NO: 162) corresponding to amino acids 122 -144 of W38346_P7 (SEQ ID
NO:46), wherein said first amino acid sequence and second amino acid sequence are
contiguous and in a sequential order,
B. An isolated polypeptide of an edge portion of W38346_P7 (SEQ ID NO:46),
comprising an amino acid sequence being at least 70%, optionally at least about 80%,
preferably at least about 85%, more preferably at least about 90% and most preferably at
least about 95% homologous to the sequence CKIQLSWKVIPAFCLESSHRNAL (SEQ ID
NO: 162) of W38346.P7 (SEQ ID NO:46).
2. Comparison report between W38346_P7 (SEQ ID NO:46) and KNOwn protein
Q6P9G4_HUMAN (SEQ ID NO:44):
A. An isolated chimeric polypeptide, comprising a first amino acid sequence being at
least 90% homologous to
MQAPRAALVFALVIALVPVGRGNYEELENSGDTTVESERPNKVTIPSTFAAVTrKET
LNANINSTNFAPDENQLEFILMVLIμlILLVLLLL corresponding to amino acids 1 - 92
of KNOwn protein Q6P9G4JHUMAN (SEQ ID NO:44), which also corresponds to amino
acids 1 - 92 of W38346_P7 (SEQ ID NO:46), a bridging amino acid S corresponding to
amino acid 93 of W38346_P7 (SEQ ED NO:46), a second amino acid sequence being at
least 90% homologous to VVFLATYYKRKRTKQEPSSQGSQSALQT corresponding to
amino acids 94 -121 of KNOwn protein Q6P9G4_HUMAN (SEQ ID NO:44), which also
corresponds to amino acids 94 -121 of W38346_P7 (SEQ ID NO:46), and a third amino
acid sequence being at least 70%, optionally at least 80%, preferably at least 85%, more
preferably at least 90% and most preferably at least 95% homologous to a polypeptide
having the sequence CKIQLSWKVIPAFCLESSHRNAL (SEQ ID NO: 162) corresponding
to amino acids 122 -144 of W38346_P7 (SEQ ID NO:46), wherein said first amino acid
sequence, bridging amino acid, second amino acid sequence and third amino acid sequence
are contiguous and in a sequential order.
B. An isolated polypeptide of an edge portion of W38346_P7 (SEQ ID NO:46),
comprising an amino acid sequence being at least 70%, optionally at least about 80%,
preferably at least about 85%, more preferably at least about 90% and most preferably at
least about 95% homologous to the sequence CKIQLSWKVIPAFCLESSHRNAL (SEQ ID
NO: 162) of W38346_P7 (SEQ ID NO:46).
The localization of the variant protein was determined according to resμlts from a
number of different software programs and analyses, including analyses from SignalP and
other specialized programs. The variant protein is believed to be located as follows with
regard to the cell: membrane.
Variant protein W38346_P7 (SEQ ID NO:46) also has the following non-silent SNPs
(Single Nucleotide Polymorphisms) as listed in Table 43, (given according to their
position(s) on the amino acid sequence, with die alternative amino acid(s) listed).
EXAMPLE 6_2: EXPRESSION ANALYSIS OF TMEM154 TRANSCRIPTS
TMEM154 transcripts were also found to be over expressed in Kidney cancer, as is
demonstrated in Figure 42 and in pancreatic cancer, as is demonstrated in Figure 43. Figures
42-43 show expression graphs of Affymetrix probe set 238063_at. Figure 42 shows the
expression of TMEM154 transcripts in microarray chips from Kidney cancer and normal
Kidney experiments. As can be seen TMEM154 transcripts are overexpressed in Kidney
cancer tissues (diamond marKers) relative to its expression in normal Kidney (circle and
triangle marKers).
Figure 43A shows the expression of TMEM154 transcripts in microarray chips from
pancreatic cancer and normal pancreas experiments. As can be seen TMEM154 transcripts
are overexpressed in pnacreatic cancer tissues (diamond marKers).
Figure 43B shows Kaμlan-Meier survival curves of the high expression of the
TMEM154 probe (238063_at, samμles over median expression), and low expression (below
median) in a samμles from Rituximab treated DLBCL (Diffuse large B-cell lymphoma). It
is evident that TMEM154 high expression is corelated with poor survival, and hance can
serve as a potential treatment for anti CD20 resistant lymphoma paetients. In Figure 43B the
time scale is shown in years; solid line represents high TMEM154 expression; fragmented
line represents low TMEM154 expression.
Expression of hypothetical protein FLJ32028, TMEM154 V/38346 transcripts which are
detectable by amμlicon as depicted in sequence name W38346^eg6-20F1R1 (SEQ ID
NO: 106) in different normal tissues and b100d specific panel
Expression of hypothetical protein FLJ32028, TMEM154 transcripts detectable by or
according to seg6-20FlRl - W38346_seg6-20F1R1 (SEQ ID NO: 106) amμlicon and
primers W38346_seg6-20F (SEQ ID NO: 104) and W38346_seg6-20R (SEQ ID NO: 105)
was measured by real time PCR in b100d panel and normal panel. The samμles used for
b100d panel are detailed in Tables 2 and 2_1. The samμles used for normal panel are
detailed in Table 3.
normal panel -
For each RT samμle, the expression of the above amμlicon was normalized to the
normalization factor calcplated from the expression of several house Keeping genes as
described in EXAMPLE 1. The normalized quantity of each RT samμle was then divided by
the median of the quantities of the Kidney samμles (samμle numbers 19-23, Table 3 above),
to obtain a value of relative expression of each samμle relative to median of the Kidney
samμles, as shown in Figure 44. High expression was observed in normal PBMCs, sμleen
and esophagus.
