METHODS AND COMPOSITIONS FOR DIAGNOSIS AND TREATMENT
The application disclosure includes the concurrently filed "sequence.txt" file
that was created on October 8,2009 and has a size of 8,856 bytes.
BACKGROUND OF THE INVENTION
Multiple sclerosis ("MS") is an inflammatory autoimmune disorder of the
central nervous system (Compston and Coles, Lancet ill, 1502-17 (2008)). With a
prevalence of about one in 1000, MS is the most common cause of neurological
disability in young adults (Polman and Uitdehaag, BMJ 321, 490-4 (2000)). MS
involves engagement of the immune system, acute inflammatory injury of axons and
glia, recovery of function and structural repair, post-inflammatory gliosis, and
neurodegeneration {see, e.g., Compston and Coles, 2008). These sequential processes
underlie a clinical course characterized by episodes with recovery, episodes leaving
persistent deficits, and secondary progression. Id.
The goal of MS treatment is to reduce the frequency and severity of relapses,
prevent disability arising from disease progression, and promote tissue repair
(Compston and Coles, 2008). The primary approach to MS treatment is modulation or
suppression of the immune system. Currently available MS drugs include interferon
beta-1a (e.g., AVONEX and REBIF), interferon beta-1b (e.g., BETASERON),
glatiramer acetate (e.g., COPAXONE), mitoxantrone (e.g., NOVANTRONE), and

natalizumab (e.g., TYSABRI). Another promising new drug for MS is alemtuzumab
(CAMPATH-1H).
Alemtuzumab is a humanized monoclonal antibody directed against CD52, a
protein widely distributed on the surface of lymphocytes and monocytes but with
unknown function. Alemtuzumab has been used to treat B-cell chronic lymphocytic
leukaemia. A single pulse of treatment leads to a rapid, profound, and prolonged
lymphopenia. Cell numbers recover but at varying rates; CD4+ T cells are particularly
slow to recover, remaining depleted for at least five years (Coles et al., Journal of
Neurology 253,98-108 (2006)). A phase 2 trial (CAMMS-223 study group; Coles et
al, TV. Engl. J. Med. 359, 1786-1801 (2008)) has shown that alemtuzumab is highly
effective in treating early relapsing-remitting multiple sclerosis. This drug reduces the
risk of disease activity and accumulation of disability by over 70% compared to
interferon-beta in patients with early relapsing-remitting multiple sclerosis. The
principal adverse effect is autoimmunity, arising in the setting of T cell lymphopenia
months to years after dosing. About 20%-30% of patients develop thyroid
autoimmunity, mainly Graves' disease (Coles et al., Lancet 354, 1691-1695 (1999)),
and 3% have immune thrombocytopenia (ITP) (Coles et al., 2008). Single cases of
Goodpasture's disease, autoimmune neutropenia (Coles et al., Journal of Neurology
253, 98-108 (2006)), and autoimmune haemolytic anaemia (unpublished observation)
also have been observed. In addition, a further 5.5% of patients develop sustained
non-thyroid autoantibodies without clinical disease (Coles et al., 2006). The timing
and spectrum of autoimmunity after alemtuzumab is similar to that seen in other
examples of "reconstitution autoimmunity" in other clinical contexts; for example,
autoimmune thyroid disease and autoimmune cytopenias also predominate months to
years after hematopoietic stem cell transplantation or antiretroviral treatment of HTV
(Chen et al., Medicine (Baltimore) 84,98-106 (2005); Daikeler and Tyndall, Best.
Pract. Res. Clin. Haematol. 20, 349-360 (2007); Jubault et al., J. Clin. Endocrinol.
Metab. 85,4254-4257 (2000); Ting, Ziegler, and Vowels, Bone Marrow Transplant.
21, 841-843 (1998); Zandman-Goddard and Shoenfeld, Autoimmun. Rev. 1, 329-337
(2002)).

While autoimmunity arising in the context of lymphopenia is well recognized
in animal models, it is rarely encountered and, hence, difficult to study in humans.
Most lymphopenic subjects do not develop autoimmunity, suggesting that additional
factors are involved (Krupica et al., Clin Immunol 120, 121-128 (2006)). It remains
unclear what those additional factors are. Depletion of T regulatory cells has been
considered as one factor, as seen in the murine colitis and gastritis models (Alderuccio
et al, J Exp. Med 178,419-426 (1993); McHugh et al, J Immunol 168, 5979-5983
(2002); Powrie et al., Int. Immunol 5, 1461-1471 (1993); Sakaguchi et al, J Immunol
155, 1151-1164 (1995)). However, it has been observed that T regulatory cells are
increased after alemtuzumab in human patients and thereafter return to normal levels
(Cox et al., Eur J Immunol 35, 3332-3342 (2005)). This observation has since been
replicated (Bloom et al., Am J Transplant. 8, 793-802 (2008)) and is in keeping with
other experimental lymphopenic models (de Kleer, I. et al., Blood 107,1696-1702
(2006); Zhang, H. et al, Nat Med 11, 1238-1243 (2005)).
SUMMARY OF THE INVENTION
We have invented new and useful methods and compositions for improving
risk management in MS treatment. The methods and compositions reduce MS
treatment side effects such as secondary autoimmunity, and help health care providers
and patients in selecting regimens for MS treatment and post-treatment monitoring.
The methods and compositions of this invention are based on our discovery that in
multiple sclerosis (MS) patients, elevated EL-21, detectable even before lymphocyte
depleting therapy such as alemtuzumab therapy, correlates with increased risk of
developing secondary autoimmunity after the therapy. We have further discovered
that an individual's IL-21 level may be genetically determined: single nucleotide
polymorphisms (SNP) genotypes of A/A at SNP rs 13151961, G/G at SNP rs6822844,
and C/C at SNP rs6840978 are associated with elevated IL-21.
Accordingly, the present invention provides methods for identifying an MS
patient who has elevated interleukin-21 (IL-21) compared to IL-21 in a subject
without an autoimmune disease. In some embodiments, the methods comprise the

step of measuring IL-21 in a blood sample from the MS patient, thereby identifying an
MS patient having elevated IL-21 compared to said subject. Alternatively, the
methods comprise the step of genotyping the patient to detect the presence or absence
in the patient of one or more genotypes of single nucleotide polymorphisms (SNPs)
associated with elevated IL-21 such as those selected from the group consisting of:
A/A at SNP rsl3151961, G/G at SNP rs6822844, and C/C at SNP rs6840978,
wherein the presence of one or more of said genotypes is associated with elevated IL-
21.
The invention further provides methods for identifying an MS patient who is at
increased risk of developing a secondary autoimmune disease following lymphocyte
depletion. In some embodiments, the methods comprise the step of ascertaining (e.g.,
by measuring) the level of interleukin-21 (IL-21) in a blood sample from the MS
patient, wherein an elevated IL-21 level compared to a subject without an autoimmune
disease indicates that the patient is at increased risk of developing a secondary
autoimmune disease compared to MS patients without elevated IL-21. Alternatively,
the methods comprise the step of ascertaining (e.g., by genotyping) the presence or
absence in the patient of one or more genotypes of single nucleotide polymorphisms
(SNPs) associated with elevated IL-21 such as those selected from the group
consisting of: A/A at SNP rsl3151961, G/G at SNP rs6822844, and C/C at SNP
rs6840978, wherein the presence of one or more (e.g., two or three) of said genotypes
is associated with an increased risk of developing a secondary autoimmune disease
compared to MS patients without said one or more genotypes. These methods
optionally comprise the step of informing the patient and/or his/her health care
provider of said increased risk, and/or the step of recording the increased risk.
The invention further provides methods for selecting or identifying an MS
patient in need of heightened monitoring for development of a secondary autoimmune
disease after lymphocyte depleting therapy. These methods may comprise the step of
measuring IL-21 in a blood sample from the MS patient, wherein elevated IL-21 in
said patient compared to a subject without an autoimmune disease indicates that the
patient is in need of heightened monitoring for development of a secondary

autoimmune disease compared to MS patients without elevated IL-21. Alternatively,
the methods may comprise the step of genotyping the patient to detect the presence or
absence of one or more genotypes of SNPs associated with elevated IL-21 such as
those selected from the group consisting of: A/A at SNP rsl3151961, G/G at SNP
rs6822844, and C/C at SNP rs6840978, wherein the presence of one or more of said
SNPs indicates that the patient is in need of heightened monitoring for development of
a secondary autoimmune disease compared to MS patients without said one or more
genotypes. These methods optionally comprise the step of informing the patient
and/or his/her health care provider of the need for heightened monitoring, and/or the
step of recording the need.
The invention also provides methods for informing a treatment for an MS
patient, comprising measuring IL-21 in a blood sample from said patient or
genotyping the patient for the presence or absence of the aforementioned three SNP
phenotypes, and selecting a treatment regimen appropriate for the IL-21 measurement
or genotype.
The invention provides methods for treating MS in a patient known to be in
need thereof, comprising the steps of (a) obtaining or ascertaining information on (i)
IL-21 in a blood sample from the patient (e.g., by measuring IL-21 in the sample); or
(ii) the presence or absence of one or more genotypes of single-nucleotide
polymorphisms (SNPs) associated with elevated IL-21 such as those selected from the
group consisting of: A/A at SNP rsl3151961, G/G at SNP rs6822844 G/G, and C/C at
SNP rs6840978 (e.g., by genotyping the patient); (b) administering a therapeutic agent
for multiple sclerosis to said patient, and (c) optionally monitoring the patient for
development of a secondary autoimmune disease. In some embodiments, the methods
of treatment are used on patients who are found to have normal IL-21 levels and/or do
not have any one of the aforementioned three IL-21 SNP genotypes. Also embraced
by the invention are anti-CD52 antibodies (e.g., alemtuzumab or a biologically similar
agent), or antigen-binding portions thereof, that are used in these treatment methods,
and uses of these antibodies or antigen-binding portions in the manufacture of a

medicament for use in these treatment methods. Further embraced by the invention
are therapeutic regimens using these methods of treatment.
The invention provides methods for reducing the occurrence or severity of a
secondary autoimmune disease in a multiple sclerosis patient who has been or will be
treated with a lymphocyte depleting therapy, wherein the secondary autoimmune
disease occurs after treatment with the lymphocyte depleting therapy, comprising the
step of administering an IL-21 antagonist, e.g., prior to, during, or subsequent to the
treatment with the lymphocyte depleting therapy. Also embraced by the invention are
IL-21 antagonists for use in these methods (e.g., an anti-IL-21 or anti-IL-21 receptor
antibody, or an antigen-binding portion thereof; or a soluble IL-21 receptor), and uses
of these IL-21 antagonists in the manufacture of a medicament for use in the methods.
The invention provides methods for assessing T cell responsiveness to
treatment with a lymphocyte depleting therapy in a multiple sclerosis patient,
comprising measuring caspase-3 in T cells obtained from said patient after said
therapy, wherein an increase in caspase-3 in said T cells compared to T cells from an
MS patient not receiving said therapy is indicative of T cell responsiveness to said
therapy. The measuring may entail determining the amount or concentration of
caspase-3 or nucleic acid encoding caspase-3.
The invention provides methods for informing an MS patient of an increased
risk of developing a secondary autoimmune disease following lymphocyte depletion,
comprising the steps of obtaining or ascertaining information on interleukin-21 (IL-
21) in a blood sample from the MS patient, wherein elevated IL-21 compared to a
subject without an autoimmune disease indicates that the patient is at increased risk of
developing a secondary autoimmune disease compared to MS patients without
elevated IL-21; and informing the patient of an increased risk or lack thereof.
Alternatively, the methods comprise obtaining or ascertaining information on the
presence or absence of one or more of the aforementioned IL-21 genotypes, instead of
information on blood IL-21 level. Accordingly, the invention also provides methods
for informing an MS patient of a need, or lack of a need, for heightened monitoring for
development of a secondary autoimmune disease following lymphocyte depleting

