Title of Invention

ISOLATED HUMAN ANTI-INTERFERON GAMMA ANTIBODIES AND COMPOSITION COMPRISING THEM

Abstract The invention relates to fully human antibodies, and fragments thereof, that bind to human interferon gamma (hIFNγ), thereby modulating the interaction between IFNγ and its receptor, IFNγ-R, and/or modulating the biological activities of IFNγ. The invention also relates to the use of such anti-IFNγ antibodies in the prevention or treatment of immune- related disorders and in the amelioration of a symptom associated with an immune-related disorder.
Full Text WO 2006/109191 PCT/IB2006/001514
Anti-Interferon Gamma Antibodies and Methods of Use Thereof
FIELD OF THE INVENTION
This invention relates generally to folly human anti-interferon gamma antibodies as
well as to methods for use thereof.
BACKGROUND OF THE INVENTION
Human interferon gamma (IFNy, IFN-gamma) is a lymphokine produced by
activated T-lymphocytes and natural killer cells. It manifests anti-proliferative, antiviral
and irnrnunomodiilatory activities and binds to IFNy-R, a lieterodimeric receptor on most
primary cells of the immune system, and niggers a cascade of events leading to
inflammation. The antiviral and immunomodulatory activity of IFNy is known to have
beneficial effects in a number of clinical conditions. However, there are many clinical
settings in which IFNy-activity is known to have deleterious effects. For example,
autoimmune diseases are associated with high levels of IFNy in the blood and diseased
> tissue from autoimmune patients. IFNy-activity has also been linked to such disease states
as cachexia and septic shock.
Accordingly, there exists a need for therapies that target IFNy activity.
SUMMARY OF THE INVENTION
The present invention provides fully human monoclonal antibodies specifically
directed against interferon gamma (IFNy, also referred to herein as IFN-gamma).
Exemplary monoclonal antibodies include NI-0501; AC1.2R3P2_A6 (also referred to
herein as "A6"); AC1.2R3P2_B4 (also referred to herein as "B4"); AD1.4R4P1_B9 (also
referred to herein as "B9"); AD1.4R4P2_C9 (also referred to herein as "C9");
AC1.4R4P2_C10 (also referred to herein as "CIO"); AC1.2R3P7_D3 (also referred to
herein as "D3"); AD1.2R2P2_D6 (also referred to herein as "D6"); AC1.2R2P2_D8 (also
referred to herein as "D8"); ADI .3R3P6_E1 (also referred to herein as "E1");
AD1.3R3P5_F8 (also referred to herein as "F8"); ADl.3R3P6_F9 (also referred to herein as
"F9"); AD1.4R4P2_G7 (also referred to herein as "G7"); AD1.1R3P3_G9 (also referred to
herein as "G9"); and AD1.3R3P6_GIO (also referred to herein as "G10") described herein.
Alternatively, the monoclonal antibody is an antibody that binds to the same epitope as NI-
1

WO 2006/109191 PCT/IB2006/001514
0501; AC1.2R3P2_B4; AD1.4R4P1JB9; AD1.4R4P2_C9; AC1.4R4P2_C10;
AC1.2R3P7_D3; ADI.2R2P2_D6; AC1.2R2P2_D8; AD1.3R3P6JE1; AD1.3R3P5JF8;
AD1.3R3P6_F9; AD1.4R4P2_G7; AD1.1R3P3_G9; or AD1.3R3P6_G10. The antibodies
are respectively referred to herein as hiilFNy antibodies.
A huIFNy antibody contains a heavy chain variable having the amino acid sequence
of SEQ ID NOS: 2, 12, 20,28, 36,42, 51, 58, 63,68, 75, 81, 88,94, or 103 and a light
chain variable having the amino acid sequence of SEQ ID NOS: 7,15,23, 31,38,47, 54,
60, 66,71,78,83, 91, 96 or 105. Preferably, the three heavy chain complementarity
determining regions (CDRs) include an amino acid sequence at least 90%, 92%, 95%, 97%
98%, 99% or more identical a sequence selected from the group consisting of SYAMS
(SEQ ID NO:3); AISGSGGSTYYADSVKG (SEQ ID NO:4); DGSSGWYVPHWF DP
(SEQ ID NO:5); DHSSGWYVISGMDV (SEQ ID NO: 13); DLTVGGPWYYFDY (SEQ ID
NO:21); DGWNALGWLES (SEQ ID NO:29); SNAMS (SEQ IDNO:43);
TLTGSGGTAYYADSVEG (SEQ ID NO:44); GTELVGGGLDN (SEQ ID NO:45);
RSFDSGGSFEY (SEQ ID NO:64); VGSWYLEDFDI (SEQ ID NO:69);
GGNYGDYFDYFDY (SEQ ID NO:76); and DFWVTTSGNDY (SEQ ID NO:89); and a
light chain with three CDR that include an amino acid sequence at least 90%, 92%, 95%,
97% 98%, 99% or more identical to a sequence selected from the group consisting of the
amino acid sequence of TRSSGSIASNYVQ (SEQ ED NO:8); EDNQRPS (SEQ ID NO:9);
QSYDGSNRWM (SEQ ID NO:10); TRSSGSIASNYVQ (SEQ ID NO:16); EDNQRPS
(SEQ ID NO:17); QSNDSDNVV (SEQ ID NO:18); DDDQRPS (SEQ ID NO:25);
QSYDSSNW (SEQ ID NO:26); TRSGGSIGSYYVQ (SEQ ID NO:32); DDKKRPS (SEQ
ID NO:33); QSYDSNNLW (SEQ ED NO:34); TRSSGTIASNYVQ (SEQ ID NO:39);
QSYDNSNHWV (SEQ ED NO:40); TGSGGSIATNYVQ (SEQ ED NO:48);
QSYDSDNHHVV (SEQ ED NO:49); TGSSGSIASNYVQ (SEQ ID NO:55);
QSYDSSNQEW (SEQ ID NO:56); QSYDSNNFWV (SEQ ID NO:61);
TRSSGSIASNYVH (SEQ ID NO:72); QSSDTTYHGGW (SEQ ID NO:73); QSYEGF
(SEQ ID NO:79); TGRNGNIASNYVQ (SEQ ID NO:84); EDTQRPS (SEQ ID NO:85);
QSSDSNRVL (SEQ ID NO:86); QSFDSTNLW (SEQ ID NO:92); AGSSGSIASNYVQ
(SEQ ID NO:97); QSYSYNNQW (SEQ ID NO:98); TRSSGSIVSNYVQ (SEQ ID
NO: 106); EDNRRPS (SEQ ID NO: 107). The antibody binds IFNy.
2

WO 2006/109191 PCT/IB2006/001514
The huIFNy antibodies of the invention include a VH CDR1 region comprising the
amino acid sequence SYAMS (SEQ ID NO:3) or SNAMS (SEQ ID NO:43); a VH CDR2
region comprising the amino acid sequence AISGSGGSTYYADSVKG (SEQ ID NO:4) or
TLTGSGGTAYYADSVEG (SEQ ID NO:44), and a VH CDR3 region comprising an amino
acid sequence selected from the group consisting of DGSSGWYVPHWFDP (SEQ ID
NO:5); DHSSGWYVISGMDV (SEQ ID NO.13); DLTVGGPWYYFDY (SEQ ID NO:21);
DGWNALGWLES (SEQ ID NO:29); GTELVGGGLDN (SEQ ID NO:45);
RSFDSGGSFEY (SEQ ID NO:64); VGSWYLEDFDI (SEQ ID NO:69);
GGNYGDYFDYFDY (SEQ ID NO:76); and DFWVITSGNDY (SEQ ID NO:89).
The huIFNy antibodies include a VL CDR1 region comprising an amino acid
sequence selected from the group consisting of TRSSGSIASNYVQ (SEQ ID NO:8);
TRSSGSIASNYVQ (SEQ ID NO: 16); TRSGGSIGSYYVQ (SEQ ID NO:32);
TRSSGTIASNYVQ (SEQ ID NO:39); TGSGGSIATNYVQ (SEQ ID NO:48);
TGSSGSIASNYVQ (SEQ ID NO:55); TRSSGSIASNYVH (SEQ ID NO:72);
TGRNGNIASNYVQ (SEQ ID NO:84); AGSSGSIASNYVQ (SEQ ID NO:97) and
TRSSGSrVSNYVQ (SEQ ID NO: 106); a VL CDR2 region comprising an amino acid
sequence selected from the group consisting of EDNQRPS (SEQ ID NO:9); EDNQRPS
(SEQ ID NO: 17); DDDQRPS (SEQ ID NO:25); DDKKRPS (SEQ EDNO.-33); EDTQRPS
(SEQ ID NO:85) and EDNRRPS (SEQ ID NO: 107); and a VL CDR3 region comprising an
amino acid sequence selected from the group consisting of QSYDGSNRWM (SEQ ID
NO: 10); QSNDSDNW (SEQ IDNO:18); QSYDSSNVV (SEQ ID NO:26);
QSYDSNNLW (SEQ ID NO:34); QSYDNSNHWV (SEQ ID NO:40); QSYDSDNHHW
(SEQ ID NO:49); QSYDSSNQEW (SEQ ID NO:56); QSYDSNNFWV (SEQ ID NO:61);
QSSDTTYHGGW (SEQ ID NO:73); QSYEGF (SEQ ID NO:79); QSSDSNRVL (SEQ ID
NO:86); QSFDSTNLW (SEQ ID NO:92); and QSYSYNNQW (SEQ ID NO:98).
The huIFNy antibodies include, for example, a VH CDR1 region comprising the
amino acid sequence SYAMS (SEQ ID NO:3) or SNAMS (SEQ ID NO:43); a VH CDR2
region comprising the amino acid sequence AISGSGGSTYYADSVKG (SEQ ID NO:4) or
TLTGSGGTAYYADSVEG (SEQ ID NO:44); a VH CDR3 region comprising an amino
acid sequence selected from the group consisting of DGSSGWYVPHWFDP (SEQ ID
NO:5); DHSSGWYVISGMDV (SEQ ID NO: 13); DLTVGGPWYYFDY (SEQ ID NO:21);
DGWNALGWLES (SEQ ID NO:29); GTELVGGGLDN (SEQ ID NO:45);
3