For b100d panel - For each RT samμle, the expression of the above amμlicon was
normalized to the normalization factor calcplated from the expression of several house
Keeping genes as described in EXAMPLE 1. The normalized quantity of each RT samμle was
then divided by the median of the quantities of the Kidney normal samμles (samμle numbers
65-67, Table 2 above), to obtain a value of relative expression of each samμle relative to
median of the Kidney normal samμles.
The resμlts of this analysis are depicted in the histogram in Figure 45. Expression of
the above-indicated hypothetical protein FLJ32028, TMEM154 transcripts is high in PMN,
moNOcytes, mμltiμle myeloma patients and several lymphomas samμles.
Forward Primer (W38346_seg6-20F) (SEQ ID NO:104):
EXAMPLE 6_3: CLONING OF CGEN928 TMEM154JT0P3 ORF FUSED TO FLAG
TAG
Cloning of TMEM154_T0_P3 open reading frame (ORF) fused to FLAG was carried out
by RT PCR as described below.
RT18 PMNs (RT-PCR product resμlted from samμle 18, Table 2) and RT19 moNOcytes
(RT-PCR product resμlted from samμle 19, Table 2) from the b100d panel were diluted 1:20
in TE buffer (10mM Tris, 1 mM EDTA pH 8) and served as a template for PCR.
PCR was done using GoTaq ReadyMix (Promega, catalog number M122) under the
following conditions: 10µl - cDNA described above; 1.5. µl - H20; and 0.5μl (10µM) - of
each primer #100-952 (SEQ ID NO:187) and #100-953 (SEQ ID NO:188) in a total reaction
volume of 25μl; with a reaction program of 2 minutes in 94°C; 35 cycles of: 30 seconds at
94°C, 30 seconds at 55°C, 1 minute at 72°C; then 10 minutes at 72°C. Primers which were
used include gene specific sequences; restriction enzyme sites; KozaK sequence and FLAG
tag.
5μl of PCR product were loaded onto a 1.2% agarose gel stained with ethidium bromide,
electrophoresed in lxTAE solution at 100V, and visualized with UV light. After verification
of expected band size, PCR product was purified using QiaQuicK™ PCR Purification Kit
(Qiagen, catalog number: 28004). The purified PCR product was digested with Nhel and
Agel restriction enzymes (New England Biolabs, Beverly, MA, U.S.A.). After digestion,
DNA was loaded onto a 1.2 % agarose gel as described above. The expected band size was
excised and extracted from the gel using QiaQuicK™ Gel Extraction Kit (Qiagen, catalog
number: 28707), The digested DNA was then ligated into pIRESpuro3 vector, previously
digested with the above restriction enzymes, using LigaFastTM Rapid DNA Ligation
System (Promega, catalog number: M8221). The resμlting DNA was transformed into
competent E.Coli bacteria DH5a (RBC Bioscience, Taipei, Taiwan, catalog number:
RH816) according to manufacturer's instructions, then plated on LB-ampicillin agar ulates
for selection of recombinant ulasmids, and incubated overnight at 37°C. The following day,
positive colonies were screened by PCR using pIRESpuro3 vector specific primer and gene
specific primer (data not shown). The PCR product was analyzed using 1.2% agarose gel as
described above. After verification of expected band size, positive colonies were grown in 5
ml Terrific Broth supulemented with 100µg/ml ampicillin, with shaKing overnight at 37°C.
ulasmid DNA was isolated from bacterial cultures using Qiaprep™ Spin Miniprep Kit
(Qiagen, catalog number: 27106). Accurate cloning was verified by sequencing the inserts
(Weizmann Institute, Rehovot, Israel). Upon verification of an error-free colony (i.e. NO
mutations within the ORF), recombinant plasmids were processed for further analyses.
The DNA sequence of the resμlting TMEM154_T0_FLAG (SEQ ID NO:189) is shown in
Figure 46; FLAG sequence is in underlined.
The amino acid sequence of TMEM154_P3_FLAG (SEQ ID NO:190) is shown in Figure
47; FLAG sequence is in underlined.
EXAMPLE 6„4: DETERMINING CELL LOCALIZATION OF TMEM154_P3
In order to determine TMEM154_P3 cellμlar localization, TMEM154_T0_P3 was cloned in
frame to FLAG tag, as described above. Protein localization was observed upon transient
transfection (Chen et al., Molecμlar Vision 2002; 8; 372-388) using confocal microscopy.
48 hours following transfection, the cells were stained with anti FLAG antibothes
conjugated to Cy-3 flurophore and were observed for the presence of fluorescent signal,
TMEM154_T0„P3_FLAG (SEQ ID NO:189) pIRESpuro3 construct was transiently
transfected into HEK-293T cells as described above. 48 hours post transient transfection,
cells on coverslip were further processed for immuNOstaining and analysis by confocal
microscopy. The cover slip was washed in phosphate buffered saline (PBS), then fixed for
15 minutes with a solution of 3.7% paraformaldehyde (PFA) (Sigma, catalog number: P-
6148)/3% glucose (Sigma, catalog number: G5767) (diluted in PBS). Quenching of PFA
was done by a 5 minute incubation in 3mM glycine (Sigma, catalog number: G7126)
(diluted in PBS). After two 5-minute washes in PBS, cells were permeabilized with 0,1%
triton-X100 (diluted in PBS) for 5 minutes. After two 5-minute washes in PBS, blocKing of
non-specific regions was done with 5% bovine serum albumin (BSA) (Sigma, catalog
number A4503) (diluted in PBS) for 20 minutes. The coverslip was then incubated, in a
humid chamber for 1 hour, with mouse anti FLAG-Cy3 antibothes (Sigma, catalog number:
A9594), diluted 1:100 in 5% BSA in PBS, followed by three 5-minute washes in PBS. The
coverslip was then mounted on a slide with Gel Mount Aqueous medium (Sigma, catalog
number: G0918) and cells were observed for the presence of fluorescent product using
confocal microscopy.