therapy on the basis of the patient's IL-21 level or the presence or absence of the IL-
21 genotypes described above.
The invention provides methods for informing a regimen for monitoring an MS
patient following lymphocyte depleting therapy, comprising the steps of obtaining or
ascertaining information on (i) IL-21 in a blood sample from the patient; or (ii) the
presence or absence of one or more genotypes of single-nucleotide polymorphisms
(SNPs) associated with elevated IL-21 such as those selected from the group
consisting of: A/A at SNP rsl3151961, G/G at SNP rs6822844 G/G, and C/C at SNP
rs6840978; and selecting a monitoring regimen appropriate for the patient based on
the information. An appropriate monitoring regimen may include, for example,
measuring auto-antibodies in the patient.
The present invention provides advantages in risk management in MS
treatment. For example, the invention provides methods for distributing a lymphocyte
depleting drug to a patient for treating multiple sclerosis, comprising the steps of
counseling the patient on the increased risk of developing a secondary autoimmune
disease following treatment with said drug, wherein the increased risk is associated
with (i) elevated IL-21; or (ii) the presence of one or more genotypes of single-
nucleotide polymorphisms (SNPs) associated with elevated IL-21 such as those
selected from the group consisting of: A/A at SNP rsl3151961, G/G at SNP
rs6822844 G/G, and C/C at SNP rs6840978; and providing the drug to the patient after
said counseling, optionally after obtaining informed consent from the patient.
The invention further provides methods for identifying an individual who is
likely to have elevated interleukin-21 (IL-21) compared to a subject without any
known inflammatory condition, comprising the step of genotyping the individual to
detect the presence or absence of one or more genotypes of single nucleotide
polymorphisms (SNPs) associated with elevated IL-21 such as those selected from the
group consisting of: A/A at SNP rsl3151961, G/G at SNP rs6822844, and C/C at
SNP rs6840978, wherein the presence of one or more of said genotypes is associated
with elevated IL-21.

In the context of this invention, lymphocyte depletion can be induced by a
treatment that targets CD52, e.g., a treatment with an anti-CD52 antibody (e.g., a
monoclonal antibody) or an antigen-binding portion thereof. The anti-CD52 antibody
can be alemtuzumab or a biologically similar agent such as an antibody that competes
for binding to CD52 with alemtuzumab.
In the methods of this invention, IL-21 measurement may entail measuring
(e.g., detecting/quantifying) the amount or concentration of IL-21 or nucleic acid
encoding IL-21 in a sample, or the amount or concentration of mRNA encoding IL-21
in IL-21-producing cells (e.g., Thl7 cells) in the sample. In some embodiments, the
measuring is of intracellular IL-21, using, for example, cytokine staining and flow
cytometry. In some embodiments, the measuring is of serum IL-21, using, for
example, an enzyme-linked immunosorbent assay (ELISA). Also embraced by the
invention are ELISA kits for detecting IL-21 levels in a human subject, comprising an
anti-IL-21 antibody, or an antigen-binding portion thereof, or a soluble IL-21 receptor.
The kits may further include an instruction directing a user to take a blood sample
from a human subject.
In the methods of this invention, IL-21 information (including measurement or
genotyping) can be obtained prior to, during, or subsequent to MS therapy. The
methods of this invention can be used in the context of any MS form, including but
not limited to relapsing-remitting multiple sclerosis, primary progressive multiple
sclerosis, and secondary progressive multiple sclerosis.
The invention also provides kits for treating multiple sclerosis, comprising a
lymphocyte depleting therapeutic agent (e.g., an anti-CD52 antibody such as
alemtuzumab); and a written instruction for informing a patient or health care provider
of the potential for an increased risk of developing a secondary autoimmune disease
following treatment with said agent, wherein the increased risk is indicated by or
associated with (i) elevated IL-21, or (ii) the presence of one or more genotypes of
single-nucleotide polymorphisms (SNPs) associated with elevated IL-21 such as those
selected from the group consisting of: A/A at SNP rs13151961, G/G at SNP
rs6822844 G/G, and C/C at SNP rs6840978.

The invention further provides kits for identifying an MS patient who is at
increased risk of developing a secondary autoimmune disease following lymphocyte
depletion, comprising an anti-interleukin-21 (IL-21) antibody and one or more
reagents for detecting the binding of said antibody to IL-21 in a blood sample from the
MS patient. The invention also provides kits for identifying an MS patient who is at
increased risk of developing a secondary autoimmune disease following lymphocyte
depletion, comprising one or more reagents suitable for identifying the genotype of
one or more single nucleotide polymorphisms (SNPs) selected from the group
consisting of: SNP rsl3151961, SNP rs6822844, and SNP rs6840978, in a sample
obtained from an individual.
Other features and advantages of the invention will be apparent from the
following figures and detailed description.
BRIEF DESCRIPTION OF THE FIGURES
FIG. 1A is a graph showing precursor frequency (PF) of T cells from healthy
controls (HC), untreated patients (Pre) and at intervals of 3 months post-alemtuzumab,
unstimulated (Unstim), or following culture with myelin basic protein (MBP) or
thyroid stimulating hormone receptor (TSHr). (* p<0.05, ** p<0.01, *** p0.00l)
FIG. 1B is a graph showing proliferative index (PI) of T cells from healthy
controls (HC), untreated patients (Pre) and at intervals of 3 months post-alemtuzumab,
unstimulated (Unstim), or following culture with myelin basic protein (MBP) or
thyroid stimulating hormone receptor (TSHr). (* p<0.05, ** p<0.01, *** p0.00l)
FIG. 1C is a graph showing the total number of viable T cells after 10 days in
culture from healthy controls (HC), untreated patients (Pre) and at intervals of 3
months post-alemtuzumab, unstimulated (Unstim), or following culture with myelin
basic protein (MBP) or thyroid stimulating hormone receptor (TSHr). (* p<0.05, **
p<0.01,*** p0.00l)
FIG. 1D is a graph showing percentage of T cells apoptosing in response to no
stimuli or following culture with MBP or TSHr in culture from healthy controls (HC),

untreated patients (Pre) and at intervals of 3 months post-alemtuzumab. (* p<0.05, **
p<0.01,***p<0.001)
FIG. 1E is plots and a graph showing passive T cell apoptosis from healthy
controls and patients before and after alemtuzumab at intervals of 3 months. (*
p<0.05, ** p<0.01, *** pO.OOl)
FIG. 1F is plots and a graph showing Fas-mediated T cell apoptosis from
healthy controls and patients before and after alemtuzumab at intervals of 3 months.
(* p<0.05, ** p<0.01, *** p0.00l)
FIG. 1G is a graph showing passive CD4+ and CD8+ T cell apoptosis from
healthy controls, pre-treatment patients and at 9 months post-alemtuzumab. (*
p0.05, ** p0.0l, *** p<0.001)
FIG. 1H is a graph showing Fas-mediated CD4+ and CD8+ T cell apoptosis
from healthy controls, pretreatment patients and at 9 months post-alemtuzumab. (*
p<0.05, ** pO.OL, *** p<0.001)
FIGS. 2A-2C are graphs showing caspase 3 mRNA expression relative to beta-
actin mRNA expression in (A) CD3+ T cells, (B) CD14+ monocytes, and (C) CD19+
B cells, respectively, either immediately ex-vivo or following stimulation with MBP or
polyclonal stimulation (anti-CD3/28 antibodies). (* p<0.05, ** p<0.01, *** p0.00l)
FIG. 3 is plots and a graph showing that autoimmunity after alemtuzumab is
associated with excessive T cell apoptosis. Percentage T cell apoptosis that is passive
(Un), Fas-mediated, or in response to MBP or TSHr stimulation in those without
autoimmunity (Ge et al., Proceedings of the National Academy of Sciences of the
United States of America 101, 3041-3046 (2004)) or those with secondary
autoimmunity (Ge et al., 2004) is shown in separate plots. (* p<0.05, ** p<0.01, ***
p0.00l)
FIGS. 4A and 4B are plots and graphs showing that rhIL-21 induces T cell
apoptosis in vitro. They show that (A) CD4+ T cells and (B) CD8+ T cells,
respectively, unstimulated or polyclonally stimulated (anti-CD3/CD28), apoptose in
response to rhIL-21 in a dose-dependent manner. (* p<0.05, ** p<0.01, *** p0.00l)

FIGS. 5A-5D are graphs showing that rhIL-21 induces T cell proliferation in
vitro. FIG. 5A is a graph showing the proliferative index of unstimulated CD4+ and
CD8+T cells in response to rhIL-21. FIG. 5B is a graph showing the proliferative
index of polyclonally stimulated (anti-CD3/CD28) CD4+ and CD8+ T cells in
response to rhIL-21. FIG. 5C is a graph showing precursor frequency of unstimulated
CD4+ and CD8+ T cells in response to rhIL-21. FIG. 5D is a graph showing
precursor frequency of polyclonally stimulated CD4+ and CD8+ T cells in response to
rhIL-21. (* p<0.05, ** p0.0l, *** p<0.001)
FIG. 5E is plots showing the number of unstimulated or polyclonally
stimulated (anti-CD3/CD28) CD4+ or CD8+ cells in different channels in the absence
of, or in response to, rhIL-21.
FIG. 6A is a graph showing serum IL-21 prior to and after alemtuzumab
treatment in 15 patients with, and 15 patients without, secondary autoimmunity. (*
p<0.05, ** p0.0l, *** p<0.001)
FIG. 6B is a graph showing pre-trearment serum IL-21 levels (pg/ml) in the
non-autoimmune patients (those who had no post-alemtuzumab autoimmunity) and the
autoimmune patients (those who had post-alemtuzumab autoimmunity).
DETAILED DESCRIPTION
This invention is based on our discovery that the occurrence of secondary
autoimmunity in an MS patient following lymphocyte depleting therapy (e.g., after
treatment with alemtuzumab) is associated with elevated IL-21 in the patient We
have discovered that IL-21 is elevated compared to the norm (see discussions below)
even before the therapy in MS patients who later develop post-therapy secondary
autoimmunity. We also have discovered that after lymphocyte depleting therapy, IL-
21 is elevated even more dramatically in those same patients, as compared to MS
patients with no signs of secondary autoimmunity, whose IL-21 is elevated to a much
smaller extent. Thus, IL-21 levels are predictive of the occurrence of secondary
autoimmunity after lymphocyte depleting therapy in an MS patient. We also have
discovered that single nucleotide polymorphism (SNP) genotypes of A/A at SNP

rsl3151961, G/G at SNP rs6822844, and C/C at SNP rs6840978 are associated with
elevated EL-21 in an individual; thus genotyping an MS patient for the presence or
absence of these specific SNP genotypes also helps predict the risk for developing
secondary autoimmunity in the patient following lymphocyte depletion.
We first described autoimmunity complicating alemtuzumab (CAMPATH-1H)
treatment in 1999 (Coles et al., 1999), and have continued to observe this
complication of, what is increasingly recognized as, a highly effective therapy for
early relapsing-remitting multiple sclerosis (Coles et al., J Neurology 253,98-108
(2006); Coles et al., 1999 and 2008). Our studies described below involved a series of
cohorts of available patients and were aimed at understanding this unprecedented
"model" of human autoimmunity occurring in a subset of MS patients treated by
alemtuzumab.
The immune state is radically altered following exposure to alemtuzumab. T
cells regenerating into the lymphopenic environment generated by alemtuzumab are
highly proliferative and skewed towards auto-reactivity. However, these cells are
highly unstable and short-lived. Whilst their fate has not previously been directly
addressed (King et al., Cell 117,265-277 (2004)), we show that these cells are dying
rapidly by apoptosis. High and sustained levels of T cell apoptosis may explain why a
single dose of alemtuzumab induces T cell lymphopenia lasting several years even
though the half-life of circulating alemtuzumab is only six days and hematological
precursors are not depleted (Gilleece et al., Blood82, 807-812 (1993)).
Against that background, we show that patients with secondary autoimmunity
have higher rates of T cell apoptosis, but no greater T cell lymphopenia, than those
without autoimmunity, suggesting increased cell cycling in this group. These
perturbations of T cell cycling are associated with significantly higher serum IL-21
expression, which we have found is genetically determined in at least some cases.
Furthermore, susceptibility to lymphopenia-associated autoimmunity is manifest
before lymphocyte depletion, with pre-treatment IL-21 levels predicting with accuracy
(positive predictive value of more than 70%, e.g., 83%, and negative predictive value
of more than 62%, e.g., 72%) the development of autoimmunity months to years after