WO 2006/109191 PCT/IB2006/001514
RSFDSGGSFEY (SEQ ID NO:64); VGSWYLEDFDI (SEQ ID NO:69);
GGNYGDYFDYFDY (SEQ ID NO:76); and DFWVITSGNDY (SEQ ID NO:89); a VL
CDR1 region comprising an amino acid sequence selected from the group consisting of
TRSSGSIASNYVQ (SEQ ID NO:8); TRSSGSIASNYVQ (SEQ ID NO: 16);
TRSGGSIGSYYVQ (SEQ ID NO:32); TRSSGTIASNYVQ (SEQ ID NO:39);
TGSGGSIATNYVQ (SEQ ED NO:48); TGSSGSIASNYVQ (SEQ ID NO:55);
TRSSGSIASNYVH (SEQ ID NO:72); TGRNGNIASNYVQ (SEQ ID NO:84);
AGSSGSIASNYVQ (SEQ IDNO:97) and TRSSGSIVSNYVQ (SEQ ID NO: 106); a VL
CDR2 region comprising an amino acid sequence selected from the group consisting of
EDNQRPS (SEQ ID NO:9); EDNQRPS (SEQ ID NO: 17); DDDQRPS (SEQ ID NO:25);
DDKKRPS (SEQ ID NO:33); EDTQRPS (SEQ ID NO:85) and EDNRRPS (SEQ ID
NO: 107); and a VL CDR3 region comprising an amino acid sequence selected from the
group consisting of QSYDGSNRWM (SEQ ID NO: 10); QSNDSDNVV (SEQ ID NO: 18);
QSYDSSNW (SEQ ID NO:26); QSYDSNNLW (SEQ ID NO:34); QSYDNSNHWV
(SEQ ID NO:40); QSYDSDNHHW (SEQ ID NO:49); QSYDSSNQEVV (SEQ ID
NO:56); QSYDSNNFWV (SEQ IDNO:61); QSSDTTYHGGW (SEQ ID NO:73);
QSYEGF (SEQ ID NO:79); QSSDSNRVL (SEQ ID NO:86); QSFDSTNLW (SEQ ID
NO:92); and QSYSYNNQW (SEQ ID NO:98).
The heavy chain of a huDFNy antibody is derived from a germ line V (variable) gene
such as, for example, the DP47 (IGHV3-23) germline gene (GenBank Accession No.
M99660) or a nucleic acid sequence homologous to the human DP47 germline gene
sequence. The nucleic acid sequence for the DP47 (IGHV 3-23) germline gene includes,
for example, the nucleic acid sequence shown below:
GAGGTGCAGCTGTTGGAGTCTGGGGGAGGCTTGGTACAGCCTGGGGC3GTCCCTGAGACTC
TCCTGTGCAGCCTCTGGATTCACCTTTAGCAGCTATGCCATGAGCTGGGTCCGCCAGGCT
CCAGGGAAGGGGCTGGAGTGGGTCTCAGCTATTAGTGGTAGTGGTGGTAGCACATACTAC
GCAGACTCCGTGAAGGGCCGGTTCACCATCTCCAGAGACAATTCCAAGAACACGCTGTAT
CTGCAAATGAACAGCCTGAGAGCCGAGGACACGGCCGTATATTACTGTGCGAAAGA (SEQ
ID NO:99)
The light chain of a huIFNy antibody is derived from a Ig lambda light chain
variable region germline gene such as, for example, the IGLV6-57 or VI-22 (GenBank
Accession No. Z73673) or a nucleic acid sequence homologous to the human IGLV6-57
4

WO 2006/109191 PCT/IB2006/001514
geTmline gene sequence. The nucleic acid sequence for the IGLV6-57 germline gene
includes, for example, the nucleic acid sequence shown below:
AATTTTATGCTGACTCAGCCCCACTCTGTGTCX3GAGTCTCCGGGGAAGACGGTAACCATC
TCCTGCACCCGCAGCAGTGGCAGCATTGCCAGCAACTATGTGCAGTGGTACCAGCAGCGC
CCGGGCAGTTCCCCCACCACTGTGATCTATGAGGATAACCAAAGACCCTCTGGGGTCCCT
GATCGGTTCTCTGGCTCCATCGACAGCTCCTCCAACTCTGCCTCCCTCACCATCTCTGGA
CTGAAGACTGAGGACGAGGCTGACTACTACTGTCAGTCTTATGATAGCAGCAATCA (SEQ
ID NO: 108)
In another aspect, the invention provides methods of treating, preventing or
alleviating a symptom of an immune-related disorder by administering a hufPNy antibody
to a subject. For example, the huIFNy antibodies are used to treat, prevent or alleviate a
symptom associated with immune-related disorders such as Crohn's Disease, systemic
lupus erythematosus, psoriasis, sarcoidosis, rheumatoid arthritis, vasculitis, atopic
dermatitis and secondary progressive multiple sclerosis. Optionally, the subject is further
administered with a second agent such as, but not limited to, an anti-cytokine or anti-
chemokine reagent that recognizes cytokines such as interleukin 1 (IL-1), IL-2, IL-4, IL-6,
IL-12, IL-13, IL-15, IL-17, IL-18, IL-20, IL-21, IL-22, IL-23, IL-27 and IL-31, and/or
chemokines such as MIP1 alpha, MEP1 beta, RANTES, MCP1, IP-10, ITAC, MTG, SDF
and firactalkine.
The subject is suffering from or is predisposed to developing an immune related
disorder, such as, for example, an autoimmune disease or an inflammatory disorder.
BRIEF DESCRIPTION OF THE DRAWINGS
Figure 1 is a series of representations of the nucleotide sequence and amino acid
sequences for the variable light and variable heavy regions of the huIFNy antibodies NI-
0501 and AC1.2R3P2_A6. Figure 1A depicts the nucleotide sequence encoding the
variable region of the heavy chain of NI-0501, and Figure IB represents the amino acid
sequence encoded by the nucleotide sequence shown in Figure 1A. The complementarity
determining regions (CDRs) are underlined in Figure IB. Figure 1C depicts the nucleotide
sequence encoding the variable region of the light chain of NI-0501, and Figure ID
represents the amino acid sequence encoded by the nucleotide sequence shown in Figure
1C. The CDRs are underlined in Figure ID. Figure IE depicts the nucleotide sequence
encoding the variable region of the heavy chain of AC1.2R3P2_A6, and Figure IF

WO 2006/109191 PCT/IB2006/001514
represents the amino acid sequence encoded by the nucleotide sequence shown in Figure
IE. The CDRs are underlined in Figure IF. Figure 1G depicts the nucleotide sequence
encoding the variable region of the light chain of AC1.2R3P2_A6, and Figure 1H represents
the amino acid sequence encoded by the nucleotide sequence shown in Figure 1G. The
CDRs are underlined in Figure 1H.
Figure 2 is a series of representations of the nucleotide sequence and amino acid
sequences for the variable light and variable heavy regions of the huIFNy antibody
AC1.2R3P2_B4. Figure 2A depicts the nucleotide sequence encoding the variable region of
the heavy chain, and Figure 2B represents the amino acid sequence encoded by the
nucleotide sequence shown in Figure 2A. The CDRs are underlined in Figure 2B. Figure
2C depicts the nucleotide sequence encoding the variable region of the light chain, and
Figure 2D represents the amino acid sequence encoded by the nucleotide sequence shown in
Figure 2C. The CDRs are underlined in Figure 2D.
Figure 3 is a series of representations of the nucleotide sequence and amino acid
sequences for the variable light and variable heavy regions of the huIFNy antibody
ADI .4R4P1_B9. Figure 3A depicts the nucleotide sequence encoding the variable region
of the heavy chain, and Figure 3B represents the amino acid sequence encoded by the
nucleotide sequence shown in Figure 3A. The CDRs are underlined in Figure 3B. Figure
3C depicts the nucleotide sequence encoding the variable region of the light chain, and
Figure 3D represents the amino acid sequence encoded by the nucleotide sequence shown in
Figure 3C. The CDRs are underlined in Figure 3D.
Figure 4 is a series of representations of the nucleotide sequence and amino acid
sequences for the variable light and variable heavy regions of the huIFNy antibody
ADI .4R4P2C9. Figure 4A depicts the nucleotide sequence encoding the variable region
of the heavy chain, and Figure 4B represents the amino acid sequence encoded by the
nucleotide sequence shown in Figure 4A. The CDRs are underlined in Figure 4B. Figure
4C depicts the nucleotide sequence encoding the variable region of the light chain, and
Figure 4D represents the amino acid sequence encoded by the nucleotide sequence shown in
Figure 4C. The CDRs are underlined in Figure 4D.
Figure 5 is a series of representations of the nucleotide sequence and amino acid
sequences for the variable light and variable heavy regions of the huIFNy antibody
AC1.4R4P2_C10. Figure 5A depicts the nucleotide sequence encoding the variable region
6