Cell localization is shown in Figure 48. TMEM154_P3 is localized to the cell membrane.
EXAMPLE 6_5: PRODUCTION OF POLYCLONAL ANTIBOtheS SPECIFIC TO
TMEM154_P3 PROTEIN
All polyclonal Abs production procedure, including peptides synthesis, peptides
conjugation, animal immunizations, bleeding and antibothes purification were performed at
Sigma-Aldrich (Israel). Two pairs of rabbits (one pair per epitope) were injected to prepare
antibothes for TMEM154_P3 (rabbit numbers 6285 and 6286, 6248 and 6249 respectively).
All animal care, handling and injections were performed by Sigma (Israel).
Peptides which were used for rabbit immunization were as follows:
RGNYEELENSGDTTVESER designated TM21 (SEQ ID NO:191) a sequence taKen from
the N' terminus corresponding to amino acids 21-39 of TMEM154_P3 protein (SEQ ID
NO:42). The second peptide sequence to be used was: YKRKRTKQEPSSQGSQS
designated TM101 (SEQ ID NO: 192), a sequence taKen from the C terminus,
corresponding to amino acids 101-117 of TMEM154_P3 protein (SEQ ID NO:42). 25mg of
each peptide were synthesized with 95% purity of which lOmg were conjugated to KLH
carrier. Each pair of rabbits was immunized with the corresponding conjugated peptide as
follows: rabbits 6285 and 6286 were immunized with TM21 peptide (SEQ ID NO:191), and
rabbits 6248 and 6249 were immunized with TM101 peptide (SEQ ID NO:192). Animals
were immunized every two weeKs. 60ml production bleeds from each rabbit were collected
and affinity purification was performed with the peptide against which the respective
antibothes were raised,
EXAMPLE 6_6: CHARACTERIZATION OF PURIFIED TMEM154_P3 ANTIBOtheS
BY IMMUNOSTAINING OF TMEM154 TRANSFECTED CELLS
In order to further characterize the affinity purified antibothes raised against TMEM154_P3,
antibody-protein interaction was stuthed using immuNOstaining of TMEM154_P3 stable
transfected HEK293T cells.
GENERATION OF STABLE POOL EXPRESSING TMEM154__P3 PROTEIN:
Two stably transfected pool were generated, TMEM154_P3 pIRESpuro3 and the negative
control empty pIRESpuro3. Both constructs were transfected into HEK-293T cells as
previously described.
IMMUNOSTAINING OF TMEM154 TRANSFECTED CELLS
500,000 cells per well of HEK-293T (ATCC, CRL-11268) stably expressing TMEM154 or
the empty vector pIRES puro3, described above, were plated on sterile glass coverslips,
13mm diameter (Marienfeld, catalog number: 01 115 30), which were μlaced in a 6 well
plate, using 2ml pre-warmed DMEM [Dulbecco's modified Eagle's Media, Biological
Industries (Beit Ha'EmeK, Israel), catalog number: 01-055-1A] + 10% FBS [Fetal Bovine
Serum, Biological Industries (Beit Ha'EmeK, Israel), catalog number: 04-001-1A] + 4mM
L-Glutamine [Biological Industries (Beit Ha'EmeK, Israel), catalog number: 03-020-1A].
48 hours post plating the cells on coverslips they were further processed for immuNOstaining
and analysis by confocal microscopy. The cover slips were washed in phosphate buffered
saline (PBS), then fixed for 25 minutes with a 3.7% paraformaldehyde (PFA) (Sigma,
catalog number: P-6148)/3% glucose (Sigma, catalog number: G5767). After 2 5-minute
washes in PBS, cells were permeabilized with 0.1% triton-X100 (diluted in PBS) for 5
minutes. After two 5-minute washes in PBS, blocKing of non-specific regions was done
with 5% bovine serum albumin (BSA) (Sigma, catalog number: A4503) (diluted in PBS) for
20 minutes. The coverslips were then incubated, in a humid chamber for 1 hour, with
purified rabbit anti-TMEM154 antibothes described above: TM21 (Rabbit 6285, 6286 ,
1mg/ml) was diluted 1:1000 in 5% BSA in PBS and TM101 (Rabbit 6248 6249, 1mg/ml)
was diluted 1:1000 in 5% BSA. The antibothes were washed 3 times for 5-minutes in PBS.
The coverslips were then incubated, in a humid chamber for 1 hour, with secondary
antibody: donKey anti-rabbit conjugated to Cy-3 flurophore (JacKson ImmuNOResearch,
catalog number: 711-165-152), diluted 1:200 in 3% BSA in PBS. After 3 5-minute washes
in PBS, the fixed coverslips were mounted on slides with Gel Mount Aqueous medium
(Sigma, catalog number: G0918) and cells were observed for the presence of fluorescent
product using confocal microscopy.