exposure to alemtuzumab. Without wishing to be bound by any theory, we believe
that by driving cycles of T cell expansion and death to excess, IL-21 increases the
stochastic opportunities for T cells to encounter self-antigen and break tolerance,
hence promoting autoimmunity.
In summary, our findings provide the first exploration of lymphopenia-induced
autoimmunity in man, and provide a conceptual framework for understanding
lymphopenia-associated autoimmunity that goes beyond the narrow context of treating
multiple sclerosis with alemtuzumab. The concept is that first therapeutic lymphocyte
depletion, and secondly genetically restricted overproduction of IL-21, leads to a state
of excess T cell cycling and reduced survival, which promotes autoimmunity in
humans. These findings provide bases for the present invention.
This invention provides methods for managing MS patients when considering
lymphocyte depleting therapy such as alemtuzumab therapy. For example, our
invention provides methods for identifying an MS patient who has elevated IL-21
compared to the norm (i.e., levels of IL-21 in control subjects) as described below),
and methods for identifying an MS patient who is at increased risk of developing
secondary autoimmunity following lymphocyte depletion. These methods comprise
the step of measuring IL-21 (e.g., intracellular or extracellular protein levels, RNA
transcript levels, or IL-21 activity levels; see discussions below) in a blood sample
from the patient, and comparing the IL-21 value to the normal IL-21 value.
Alternatively, in lieu of or in addition to the blood test, one can genotype the patient
for the presence or absence of one or more of SNP genotypes of A/A at SNP
rsl3151961, G/G at SNP rs6822844, and C/C at SNP rs6840978, where the presence
of one, two or all three of these genotypes is associated with elevated IL-21. As
discussed above, elevated IL-21 is associated with increased risk of developing
secondary autoimmunity in the MS patient following lymphocyte depletion, as
compared to MS patients who do not have elevated IL-21.
Identification of a patient by the methods of the invention may be followed by
a number of further steps contemplated by the invention. For example, the patient can
be informed of the increased risk of developing secondary autoimmunity following

lymphocyte depleting therapy, or lack of such risk, based on his/her IL-21 level or
genotype. Thus, the invention will allow individualized counseling of the risks of the
therapy before commitment to the therapy. The health care provider can consider
therapeutic options in view of the risk of secondary autoimmunity and provide a
recommendation, including, for example, administering an IL-21 antagonist prior to,
during, or after lymphocyte depleting therapy, or selecting a treatment regimen that
does not involve lymphocyte depletion.
The health care provider also can consider risk management plans for a patient
who elects to undergo lymphocyte depleting therapy. For example, the health care
provider can inform the patient of a need for heightened monitoring for development
of secondary autoimmunity after lymphocyte depleting therapy in view of his/her
increased risk of developing secondary autoimmunity. The health care provider also
can recommend an appropriate monitoring regimen following lymphocyte depleting
therapy. An appropriate monitoring regimen for patients at risk may include, without
limitation, more frequent monitoring for secondary autoimmunity after lymphocyte
depleting therapy at an interval of, for example, one week, two weeks, one month, two
months, three months, six months, or one year. The monitoring may need to be
continued for an extended period of time, for example, more than one year, two years,
three years, four years, five years, or more, because some patients may not present
with secondary autoimmunity until well after one year following lymphocyte
depletion therapy. Heightened monitoring also may entail, for example, more
thorough medical examination (e.g., more blood tests) by a specialist for any signs of
secondary autoimmunity. Moreover, pharmacists or clinical staff who distribute a
lymphocyte depleting drug to a patient for treating MS may be required to counsel the
patient on the increased risk of developing secondary autoimmunity following the
drug use, in the event that the patient has an elevated level of IL-21 and/or has the
particular IL-21 genotypes described herein that have been associated with elevated
serum IL-21. The pharmacists or clinical staff may also be required to obtain
informed consent from the patient prior to distributing the drug to the patient.

Multiple Sclerosis Patients
The methods and compositions of this invention can be used in the context of
any form of MS, for example, relapsing-remitting MS, primary progressive MS, and
secondary progressive MS. MS patients in the context of this invention are those who
have been diagnosed as having a form of MS by, for example, the history of symptoms
and neurological examination with the help of tests such as magnetic resonance
imaging (MRI), spinal taps, evoked potential tests, and laboratory analysis of blood
samples.
Multiple sclerosis ("MS"), also known as disseminated sclerosis, is an
autoimmune condition in which the immune system attacks the central nervous
system, leading to demyelination (Compston and Coles, 2008). MS destroys a fatty
layer called the myelin sheath that wraps around and electrically insulates nerve fibers.
Almost any neurological symptom can appear with the disease, and often progresses to
physical and cognitive disability (Compston and Coles, 2008). MS takes several
forms. New symptoms can occur in discrete attacks (relapsing forms), or slowly
accumulate over time (progressive forms) (Lublin et al., Neurology 46 (4), 907-11
(1996)). Between attacks, symptoms may go away completely (remission), but
permanent neurological problems often occur, especially as the disease advances
(Lublin et al., 1996). Several subtypes, or patterns of progression, have been
described, and they are important for prognosis as well as therapeutic decisions. In
1996 the United States National Multiple Sclerosis Society standardized four subtype
definitions: relapsing-remitting, secondary progressive, primary progressive, and
progressive relapsing (Lublin et al., 1996).
The relapsing-remitting subtype is characterized by unpredictable acute
attacks, called exacerbations or relapses, followed by periods of months to years of
relative quiet (remission) with no new signs of disease activity. This describes the
initial course of most individuals with MS (Lublin et al., 1996).
Secondary progressive MS begins with a relapsing-remitting course, but
subsequently evolves into progressive neurologic decline between acute attacks

without any definite periods of remission, even though occasional relapses and minor
remissions may appear (Lublin et al., 1996).
The primary progressive subtype is characterized by a gradual but steady
progression of disability with no obvious remission after their initial MS symptoms
appear (Miller et al., Lancet Neurol 6(10), 903-12 (2007)). It is characterized by
progression of disability from onset, with no, or only occasional and minor, remissions
and improvements (Lublin et al., 1996). The age of onset for the primary progressive
subtype is usually later man other subtypes (Miller et al., 2007)).
Progressive relapsing MS is characterized by a steady neurological decline
with acute attacks that may or may not be followed by some recovery. This is the
least common of all the subtypes described hereinabove (Lublin et al., 1996).
Cases with non-standard behavior have also been described, sometimes
referred to as borderline forms of MS (Fontaine, Rev. Neurol (Paris) 157 (8-9 Pt 2):
929-34 (2001)). These forms include Devic's disease, Balo concentric sclerosis,
Schilder's diffuse sclerosis, and Marburg multiple sclerosis (Capello et al, Neurol.
Sci. 25 Suppl 4: S361 3 (2004); Hainfellner et al., J. Neurol. Neurosurg. Psychiatr.
55(12): 1194-6(1992)).
Lymphocyte Depletion in Multiple Sclerosis Patients
As used herein, "lymphocyte depletion" is a type of immunosuppression by
reduction of circulating lymphocytes, e.g., T cells and/or B cells, resulting in
lymphopenia. Prolonged lymphocyte depletion is seen when, for example, autologous
bone marrow transplantation (BMT) or total lymphoid irradiation is used to treat
multiple sclerosis. See, e.g., Cox et al., Eur. J. Immunol. 35, 3332-3342 (2005). For
example, lymphocyte depletion can be achieved by a combined use of thymoglobulin,
cyclophosphamide and whole body irradiation. Lymphocyte depletion in MS patients
also can be achieved by a number of drug treatments. For example, a humanized anti-
CD52 monoclonal antibody, CAMPATH-1H (alemtuzumab), has been used in
lymphocyte depleting therapy to treat MS patients. CAMPATH-lH-induced
lymphopenia has been shown to effectively reduce central nervous system

inflammation both clinically and radiologically (Coles et al., Ann. Neurol. 46,296
304 (1999); Coles et al., 2008).
Other agents can also be used in lymphocyte depleting therapy to treat MS
patients. These agents can be those that cause lymphocyte cell death or inhibit
lymphocyte functions. They include, without limitation, (1) agents targeting CD-52-
bearing cells, such as agents biologically similar to alemtuzumab, i.e., other anti-CD52
antibodies (e.g., chimeric, humanized, or human antibodies) that bind to the same or a
different epitope as alemtuzumab or compete with alemtuzumab for binding to CD52,
and soluble CD52 polypeptides that compete with cell surface CD52 for binding to
ligand(s) of CD52; (2) biomolecules such as peptides, proteins, and antibodies (e.g.,
chimeric, humanized, or human antibodies) that target cell-surface molecules on
lymphocytes, such as anti-CD4 antibodies, anti-CD20 antibodies (e.g., rituximab),
anti-TCR antibodies, and anti-integrin antibodies (e.g., natalizumab); (3) cytotoxins
(e.g., apoptosis-inducing agents, cyclophosamide, alkylating agents, and DNA
intercalators) delivered specifically or nonspecifically to lymphocytes; and (4)
antigen-binding portions of the aforementioned antibodies. The antibodies may
include, without limitation, monoclonal antibodies, bifunctional antibodies,
oligoclonal antibodies, and polyclonal antibodies.
The term "antigen-binding portion" as used herein refers to one or more
fragments of an antibody that retain the ability to specifically bind to the same antigen
as the whole antibody from which the portion is derived. Examples of "antigen-
binding portion" include, without limitation, a Fab fragment, a F(ab')2 fragment, a Fd
fragment, a Fv fragment, a dAb fragment, an isolated complementarity determining
region (CDR), scFv, and a diabody. The antibodies and antigen-binding portions
thereof useful in this invention can be made by any methods well known in the art.
Any of the above lymphocyte depleting therapies can cause lymphopenia, and
in some patients, the lymphopenia leads to secondary autoimmunity.
Secondary Autoimmunity in MS Patients
Autoimmunity is referred to herein as "secondary autoimmunity" when it
arises subsequent to the onset of a first ("primary") disease, for example, a "primary"

autoimmune disease. Secondary autoimmunity sometimes arises in MS patients
having, or having had, lymphopenia following, e.g., lymphocyte depleting therapy. In
some individuals, secondary autoimmunity arises soon after lymphocyte depleting
therapy (e.g., treatment with alemtuzumab). In other individuals, secondary
autoimmunity may not arise until months or years after lymphocyte depleting therapy;
in some of those individuals, by the time they develop secondary immunity,
substantial lymphocyte recovery (total lymphocyte count) may have occurred so that
they may no longer be lymphopenic.
Secondary autoimmunity arising in lymphopenic MS patients can be any type
of autoimmune condition other than MS, including but not limited to thyroid
autoimmunity (e.g., Graves' disease), immune thrombocytopenia (ITP),
Goodpasture's disease, autoimmune neutropenia, autoimmune hemolytic anemia, and
autoimmune lymphopenia. Techniques for diagnosing and monitoring these
autoimmune diseases are well known to those skilled in the art, including assessment
of symptoms and medical examination such as blood analysis. The invention
contemplates the use of any known methods. For example, autoantibody levels in a
patient's body fluid (e.g., blood) can be determined as a means of detecting signs of
autoimmunity. Specifically, anti-nuclear antibodies, anti-smooth muscle antibodies,
and anti-mitochrondrial antibodies can be measured. In the event anti-nuclear
antibodies are detected, additional assays can be performed to measure anti-double-
stranded DNA antibodies, anti-ribonucleoprotein antibodies, and anti-La antibodies.
Anti-thyroid peroxidase (TPO) and anti-thyroid stimulating hormone (TSH) receptor
antibodies can be measured to detect autoimmune thyroid diseases; if anti-TPO or
anti-TSH receptor antibodies are detected, one can measure whether thyroid function
is affected by measuring free T3, free T4 and TSH levels. Anti-platelet antibodies can
be measured to detect autoimmune thrombocytopenia; and a measurement of blood
platelet levels may serve to determine if the presence of anti-platelet antibodies is
causing a reduction in platelet number.