WO 2006/109191 PCT/IB2006/001514
of the heavy chain, and Figure 5B represents the amino acid sequence encoded by the
nucleotide sequence shown in Figure 5A. The CDRs are underlined in Figure 5B. Figure
5C depicts the nucleotide sequence encoding the variable region of the light chain, and
Figure 5D represents the amino acid sequence encoded by the nucleotide sequence shown in
Figuie 5C. The CDRs are underlined in Figure 5D.
Figure 6 is a series of representations of the nucleotide sequence and amino acid
sequences for the variable light and variable heavy regions of the huIFNy antibody
AC1.2R3P7_D3. Figure 6A depicts the nucleotide sequence encoding the variable region
of the heavy chain, and Figure 6B represents the amino acid sequence encoded by the
nucleotide sequence shown in Figure 6A. The CDRs are underlined in Figure 6B. Figure
6C depicts the nucleotide sequence encoding the variable region of the light chain, and
Figure 6D represents the amino acid sequence encoded by the nucleotide sequence shown in
Figure 6C. The CDRs are underlined in Figure 6D.
Figure 7 is a series of representations of the nucleotide sequence and amino acid
sequences for the variable light and variable heavy regions of the huIFNy antibody
AD1.2R2P2_D6. Figure 7A depicts the nucleotide sequence encoding the variable region
of the heavy chain, and Figure 7B represents the amino acid sequence encoded by the
nucleotide sequence shown in Figure 7A. The CDRs are underlined in Figure 7B. Figure
7C depicts the nucleotide sequence encoding the variable region of the light chain, and
Figure 7D represents the amino acid sequence encoded by the nucleotide sequence shown in
Figure 7C. The CDRs are underlined in Figure 7D.
Figure 8 is a series of representations of the riucleotide sequence and amino acid
sequences for the variable light and variable heavy regions of the huIFNy antibody
AC1.2R2P2_D8. Figure 8A depicts the nucleotide sequence encoding the variable region
of the heavy chain, and Figure 8B represents the amino acid sequence encoded by the
nucleotide sequence shown in Figure 8A. The CDRs are underlined in Figure 8B. Figure
8C depicts the nucleotide sequence encoding the variable region of the light chain, and
Figure 8D represents the amino acid sequence encoded by the nucleotide sequence shown in
Figure 8C. The CDRs are underlined in Figure 8D.
Figure 9 is a series of representations of the nucleotide sequence and amino acid
sequences for the variable light and variable heavy regions of the hulFNy antibody
AD1.3R3P6JB1. Figure 9A depicts the nucleotide sequence encoding the variable region of
7

WO 2006/109191 PCT/IB2006/001514
the heavy chain, and Figure 9B represents the amino acid sequence encoded by the
nucleotide sequence shown in Figure 9A. The CDRs are underlined in Figure 9B. Figure
9C depicts the nucleotide sequence encoding the variable region of the light chain, and
Figure 9D represents the amino acid sequence encoded by the nucleotide sequence shown in
Figure 9C. The CDRs are underlined in Figure 9D.
Figure 10 is a series of representations of the nucleotide sequence and amino acid
sequences for the variable light and variable heavy regions of the huIFNy antibody
ADI .3R3P5F8. Figure 10A depicts the nucleotide sequence encoding the variable region
of the heavy chain, and Figure 10B represents the amino acid sequence encoded by the
nucleotide sequence shown in Figure 10A. The CDRs are underlined in Figure 10B. Figure
IOC depicts the nucleotide sequence encoding the variable region of the light chain, and
Figure 10D represents the amino acid sequence encoded by the nucleotide sequence shown
in Figure IOC. The CDRs are underlined in Figure 10D.
Figure 11 is a series of representations of the nucleotide sequence and amino acid
sequences for the variable light and variable heavy regions of the huIFNy antibody
AD1.3R3P6JF9. Figure 11A depicts the nucleotide sequence encoding the variable region
of the heavy chain, and Figure 1 IB represents the amino acid sequence encoded by the
nucleotide sequence shown in Figure 11A. The CDRs are underlined in Figure 1 IB. Figure
11C depicts the nucleotide sequence encoding the variable region of the light chain, and
Figure 1 ID represents the amino acid sequence encoded by the nucleotide sequence shown
in Figure 11C. The CDRs are underlined in Figure 1 ID.
Figure 12 is a series of representations of the nucleotide sequence and amino acid
sequences for the variable light and variable heavy regions of the huIFNy antibody
AD1.4R4P2J37. Figure 12A depicts the nucleotide sequence encoding the variable region
of the heavy chain, and Figure 12B represents the amino acid sequence encoded by the
nucleotide sequence shown in Figure 12A. The CDRs are underlined in Figure 12B. Figure
12C depicts the nucleotide sequence encoding the variable region of the light chain, and
Figure 12D represents the amino acid sequence encoded by the nucleotide sequence shown
in Figure 12C. The CDRs are underlined in Figure 12D.
Figure 13 is a series of representations of the nucleotide sequence and amino acid
sequences for the variable light and variable heavy regions of the huIFNy antibody
AD1.1R3P3_G9. Figure 13A depicts the nucleotide sequence encoding the variable region
8

WO 2006/109191 PCT/IB2006/OO1514
of the heavy chain, and Figure 13B represents the amino acid sequence encoded by the
nucleotide sequence shown in Figure 13A. The CDRs are underlined in Figure 13B. Figure
13C depicts the nucleotide sequence encoding the variable region of the light chain, and
Figure 13D represents the amino acid sequence encoded by the nucleotide sequence shown
in Figure 13C. The CDRs are underlined in Figure 13D.
Figure 14 is a series of representations of the nucleotide sequence and amino acid
sequences for the variable light and variable heavy regions of the huIFNy antibody
AD1.3R3P6_G10. Figure 14A depicts the nucleotide sequence encoding the variable region
of the heavy chain, and Figure 14B represents the ammo acid sequence encoded by the
nucleotide sequence shown in Figure 14A. The CDRs are underlined in Figure 14B. Figure
14C depicts the nucleotide sequence encoding the variable region of the light chain, and
Figure 14D represents the amino acid sequence encoded by the nucleotide sequence shown
in Figure 14C. The CDRs are underlined in Figure 14D.
Figure 15 is a graph depicting the inhibition of IFNy-induced reporter gene
expression using periplasmic scFv extracts. Quantified scFv extracts inhibited the IFNy-
induced reporter gene in a dose dependant fashion. For each scFv clone various
concentrations (2.7,0.68,0.17,0.043 and 0.011 nM) were tested as shown by the columns
above each clone name (descending concentration from left to right, see also Table 3
below).
Figure 16, Panels 1-12 are a series of graphs depicting the inhibition of IFNy-
induced MHC class II expression on melanoma cells using scFv extracts. Purified fully
human scFv inhibited IFNy-induced MHC II expression on melanoma cells. scFv clones (
) and the mouse anti-human IFNy mAb 16C3 (—) are depicted.
Figure 17, Panels 1-7 are a series of graphs depicting the inhibition of IFNy-induced
MHC class II expression on melanoma cells using scFv extracts that were reformatted onto
a fully human IgG backbone. Purified fully IgG mAbs inhibited IFNy-induced MHC II
expression on melanoma cells. Fully IgG clones (-X-), the mouse anti-human IFNy mAb
16C3 (- A.-), and the R&D Systems, Inc. (Minneapolis, MN) mouse anti-human IFNy
MAB285 (-•-) are depicted.
Figure 18 is a graph depicting the affinity of the NI-0501 huIFNy antibody for
human IFNy.
9

WO 2006/109191 PCT/IB2006/001514
Figure 19 is a graph comparing the activity of antibodies produced by the A6 and
NI-0501 (also referred to herein as "A6 back-mutated to germline" or "back-mutated A6")
clones.
Figure 20 is a graph depicting the activity of the NI-0501 huIFNy antibody on native
human IFNy.
Figures 21A-21F are a series of graphs depicting the binding of the NI-0501 huIFNy
antibody with recombinant IFNy from various species.
Figure 22 is a graph depicting the ability of the NI-0501 huIFNy antibody to
neutralize the MHC class II upregulation induced by native cynomolgus IFNy.
Figure 23 is a graph depicting the ability of the NI-0501 huIFNy antibody to block
IFNy-induced IP-10 production in whole blood.
DETAILED DESCRIPTION
The present invention provides fully human monoclonal antibodies specific against
interferon gamma (IFNy). The antibodies are collectively referred to herein is huIFNy
antibodies.
The huIFNy antibodies are, for example, IFNy antagonists or inhibitors that
modulate at least one biological activity of IFNy. Biological activities of IFNy include, for
example, binding the IFNy receptor (IFNy-R), modulating, e.g., reducing or inhibiting,
major histocompatibility complex (MHC) class II expression on a cell surface, and
modulating, e.g., reducing or inhibiting, cell proliferation. For example, the huIFNy
antibodies completely or partially inhibit IFNy activity by partially or completely blocking
the binding of IFNy and the IFNy receptor (IFNy-R). The IFNy antibodies are considered to
completely inhibit IFNy activity when the level of IFNy activity in the presence of the
huIFNy antibody is decreased by at least 95%, e.g., by 96%, 97%, 98%, 99% or 100% as
compared to the level of IFNy activity in the absence of binding with a huIFNy antibody
described herein. The IFNy antibodies are considered to partially inhibit IFNy activity
when the level of IFNy activity in the presence of the huTFNy antibody is decreased by less
than 95%, e.g., 10%, 20%, 25%, 30%, 40%, 50%, 60%, 75%, 80%, 85% or 90% as
compared to the level of IFNy activity in the absence of binding with a huIFNy antibody
described herein.
10