Specific cell staining localized to the cell membrane was observed using purified TM21 and
TM101 antibothes on TMEM154 transfected cells (Figure 49 and Figure 50 respectively),
while, NO staining was observed using these antibothes on the negative control pIRESpuro3
HEK-293T transfected cells (Figure 51). The red fluorescence obtained in Figures 49 and
50 as opposed to the absence of signal in Figure 51 demonstrates the specificity of TM21
and TM101 antibothes to TMEM154_P3 (SEQ ID NO:42).
EXAMplE 6_7: DEMONSTRATION OF ENDOGENOUS EXPRESSION OF
TMEM154_P3 BY IMMUNOSTAINING OF LYMPHOBLAST CELL LINES
In order to determine endogeNOus expression of TMEM154, three cell lines were selected
for immustaining using specific antibothes against TMEM154_P3 protein described above.
500000 cells from each cell line: Ramos (ATCC cat NO CRL-1923), CESS (ATCC cat NO
TIB-190), Daudi (ATCC cat NO CCL-213) were fixed with 3.7% PFA containing 3%
Glucose and plated on coverslips previously treated with poly-L-Lysin 0.01 % (Sigma cat NO
P4832), Cells were further processed for immunostaining as describe above and analyzed by
confocal microscopy.
Specific cell staining localized to the cell membrane was observed using purified TM21 and
TM101 antibothes on all three cell lines as shown in Figure 52.
[00573] EXAMPLE 7
[00574] DEVELOPMENT OF FμlLY HUMAN ANTI-KRTCAP3, ANTI-FAM26F,
ANTI-MGC52498, ANTI-FAM70A AND ANTI-TMEM154 ANTBODIES
[00575] Generation Of Human monoclonal Antibothes Against KRTCAP3, FAM26F,
MGC52498, FAM70A and TMEM154 Antigen
[00576] Fusion proteins composed of the extracellular domain of the KRTCAP3,
FAM26F, MGC52498, FAM70A and TMEM154 linKed to an IgG2 Fc polypeptide are
generated by standard recombinant methods and used as antigen for immunization.
[00577] Transgenic HuMab Mouse.
[00578] Fully human monoclonal antibothes to KRTCAP3, FAM26F, MGC52498,
FAM70A and TMEM154 are prepared using mice from the HCo7 strain of the transgenic
HuMab Mouse®, which expresses human antibody genes. In this mouse strain, the
endogeNOus mouse Kappa light chain gene has been homozygously disrupted as described in
Chen et al. (1993) EMBO J. 12:811-820 and the endogeNOus mouse heavy chain gene has
been homozygously disrupted as described in EXAMPLE 1 of PCT Publication WO 01/09187.
Furthermore, this mouse strain carries a human Kappa light chain transgene, KCo5, as
described in Fishwild et al. (1996) Nature BiotechNOlogy 14:845-851, and a human heavy
chain transgene, HCo7, as described in U.S. Pat. NOs. 5,545,806; 5,625,825; and 5,545,807.
[00579] HuMab Immunizations:
[00580] To generate fμlly human monoclonal antibothes to KRTCAP3, FAM26F,
MGC52498, FAM70A and TMEM154 polypeptides, mice of the HCo7 HuMab Mouse®
strain can be immunized with purified recombinant KRTCAP3, FAM26F, MGC52498,
FAM70A or TMEM154 fusion protein derived from mammalian cells mat are transfected
with an expression vector containing the gene encoding the fusion protein. General
immunization schemes for the HuMab Mouse® are described in Lonberg, N. et al (1994)
Nature 368(6474): 856-859; Fishwild, D. et al. (1996) Nature BiotechNOlogy 14: 845-851
and PCT Publication WO 98/24884. The mice are 6-16 weeKs of age upon the first infusion
of antigen. A purified recombinant KRTCAP3, FAM26F, MGC52498, FAM70A or
TMEM154 antigen preparation (5-50 micro-grams, purified from transfected mammalian
cells expressing KRTCAP3, FAM26F, MGC52498, FAM70A or TMEM154 fusion protein)
is used to immunize the HuMab mice intraperitoneally.
[00581] Transgenic mice are immunized twice with antigen in comμlete Freund's
adjuvant or Ribi adjuvant IP, followed by 3-21 days IP (up to a total of 11 immunizations)
with the antigen in incomμlete Freund's or Ribi adjuvant. The immune response is
monitored by retroorbital bleeds. The μlasma is screened by ELISA (as described below),
and mice with sufficient titers of anti- KRTCAP3, anti-FAM26F, anti-MGC52498, anti-
FAM70A or anti-TMEM154 human immunogloulin are used for fusions. Mice are boosted
intraveNOusly with antigen 3 days before sacrifice and removal of the sμleen.