Measurement of IL-21
In the methods of this invention, EL-21 can be measured by a number of
techniques. IL-21 is a member of the gamma-c-related cytokine family, and has
potent activity in promoting T and B cell proliferation and natural killer (NK) cell
cytotoxicity. IL-21 is mainly expressed by activated CD4+ T cells (e.g., Thl7 cells)
and is important in T helper type I (Thl) immune responses (Weiss et al., Expert Opin
Biol. Ther. 7, 1705-1721 (2007); Sivakumar et al, Immunology 112, 177-182 (2004)).
The human IL-21 gene encodes a polypeptide precursor of 162 amino acid residues
and a fully processed mature protein of 133 amino acid residues (about 15 kD); the
gene is located on human chromosome 4q26-27 (Sivakumar et al., 2004). The
receptor for IL-21 (IL-21 R) has been found on resting peripheral B cells, activated
peripheral blood mononuclear cells, and in germinal center of human lymph nodes
(Marleau et al., J. Leukocyte Biol. 78, 575-584 (2005)).
Methods of measuring IL-21 are well known to those skilled in the art.
According to some embodiments of the present invention, a body fluid sample (e.g.,
blood, serum, plasma, urine, saliva, or cerebrospinal fluid) is obtained from a patient,
and the IL-21 level in die sample is measured, by any assay suitable for protein
detection, including but not limited to, immunoassays such as enzyme-linked
immunosorbent assays (ELISA). Commercial ELISA kits for measuring human IL-21
are available from, for example, KOMABIOTECH (Seoul, Korea), Bender
MedSystems (Burlingame, CA), and eBioscience (San Diego, CA).
Alternatively, IL-21 transcript levels in IL-21 producing cells (e.g., Th17 cells)
obtained from the patient can be measured by Northern blot analysis and quantitative
polymerase chain reaction (Q-PCR). Methods of isolating Thl 7 cells are well known
in the art, and isolation can be done by using commercially available kits, e.g., kits
from Miltenyi Biotec (Auburn, CA), eBioscience (San Diego, CA). In some
embodiments, IL-21 levels are measured by cytokine staining and flow cytometry in
which an anti-IL-21 antibody linked to a detectable moiety is used to detect the
intracellular level of IL-21 in IL-21 producing cells from the patient. IL-21 also can
be measured in terms of activity in a biological assay, e.g., by measuring proliferative

responses of T cells to a combination of IL-21 and IL-15 using, e.g., CFSE
(carboxyfluorescein succinimidyl ester) (Zeng et al., Curr. Protoc. Immunol.
78:6.30.1-6.30.8 (2007)). Another method of measuring IL-21 is based on IL-21-
induced tyrosine phosphorylation of Stat3 in splenic CD8(+) T cells using a flow
cytometry-based analysis (Zeng et al., 2007). Those of skill in the art will readily
appreciate other suitable means for measuring IL-21.
In the methods of this invention, the reference (or index) value for determining
whether a patient has elevated (abnormally high) IL-21 is the value of IL-21 of a
control subject, or the mean value of IL-21 of a group of control subjects, obtained
using the same assay that is conducted at the same or a different time. The control
subject is a normal or healthy subject, who, in this context, is an individual without
any ongoing known inflammatory condition, including without an autoimmune
disease (without any detectable symptoms of an autoimmune disease). In some
embodiments, the control subjects are not lymphopenic. An increase of IL-21 level by
about 10%, 20%, 30%, 40%, 50%, 100%, two-fold, three-fold, four-fold, five-fold,
ten-fold, twenty-fold, thirty-fold, forty-fold, fifty-fold, one hundred-fold or more may
be considered a significant increase. Certain statistical analyses can be applied to
determine if the IL-21 level in a test sample is significantly different from the control
level. Such statistical analyses are well known to those skilled in the art and may
include, without limitation, parametric (e.g., two-tailed Student's t-test) or non-
parametric (e.g., Wilcoxon-Mann-Whitney U test) tests.
Detecting IL-21 SNP Genotypes
In some methods of this invention, genotyping is used to predict whether a
patient is prone to having (i.e., at risk of having or likely to have) elevated IL-21 and
hence at risk of developing secondary autoimmunity while having lymphopenia.
"Genotyping" refers to the process of determining the genotype of an individual by the
use of biological assays. Methods of genotyping are well known to those skilled in the
art, and include, without limitation, PCR, DNA sequencing, allele-specific oligo
(ASO) probes, and hybridization to DNA microarrays or beads. Genotyping can be
partial, i.e., only a small fraction of an individual's genotype is determined. In the

context of this invention, only certain SNPs need to be detected. A SNP is a DNA
sequence variation occurring when a single nucleotide A, T, C, or G - in a
corresponding portion of the genome differs between members of a species or between
paired chromosomes in an individual. Known human SNPs are assigned reference
SNP (refSNP or rs) identification numbers in the public-domain archive Single
Nucleotide Polymorphism Database (dbSNP) hosted at the National Center for
Biotechnology Information (NCBI).
The present inventors have discovered that the minor SNP genotypes of
rs 13151961 A/A, rs6822844 G/G and rs6840978 C/C are associated with significantly
higher levels of serum IL-21 compared to individuals who do not have these
genotypes. MS patients having one or more of these SNP phenotypes, thus, have an
increased susceptibility to developing secondary autoimmunity after lymphocyte
depletion, compared to MS patients who do not have these genotypes.
Timing of Obtaining IL-21 Information
Obtaining information on IL-21 (IL-21 levels or IL-21-related SNP genotypes)
of an MS patient is useful in selecting treatment and post-treatment monitoring
regimens for the patient. When the information is obtained prior to MS therapy, the
patient can be informed of the relative risk of developing secondary autoimmunity
following lymphocyte depleting therapy and treatment decisions can be made
accordingly. The patient also can be informed of a need for heightened post-treatment
monitoring, e.g., more frequent and more thorough examination by a specialist, if he is
classified as "at risk." Thus, the IL-21 information improves risk management (by
physicians, pharmacists, and patients) in MS treatment.
Obtaining IL-21 information during or after MS treatment also will be helpful
in monitoring secondary autoimmunity development and treatment As noted above
and further described below, we have discovered that following lymphocyte depleting
therapy, MS patients who go on to develop secondary autoimmunity have a much
larger increase in their serum IL-21, as compared to MS patients who do not develop
secondary autoimmunity. The latter group of MS patients produce only slightly more
IL-21 following lymphocyte depletion. Thus, by measuring IL-21 production after

lymphocyte depleting treatment, one also can predict the risk of secondary
autoimmunity, which may not occur until months or years after the treatment.
Treating Secondary Autoimmunity
A secondary autoimmunity disease arising in MS patients can he treated based
on the type of the disease. In some embodiments of the present invention, the
secondary autoimmunity can be treated by using an effective dose of an IL-21
antagonist. An IL-21 antagonist can be a therapeutic agent that inhibits IL-21 activity,
e.g., an agent that inhibits the interaction between IL-21 and IL-21R. "An effective
dose" refers to the amount of an inhibiting agent sufficient to inhibit IL-21 activity in a
patient such that symptoms of the secondary autoimmune disease are alleviated or
prevented. IL-21 antagonists can be, for example, chimeric, humanized, or human
monoclonal antibodies to human IL-21 or IL-21 R, or soluble IL-21 R proteins. See
also, e.g., U.S. Patent No. 7,410,780 and U.S. Patent Application Publication No.
20080241098, the entire teachings of which are incorporated herein by reference.
Pharmaceutical compositions containing an IL-21 antagonist can be made according to
methods known to those in the art. Pharmaceutical compositions containing IL-21
antagonists can be administered to a patient using a suitable method known in the art,
e.g., intravenously, intramuscularly, or subcutaneously.
Kits for Treating and Testing MS Patients
The present invention provides kits for treating multiple sclerosis. A kit of this
invention can contain, inter alia, a lymphocyte depleting drug (e.g., alemtuzumab),
and a written instruction for informing a patient or a healthy care provider of
contraindications of the drug, for example, the potential for an increased risk of
developing a secondary autoimmune disease following treatment with the drug. The
increased risk can be associated with or indicated by (i) elevated IL-21, or (ii) the
presence of one or more genotypes of single-nucleotide polymorphisms (SNPs)
selected from the group consisting of: A/A at SNP rsl3151961, G/G at SNP
rs6822844, and CIC at SNP rs6840978.
In other embodiments, the invention provides kits for detecting serum IL-21 in
an MS patient, and/or for identifying MS patients at increased risk of developing a

secondary autoimmune disease following lymphocyte depletion. Such kits can
comprise an anti-EL-21 antibody, or an antigen-binding portion thereof, or a soluble
IL-21 receptor, and optionally an instruction directing a user to take a blood sample
from a patient, and optionally one or more reagents for detecting the binding of the
antibody, portion, or soluble IL-21 receptor to IL-21 in the blood sample from the MS
patient. Such kits will have been validated or approved by an appropriate regulatory
authority for making medical diagnosis in patients, such as MS patients.
In still other embodiments, the invention provides kits for identifying an MS
patient who is at increased risk of developing a secondary autoimmune disease
following lymphocyte depletion. The kits can comprise one or more reagents suitable
for identifying the presence or absence of one or more SNP genotypes selected from
the group consisting of: SNP rsl3151961, SNP rs6822844, and SNP rs6840978, in a
sample obtained from an MS patient, and an instruction directing a user to take a
sample from an MS patient.
Assessing T Cell Responsiveness to MS Treatment
This invention provides methods for assessing T cell responsiveness to
treatment with lymphocyte depleting therapy in an MS patient. The methods entail
measuring caspase-3 in T cells obtained from the patient after the treatment. An
increase in caspase-3 (e.g., caspase-3 protein, RNA transcript, and/or activity levels)
in the T cells compared to T cells from an MS patient not receiving the treatment
indicates that the T cells in the treated patient have responded to the treatment. These
methods are based on our discovery that T cells from people with untreated MS are
apoptosis-resistant, and that this resistance is associated with under-expression of
caspase-3. But after lymphocyte depleting therapy, caspase-3 expression is
significantly increased in T cells, reaching levels seen in healthy people.
Techniques of measuring caspase-3 in T cells are well known in the art. For
example, one can obtain cell extracts from T cells using techniques well known in the
art, and measure caspase-3 protein levels by, e.g., ELISA. Commercial ELISA kits for
measuring human caspase-3 are available from, e.g., Bender MedSystems
(Burlingame, CA), EMD Chemicals, Inc. (San Diego, CA), and R&D Systems, Inc.