WO 2006/109191 PCT/IB2006/001514
Additionally, the huIFNy antibodies of the invention inhibit IFNy-induced MHC
class II expression on cells (see e.g., Examples 4 and 5). Preferably, the huIFNy antibodies
exhibit greater than 50% inhibition of IFNy-induced MHC class II expression in the hitman
melanoma cell line Me67.8 at a concentration of at least 0.02 nM. For example, the
antibodies exhibit greater than 50% inhibition of IFNy-induced MHC class II expression in
the Me67.8 cell line at a concentration in the range of 0.022 nM to 0.044 nM, eg., at a
concentration of 0.022 nM, 0.028 nM or 0.044 nM.
The huIFNy antibodies modulate an immune response in a subject, e.g., in a human
subject. Preferably, the huIFNy antibodies modulate an adaptive immune response in a
subject. More preferably, the huIFNy antibodies modulate the cellular or cell-mediated
immune response, also known as Thl-type or Thl-mediated response.
For example, the huIFNy antibodies described herein modulate, e.g., reduce, inhibit
or prevent an exaggerated Thl-mediated immune response, such as an exaggerated Thl-
mediated immune response associated with an autoimmune or inflammatory disorder such
as, for example, Crohn's disease, system lupus erythematosus, psoriasis, sarcoidosis,
Theumatoid arthritis, vasculitis, atopic dermatitis and secondary progressive multiple
sclerosis. As used herein, the term "exaggerated" Thl-mediated immune response refers to
the presence of an elevated level of Thl cytokine(s), such as IL-2, IL-3, TNF-alpha (TNFa)
and IFNy, in a subject as compared to the level of Thl cytokine production in a subject not
suffering from a disease or disorder associated with an exaggerated Thl immune response.
To classify a Till -mediated immune response as an exaggerated response, the level of a Till
cytokine production response is evaluated, e.g., by measuring and analyzing the level of
secreted cytokines using an ELISA or other assay.
The huIFNy antibodies described herein modulate, e.g., inhibit, reduce or prevent,
class switching to an IgG isotype, such as IFNy-induced class switching. These huIFNy
antibodies modulate, e.g., inhibit, prevent or reduce a Thl-mediated response and
consequently decrease IFNy-induced switching.
The huIFNy antibodies of the invention were produced by immunizing an animal
with IFNy, such as, for example, murine or human IFNy (see e.g., Genbank Accession No.
X13274) or an immunogenic fragment, derivative or variant thereof. Alternatively, the
animal is immunized with cells transfected with a vector containing a nucleic acid molecule
encoding IFNy, such that IFNy is expressed and associated with the surface of the
11

WO 2006/109191

PCT/IB2006/001514

transfected cells. Alternatively, the antibodies are obtained by screening a library that
contains antibody or antigen binding domain sequences for binding to IFNy. This library is
prepared, e.g., in bacteriophage as protein or peptide fusions to a bacteriophage coat protein
that is expressed on the surface of assembled phage particles and the encoding DNA
sequences contained within the phage particles (i.e., "phage displayed library").
huIFNy antibodies of the invention include, for example, the heavy chain
complementarity determining regions (CDRs) shown below in Table 1, the light chain
CDRs shown in Table 2, and combinations thereof.
Table 1. VH sequences from antibody clones that bind and neutralize IFNy

10
12

WO 2006/109191

PCT/IB2006/0O1514


Table 2. VL sequences from antibody clones that bind and neutralize IFNy
An exemplary huIFNy monoclonal antibody is the NI-0501 antibody described
herein. The NI-0501 antibody is a back-mutated version of the AC1.2R3.P2_A6 antibody.
As used herein, the term "back-mutated" refers to mutating a nucleotide or amino acid
residue back to the nucleotide or residue found at the corresponding location in the germline
sequence. The NI-0501 antibody includes a heavy chain variable region (SEQ ID NO:2)
13

WO 2006/109191 PCT7IB2006/001514
encoded by the nucleic acid sequence shown in SEQ ID NO: 1, and a light chain variable
region (SEQ ID NO:7) encoded by the nucleic acid sequence shown in SEQ ID NO:6
(Figures 1A-1D).
The amino acids encompassing the complementarity determining regions (CDR) as
defined by Chothia et al. and E.A. Kabat et al. are underline in Figures IB and ID. (See
Chothia, C, etal, Nature 342:877-883 (1989); Kabat, EA, et al, Sequences of Protein of
immunological interest, Fifth Edition, US Department of Health and Human Services, US
Government Printing Office (1991)). The heavy chain CDRs of the A6 antibody have the
following sequences: SYAMS (SEQ ID NO:3); AISGSGGSTYYADSVKG (SEQ ID
NO:4); and DGSSGWYVPHWFDP (SEQ ID NO:5). The light chain CDRs of the A6
antibody have the following sequences: TRSSGSIASNYVQ (SEQ ID NO:8); EDNQRPS
(SEQ ID NO:9); and QSYDGSNRWM (SEQ ID NO: 10).
Another exemplary huIFNT monoclonal antibody is the AC12R3.P2_A6 antibody
("A6") described herein. The A6 antibody includes a heavy chain variable region (SEQ ID
NO: 103) encoded by the nucleic acid sequence shown in SEQ ID NO: 102, and a light chain
variable region (SEQ ID NO:105) encoded by the nucleic acid sequence shown in SEQ ID
NO:104 (Figures 1E-1H). The amino acids encompassing the complementarity determining
regions (CDR) as defined by Chothia et al. and E.A. Kabat et al, are underline in Figures IF
and 1H. {See Chothia, C, et al., Nature 342:877-883 (1989); Kabat, EA, et al., Sequences of
Protein of immunological interest, Fifth Edition, US Department of Health and Human
Services, US Government Printing Office (1991)). The heavy chain CDRs of the A6
antibody have the following sequences: SYAMS (SEQ DD NO:3);
AISGSGGSTYYADSVKG (SEQ ID NO:4); and DGSSGWYVPHWFDP (SEQ ID NO:5).
The light chain CDRs of the A6 antibody have the following sequences:
TRSSGSIVSNYVQ (SEQ ID NO:106); EDNRRPS (SEQ ED NO:107); and
QSYDGSNRWM (SEQ ID NO:10).
The AC1.2R3P2_B4 antibody (also referred to herein as "B4") includes a heavy
chain variable region (SEQ ID NO: 12) encoded by the nucleic acid sequence shown in SEQ
ID NO:11, and a light chain variable region (SEQ ID NO:15) encoded by the nucleic acid
sequence shown in SEQ ED NO: 14 (Figures 2A-2D). The amino acids encompassing the
CDR as defined by Chothia et al. 1989, E.A. Kabat et al., 1991 are underlined in Figures 2B
and 2D. The heavy chain CDRs of the B4 antibody have the following sequences: SYAMS
14

WO 2006/109191 PCT/IB2006/001514
(SEQ ID NO:3); AISGSGGSTYYADSVKG (SEQ ID NO:4); and DHSSGWYVTSGMDV
(SEQ ID NO:13). The light chain CDRs of the B4 antibody have the following sequences:
TRSSGSIASNYVQ (SEQ ID NO:16); EDNQRPS (SEQ ID NO:17); and QSNDSDNVV
(SEQ ID NO: 18).
The AD1.4R4P1_B9 antibody (also referred to herein as "B9") includes a heavy
chain variable region (SEQ ID NO:20) encoded by the nucleic acid sequence shown in SEQ
ID NO: 19, and a light chain variable region (SEQ ID NO:23) encoded by the nucleic acid
sequence shown in SEQ ID NO:22 (Figures 3A-3D). The amino acids encompassing the
CDR as defined by Chothia et al. 1989, E.A. Kabat et al., 1991 are underlined in Figures 3B
and 3D. The heavy chain CDRs of the B9 antibody have the following sequences: SYAMS
(SEQ ID NO:3); AISGSGGSTYYADSVKG (SEQ ID NO:4); and DLTVGGPWYYFDY
(SEQ ID NO:21). The light chain CDRs of the B9 antibody have the following sequences:
TRSSGSIVSNYVQ (SEQ ID NO;8); DDDQRPS (SEQ ID NO:25); and QSYDSSNVV
(SEQ ID NO:26).
The AD1.4R4P2_C9 antibody (also referred to herein as "C9") includes a heavy
chain variable region (SEQ ID NO:28) encoded by the nucleic acid sequence shown in SEQ
ID NO:27, and a light chain variable region (SEQ ID NO:31) encoded by the nucleic acid
sequence shown in SEQ ID NO:30 (Figures 4A-4D). The amino acids encompassing the
CDR as defined by Chothia et al. 1989, E.A. Kabat et al., 1991 are underlined in Figures 4B
and 4D. The heavy chain CDRs of the C9 antibody have the following sequences: SYAMS
(SEQ ID NO:3); AISGSGGSTYYADSVKG (SEQ ID NO:4); and DGWNALGWLES
(SEQ ID NO:29). The light chain CDRs of the C9 antibody have the following sequences:
TRSGGSIGSYYVQ (SEQ ID NO:32); DDKKRPS (SEQ ID NO:33); and QSYDSNNLW
(SEQ ID NO.-34).
The AC1.4R4P2_C 10 antibody (also referred to herein as "CIO") includes a heavy
chain variable region (SEQ ID NO:36) encoded by the nucleic acid sequence shown in SEQ
ID NO:35, and a light chain variable region (SEQ ID NO:38) encoded by the nucleic acid
sequence shown in SEQ ID NO:37 (Figures 5A-5D). The amino acids encompassing the
CDR as defined by Chothia et al. 1989, E.A. Kabat et al., 1991 are underlined in Figures 5B
and 5D. The heavy chain CDRs of the CIO antibody have the following sequences:
SYAMS (SEQ ID NO:3); AISGSGGSTYYADSVKG (SEQ ID NO:4); and
DGSSGWYVPHWF DP (SEQ ID NO:5). The light chain CDRs of the CIO antibody have
15