[00582] Selection of HuMab mice® Producing Anti- KRTCAP3, Anti-FAM26F, Anti-
MGC52498, Anti-FAM70A or Anti-TMEM154 Antibothes:
[00583] To select HuMab mice® producing antibothes that bind KRTCAP3, FAM26F,
MGC52498, FAM70A or TMEM154 polypeptides, sera from immunized mice is tested by
a modified ELISA as originally described by Fishwild, D. et al. (1996). Briefly, microtiter
plates are coated with purified recombinant KRTCAP3, FAM26F, MGC52498, FAM70A
or TMEM154 fusion protein at l-2,mu.g/ml in PBS, 50.mu.l/wells incubated 4 degrees C.
overnight then blocKed with 200.mu.l/well of 5% BSA in PBS. Dilutions of μlasma from
KRTCAP3, FAM26F, MGC52498, FAM70A or TMEMI54 -immunized mice are added to
each well and incubated for 1-2 hours at ambient temperature. The plates are washed with
PBS/Tween and then incubated with a goat-anti-human Kappa light chain polyclonal
antibody conjugated with alKaline phosphatase for 1 hour at room temperature. After
washing, the plates are developed with pNPP substrate and analyzed by spectrophotometer
at OD 415-650. Mice that developed the highest titers of anti-KRTCAP3, anti-FAM26F,
anti-MGC52498, anti-FAM70A or anti-TMEM154 antibothes are used for fusions. Fusions
are performed as described below and hybridoma supernatants are tested for anti-
KRTCAP3, anti-FAM26F, anti-MGC52498, anti-FAM70A or anti-TMEM154 activity by
ELISA.
[00584] Generation Of Hybridomas Producing Human monoclonal Antibothes To
KRTCAP3, FAM26F, MGC52498, FAM70A or TMEM154 polypeptides
[00585] The mouse sμleNOcytes, isolated from the HuMab mice, are fused with PEG to a
mouse myeloma cell line based upon standard protocols. The resμlting hybridomas are then
screened for the production of antigen-specific antibothes. Single cell suspensions of sμlenic
lymphocytes from immunized mice are fused to one-fourth the number of P3X63 Ag8.6.53
(ATCC CRL 1580) nonsecreting mouse myeloma cells with 50% PEG (Sigma). Cells are
plated at approximately 1X10 -5 /well in flat bottom microliter plate, followed by about two
weeK incubation in selective medium containing 10% fetal calf serum, supμlemented with
origen (IGEN) in RPMI, L-glutamine, sodium pyruvate, HEPES, penicillin, streptamycin,
gentamycin, lx HAT, and beta-mercaptoethaNOl. After 1-2 weeKs, cells are cμltured in
medium in which the HAT is reμlaced with HT. Individual wells are then screened by
ELISA (described above) for human anti-KRTCAP3, anti-FAM26F, anti-MGC52498, anti-
FAM70A or anti-TMEM154 monoclonal IgG antibothes. Once extensive hybridoma growth
occurred, medium is monitored usually after 10-14 days. The antibody secreting
hybridomas are replated, screened again and, if still positive for human IgG, anti-
KRTCAP3, anti-FAM26F, anti-MGC52498, anti-FAM70A or anti-TMEM154 monoclonal
antibothes are subcloned at least twice by limiting dilution. The stable subclones are then
cμltured in vitro to generate small amounts of antibody in tissue cμlture medium for further
characterization.
[00586] Hybridoma clones are selected for further analysis.
[00587] Structural Characterization Of Desired anti-KRTCAP3, anti-FAM26F, anti-
MGC52498, anti-FAM70A or anti-TMEM154Human monoclonal Antibothes
[00588] The cDNA sequences encoding the heavy and light chain variable regions of the
obtained anti-KRTCAP3, anti-FAM26F, anti-MGC52498, anti-FAM70A or anti-
TMEM154 monoclonal antibothes are obtained from the resμltant hybridomas, respectively,
using standard PCR techniques and are sequenced using standard DNA sequencing
techniques,
[00589] The nucleotide and amino acid sequences of the heavy chain variable region and
of the light chain variable region are identified. These sequences may be compared to
KNOwn human germline immunogloulin light and heavy chain sequences and the CDRs of
each heavy and light of the obtained anti-KRTCAP3, anti-FAM26F, anti-MGC52498, anti-
FAM70A or anti-TMEM154 sequences identified.
[00590] Characterization Of Binding Specificity And Binding Kinetics Of anti-
KRTCAP3, anti-FAM26F, anti-MGC52498, anti-FAM70A or anti-TMEM154 Human
monoclonal Antibothes
[00591] The binding affinity, binding Kinetics, binding specificity, and cross-competition
of anti-KRTCAP3, anti-FAM26F, anti-MGC52498, and-FAM70A or anti-TMEM154
antibothes are examined by Biacore analysis. Also, binding specificity is examined by flow
cytometry.
[00592] Binding affinity and Kinetics
[00593] Anti-KRTCAP3, anti-FAM26F, anti-MGC52498, anti-FAM70A or anti-
TMEM154 antibothes produced according to the invention are characterized for affinities
and binding Kinetics by Biacore analysis (Biacore AB, Uppsala, Sweden). Purified
recombinant human KRTCAP3, FAM26F, MGC52498, FAM70A or TMEM154 fusion
protein is covalently linKed to a CM5 chip (carboxy methyl dextran coated chip) via
primary amines, using standard amine couμling chemistry and Kit provided by Biacore.
Binding is measured by providing the antibothes in HBS EP buffer (provided by BIAcore
AB) at a concentration of 267 nM and a flow rate of 50.mu.l/min. The antigen- antibody
association Kinetics are followed for 3 minutes and the dissociation Kinetics are followed for
7 minutes. The association and dissociation curves are fit to a 1:1 Langmuir binding model
using BlAevaluation software (Biacore AB). To minimize the effects of avidity in the
estimation of the binding constants, only the initial segments of data corresponding to
association and dissociation phases are used for fitting.