(Minneapolis, MN). Alternatively, caspase-3 transcript levels can be measured in T
cells by, for example, Northern blot analysis or quantitative PCR. Caspase-3 can also
be measured in terms of activity in a biological assay, e.g., by measuring its protease
activity. Commercial kits for measuring caspase-3 activity are available from, e.g.,
Roche Applied Science (Indianapolis, IN), and Invitrogen (Carlsbad, CA).
Unless otherwise defined, all technical and scientific terms used herein have
the same meaning as commonly understood by one of ordinary skill in the art to which
this invention belongs. Exemplary methods and materials are described below,
although methods and materials similar or equivalent to those described herein can
also be used in the practice or testing of the present invention. All publications and
other references mentioned herein are incorporated by reference in their entirety. In
case of conflict, the present specification, including definitions, will control. Although
a number of documents are cited herein, this citation does not constitute an admission
that any of these documents forms part of the common general knowledge in the art.
Throughout this specification and embodiments, the word "comprise," or variations
such as "comprises" or "comprising" will be understood to imply the inclusion of a
stated integer or group of integers but not the exclusion of any other integer or group
of integers. The materials, methods, and examples are illustrative only and not
intended to be limiting.
The following examples are meant to illustrate the methods and materials of
the present invention. Suitable modifications and adaptations of the described
conditions and parameters normally encountered in the art which are obvious to those
skilled in the art are within the spirit and scope of the present invention.
EXAMPLES
In the following examples, all patients had relapsing-remitting multiple
sclerosis and were participants in one of two clinical trials: CAMMS-223 and
CAMMS-224 (REC 02/315 and 03/078) in which alemtuzumab was given by
intravenous infusion of 12-24 mg/day for five days, followed by re-treatment at 12
months. Patients and controls consented to venesection for research purposes (LREC

02/263) and all were free from exposure to other disease modifying agents, including
steroids, for at least one month at the time of blood sampling.
Lymphocyte proliferation and apoptosis data were generated by a cross-
sectional study of fresh, ex vivo cells from 65 patients and 21 healthy controls (7
males, mean age 34 years). This generated hypotheses about T-cell cycling in the
pathogenesis of secondary autoimmunity, which were tested on samples available at
nine months after alemtuzumab treatment, which was chosen as the earliest time point
in which T cell apoptosis could be robustly analyzed. Of the 29 samples available at
this time point, 10 met our study definition of autoimmunity (1 male, mean age 36
years) compared to 10 without autoimmunity (3 male, mean age 38 years).
Autoimmunity was defined as development of a novel autoimmune disease (with or
without autoantibodies), or persistent significant titers of autoantibodies (present on at
least two occasions at least three months apart) without clinical disease. "No
autoimmunity" was defined as the absence of an autoimmune disease and
autoantibodies for at least 18 months post-alemtuzumab in this study. Of the ten
patients with autoimmunity, three had autoantibodies only (antinuclear antibodies).
Next, serum EL-21 was measured serially in: 15 randomly selected patients with
autoimmunity five of whom had been studied as above (three males, mean age 34
years; twelve with thyroid autoimmunity, one with Goodpasture's disease, one with
ITP, and one with antinuclear antibodies only), and fifteen randomly selected patients
without autoimmunity - six of whom had been studied as above, (five males, mean
age 31 years) and nineteen healthy controls (seven male, mean age 33 years).
73 subjects were studied for genetic analysis. Of these, 23 met the definition
of "no autoimmunity" and 27 had secondary autoimmunity after alemtuzumab (six
with autoantibodies only: four with antinuclear and two with anti-smooth muscle
antibodies; eighteen with thyroid autoimmunity, two with ITP and one with
Goodpasture's disease). The 23 remaining subjects could not be categorised on the
basis of transient autoantibody production and/or insufficient time since treatment
with alemtuzumab.

For all the statistical analysis described in the following examples, data were
analyzed using SPSS 12.0.1 for Windows. Following assessment for normality,
parametric (Student's t-test) or non-parametric (Wilcoxon-Mann-Whitney) tests were
performed. P values are stated throughout the text, where a value of p<0.05 was
considered as statistically significant, modified by a Bonferroni correction where
indicated.
Example 1: Alemtuzumab induces a T cell lymphopenia.
A single dose of alemtuzumab resulted in the depletion of CD4+ and CD8+ T
lymphocytes to 5.6% and 6.8% respectively of baseline values at month 1, and 30.3%
and 40.8% respectively at month 12 (data not shown).
Example 2: T cells from patients with untreated multiple sclerosis are resistant to
cell death
For various assays performed in this Example, different cross-sectional and
longitudinal samples were used according to availability. As a prelude to measuring
lymphocyte cell cycling after alemtuzumab, we examined the proliferative response of
T cells, unstimulated or in culture with myelin basic protein (MBP) or the thyroid-
stimulating hormone receptor (TSHr), between untreated patients with multiple
sclerosis and normal controls (FIGS. 1A and 1B).
A. Peripheral mononuclear cell cultures
Peripheral blood mononuclear cells (PBMCs) were isolated from heparinized
blood by centrifugation on a Ficoll-Paque density gradient (Amersham Pharmacia
Biotech). Whole PBMCs were immediately suspended in culture medium (RPMT)
containing 1% penicillin, 1% streptomycin and 10% fetal calf serum (Sigma S5394)
and adjusted to a concentration of 106/mL viable cells (determined by trypan blue
exclusion). To induce passive cell death, PBMCs were incubated for 72 hours in
media alone without additional growth factors. Fas-mediated apoptosis was induced
by culturing PBMCs for 48 hours with soluble anti-CD28 (lμg/mL: kindly donated by
M. Frewin, University of Oxford) in anti-CD3 mAb-precoated plates (lμg/mL -BD
Pharmingen), followed by 18 hours incubation with activating anti-human Fas (clone
CH11,1μg/mL - Upstate Biotechnology, Lake Placid, NY).

B. Detection of apoptosis
Apoptotic T cells were detected by staining cells with: allophycocyanin-
conjugated mouse anti-human monoclonal antibodies against CD3 (Serotec
MCA463APC), CD4 (Serotec MCA1267APC) and CD8 (Serotec MCA1226APC),
FITC-conjugated annexin-V and Propidium Iodide (BD Pharmingen). Fluorescence
was detected by flow cytometry (FACSCALIBUR: Becton Dickinson, Mountain
View, CA). Based on forward and side scatter, a wide lymphocyte gate was drawn to
include live and apoptotic lymphocytes (having reduced FSc and increased SSc). At
least 15,000 events within the gate were collected and analyzed using WinMDI 2.8
software. Early apoptotic cells were defined as annexinV+Pr, and late apoptotic or
necrotic cells as annexinV+PI+ (Aubry et ah, Cytometry 37,197-204 (1999)).
Apoptotic cell death was defined as total cell death (annexinV+Pr plus annexinV+PI+)
blocked by pan-caspase inhibition with Q-VD-OPh (RnD Systems OPH001).
C. Proliferation assays
PBMCs were loaded with the cell division tracking dye CFSE
(carboxyfluorescein diacetate succinimidyl ester) (Lyons et al. Methods Cell Biol. 63,
375-398 (2001)) and cultured with 50ug/mL myelin basic protein (MBP: RDI-
TRK.8M79/LYO) or1μg/mL thyroid stimulating hormone receptor extracellular
domain bound to a matrix binding protein (TSHr: kindly donated by M. Ludgate,
Cardiff University). After 10 days CFSE staining in cells, identified by specific
surface markers (CD4, CD8), was analysed by flow cytometry. Precursor frequency
(defined as the proportion of lymphocytes that left the parent population to undergo at
least two cell divisions) and proliferation index (defined as the sum of the cells in all
generations divided by the computed number of parent cells) were calculated using
Modfit LT 3.0 (Verity Software). Absolute number of surviving cells was measured
by comparison with a fixed number of inert beads (BD CALIBRITE, BD
Biosciences), included in cultures.
D. Results
There was no difference in the proliferative response of T cells, unstimulated
or in culture with myelin basic protein (MBP) or the thyroid stimulating hormone

receptor (TSHr), between untreated patients with multiple sclerosis and normal
controls (FIGS. 1A and 1B). Conversely, survival of T cells from untreated patients
with multiple sclerosis was > 4 fold greater than that of controls (p<0.005; FIG. 1C),
suggesting that reduced T cell death is a feature of untreated multiple sclerosis. We
confirmed this by demonstrating that T cells from untreated patients are resistant both
to passive and Fas-mediated apoptosis compared with healthy controls (passive: 0.3%
v. 6.7%, p=0.0016; and Fas-mediated: 2.9% v. 15.5%, p=0.0018; FIGS. 1E and 1F).
Example 3: T cells that regenerate after alemtuzumab are highly proliferative,
skewed towards self reactivity and susceptible to apoptosis
Using the assays described in Example 2, we found that following
alemtuzumab, the proportion of T cells responding to self-antigens (precursor
frequency) and the degree of proliferation (proliferative index) were significantly
increased compared to untreated patients and healthy controls. For example at month
3, unstimulated T cell proliferation was >6.5 fold that of untreated patients and
proliferation in response to MBP and TSHr stimulation was increased by 900% and
700% respectively (all p0.01: FIGS. 1A and 1B). T cell apoptosis was also
significantly increased post-alemtuzumab. In response to antigenic stimulation, the
proportion of T cells undergoing apoptosis at six months was 10 fold greater than at
baseline (FIG. 1D; p0.00l for all antigens) resulting in fewer viable T cells at the end
of culture (FIG. 1C). Passive and Fas-mediated apoptosis were also increased after
alemtuzumab, with rates at least double those observed in the healthy control group
(passive: 24.5%, 22.2% and 17.9% at 6, 9 and 12 months, respectively, compared to
6.7% in controls, all p0.00l; Fas-mediated 37.8%, 35.8% and 29.9% at 6, 9 and 12
months, respectively, compared to 15.5% in controls, all p<0.01; FIGS. 1E and 1F).
Increased lymphocyte apoptosis after alemtuzumab was seen in both the CD4+ and
CD8+ subpopulations (FIGS. 1G and 1H) and persisted for at least 18 months after
alemtuzumab treatment (data not shown).
Example 4: T cells from untreated patients with multiple sclerosis under-express
caspase 3
A. mRNA analysis

PBMCs, immediately ex-vivo or after culture with MBP or polyclonal
stimulation, were positively separated, using 20 μL of magnetic beads (Miltenyi
Biotec; CD19 Microbeads, CD3 Microbeads, CD14 Microbeads) per 1x107 cells
loaded into a MACS® LS Column. Magnetically retained cells were eluted, washed
and stored in RNAlater™ at -70°C (cell purity consistently 95-98%, data not shown).
Fas, FasL, Bcl-2, Bcl-X1, Bad, Bax, Bid, Bim, Survivin, c-FLIP, and Caspase
3, 8 and 9 expression was determined by semi-quantitative RT-PCR. mRNA was
extracted from cells stored in RNAlater™ using the RNEASY Mini Kit (QIAgen) and
reverse transcribed to cDNA using the PRO-STAR First Strand RT-PCR Kit
(Stratagene). PCR primers and probes were designed using PRIMER EXPRESS (PE
Biosystems, Foster City, CA, USA), and purchased from Oswel DNA service. mRNA
sequence information was obtained from GenBank. Quantitative real-time PCR was
performed on an ABI Prism 7900HT Sequence Detection System (Perkin Elmer) using
PCR Mastermix containing ROX (Eurogentec RT-QP2X-03). Primer and probe
sequences were: Bcl-2 For: 5'-CCT GTG GAT GAC TGA GTA CCT GAA-3' (SEQ
ID NO: 1), Rev 5'-CAC CTA CCC AGC CTC CGT TA-3' (SEQ ID NO:2), JOE-
labelled probe 5'-CGG CAC CTG CAC ACC TGG ATC-3' (SEQ ID NO:3); Bcl-Xl
For 5'-TTC AGT CGG AAA TGA CCA GAC A-3' (SEQ ID NO:4), Rev 5'- GAG
GAT GTG GTG GAG CAG AGA-3' (SEQ ID NO:5), FAM-labelled probe 5'-TGA
CCA TCC ACT CTA CCC TCC CAC CC-3' (SEQ ID NO:6); Fas For 5'- AAA AGC
ATT TTG AGC AGG AGA GTA TT-3' (SEQ ID NO:7), Rev 5'- GGC CAT TAA
GAT GAG CAC CAA-3' (SEQ ID NO:8), JOE-labelled probe 5'- CTA GAG CTC
TGC CAC CTC TCC ATT -3' (SEQ ID NO:9); FasL For 5'- AAG AAA GTG GCC
CAT TTA ACA G-3' (SEQ ID NO: 10), Rev 5'- AGA AAG CAG GAC AAT TCC
ATA GGT-3' (SEQ ID NO: 11), FAM-labelled probe 5'- CAA CTC AAG GTC CAT
GCC TCT GG-3' (SEQ ID NO: 12); Survivin For 5'- CTG CCT GGC AGC CCT TT-
3' (SEQ ID NO: 13), Rev 5'- CTC CAA GAA GGG CCA GTT CTT - 3' (SEQ ID
NO: 14), FAM-labelled probe 5'- TCA AGG ACC ACC GCA TCT CTA CAT T-3'
(SEQ ID NO: 15); c-FLIP For 5'- GTG GAG ACC CAC CTG CTC -3' (SEQ ID
NO: 16), Rev 5'- GGA CAC ATC AGA TTT ATC CAA ATC C -3' (SEQ ID NO:17),