WO 2006/109191 PCT/IB2006/001514
the following sequences: TRSSGTIASNYVQ (SEQ ID NO:39); EDNQRPS (SEQ ID
NO:17); and QSYDNSNHWV (SEQ ID NO.40).
The AC1.2R3P7J33 antibody (also referred to herein as "D3") includes a heavy
chain variable region (SEQ ID NO:42) encoded by the nucleic acid sequence shown in SEQ
ID KO:41, and a light chain variable region (SEQ ID NO:47) encoded by the nucleic acid
sequence shown in SEQ ID NO:46 (Figures 6A-6D). The amino acids encompassing the
CDR as defined by Chothia et al. 1989, E.A. Kabat et al., 1991 are underlined in Figures 6B
and 6D. The heavy chain CDRs of the D3 antibody have the following sequences: SNAMS
(SEQ ID NO:43); TLTGSGGTAYYADSVEG (SEQ ID NO:44); and GTELVGGGLDN
(SEQ ID NO:45). The light chain CDRs of the D3 antibody have the following sequences:
TGSGGSIATNYVQ (SEQ ED NO:48); EDNQRPS (SEQ ID NO: 17) and
QSYDSDNHHW (SEQ ID NO:49).
The ADI .2R2P2_D6 antibody (also referred to herein as "D6") includes a heavy
chain variable region (SEQ ID NO: 51) encoded by the nucleic acid sequence shown in SEQ
ID NO:50, and a light chain variable Tegion (SEQ ID NO:54) encoded by the nucleic acid
sequence shown in SEQ ID NO: 53 (Figures 7A-7D). The amino acids encompassing the
CDR as defined by Chothia et al. 1989, E.A. Kabat et al., 1991 are underlined in Figures 7B
and 7D. The heavy chain CDRs of the D6 antibody have the following sequences: SYAMS
(SEQ ID NO:3); AISGSGGSTYYADSVKG (SEQ ID NO:4); and DGWNALGWLES
(SEQ ID NO:29). The light chain CDRs of the D6 antibody have the following sequences:
TGSSGSIASNYVQ (SEQ ID NO:55); EDNQRPS (SEQ ID NO:17); and
QSYDSSNQEVV (SEQ ID NO:56).
The AC1.2R2P2_D8 antibody (also referred to herein as "D8") includes a heavy
chain variable region (SEQ ID NO:58) encoded by the nucleic acid sequence shown in SEQ
ID NO:57, and a light chain variable region (SEQ ID NO:60) encoded by the nucleic acid
sequence shown in SEQ ID NO:59 (Figures 8A-8D). The amino acids encompassing the
CDR as defined by Chothia et al. 1989, E.A. Kabat et al., 1991 are underlined in Figures 8B
and 8D. The heavy chain CDRs of the D8 antibody have the following sequences: SYAMS
(SEQ ID NO:3); AISGSGGSTYYADSVKG (SEQ ID NO:4); and DGSSGWYVPHWF DP
(SEQ ID NO: 5). The light chain CDRs of the D8 antibody have the following sequences:
TRSSGSIVSNYVQ (SEQ ID NO:8); EDNQRPS (SEQ ID NO:17); and QSYDSNNFWV
(SEQ ID NO:61).
16

WO 2006/109191 PCT/IB2006/001514
The ADI .3R3P6_E1 antibody (also referred to herein as "El") includes a heavy
chain variable region (SEQ ED NO:63) encoded by the nucleic acid sequence shown in SEQ
ID NO:62, and a light chain variable region (SEQ ID NO:66) encoded by the nucleic acid
sequence shown in SEQ ID NO:65 (Figures 9A-9D). The amino acids encompassing the
CDR as defined by Chothia et al. 1989, EA Kabat et al, 1991 are underlined in Figures 9B
and 9D. The heavy chain CDRs of the El antibody have the following sequences: SYAMS
(SEQ ID NO:3); AISGSGGSTYYADSVKG (SEQ ID NO:4); and RSFDSGGSFEY (SEQ
ID NO:64). The light chain CDRs of the El antibody have the following sequences:
TRSSGSIVSNYVQ (SEQ ID NO:8); DDDQRPS (SEQ ID NO:25); and QSYDSSNW
(SEQ ID NO:26).
The AD1.3R3P5_F8 antibody (also referred to herein as "F8") includes a heavy
chain variable region (SEQ ID NO:68) encoded by the nucleic acid sequence shown in SEQ
ID NO:67, and a light chain variable region (SEQ ID NO:71) encoded by the nucleic acid
sequence shown in SEQ ID NO:70 (Figures 10A-10D). The amino acids encompassing the
CDR as defined by Chothia et al. 1989, E.A. Kabat et al., 1991 are underlined in Figures
10B and 10D. The heavy chain CDRs of the F8 antibody have the following sequences:
SYAMS (SEQ ID NO:3); AISGSGGSTYYADSVKG (SEQ ID NO:4); and
VGSWYLEDFDI (SEQ ID NO:69). The light chain CDRs of the F8 antibody have the
following sequences: TRSSGSIASNYVH (SEQ ID NO:72); EDNRRPS (SEQ ID NO:9);
and QSSDTTYHGGW (SEQ ID NO:73).
The AD1.3R3P6_F9 antibody (also referred to herein as "F9") includes a heavy
chain variable region (SEQ ID NO:75) encoded by the nucleic acid sequence shown in SEQ
ID NO:74, and a light chain variable region (SEQ ID NO:78) encoded by the nucleic acid
sequence shown in SEQ ID NO:77 (Figures 11A-1 ID). The amino acids encompassing the
CDR as defined by Chothia et al. 1989, E.A. Kabat et al., 1991 are underlined in Figures
1 IB and 1 ID. The heavy chain CDRs of the F9 antibody have the following sequences:
SYAMS (SEQ ID NO:3); AISGSGGSTYYADSVKG (SEQ ID NO:4); and
GGNYGDYFDYFDY (SEQ ID NO:76). The light chain CDRs of the F9 antibody have the
following sequences: TRSSGSIASNYVQ (SEQ ID NO: 16); EDNQRPS (SEQ ID NO: 17);
and QSYEGF (SEQ ID NO:79).
The ADI .4R4P2_G7 antibody (also referred to herein as "G7") includes a heavy
chain variable region (SEQ ID NO:81) encoded by the nucleic acid sequence shown in SEQ
17

WO 2006/109191 PCT/IB2006/001514
ID NO:80, and a light chain variable region (SEQ ID NO:83) encoded by the nucleic acid
sequence shown in SEQ ID NO:82 (Figures 12A-12D). The amino acids encompassing the
CDR as defined by Chothia et al. 1989, E.A. Kabat et al., 1991 are underlined in Figures
12B and 12D. The heavy chain CDRs of the G7 antibody have the following sequences:
5 SYAMS (SEQ ID NO:3); AISGSGGSTYYADSVKG (SEQ ID NO:4); and
DGWNALGWLES (SEQ ID NO:29). The light chain CDRs of the G7 antibody have the
following sequences; TGRNGNIASNYVQ (SEQ ID NO:84); EDTQRPS (SEQ ID NO:85);
and QSSDSNRVL (SEQ ID NO:86).
The ADI .1R3P3_G9 antibody (al.so referred to herein as "G9") includes a heavy
10 chain variable region (SEQ ID NO:88) encoded by the nucleic acid sequence shown in SEQ
ID NO:87, and a light chain variable region (SEQ ID NO:91) encoded by the nucleic acid
sequence shown in SEQ ID NO:90 (Figures 13A-13D). The amino acids encompassing the
CDR as defined by Chothia et al. 1989, E.A. Kabat et al., 1991 are underlined in Figures
13B and 13D. The heavy chain CDRs of the G9 antibody have the following sequences:
15 SYAMS (SEQ ID NO:3); AISGSGGSTYYADSVKG (SEQ ID NO:4); and
DFWV1TSGNDY (SEQ ID NO:89). The light chain CDRs of the Q9 antibody have the
following sequences: TRSSGSIASNYVQ (SEQ ID NO: 16); EDNRRPS (SEQ ID NO:9);
and QSFDSTNLVV (SEQ ID NO:92).
The ADI .3R3P6_G10 antibody (also referred to herein as "G10") includes a heavy
20 chain variable region (SEQ ID NO;94) encoded by the nucleic acid sequence shown in SEQ
ID NO:93, and a light chain variable region (SEQ ID NO:96) encoded by the nucleic acid
sequence shown in SEQ ID NO;95 (Figures 14A-14D). The amino acids encompassing the
CDR as defined by Chothia et al. 1989, E.A. Kabat et al., 1991 are underlined in Figures
14B and 14D. The heavy chain CDRs of the G10 antibody have the following sequences:
25 SYAMS (SEQ ID NO:3); AISGSGGSTYYADSVKG (SEQ ID NO:4); and
DGWNALGWLES (SEQ ID NO:29). The light chain CDRs of the G10 antibody have the
following sequences: AGSSGSIASNYVQ (SEQ IDNO:97); EDNQRPS (SEQ ID NO: 17);
and QSYSYNNQW (SEQ ID NO:98).
huIFNy antibodies of the invention also include antibodies that include a heavy
30 chain variable amino acid sequence that is at least 90%, 92%, 95%, 97% 98%, 99% or more
identical the amino acid sequence of SEQ ID NO: 2,12,20,28, 36,42, 51, 58, 63, 68, 75,
81, 88, 94, or 103 (Figures 1-14) and/or a light chain variable amino acid that is at least
18