[00594] Epitope Mapping of Obtained anti-KRTCAP3, anti-FAM26F, anti-MGC52498,
anti-FAM70A oranti-TMEM154 Antibothes
[00595] Biacore is used to determine epitope grouping of anti-KRTCAP3, anti-
FAM26F, anti-MGC52498, anti-FAM70A or anti-TMEM154 antibothes are used to map
their epitopes on the KRTCAP3, FAM26F, MGC52498, FAM70A or TMEM154 antigen,
respectively. These different antibothes are coated on three different surfaces of the same
chip to 8000 RUs each. Dilutions of each of the mAbs are made, starting at 10 mu.g/mL and
is incubated with Fc fused KRTCAP3, FAM26F, MGC52498, FAM70A or TMEM154 (50
nM) for one hour. The incubated comμlex is injected over all the three surfaces (and a blanK
surface) at the same time for 1.5 minutes at a flow rate of 20.mu,L/min. Signal from each
surface at end of 1.5 minutes, after subtraction of appropriate blanKs, has been μlotted
against concentration of mAb in the comμlex. Upon analysis of the data, me anti-
KRTCAP3, anti-FAM26F, anti-MGC52498, anti-FAM70A or anti-TMEM154 antibothes
are categorized into different epitope groups depending on the epitope mapping resμlts. The
functional properties thereof are also compared.
[00596] Chinese hamster ovary (CHO) cell lines that express KRTCAP3, FAM26F,
MGC52498, FAM70A or TMEM154 protein at the cell surface are developed and used to
determine the specificity of the KRTCAP3, FAM26F, MGC52498, FAM70A or TMEM154
HuMAbs by flow cytometry. CHO cells are transfected with expression plasmids containing
fμll length cDNA encoding transmembrane forms of KRTCAP3, FAM26F, MGC52498,
FAM70A or TMEM154 antigen or a variant thereof. The transfected proteins contained an
epitope tag at the N-terminus are used for detection by an antibody specific for the epitope.
Binding of an anti-KRTCAP3, anti-FAM26F, anti-MGC52498, anti-FAM70A or anti-
TMEM154 MAb is assessed by incubating the transfected cells with each of the KRTCAP3,
FAM26F, MGC52498, FAM70A or TMEM154 antibothes at a concentration of 10 micro-
grams/ml. The cells are washed and binding is detected with a FITC-labeled anti-human
IgG Ab. A murine anti-epitope tag Ab, followed by labeled anti-murine IgG, is used as the
positive control. non-specific human and murine Abs are used as negative controls. The
obtained data is used to assess the specificity of the HuMAbs for the KRTCAP3, FAM26F,
MGC52498, FAM70A orTMEM154 antigen target.
[00597] These antibothes and other antibothes specific to KRTCAP3, FAM26F,
MGC52498, FAM70A or TMEM154 polypeptides may be used in the afore-described anti-
KRTCAP3, anti-FAM26F, anti-MGC52498, anti-FAM70A or anti-TMEM154 related
therapies such as treatment of cancers wherein KRTCAP3, FAM26F, MGC52498,
FAM70A or TMEM154 antigen is differentially expressed, such as ovarian cancer, lung
cancer, breast cancer, Kidney cancer, liver cancer, pancreatic cancer, prostate cancer,
melaNOma and hematological malignancies such as Mμltiμle Myeloma, lymphoma, non-
HodgKin's lymphoma, anti CD20 (i.e. Rituximab) resistant lymphoma, leuKemia and T cell
leuKemia, involving the KRTCAP3, FAM26F, MGC52498, FAM70A or TMEM154
antigen, such as in the treatment of cancers and inflammatory or autoimmune diseases
wherein such antibothes will e.g., prevent negative stimμlation of T cell activity against
desired target cancer cells or prevent the positive stimμlation of T cell activity thereby
eliciting a desired anti-autoimmune effect.
[00598] The invention has been described and prophetic embodiments provided relating
to manufacture and selection of desired anti-KRTCAP3, anti-FAM26F, anti-MGC52498,
anti-FAM70A or anti-TMEM154 antibothes for use as therapeutics and diagNOstic methods
wherein the disease or condition is associated with KRTCAP3, FAM26F, MGC52498,
FAM70A or TMEM154 antigen. The invention is NOw further described by the claims
which follow.
We Claim:
1. A polyclonal or monoclonal antibody or fragment that specifically binds to at least one
of the TMEM154 polypeptides selected from the group consisting of SEQ ID NOs:
42-46, 63, 64, 161, 162, 191, 192, or a fragment or a variant, or a homolog thereof
possessing at least 85% sequence identity therewith,
2. An antibody or a fragment according to claim 1, wherein said antibody blocKs or
inhibits the interaction of at least one of the polypeptides selected from the group
consisting of SEQ ID NOs: 42-46 with a counterpart.
3. The antibody or fragment of claim 1, wherein said antibody or fragment replaces or
augments the interaction of at least one of the polypeptides selected from the group
consisting of SEQ ED NOs: 42-46 with a counterpart.
4. An antibody or fragment according to claim 1, which is suitable for treatment or
prevention of cancer or immune related condition, by modplating the activity of at
least one of the TMEM154 proteins selected from the group consisting of SEQ ID
NOs: 42-46.
5. The antibody or fragment according to claim 4, wherein the cancer is selected from the
group consisting of non-HodgKin's Lymphoma, HodgKin's Lymphoma, anti CD20
(i.e. Rituximab) resistant lymphoma, Mμltiμle Myeloma, Kidney cancer and
pancreatic cancer.