FAM-labelled probe 5'- CTG CCA TCA GCA CTC TAT AGT CCG AAA CAA -3'
(SEQ ID N0.18); Caspase 8 For 5'- AGG AGG AGA TGG AAA GGG AAC TT -3'
(SEQ ID N0:19), Rev 5'- ACC TCA ATT CTG ATC TGC TCA CTT CT -3' (SEQ
ID NO:20), JOE-labeled probe 5'- CTC CCT ACA GGG TCA TGC TCT ATC AGA
TTT CAG -3' (SEQ ID N0:21); Caspase 3 For 5'- AAG ATC ATA CAT GGA AGC
GAA TCA -3' (SEQ ID NO:22), Rev 5'- CGA GAT GTC ATT CCA GTG CTT TTA
-3' (SEQ ID NO:23), FAM-labeled probe 5'- CTG GAA TAT CCC TGG ACA ACA
GTT ATA AA -3' (SEQ ID NO:24); Caspase 9 For 5'- TGC GAA CTA ACA GGC
AAG CA -3' (SEQ ID NO:25), Rev 5'- GAA CCT CTG GTT TGC GAA TCT C -3'
(SEQ ID NO:26), FAM-labeled probe 5'- CAA AGT TGT CGA AGC CAA CCC
TAG AAA ACC TTA -3' (SEQ ID NO:27); Bad For 5'- CAG TGA CCT TCG CTC
CAC ATC - 3' (SEQ ID NO:28), Rev 5' - ACG GAT CCT CTT TTT GCA TAG -3'
(SEQ ID NO:29), JOE-labeled probe 5'- ACT CCA CCC GTT CCC ACT GCC C-3'
(SEQ ID NO:30); Bax For 5'-TTT CTG ACG GCA ACT TCA ACT -3' (SEQ ID
NO:31), Rev 5'-GGT GCA CAG GGC CTT GAG-3' (SEQ ID NO:32), JOE-labeled
probe 5'-TGT CGC CCT TTT CTA CTT TGC CAG CA-3' (SEQ ID NO:33); Bid For
5'- GCT GTA TAG CTG CTT CCA GTG TAG -3' (SEQ ID NO:34), Rev 5'-GCT
ATC TTC CAG CCT GTC TTC TCT -3' (SEQ ID NO:35), JOE-labeled probe 5'-
AGC CCT GGC ATG TCA ACA GCG TTC -3' (SEQ ID NO:36) and Bim For 5'-
ACC ACA AGG ATT TCT CAT GAT ACC -3' (SEQ ID NO:37), Rev 5'- CCA TAT
GAC AAA ATG CTC AAG GAA -3' (SEQ ID NO:38), FAM-labeled probe 5'- TAG
CCA CAG CCA CCT CTC TCC CT-3' (SEQ ID NO:39).
B. Results
T cell mRNA expression of caspase 3, the effector caspase common to both
apoptotic pathways, from untreated multiple sclerosis patients was reduced compared
to controls; this was significant for unstimulated and MBP-stimulated PBMCs (by
78% and 87% respectively, both p<0.05, after correction for multiple comparisons),
but not for polyclonal stimulated cultures (FIG. 2A). A similar trend was seen in
CD 14+ cells (but not CD 19+ cells) although this difference did not survive correction
for multiple comparisons (FIG. 2B). After alemtuzumab, caspase 3 expression was

significantly increased in T cells and monocytes, reaching levels seen in healthy
controls (p<0.05; FIGS. 2A and 2B). Expression of all other genes tested (listed in
methods) was unchanged after alemtuzumab.
Thus, our studies show that T cells from people with untreated multiple
sclerosis are resistant to apoptosis, and this resistance is associated with under-
expression of caspase 3. Consistent with the position of this effector caspase at the
convergence point of the extrinsic and intrinsic apoptotic pathways, we have
demonstrated T cell resistance both to Fas-mediated and passive apoptosis in our
patients. Under-expression of caspase 3 has been described in some autoimmune
diseases, including Type I diabetes (Vendrame et al., Eur J Endocrinol 152, 119-125
(2005)), Hashimoto's thyroiditis and autoimmune polyendocrine syndrome-2
(Vendrame et al., J Clin Endocrinol Metabjc (2006)). This is, however, a novel
finding in multiple sclerosis.
Example 5: Secondary autoimmunity after alemtuzumab is associated with
excessive T cell apoptosis
Having demonstrated increased lymphocyte proliferation and apoptosis as a
generic response to treatment, we tested the relationship between T cell apoptosis and
development of autoimmunity after alemtuzumab, defined as development of a novel
autoimmune disease and/or persistent autoantibodies above the normal range, after
alemtuzumab, sustained over at least 3 months. Using this definition, T cells derived
from patients with autoimmunity (n = 10) showed significantly higher levels of
apoptotic cell death in all culture conditions at 9 months post-treatment, when
compared to T cells from non-autoimmune patients (n = 10) studied at the same time
point (unstimulated 4.7% vs. 14.4%, Fas-mediated 18.2% vs. 32.1%, MBP 7.6% vs.
17.6%, and TSHr 9.5% vs. 25.5%, p<0.01 for all comparisons; FIG. 3). If a stricter
definition of autoimmunity was applied, that being development of an autoimmune
disease, excluding nonpathogenic antibody production, the difference remained,
despite reducing the number in the autoimmune group to 7 (unstimulated, 4.7% vs.
15.4%; Fas mediated, 18.2% vs. 31.7%; MBP, 7.6% vs. 20.2%; TSHr, 9.5% vs.
13.4%; P < 0.02 for all comparisons).

There was no difference in the rate of T cell reconstitution between the two
groups (e.g., at 6 months, CD4 counts are 0.15 x 109/L vs. 0.19 x 109/L; and CD8
counts 0.11 x 109/L vs. 0.11 x 109/L in those with and without autoimmunity,
respectively), suggesting increased T cell cycling in the autoimmune group (data not
shown).
Example 6: IL-21 induces T cell proliferation and apoptosis
A. IL-21 assays and spiking
Serum IL-21 was measured using the EBIOSCIENCE kit (88-7216-86) as per
instructions. Plates were read using a microplate reader (model 680, BioRad) at
450nm. Unstimulated and polyclonally stimulated (lug/mL plate-bound anti-CD3 and
1μg/mL soluble anti-CD28) PBMCs were spiked with 5pg/mL and 20pg/mL rhIL-21
(EBIOSCIENCE 14-8219). CD4+ and CD8+ apoptosis and proliferation were
assessed as described above.
B. Results
We tested the effect of exogenous IL-21 on apoptosis and proliferation of
human T cells in vitro. Spiking PBMCs from healthy controls with rhIL-21 led to an
increase in the apoptotic death of unstimulated and polyclonally stimulated CD4+
(FIG. 4A) and CD8+ (FIG. 4B) T cells in a dose dependent manner (p<0.05 for all
conditions). Spiking unstimulated cells with rhIL-21 led to a small but significant
increase in the proliferation of both CD4+ and CD8+ T cells; with an increase both in
proliferative index (CD4+ and CD8+: 1.07 vs. 1.25, p=0.017; and 1.09 vs. 1.32,
p=0.017 respectively; FIG. 5A) and precursor frequency (CD4+ 0.007 vs. 0.014,
p=0.016; CD8+ 0.007 vs. 0.015, p=0.026; FIG. 5C). IL-21 did not affect the
proportion of CD4+ or CD8+ T cells proliferating in response to polyclonal
stimulation (FIG. 5D), suggesting that they were already maximally stimulated. IL-
21, however, did lead to a significant increase in the extent of CD8+ cell proliferation
(proliferative index 11.59 vs. 19.39, p=0.012; FIG. 5B).
Example 7: IL-21 predicts the development of secondary autoimmunity after
alemtuzumab

At all time points in Example 6, the concentration of serum IL-21 was
significantly greater in patients who developed secondary autoimmunity compared to
the non-autoimmune group (for all comparisons p<0.05; FIG. 6A). We examined all
pre-treatment serum samples from 84 patients who subsequently went on to have
alemtuzumab. After at least two years of follow up with these patients, we
categorized them as being in the "autoimmune" group (n = 35: 32 patients with
thyroid diseases, one ITP, one Goodpasture's, and one Alopecia) or "non-
autoimmune" group (n = 49: patients with no or only transient (unsustained over six
months) autoantibodies)). These pre-treatment sera had a statistically greater mean
concentration of IL-21 than controls; however, this was entirely accounted for by high
IL-21 levels in those patients who went on to develop secondary autoimmunity. There
was a highly significant difference in mean pre-treatment IL-21 levels between those
that went on to develop autoimmunity (464pg/ml) and those that did not (229pg/ml;
p= 0.0002) (FIG. 6B).
The association between induced-lymphopenia and autoimmunity has been
observed in animal models. Under lymphopenic conditions, the remaining T cells
undergo extensive compensatory expansion in order to reconstitute the immune
system. This process, termed homeostatic proliferation, relies on stimulation through
the TCR-self-peptide-MHC complex (Ge et al, P.N.A.S. 101, 3041-3046 (2004); Ge et
al., P.N.A.S. 98, 1728-1733 (2001); Kassiotis et al., J Exp. Med. 197,1007-1016
(2003)) and results in a population skewed towards increased recognition of self-
antigen, as seen in our studies. In addition, rapidly expanding T cells acquire the
phenotype and functional characteristics of memory cells including: reduced
dependence on co-stimulation, the ability to respond to lower doses of antigen than
naive cells, and the rapid secretion of inflammatory cytokines on restimulation, so
further promoting the breakdown of self tolerance (Cho et al.,J Exp. Med. 192, 549-
556 (2000); Goldrath et al. J Exp. Med. 192, 557-564 (2000); Murali-Krishna et al., J
Immunol 165,1733-1737 (2000); Wu et al., Nat Med. 10, 87-92 (2004)). Yet, despite
these changes, autoimmunity is not an inevitable consequence of lymphopenia.