WO 2006/109191 PCT/IB2006/001514
90%, 92%, 95%, 97% 98%, 99% or more identical the amino acid sequence of SEQ ID NO:
7,15,23,31,38,47,54,60,66,71, 78,83,91,96 or 105 (Figures 1-14).
Alternatively, the monoclonal antibody is an antibody that binds to the same epitope
as NI-0501, A6, B4, B9, C9, C10, D3, D6, D8, El, F8, F9, G7, G9 or G10.
Unless otherwise defined, scientific and technical terms used in connection with the
present invention shall have the meanings that are commonly understood by those of
ordinary skill in the art. Further, unless otherwise required by context, singular terms shall
include pluralities and plural terms shall include the singular. Generally, nomenclatures
utilized in connection with, and techniques of, cell and tissue culture, molecular biology,
and protein and oligo- or polynucleotide chemistry and hybridization described herein are
those well known and commonly used in the art. Standard techniques are used for
recombinant DNA, oligonucleotide synthesis, and tissue culture and transformation (e.g.,
electroporation, lipofection). Enzymatic reactions and purification techniques are
performed according to manufacturer's specifications or as commonly accomplished in the
art or as described herein. The foregoing techniques and procedures are generally
performed according to conventional methods well known in the art and as described in
various general and more specific references that are cited and discussed throughout the
present specification. See e.g., Sambrook et at. Molecular Cloning: A Laboratory Manual
(2d ed., Cold Spring Harbor Laboratory Press, Cold Spring Harbor, N.Y. (1989)). The
nomenclatures utilized in connection with, and the laboratory procedures and techniques of,
analytical chemistry, synthetic organic chemistry, and medicinal and pharmaceutical
chemistry described herein are those well known and commonly used in the art. Standard
techniques are used for chemical syntheses, chemical analyses, pharmaceutical preparation,
formulation, and delivery, and treatment of patients.
As utilized in accordance with the present disclosure, the following terms, unless
otherwise indicated, shall be understood to have the following meanings:
As used herein, the term "antibody" refers to immunoglobulin molecules and
immunologically active portions of immunoglobulin (Ig) molecules, i.e., molecules that
contain an antigen binding site that specifically binds (immunoreacts with) an antigen.
Such antibodies include, but are not limited to, polyclonal, monoclonal, chimeric, single
chain, Fab, Fab and F(ab)2 fragments, and an Fab expression library. By "specifically bind" or
"immunoreacts with" is meant that the antibody reacts with one or more antigenic
19

WO 2006/109191 PCT/1B2006/001514
determinants of the desired antigen and does not react (i.e., bind) with other polypeptides or
binds at much lower affinity (Kd > 10'6) with other polypeptides.
The basic antibody structural unit is known to comprise a tetramer. Each tetramer is
composed of two identical pairs of polypeptide chains, each pair having one "light" (about
25 kDa) and one "heavy" chain (about 50-70 kDa). The ammo-terminal portion of each
chain includes a variable region of about 100 to 110 or more amino acids primarily
responsible for antigen recognition. The carboxy-terminal portion of each chain defines a
constant Tegion primarily responsible for effector function. Human light chains are
classified as kappa and lambda light chains. Heavy chains are classified as mu, delta,
gamma, alpha, or epsilon, and define the antibody's isotype as IgM, IgD, IgA, and IgE,
respectively. Within light and heavy chains, the variable and constant regions are joined by
a "J" region of about 12 or more amino acids, with the heavy chain also including a "D"
region of about 10 more amino acids. See generally, Fundamental Immunology Ch. 7 (Paul,
W., ea., 2nd ed. Raven Press, N.Y. (1989)). The variable regions of each light/heavy chain
pair form the antibody binding site.
The term "monoclonal antibody" (MAb) or "monoclonal antibody composition", as
used herein, refers to a population of antibody molecules that contain only one molecular
species of antibody molecule consisting of a unique light chain gene product and a unique
heavy chain gene product. In particular, the complementarity determining regions (CDRs)
of the monoclonal antibody are identical in all the molecules of the population. MAbs
contain an antigen binding site capable of immunoreacting with a particular epitope of the
antigen characterized by a unique binding affinity for it.
In general, antibody molecules obtained from humans relate to any of the classes
IgG, IgM, IgA, IgE and IgD, which differ from one another by the nature of the heavy chain
present in the molecule. Certain classes have subclasses as well, such as IgG1 IgG2, and
others. Furthermore, in humans, the light chain may be a kappa chain or a lambda chain.
The term "antigen-binding site," or "binding portion" refers to the part of the
immunoglobulin molecule that participates in antigen binding. The antigen binding site is
formed by amino acid residues of the N-terminal variable ("V") regions of the heavy ("H")
and light ("L") chains. Three highly divergent stretches within the V regions of the heavy
and light chains, referred to as "hypervariable regions," are interposed between more
conserved flanking stretches known as "framework regions," or "FRs". Thus, the term "FR"
20

WO 2006/109191 PCT/IB2006/001514
refers to amino acid sequences which are naturally found between, and adjacent to,
hypervariable regions in immunoglobulins. In an antibody molecule, the three hypervariable
regions of a light chain and the three hypervariable regions of a heavy chain are disposed
relative to each other in three dimensional space to form an antigen-binding surface. The
antigen-binding surface is complementary to the three-dimensional surface of a bound
antigen, and the three hypervariable regions of each of the heavy and light chains are
referred to as "complementarity-determining regions," or "CDRs." The assignment of
amino acids to each domain is in accordance with the definitions of Kabat Sequences of
Proteins of Immunological Interest (National Institutes of Health, Bethesda, Md. (1987 and
1991)), or Chothia &Lesk J. Mol. Biol. 196:901-917 (1987), Chothia et al. Nature 342:878-
883 (1989).
As used herein, the term "epitope" includes any protein determinant capable of
specific binding to an imrnunoglobulin, a scFv, or a T-cell Teceptor. The term "epitope"
includes any protein determinant capable of specific binding to an immunoglobulin or T-
cell receptor. Epitopic determinants usually consist of chemically active surface groupings
of molecules such as amino acids or sugar side chains and usually have specific three
dimensional structural characteristics, as well as specific charge characteristics. An
antibody is said to specifically bind an antigen when the dissociation constant is preferably As used herein, the terms "immunological binding," and "immunological binding
properties" refer to the non-covalent interactions of the type which occur between an
immunoglobulin molecule and an antigen for which the immunoglobulin is specific. The
strength, or affinity of immunological binding interactions can be expressed in terms of the
dissociation constant (K affinity. Immunological binding properties of selected polypeptides are quantified using
methods well known in the art. One such method entails measuring the rates of antigen-
binding site/antigen complex formation and dissociation, wherein those rates depend on the
concentrations of the complex partners, the affinity of the interaction, and geometric
parameters that equally influence the rate in both directions. Thus, both the "on rate
constant" (Kon) and the "off rate constant" (Koff) can be determined by calculation of the
concentrations and the actual rates of association and dissociation. {See Nature 361:186-87
(1993)). The ratio of Koff/Kon enables the cancellation of all parameters not related to
21

WO 2006/109191 PCT/IB2006/001514
affinity, and is equal to the dissociation constant Kd. {See, generally, Davies et al. (1990)
Annual Rev Biochem 59:439-473). An antibody of the present invention is said to
specifically bind to an IFNy epitope when the equilibrium binding constant (Kd) is :S1 mM,
preferably pM, as measured by assays such as radioligand binding assays or similar assays known to
those skilled in the art.
Those skilled in the art will recognize that it is possible to determine, without undue
experimentation, if a human monoclonal antibody has the same specificity as a hitman
monoclonal antibody of the invention (e.g., monoclonal antibody NI-0501, A6, B4, B9, C9,
C10, D3, D6, D8, El, F8, F9, G7, G9 or G10) by ascertaining whether the former prevents
the latter from binding to a IFNy antigen polypeptide. If the human monoclonal antibody
being tested competes with a human monoclonal antibody of the invention, as shown by a
decrease in binding by the human monoclonal antibody of the invention, then the two
monoclonal antibodies bind to the same, or a closely related, epitope. Another way to
determine whether a human monoclonal antibody has the specificity of a human
monoclonal antibody of the invention is to pre-incubate the human monoclonal antibody of
the invention with the IFNy antigen polypeptide with which it is normally reactive, and then
add the human monoclonal antibody being tested to determine if the human monoclonal
antibody being tested is inhibited in its ability to bind the IFNy antigen polypeptide. If the
human monoclonal antibody being tested is inhibited then, in all likelihood, it has the same, .
or functionally equivalent, epitopic specificity as the monoclonal antibody of the invention.
Various procedures known within the art aie used for the production of the
monoclonal antibodies directed against a protein such as an IFNy protein, or against
derivatives, fragments, analogs homologs or orthologs thereof. (See, e.g., Antibodies: A
Laboratory Manual, Harlow E, and Lane D, 1988, Cold Spring Harbor Laboratory Press,
Cold Spring Harbor, NY, incorporated herein by reference). Fully human antibodies are
antibody molecules in which the entire sequence of both the light chain and the heavy chain,
including the CDRs, arise from human genes. Such antibodies are termed "human
antibodies", or "fully human antibodies" herein. Human monoclonal antibodies are
prepared, for example, using the procedures described in the Examples provided below.
Human monoclonal antibodies can be also prepared by using trioma technique; the human
B-cell hybridoma technique (see Kozbor, et al., 1983 Immunol Today 4: 72); and the EBV
22