6. The antibody or fragment according to claim 4, wherein the immune related condition
is SLE (systemic lupus erythematosus).
7. An antibody or fragment according to claim 1, wherein the antigen binding site
contains from about 3-7 contiguous or non-contiguous amino acids of any of the
above sequences.
8. An antibody or fragment according to claim 1, wherein the antibody is a fμlly human
antibody, a humanized or primatized antibody, or a chimeric antibody.
9. An antibody or fragment according to claim 1, wherein the antibody is selected from
me group consisting of Fab, Fab', F(ab')2, F(ab'), F(ab), Fv or scFv fragment and
minimal recognition unit.
10. An antibody or fragment according to claim 1, wherein the antibody is couμled to a
detectable marKer, or to an effector moiety.
11. An antibody or fragment according to claim 10, wherein the effector moiety is one or
more of a radionuclide, fluorophore, an enzyme, a toxin, a therapeutic agent, a
chemotherapeutic agent, a cytoKine antibody, a cytoKine receptor, or an
immuNOmodμlatory agent.
12. An antibody or fragment according to claim 10, wherein the detectable marKer is one
or more of a radioisotope, a metal chelator, an enzyme, a fluorescent compound, a
bioluminescent compound or a chemiluminescent compound.
13. A pharmaceutical composition that comprises an antibody or a fragment according to
any one of claims 1-12.
14. A method for modplating lymphocyte activity, comprising contacting a lymphocyte,
positive for a TMEM154 polypeptide selected from the group consisting of SEQ ID
NOs: 42-46, with a bioactive agent capable of modplating TMEM154-mediated
signaling in an amount effective to modplate at least one lymphocyte activity.
15. A method according to claim 14, wherein said agent comprises an antagonist of
TMEM154-mediated signaling, and wherein said contacting inhibits the attenuation
of lymphocyte activity mediated by such signaling,
16. The method of claim 15, wherein said contacting increases lymphocyte activity.
17. The method of claim 15, wherein said antagonist comprises a blocKing agent capable
of interfering with the functional interaction of TMEM154 antigen and its
counterpart,
18. The method of claim 15, wherein the administered antagonist is an antibody or
fragment which is suitable for treatment or prevention of cancer by modplating the
activity of any one of the TMEM154 proteins.
19. The method of claim 15, wherein the administered antibody or fragment inhibits
negative stimμlation of T cell activity against cancer cells.
20. A method of treating or preventing TMEM154 positive cancer or immune related
condition, comprising administering to the patient a therapeutically effective amount
of an antibody or fragment or pharmaceutical composition according to anyone of
claims 1-13.
21. The method of claim 20, wherein the treatment is provided in combination with
another medicament or therapeutic method.
22. The method of claim 20, wherein the cancer is selected from the group consisting of
non-HodgKin's Lymphoma, HodgKin's Lymphoma, anti CD20 (i.e. Rituximab)
resistant lymphoma, Mμltiμle Myeloma, Kidney cancer and pancreatic cancer.
23. The method of claim 20, wherein the immune related condition is SLE (systemic lupus
erythematosus).
24. An antibody or fragment that specifically binds at least one polypeptide of any of SEQ
ID NOs:42-46, 63, 64, 161, 162, 191, 192, or a fragment or variant thereof, for
diagNOsing cancer or immune related condition characterized by differential
expression of at least one of the TMEM154 polypeptides selected from the group
consisting of SEQ ID NOs: 42-46, or a fragment or variant thereof.
25. The antibody according to claim 24, wherein the cancer is selected from the group
consisting of non-HodgKin's Lymphoma, HodgKin's Lymphoma, anti CD20 (i.e.
Rituximab) resistant lymphoma, Mμltiμle Myeloma, Kidney cancer and pancreatic
cancer.
26. The antibody according to claim 24, wherein the immune related condition is SLE
(systemic lupus erythematosus).
27. A method for diagNOsing a cancer or an immune related condition in a subject,
comprising detecting in the subject or in a samμle obtained from said subject the
presence of a polypeptide and/or an overexpressed level of said polypeptide having a
sequence at least 85% homologous to any one of the TMEM154 polypeptides, having
an amino acid sequence selected from the group consisting of SEQ ID NOs; 42-46,
63, 64, 161, 162, or a fragment thereof; wherein said overexpressed level is
determined with regard to a normal level of said polypeptide in a corresponding
normal tissue.
28. The method of claim 27, wherein the detection is conducted by immuNOassay.
29. The method of claim 28, wherein the immuNOassay utilizes an antibody according to
any of claims 1, 10, or 24.
30. An assay for detecting the presence of any one of the TMEM154 proteins, selected
from the group consisting of any of SEQ ID NOs: 42-46, or a fragment or variant
thereof in a biological samμle comprising contacting the samμle with an antibody or
a fragment according to any of claims 1,10, or 24, in the samμle.
31. The method of claim 27, wherein detecting the presence and/or the overexpressed level
of the TMEM154 polypeptides, or a fragment or variant thereof is performed in vivo
or in vitro.
32. A method for diagNOsing a cancer or an immune related condition in a subject,
comprising detecting in the subject or in a samμle obtained from said subject a
polynucleotide and/or an overexpressed level of said polynucleotide having a
sequence at least 85% homologous to the nucleic acid sequence as set forth in at least
one of SEQ ID NOs:23, 38-41, or 106; wherein said overexpressed level is
determined with regard to a normal level of said polynucleotide in a corresponding
normal tissue.