Indeed, as with our patients, most lymphopenic subjects did not develop
autoimmunity, suggesting that additional "co-factors" are required.
We have demonstrated here for the first time in man that overproduction of IL-
21 is the "second hit" required in the development of secondary autoimmunity
following otherwise successful treatment of multiple sclerosis with a lymphocyte
depleting agent such as alemtuzumab. Our studies show that autoimmunity arises in
lymphocyte-depleted patients, with greater T cell apoptosis and cell cycling driven by
genetically influenced higher levels of IL-21 that are detectable even before treatment.
Even before treatment, patients who went on to develop secondary autoimmunity had
more than 2-fold greater levels of serum IL-21 than the nonautoimmune group,
suggesting that serum IL-21 may serve as a biomarker for the risk of developing
autoimmunity months to years after alemtuzumab treatment. Without wishing to be
bound by any theory, we believe that, by driving cycles of T cell expansion and death
to excess, IL-21 increases the probability of generating self-reactive T cells, and
hence, for autoimmunity. Thus, cytokine-induced abnormal T cell cycling is a general
principle of lymphopenia-associated autoimmunity.
Example 8: IL-21 genotype influences IL-21 expression and associates with
autoimmunity
A. IL-21 genotyping
In total, four SNPs, rsl3151961, rs6822844, rs4833837 and rs6840978, which
lie in a region of strong linkage disequilibrium containing four genes, KIAA1109-
ADAD1-1L2-IL21, on chromosome 4q27 were tested. All four SNPs were available as
Applied Biosystems Assay-On-Demand (AoD) products. SNP genotyping was
performed using Applied Biosystems TaqMan methodology according to the
manufacturer's recommended conditions. Polymerase chain reaction (PCR) was
performed on Applied Biosystems 384-well 9700 Viper PCR machines, after which
genotypes were called on a 7900 High Throughput Sequence Detection System (SDS)
using SDS Software Version 2.1. Each individual was genotyped in duplicate. All
individuals were additionally genotyped for the multiple sclerosis associated genetic
factors: HLA-DRB1*1501, rs2104286 (IL2RA) and rs6897932 (1L7R).

B. Results
In order to determine whether there is an association between genetic variation
and IL-21 production, we genotyped 73 subjects, in whom pre-alemtuzumab serum
IL-21 concentration had been determined, for four single nucleotide polymorphisms
(SNPs) that lie within a block of linkage disequilibrium (LD) on chromosome 4q27
encoding the IL-21 gene. The minor allele frequency for all four SNPs was in line
with published data: rsl3151961G (14.5%), rs6822844T (14.6%), rs4833837G
(38.0%) and rs6840978T (18.1%) (Glas et al., Am. J. Gastroenterol. 104, 1737-1744
(2009)). We found that the genotype at 3 of the 4 SNPs (rsl3151961 A/A, rs6822844
G/G and rs6840978 C/C) was associated with significantly higher levels of serum IL-
21 (p values: 0.0076, 0.0098 and 0.0067 respectively). The genotype at rs4833837 did
not influence IL-21 production. The LD between rs4833837 and the three other SNPs
is low (r2<0.15), therefore a SNP which lies on the haplorype rsl3151961(A)-
rs6822844(G)-rs6840978(C) is most likely to be associated with increased IL-21
production. The genotype frequencies for HLA-DRB1 *1501, rs2104286 (IL2RA) and
rs6897932 (IL7R) did not differ from published data for other unselected patients with
multiple sclerosis(International Multiple Sclerosis Genetics Consortium (IMSGC),
Lancet Neurol. 7, 567-569 (2008); Yeo et al., Ann Neurol 61, 228-236 (2007)).
Finally, in order to address whether genotype influences susceptibility to
autoimmunity after alemtuzumab, we categorized as many patients as possible into
those who did (27 subjects) and definitely did not (23 subjects) develop autoimmunity
post-alemtuzumab. 23 patients could not be categorized due to transient autoantibody
production and/or insufficient time since exposure to alemtuzumab. The genotypes
(rsl3151961 A/A, rs6822844 G/G, rs6840978 C/C), shown to be associated with
higher serum IL-21 concentration, were also found to be associated with
autoimmunity after alemtuzumab.

What is claimed is:
1. A method for identifying a multiple sclerosis (MS) patient who has
elevated interleukin-21 (IL-21) compared to IL-21 in a subject without an autoimmune
disease, comprising the step of:
measuring IL-21 in a blood sample from the MS patient, thereby identifying
an MS patient having elevated IL-21 compared to said subject.
2. A method for identifying a multiple sclerosis patient who is likely to
have elevated interleukin-21 (TL-21) compared to a subject without an autoimmune
disease, comprising the step of genotyping the patient to detect the presence or
absence of one or more genotypes of single nucleotide polymorphisms (SNPs)
selected from the group consisting of: A/A at SNP rsl3151961, G/G at SNP
rs6822844, and C/C at SNP rs6840978, wherein the presence of one or more of said
genotypes is associated with elevated IL-21.
3. A method for identifying a multiple sclerosis (MS) patient who is at
increased risk of developing a secondary autoimmune disease following lymphocyte
depletion, comprising the step of:
measuring interleukin-21 (IL-21) in a blood sample from the MS patient,
wherein elevated IL-21 compared to a subject without an autoimmune disease
indicates that the patient is at increased risk of developing a secondary autoimmune
disease compared to MS patients without elevated IL-21; and
informing the patient of said increased risk.
4. A method for identifying a multiple sclerosis patient who is at
increased risk of developing a secondary autoimmune disease following lymphocyte
depletion, comprising the step of:

genotyping the patient to detect the presence or absence in the patient of one or
more genotypes of single nucleotide polymorphisms (SNPs) selected from the group
consisting of: A/A at SNP rsl3151961, G/G at SNP rs6822844, and C/C at SNP
rs6840978, wherein the presence of one or more of said genotypes is associated with
an increased risk of developing a secondary autoimmune disease compared to MS
patients without said one or more genotypes; and
informing the patient of said increased risk.
5. The method of claim 3, wherein said lymphocyte depletion is induced
by a treatment that targets CD52.
6. The method of claim 5, wherein the treatment that targets CD52
comprises treatment with an anti-CD52 antibody or an antigen-binding portion
thereof.
7. The method of claim 6, wherein the anti-CD52 antibody is
alemtuzumab or a biologically similar agent.
8. The method of claim 4, wherein said lymphocyte depletion is induced
by a treatment that targets CD52.
9. The method of claim 8, wherein the treatment that targets CD52
comprises treatment with an anti-CD52 antibody or an antigen-binding portion
thereof.
10. The method of claim 9, wherein the anti-CD52 antibody is
alemtuzumab or a biologically similar agent.

11. A method for selecting a multiple sclerosis (MS) patient in need of
heightened monitoring for development of a secondary autoimmune disease after
lymphocyte depleting therapy, comprising the step of:
measuring IL-21 in a blood sample from the MS patient, wherein elevated IL-
21 in said patient compared to a subject without an autoimmune disease indicates that
the patient is in need of heightened monitoring for development of a secondary
autoimmune disease compared to MS patients without elevated IL-21.
12. A method for selecting a multiple sclerosis patient in need of
heightened monitoring for development of a secondary autoimmune disease after
lymphocyte depleting therapy, comprising the step of:
genotyping the patient to detect the presence or absence of one or more
genotypes of single nucleotide polymorphisms (SNPs) selected from the group
consisting of: A/A at SNP rs 13151961, G/G at SNP rs6822844, and C/C at SNP
rs6840978, wherein the presence of one or more of said SNPs indicates that the patient
is in need of heightened monitoring for development of a secondary autoimmune
disease compared to MS patients without said one or more genotypes.
13. A method for informing a treatment decision for a multiple sclerosis
patient, comprising the steps of:
measuring IL-21 in a blood sample from said patient; and
selecting a treatment regimen appropriate for the IL-21 measurement.
14. A method for informing a treatment decision for a multiple sclerosis
patient, comprising the steps of:
genotyping the patient for the presence or absence of one or more genotypes of
single polynucleotide polymorphisms (SNPs) selected from the group consisting of:
A/A at SNP rsl3151961, G/G at SNP rs6822844, and C/C at SNP rs6840978; and
selecting a treatment regimen appropriate for the patient's genotype.

15. A method for treating multiple sclerosis in a patient known to be in
need thereof, comprising the steps of:
obtaining information on (i) IL-21 in a blood sample from the patient; or (ii)
the presence or absence of one or more genotypes of single-nucleotide polymorphisms
(SNPs) selected from the group consisting of: A/A at SNP rsl3151961, G/G at SNP
rs6822844 G/G, and C/C at SNP rs6840978; and
administering a therapeutic agent for multiple sclerosis to said patient.
16. The method of claim 15, further comprising, after the administering
step, monitoring said patient for development of a secondary autoimmune disease.
17. An antibody that binds CD52, or an antigen-binding portion of said
antibody, for use in a method of treating multiple sclerosis in a patient known to be in
need thereof, the method comprising the steps of:
obtaining information on (i) IL-21 in a blood sample from the patient; or (ii)
the presence or absence of one or more genotypes of single-nucleotide polymorphisms
(SNPs) selected from the group consisting of: A/A at SNP rsl3151961, G/G at SNP
rs6822844 G/G, and C/C at SNP rs6840978; and
administering the antibody or antigen-binding portion to said patient.
18. An antibody that binds CD52, or an antigen-binding portion of said
antibody, for use in a method of treating multiple sclerosis in a patient known to be in
need thereof,
wherein the method comprises (i) measuring IL-21 in a blood sample from the
MS patient and/or (ii) genotyping the patient to detect the presence or absence of one
or more genotypes of single nucleotide polymorphisms (SNPs) selected from the
group consisting of: A/A at SNP rs 13151961, G/G at SNP rs6822844, and C/C at
SNP rs6840978.

19. An antibody that binds CD52, or an antigen-binding portion of said
antibody, for use in a method of treating multiple sclerosis in a patient known to be in
need thereof,
wherein the patient has been found (i) to have normal levels of IL-21 and/or
(ii) not to have one or more genotypes of single-nucleotide polymorphisms (SNPs)
selected from the group consisting of: A/A at SNP rsl3151961, G/G at SNP
rs6822844 G/G, and C/C at SNP rs6840978.
20. An antibody for use according to claim 18 or 19 wherein the method
comprises identifying the patient by a method of any one of claims 1 to 10.
21. The antibody according to any one of claims 17, 18, and 19, wherein
the antibody is alemtuzumab or a biologically similar agent.
22. The antibody according to claim 20, wherein the antibody is
alemtuzumab or a biologically similar agent.
23. Use of an antibody that binds CD52, or an antigen-binding portion of
said antibody, in the manufacture of a medicament for use in a method of treating
multiple sclerosis in a patient known to be in need thereof, the method comprising the
steps of:
obtaining information on (i) IL-21 in a blood sample from the patient; or (ii)
the presence or absence of one or more genotypes of single-nucleotide polymorphisms
(SNPs) selected from the group consisting of: A/A at SNP rsl3151961, G/G at SNP
rs6822844 G/G, and C/C at SNP rs6840978; and
administering the antibody or antigen-binding portion to said patient.
24. Use of an antibody that binds CD52, or an antigen-binding portion of
said antibody, in the manufacture of a medicament for use in a method of treating
multiple sclerosis in a patient known to be in need thereof,

wherein the method comprises (i) measuring IL-21 in a blood sample from the
MS patient and/or (ii) genotyping the patient to detect the presence or absence of one
or more genotypes of single nucleotide polymorphisms (SNPs) selected from the
group consisting of: A/A at SNP rsl3151961, G/G at SNP rs6822844, and C/C at
SNP rs6840978.
25. Use of an antibody that binds CD52, or an antigen-binding portion of
said antibody, in the manufacture of a medicament for use in a method of treating
multiple sclerosis in a patient known to be in need thereof,
wherein the patient has been found (i) to have normal levels of IL-21 and/or
(ii) not to have one or more genotypes of single-nucleotide polymorphisms (SNPs)
selected from the group consisting of: A/A at SNP rsl3151961, G/G at SNP
rs6822844 G/G, and C/C at SNP rs6840978.
26. Use according to claim 23, 24 or 25, wherein the method comprises
identifying the patient by a method of any one of claims 1 to 10.
27. Use according to claim 23, 24, or 25, wherein the antibody is
alemtuzumab or a biologically similar agent.
28. Use according to claim 26, wherein the antibody is alemtuzumab or a
biologically similar agent.
29. A method for reducing the occurrence or severity of a secondary
autoimmune disease in a multiple sclerosis patient who has been or will be treated
with a lymphocyte depleting therapy, wherein the secondary autoimmune disease
occurs after treatment with the lymphocyte depleting therapy, comprising the step of
administering an IL-21 antagonist.