WO 2006/109191 PCT/IB2006/001514
hybridoma technique to produce human monoclonal antibodies (see Cole, et al., 1985 In:
MONOCLONAL ANTIBODIES AND CANCER THERAPY, Alan R. Liss, Inc., pp. 77-96). Human
monoclonal antibodies may be utilized and may be produced by using human hybridomas
(see Cote, et al., 1983. Proc Natl Acad Sci USA 80: 2026-2030) or by transforming human
B-cells with Epstein Barr Virus in vitro (see Cole, et al., 1985 In: MONOCLONAL
ANTIBODIES AND CANCER THBRAPY, Alan R. Liss, Inc., pp. 77-96).
Antibodies are purified by well-known techniques, such as affinity chromatography
using protein A or protein G, which provide primarily the IgG fraction of immune serum.
Subsequently, or alternatively, the specific antigen which is the target of the
immunoglobulin sought, or an epitope thereof, may be immobilized on a column to purity
the immune specific antibody by immunoaffinity chromatography. Purification of
immunoglobulins is discussed, for example, by D. Wilkinson (The Scientist, published by
The Scientist, Inc., Philadelphia PA, Vol. 14, No. 8 (April 17,2000), pp. 25-28).
It is desirable to modify the antibody of the invention with respect to effector
function, so as to enhance, e.g., the effectiveness of the antibody in treating immune-related
diseases. For example, cysteine residue(s) can be introduced into the Fc region, thereby
allowing interchain disulfide bond formation in this region. The homodimeric antibody
thus generated can have improved intemalization capability and/or increased
complement-mediated cell killing and antibody-dependent cellular cytotoxicity (ADCC).
(See Caron et al., J. Exp Med., 176:1191-1195 (1992) and Shopes, J. Immunol., 148:
2918-2922 (1992)). Alternatively, an antibody can be engineered that has dual Fc regions
and can thereby have enhanced complement lysis and ADCC capabilities. (See Stevenson
et al., Anti-Cancer Drug Design, 3:219-230 (1989)).
The invention also includes Fv, Fab, Fab" and F(ab')2 huIFNy fragments, single chain
huIFNy antibodies, bispecific huIFNy antibodies and heteroconjugate huIFNy antibodies.
Bispecific antibodies are antibodies that have binding specificities for at least two
different antigens. In the present case, one of the binding specificities is for IFNy. The
second binding target is any other antigen, and advantageously is a cell-surface protein or
receptor or receptor subunit.
Methods for making bispecific antibodies are known in the art. Traditionally, the
recombinant production of bispecific antibodies is based on the co-expression of two
immunoglobulin heavy-chain/light-chain pairs, where the two heavy chains have different
23

WO 2006/109191 PCT/IB2006/001514
specificities (Milstein and Cuello, Nature, 305:537-539 (1983)). Because of the random
assortment of immunoglobulin heavy and light chains, these hybridomas (quadromas)
produce a potential mixture often different antibody molecules, of which only one has the
correct bispecific structure. The purification of the correct molecule is usually
accomplished by affinity chromatography steps. Similar procedures are disclosed in WO
93/08829, published 13 May 1993, and in Traunecker et al., EMBO J., 10:3655-3659
(1991).
Antibody variable domains with the desired binding specificities (antibody-antigen
combining sites) can be fused to immunoglobulin constant domain sequences. The fusion
preferably is with an immunoglobulin heavy-chain constant domain, comprising at least part
of the hinge, CH2, and CH3 regions. It is preferred to have the first heavy-chain constant
region (CHI) containing the site necessary for light-chain binding present in at least one of
the fusions. DNAs encoding the immunoglobulin heavy-chain fusions and, if desired, the
immunoglobulin light chain, are inserted into separate expression vectors, and are
co-transfected into a suitable host organism. For further details of generating bispecific
antibodies see, for example, Suresh et al., Methods in Enzymology, 121:210 (1986).
According to another approach described in WO 96/27011, the interface between a
pair of antibody molecules can be engineered to maximize the percentage of heterodimers
which are recovered from recombinant cell culture. The preferred interface comprises at
least a part of the CH3 region of an antibody constant domain. In this method, one or more
small amino acid side chains from the interface of the first antibody molecule are replaced
with larger side chains (e.g. tyrosine or tryptophan). Compensatory "cavities" of identical
or similar size to the large side chain(s) are created on the interface of the second antibody
molecule by replacing large amino acid side chains with smaller ones (e.g. alanine or
threonine). This provides a mechanism for increasing the yield of the heterodimer over
other unwanted end-products such as homodimers.
Bispecific antibodies can be prepared as full length antibodies or antibody fragments
(e.g. F(ab')2 bispecific antibodies). Techniques for generating bispecific antibodies from
antibody fragments have been described in the literature. For example, bispecific antibodies
can be prepared using chemical linkage. Brennan et al., Science 229:81 (1985) describe a
procedure wherein intact antibodies are proteolytically cleaved to generate F(ab')2
fragments. These fragments are reduced in the presence of the dithiiol complexing agent
24

WO 2006/109191 PCT/IB2006/OO1514
sodium arsenite to stabilize vicinal dithiols and prevent intermolecular disulfide formation.
The Fab' fragments generated are then converted to thionitrobenzoate (TNB) derivatives.
One of the Fab'-tNB derivatives is then reconverted to the Fab'-thiol by reduction with
mercaptoethylamine and is mixed with an equimolar amount of the other Fab'-TNB
derivative to form the bispecific antibody. The bispecific antibodies produced can be used
as agents for the selective immobilization of enzymes.
Additionally, Fab' fragments can be directly recovered from E. coli and chemically
coupled to form bispecific antibodies. Shalaby et al., J. Exp. Med. 175:217-225 (1992)
describe the production of a fully humanized bispecific antibody F(ab')2 molecule. Each
Fab' fragment was separately secreted from E. coli and subjected to directed chemical
coupling in vitro to form the bispecific antibody. The bispecific antibody thus formed was
able to bind to cells overexpressing the ErbB2 receptor and normal human T cells, as well
as trigger the lytic activity of human cytotoxic lymphocytes against human breast tumor
targets.
Various techniques for making and isolating bispecific antibody fragments directly
from recombinant cell culture have also been described. For example, bispecific antibodies
have been produced using leucine zippers. Kostelny et al., J. Immunol. 148(5):1547-1553
(1992). The leucine zipper peptides from the Fos and Jun proteins were linked to the Fab'
portions of two different antibodies by gene fusion. The antibody homodimers were
reduced at the hinge region to form monomers and then re-oxidized to form the antibody
heterodimers. This method can also be utilized for the production of antibody homodimers.
The "diabody" technology described by Hollinger et al., Proc. Natl Acad. Sci. USA
90:6444-6448 (1993) has provided an alternative mechanism for making bispecific antibody
fragments. The fragments comprise a heavy-chain variable domain (VH) connected to a
light-chain variable domain (VL) by a linker which is too short to allow pairing between the
two domains on the same chain. Accordingly, the VH and VL domains of one fragment are
forced to pair with the complementary VL and VH domains of another fragment, thereby
forming two antigen-binding sites. Another strategy for making bispecific antibody
fragments by the use of single-chain Fv (sFv) dimers has also been reported. See, Gruber et
al., J. Immunol. 152:5368 (1994).
Antibodies with more than two valencies are contemplated. For example, trispecific
antibodies can be prepared. Tutt et al., J. Immunol. 147:60 (1991).
25

WO 2006/109191 PCT/IB2006/001514
Exemplary bispecific antibodies can bind to two different epitopes, at least one of
which originates in the protein antigen of the invention. Alternatively, an anti-antigenic arm
of an immunoglobulin molecule can be combined with an arm which binds to a triggering
molecule on a leukocyte such as a T-cell receptor molecule (e.g. CD2, IFNy, CD28, or B7),
or Fc receptors for IgG (FcyR), such as FcyRI (CD64), FcyRII (IFNy2) and FcyRllI (CD 16)
so as to focus cellular defense mechanisms to the cell expressing the particular antigen.
Bispecific antibodies can also be used to direct cytotoxic agents to cells which express a
particular antigen. These antibodies possess an antigen-binding arm and an arm which
binds a cytotoxic agent or a radionuclide chelator, such as EOTUBB, DPTA, DOTA, or
TETA. Another bispecific antibody of interest binds the protein antigen described herein
and further binds tissue factor (TF).
Heteroconjugate antibodies are also within the scope of the present invention.
Heteroconjvtgate antibodies are composed of two covalently joined antibodies. Such
antibodies have, for example, been proposed to target immune system cells to unwanted
cells (U.S. Patent No. 4,676,980), and for treatment of fflV infection (WO 91/00360; WO
92/200373; EP 03089). It is contemplated that the antibodies can be prepared in vitro using
known methods in synthetic protein chemistry, including those involving crosslinking
agents. For example, immunotoxins can be constructed using a disulfide exchange reaction
or by forming a thioether bond. Examples of suitable reagents for this purpose include
iminothiolate and methyl-4-mercaptobutyrimidate and those disclosed, for example, in U.S.
Patent No. 4,676,980.
The invention also pertains to immunoconjugates comprising an antibody
conjugated to a cytotoxic agent such as a toxin (e.g., an enzymatically active toxin of
bacterial, fungal, plant, or animal origin, or fragments thereof), or a radioactive isotope (i e.,
a radioconjugate).
Enzymatically active toxins and fragments thereof that can be used include
diphtheria A chain, nonbinding active fragments of diphtheria toxin, exotoxin A chain (from
Pseudomonas aeruginosa), ricin A chain, abrin A chain, modeccin A chain, alpha-sarcin,
Aleurites fordii proteins, dianthin proteins, Phytolaca americana proteins (PAPI, PAPII, and
PAP-S), momordica charantia inhibitor, curcin, crotin, sapaonaria officinalis inhibitor,
gelonin, mitogellin, restrictocin, phenomycin, enomycin, and the tricothecenes. A variety of
26