33. The method of either of claims 27 or 32, wherein diagNOsing comprises screening for
cancer or immune related condition in a subject, detecting a presence or a severity of
cancer or immune related condition in a subject, distinguishing cancer or immune
related condition from other diseases, providing progNOsis of cancer or immune
related condition, monitoring progression or relapse of cancer or immune related
condition in a subject, assessment of treatment efficacy or relapse of cancer or
immune related condition in a subject, selecting a therapy and a treatment for cancer
or immune related condition in a subject, optimization of a given therapy for cancer
or immune related condition in a subject, monitoring the treatment of cancer or
immune related condition in a subject, predicting the suitability of a therapy for
specific patients or subpopμlations, determining the appropriate dosing of a
therapeutic product in patients or subpopμlations.
34. The method of either of claims 27 or 32, wherein the cancer is selected from the group
consisting of non-HodgKin's Lymphoma, HodgKin's Lymphoma, anti CD20 (i.e.
Rituximab) resistant lymphoma, Mμltiμle Myeloma, Kidney cancer and pancreatic
cancer.
35. The method of either of claims 27 or 32, wherein the immune related condition is SLE
(systemic lupus erythematosus).
36. The method of claim 32, wherein the detection is performed using an oligonucleotide
pair capable of hybridizing to at least a portion of a nucleic acid sequence at least
85% homologous to the nucleic acid sequence set forth in any of SEQ. ID NOs: 23,
38-41, or 106.
37. The method of claim 36, wherein the detection is performed using an oligonucleotide
pair as set forth in any one of SEQ. ID NOs:104-105,
38. An isolated polynucleotide, comprising an amμlicon having a nucleic acid sequence
set forth in SEQ ID NO: 106, or fragments thereof, or polynucleotides homologous
thereto.
39. A primer pair, comprising a pair of isolated oligonucleotides capable of amμlifying the
nucleic acid sequence as set forth in at least one of SEQ ID NOs:23, 38-41, or 106 or
fragments thereof, or polynucleotides homologous thereto.
40. A primer pair, according to claim 39, comprising a pair of isolated oligonucleotides
having a sequence selected from the group consisting of SEQ. ID NOs: 104-105.
41. An isolated polypeptide of TMEM154 ectodomain, or fragment or variant thereof that
possesses at least 95% sequence identity therewith.
42. A polypeptide according to claim 41, comprising an amino acid sequence having at
least 95% sequence identity with a sequence selected from the group consisting of
amino acid residues 23-75 of the sequences W38346_P3 (SEQ ID NO:42), or
W38346_P7 (SEQ ID NO:46), corresponding to amino acid sequence depicted in
SEQ ID NO:63, or amino acid residues 20-105 of the sequence W38346_P4 (SEQ ID
NO:45), corresponding to the amino acid sequence depicted in SEQ ID NO:64, or
fragment thereof, having at least 95% sequence identity with the amino acid
sequence set forth in any one of SEQ ID NOs: 63, 64,161,162,191, or 192.
43. A polypeptide according to either of claims 41 or 42, which is fused to a non-
TMEM154 protein sequence, or attached to a detectable or therapeutic moiety.
44. A fused protein according to claim 43 wherein the non-TMEM154 protein is at least a
portion of an immunogloulin molecμle.
45. A nucleic acid sequence encoding a TMEM154 ectodomain polypeptide according to
any of claims 41, 42, 43 or 44.
46. The nucleic acid sequence according to claim 45, having a sequence as set forth in
SEQ ID NO:23, or fragment or variant thereof that possesses at least 95% sequence
identity therewith.
47. An expression vector containing a nucleic acid sequence according to either claims 45
or 46.
48. A host cell comprising an expression vector of claim 47.
49. A method of producing a TMEM154 ectodomain polypeptide, or fragment or
conjugate thereof, comprising cμlturing the host cell according to claim 48, under
conditions whereby the cell expresses the polypeptide encoded by the DNA segment
or nucleic acid and recovering said polypeptide.
50. A pharmaceutical composition comprising at least one polypeptide according to any of
claims 41, 42, 43, or 44, and further comprising a pharmaceutically acceptable
diluent or carrier.
51. A method for treating or preventing cancer or immune related condition, comprising
administering to a subject in need thereof a pharmaceutical composition according to
claim 50.
52. The method of claim 51, wherein the cancer is selected from the group consisting of
non-HodgKin's Lymphoma, HodgKin's Lymphoma, anti CD20 (i.e. Rituximab)
resistant lymphoma, Mμltiμle Myeloma, Kidney cancer, and pancreatic cancer.
53. The method of claim 51, wherein the immune related condition is systemic lupus
erythematosus (SLE).
54. An siRNA, antisense RNA, or ribozyme that binds the transcript encoding any one of
the TMEM154 polypeptides, and inhibits its expression.
55. The pharmaceutical composition according to either of claims 13 or 50, for use in
combination with another medicament or therapeutic method.
This invention relates to a novel target for production of immune and non-immune based
therapeutics and for disease diagNOsis. More particμlarly, the invention provides
therapeutics antibothes against KRTCAP3, FAM26F, MGC52498, FAM70A or TMEM154
antigens, which are differentially expressed in cancer, and diagNOstic and therapeutic
usages. This invention further relates to extracellular domains KRTC AP3, FAM26F,
MGC52498, FAM70A and TMEM154 proteins and variants and therapeutic usages thereof,