30. The method of claim 29, wherein the administering step takes place
prior to, during, or subsequent to the treatment with the lymphocyte depleting therapy.
31. An IL-21 antagonist for use in a method of reducing the occurrence or
severity of a secondary autoimmune disease in a multiple sclerosis patient who has
been or will be treated with a lymphocyte depleting therapy, wherein the secondary
autoimmune disease occurs after treatment with the lymphocyte depleting therapy, the
method comprising administering the IL-21 antagonist to said patient.
32. The IL-21 antagonist according to claim 31, wherein the IL-21
antagonist is an antibody or antigen-binding portion thereof.
33. Use of an IL-21 antagonist in the manufacture of a medicament for
reducing the occurrence or severity of a secondary autoimmune disease in a multiple
sclerosis patient who has been or will be treated with a lymphocyte depleting therapy,
wherein the secondary autoimmune disease occurs after treatment with the
lymphocyte depleting therapy, the method comprising administering the IL-21
antagonist to said patient.
34. Use according to claim 33, wherein the IL-21 antagonist is an antibody
or antigen-binding portion thereof.
35. A therapeutic regimen for treating multiple sclerosis in a patient known
to be in need thereof, said regimen comprising:
measuring IL-21 in a blood sample from the patient and/or genotyping the
patient to detect the presence or absence of one or more genotypes of single-nucleotide
polymorphisms (SNPs) selected from the group consisting of: A/A at SNP
rsl3151961, G/G at SNP rs6822844, and C/C at SNP rs6840978; and
administering a therapeutic agent for multiple sclerosis to said patient.

36. An antibody that binds CD52, or an antigen-binding portion of said
antibody, for use in a method of treating multiple sclerosis in a patient known to be in
need thereof, the method comprising:
measuring IL-21 in a blood sample from the patient and/or genotyping the
patient to detect the presence or absence of one or more genotypes of single-nucleotide
polymorphisms (SNPs) selected from the group consisting of: A/A at SNP
rsl3151961, G/G at SNP rs6822844, and C/C at SNP rs6840978; and
administering the antibody or antigen-binding portion to said patient.
37. Use of an antibody that binds CD52, or an antigen-binding portion of
said antibody, in the manufacture of a medicament for use in a method of treating
multiple sclerosis in a patient known to be in need thereof, the method comprising:
measuring IL-21 in a blood sample from the patient and/or genotyping the
patient to detect the presence or absence of one or more genotypes of single-nucleotide
polymorphisms (SNPs) selected from the group consisting of: A/A at SNP
rsl3151961, G/G at SNP rs6822844, and C/C at SNP rs6840978; and
administering the antibody or antigen-binding portion to said patient.
38. An enzyme-linked immunosorbent assay (ELISA) kit for detecting serum
EL-21 level in a subject, comprising an antibody that binds IL-21, or an antigen-
binding portion of said antibody, or a soluble IL-21 receptor, and an instruction
directing a user to take a blood sample from the subject.
39. The method of any one of claims 1,3,11, and 13, wherein the
measuring comprises determining the amount or concentration of IL-21 or nucleic acid
encoding IL-21 in the sample.
40. The method of any one of claims 1,3, 11,and 13,wherein the
measuring is of mRNA encoding IL-21 in IL-21-producing cells in the sample.

41. The method of claim 40, wherein the IL-21 -producing cells are Thl 7
cells.
42. The method of any one of claims 1, 3, 11, and 13, wherein the
measuring is of intracellular IL-21.
43. The method of claim 42, wherein the measuring comprises cytokine
staining and flow cytometry.
44. The method of any one of claims 1,3,11, and 13, wherein the
measuring is of serum IL-21.
45. The method of claim 44, where the measuring comprises the use of an
enzyme-linked immunosorbent assay (ELISA).
46. The method of any one of claims 1-4, 11,12, and 29, wherein the
autoimmune disease is selected from the group consisting of: immune
thrombocytopenic purpura (ITP), Graves' disease, Goodpasture's disease,
autoimmune thyroid disease, autoimmune hemolytic anemia, autoimmune
neutropenia, and autoimmune lymphopenia.
47. The method of claim 3 or 4, wherein the lymphocyte depletion occurs
during or subsequent to treatment with a lymphocyte depleting therapy.
48. The method of any one of claims 11,12, and 29, wherein the
lymphocyte depleting therapy targets CD52-bearing cells.
49. The method of claim 48, wherein the lymphocyte depleting therapy that
targets CD52-bearing cells comprises administering an antibody that binds CD52, or
an antigen-binding portion of said antibody.

50. The method of claim 49, wherein the antibody is a monoclonal
antibody.
51. The method of claim 49 or 50, wherein the antibody competes for
binding to CD52 with alemtuzumab.
52. The method of claim 50, wherein the antibody competes for binding to
CD52 with alemtuzumab.
53. The method of claim 50, wherein the antibody is alemtuzumab or a
biologically similar agent.
54. The method of any one of claims 1,3,11,13, and 15, wherein the
blood sample is obtained from the patient prior to, during, or subsequent to therapy for
multiple sclerosis.
55. The method of claim 54, wherein the blood sample is obtained from the
patient prior to a lymphocyte depleting therapy.
56. The method of any one of claims 1-16,29, and 30, wherein the multiple
sclerosis is relapsing-remitting multiple sclerosis.
57. The method of any one of claims 1-16,29, and 30, wherein the multiple
sclerosis is primary progressive multiple sclerosis.
58. The method of any one of claims 1-16,29, and 30, wherein the multiple
sclerosis is secondary progressive multiple sclerosis.

59. A method for assessing T cell responsiveness to treatment with a
lymphocyte depleting therapy in a multiple sclerosis patient, comprising:
measuring caspase-3 in T cells obtained from said patient after said therapy,
wherein an increase in caspase-3 in said T cells compared to T cells from an MS
patient not receiving said therapy is indicative of T cell responsiveness to said therapy.
60. The method of claim 59, wherein the lymphocyte depleting therapy
targets CD52.
61. The method of claim 60, wherein the lymphocyte depleting therapy
comprises treatment with an anti-CD52 antibody or an antigen-binding portion
thereof.
62. The method of claim 61, wherein the CD52 antibody is alemtuzumab
or a biologically similar agent.
63. The method of any one of claims 60-62, wherein the measuring
comprises determining the amount or concentration of caspase-3 or nucleic acid
encoding caspase-3.
64. A method for identifying an individual who is likely to have elevated
interleukin-21 (IL-21) compared to a subject without any known inflammatory
condition, comprising the step of genotyping the individual to detect the presence or
absence of one or more genotypes of single nucleotide polymorphisms (SNPs)
selected from the group consisting of: A/A at SNP rs 13151961, G/G at SNP
rs6822844, and C/C at SNP rs6840978, wherein the presence of one or more of said
genotypes is associated with elevated IL-21.

65. A method for informing an MS patient of an increased risk of
developing a secondary autoimmune disease following lymphocyte depletion,
comprising the steps of:
obtaining information on interleukin-21 (IL-21) in a blood sample from the MS
patient, wherein elevated IL-21 compared to a subject without an autoimmune disease
indicates that the patient is at increased risk of developing a secondary autoimmune
disease compared to MS patients without elevated IL-21; and
informing the patient of said increased risk or lack thereof.
66. A method for informing an MS patient of an increased risk of
developing a secondary autoimmune disease following lymphocyte depletion,
comprising the steps of:
obtaining information on the presence or absence of one or more genotypes of
single nucleotide polymorphisms (SNPs) selected from the group consisting of: A/A at
SNP rsl3151961, G/G at SNP rs6822844, and C/C at SNP rs6840978, wherein the
presence of one or more of said genotypes is associated with an increased risk of
developing a secondary autoimmune disease compared to MS patients without said
one or more genotypes; and
informing the patient of said increased risk or lack thereof.
67. A method for informing an MS patient of a need for heightened
monitoring for development of a secondary autoimmune disease following
lymphocyte depleting therapy, comprising the steps of:
obtaining information on IL-21 in a blood sample from the MS patient,
wherein elevated IL-21 in said patient compared to a subject without an autoimmune
disease indicates that the patient is in need of heightened monitoring for development
of a secondary autoimmune disease compared to MS patients without elevated IL-21;
and
informing the patient of said need or lack thereof.

68. A method for informing an MS patient of a need for heightened
monitoring for development of a secondary autoimmune disease following
lymphocyte depleting therapy, comprising the step of:
obtaining information on the presence or absence of one or more genotypes of
single nucleotide polymorphisms (SNPs) selected from the group consisting of: A/A
at SNP rs 13151961, G/G at SNP rs6822844, and C/C at SNP rs6840978, wherein the
presence of one or more of said SNPs indicates that the patient is in need of
heightened monitoring for development of a secondary autoimmune disease compared
to MS patients without said one or more genotypes; and
informing the patient of said need or lack thereof.
69. A method for informing a regimen for monitoring an MS patient
following lymphocyte depleting therapy, comprising the steps of:
obtaining information on (i) IL-21 in a blood sample from the patient; or (ii)
the presence or absence of one or more genotypes of single-nucleotide polymorphisms
(SNPs) selected from the group consisting of: A/A at SNP rsl3151961, G/G at SNP
rs6822844 G/G, and C/C at SNP rs6840978; and
selecting a monitoring regimen appropriate for the patient based on the
information.
70. The method of any one of claims 65-69, wherein the obtaining step
takes place prior to lymphocyte depletion.
71. The method of claim 69, wherein the monitoring regimen comprises
measuring auto-antibodies in the patient.
72. A method for distributing a lymphocyte depleting drug to a patient for
treating multiple sclerosis, comprising the steps of:
counseling the patient on the increased risk of developing a secondary
autoimmune disease following treatment with said drug, wherein the increased risk is

associated with (i) elevated IL-21; or (ii) the presence of one or more genotypes of
single-nucleotide polymorphisms (SNPs) selected from the group consisting of: A/A
at SNP rsl3151961, G/G at SNP rs6822844 G/G, and C/C at SNP rs6840978; and
providing the drug to the patient after said counseling.
73. The method of claim 72, further comprising obtaining informed
consent from the patient, prior to the providing step.
74. The method of claim 73, wherein the drug is an anti-CD52 antibody.
75. The method of claim 74, wherein the drug is alemtuzumab.
76. A kit for treating multiple sclerosis, comprising:
a lymphocyte depleting therapeutic agent; and
a written instruction for informing a health care provider or a patient of
the potential for an increased risk of developing a secondary autoimmune disease
following treatment with said agent, wherein said increased risk is associated with (i)
elevated EL-21, or (ii) the presence of one or more genotypes of single-nucleotide
polymorphisms (SNPs) selected from the group consisting of: A/A at SNP
rs 13151961, G/G at SNP rs6822844 G/G, and C/C at SNP rs6840978.
77. The kit of claim 76, wherein the agent is an anti-CD52 antibody.
78. The kit of claim 77, wherein the agent is alemtuzumab.
79. A kit for identifying a multiple sclerosis (MS) patient who is at
increased risk of developing a secondary autoimmune disease following lymphocyte
depletion, comprising:
an anti-interleukin-21 (IL-21) antibody and one or more reagents for detecting
the binding of said antibody to IL-21 in a blood sample from the MS patient.

80. A kit for identifying a multiple sclerosis patient who is at increased risk
of developing a secondary autoimmune disease following lymphocyte depletion,
comprising:
one or more reagents suitable for identifying the genotype of one or more
single nucleotide polymorphisms (SNPs) selected from the group consisting of: SNP
rsl3151961, SNP rs6822844, and SNP rs6840978, in a sample obtained from an
individual.

The invention provides methods of diagnosing multiple sclerosis (MS) patients, including methods of identifying
multiple sclerosis patients who are at increased risk of developing a secondary autoimmune disease following lymphocyte depletion,
caused, e.g., by treatment with an anti-CD52 antibody. Also embraced are methods of selecting treatment regimens for MS
patients, and reagents useful in the above methods.