WO 2006/109191 PCT/IB2006/001514
radionuclides are available for the production of radioconjugated antibodies. Examples
include 212Bi,13V31In,9°Y, and I86Re.
Conjugates of the antibody and cytotoxic agent are made using a variety of
bifunctional protein-coupling agents such as N-succinirnidyl-3-(2-pyridyldithiol) propionate
(SPDP), iminothiolane (IT), biftmctioiial derivatives of imidoesters (such as dimethyl
adipimidate HCL), active esters (such as disuccinimidyl suberate), aldehydes (such as
glutareldehyde), bis-azido compounds (such as bis (p-azidobenzoyl) hexanediamine),
bis-diazonium derivatives (such as bis-(p-diazoniumbenzoyl)-ethy]enediamine),
diisocyanates (such as tolyene 2,6-diisocyanate), and bis-active fluorine compounds (such
as l,5-difluoro~2,4-dinitrobenzene). For example, a ricin immunotoxin can be prepared as
described in Vitetta et al., Science 238:1098 (1987). Carbon-14-labeled
l-isothiocyanatobenzyl-3-methyldiethylenetriaminepentaacetic acid (MX-DTPA) is an
exemplary chelating agent for conjugation of radionucleotide to the antibody. (See
WO94/11026).
Those of ordinary skill in the art will recognize that a large variety of possible
moieties can be coupled to the resultant antibodies or to other molecules of the invention.
(See, for example, "Conjugate Vaccines", Contributions to Microbiology and Immunology,
J. M. Cruse and R. E. Lewis, Jr (eds), Carger Press, New York, (1989), the entire contents
of which are incorporated herein by reference).
Coupling is accomplished by any chemical reaction that will bind the two molecules
so long as the antibody and the other moiety retain their respective activities. This linkage
can include many chemical mechanisms, for instance covalent binding, affinity binding,
intercalation, coordinate binding and complexation. The preferred binding is, however,
covalent binding. Covalent binding is achieved either by direct condensation of existing side
chains or by the incorporation of external bridging molecules. Many bivalent or polyvalent
linking agents are useful in coupling protein molecules, such as the antibodies of the present
invention, to other molecules. For example, representative coupling agents can include
organic compounds such as thioesters, carbodiimides, succinimide esters, diisocyanates,
glutaraldehyde, diazobenzenes and hexametliylene diamines. This listing is not intended to
be exhaustive of the various classes of coupling agents known in the art but, rather, is
exemplary of the more common coupling agents. (See Killen and Lindstrom, Jour. Immun.
133:1335-2549 (1984); Jansen et al., Immunological Reviews 62:185-216 (1982); and
27

WO 2006/109191 PCT/IB2006/001514
Vitetta et al., Science 238:1098 (1987). Preferred linkers are described in the literature.
{See, for example, Ramakrishnan, S. et al., Cancer Res. 44:201-208 (1984) describing vise of
MBS (M-maleimidoberizoyl-N-hydroxysuccrnimide ester). See also, U.S. Patent No.
5,030,719, describing use of halogenated acetyl hydrazide derivative coupled to an antibody
by way of an oligopeptide linker. Particularly preferred linkers include: (i) EDC (l-ethyl-3-
(3-dirnethylamino-propyl) carbodiimide hydrochloride; (ii) SMPT (4-
succimmidyloxycarbonyl-alpha-methyl-alpha-(2-pridyl-dithio)-toluene (Pierce Cbem. Co.,
Cat. (21558G); (iii) SPDP (succinimidyl-6 [3-(2-pyridyldithio) propionamido] hexanoate
(Pierce Chem. Co., Cat#21651G); (iv) Snlfo-LC-SPDP (sulfosuccinimidyl 6 [3-(2-
pyridyldithio)-propianaraide] hexanoate (Pierce Chem. Co. Cat. #2165-G); and (v) sulfo-
NHS (N-hydroxysulfo-succinimide: Pierce Chem. Co., Cat. #24510) conjugated to EDC.
The linkers described above contain components that have different attributes, thus
leading to conjugates with differing physio-chemical properties. For example, sulfo-NHS
esters of alkyl carboxylates are more stable than sulfo-NHS esters of aromatic carboxylates.
NHS-ester containing linkers are less soluble than sulfo-NHS esters. Further, the linker
SMPT contains a sterically hindered disulfide bond, and can form conjugates with increased
stability. Disulfide linkages, are in general, less stable than other linkages because the
disulfide linkage is cleaved in vitro, resulting in less conjugate available. Sulfo-NHS, in
particular, can enhance the stability of carbodimide couplings. Carbodimide couplings (such
as EDC) when used in conjunction with sulfo-NHS, forms esters that are more resistant to
hydrolysis than the carbodimide coupling reaction alone.
The term "isolated polynucleotide" as used herein shall mean a polynucleotide of
genomic, cDNA, or synthetic origin or some combination thereof, which by virtue of its
origin the "isolated polynucleotide" (1) is not associated with all or a portion of a
polynucleotide in which the "isolated polynucleotide" is found in nature, (2) is operably
linked to a polynucleotide which it is not linked to in nature, or (3) does not occur in nature
as part of a larger sequence.
The term "isolated protein" referred to herein means a protein of cDNA,
recombinant RNA, or synthetic origin or some combination thereof, which by virtue of its
origin, or source of derivation, the "isolated protein" (1) is not associated with proteins
found in nature, (2) is free of other proteins from the same source, e.g., free of marine
proteins, (3) is expressed by a cell from a different species, or (4) does not occur in nature.
28

WO 2006/109191 PCT/IB2006/001514
The term "polypeptide" is used herein as a generic term to refer to native protein,
fragments, or analogs of a polypeptide sequence. Hence, native protein fragments, and
analogs are species of the polypeptide genus. Preferred polypeptides in accordance with the
invention comprise the human heavy chain hnmunoglobulin molecules represented by
Figures IB, 2B, 3B and 4B and the human light chain immunoglobulin molecules
represented by Figures ID, 2D, 3D and 4D, as well as antibody molecules formed by
combinations comprising the heavy chain immunoglobulin molecules with light chain
immunoglobulin molecules, such as kappa light chain immunoglobulin molecules, and vice
versa, as well as fragments and analogs thereof.
The term "naturally-occurring" as used herein as applied to an object refers to the
fact that an object can be found in nature. For example, a polypeptide or polynucleotide
sequence that is present in an organism (including viruses) that can be isolated from a
source in nature and which has not been intentionally modified by man in the laboratory or
otherwise is naturally-occurring.
The term "operably linked" as used herein Tefers to positions of components so
described are in a relationship permitting them to function in their intended manner. A
control sequence "operably linked" to a coding sequence is ligated in such a way that
expression of the coding sequence is achieved under conditions compatible with the control
sequences.
The term "control sequence" as used herein refers to polynucleotide sequences
which are necessary to effect the expression and processing of coding sequences to which
they are ligated. The nature of such control sequences differs depending upon the host
organism in prokaryotes, such control sequences generally include promoter, ribosomal
binding site, and transcription termination sequence in eukaryotes, generally, such control
sequences include promoters and transcription termination sequence. The term "control
sequences" is intended to include, at a minimum, all components whose presence is
essential for expression and processing, and can also include additional components whose
presence is advantageous, for example, leader sequences and fusion partner sequences. The
term "polynucleotide" as referred to herein means a polymeric boron of nucleotides of at
least 10 bases in length, either ribonucleotides or deoxynucleotides or a modified form of
either type of nucleotide. The term includes single and double stranded forms of DNA.
29

WO 2006/109191 PCT/IB2006/001514
The term oligonucleotide referred to herein includes naturally occurring, and
modified nucleotides linked together by naturally occurring, and non-naturally occurring
oligonucleotide linkages. Oligonucleotides are a polynucleotide subset generally
comprising a length of 200 bases or fewer. Preferably oligonucleotides are 10 to 60 bases in
length and most preferably 12,13,14,15, 16,17,18, 19, or 20 to 40 bases in length.
Oligonucleotides are usually single stranded, e.g., for probes, although oligonucleotides
may be double stranded, e.g., for use in the construction of a gene mutant. Oligonucleotides
of the invention are either sense or antisense oligomicleotides.
The term "naturally occurring nucleotides" referred to herein includes
deoxyribonucleotides and ribonucleotides. The term "modified nucleotides" referred to
herein includes nucleotides with modified or substituted sugar groups and the like. The
term "oligonucleotide linkages" referred to herein includes Oligonucleotides linkages such
as phosphorothioate, phosphorodithioate, phosphoroselerloate, phosphorodiselenoate,
phosphoroanilothioate, phoshoraniladate, phosphoronmidate, and the like. See e.g.,
LaPlanche et al. Nucl. Acids Res. 14:9081 (1986); Stec et al J. Am. Chem. Soc. 106:6077
(1984), Stein et al. Nucl. Acids Res. 16:3209 (1988), Zon et al. Anti Cancer Drug Design
6:539 (1991); Zon et al. Oligonucleotides and Analogues: A Practical Approach, pp. 87-108
(F. Eckstein, Ed., Oxford University Press, Oxford England (1991)); Stec et al. U.S. Patent
No. 5,151,510; Uhlmann and Peyman Chemical Reviews 90:543 (1990). An
oligonucleotide can include a label for detection, if desired.
The term "selectively hybridize" referred to herein means to detectably and
specifically bind. Polynucleotides] oligonucleotides and fragments thereof in accordance
with the invention selectively hybridize to nucleic acid strands under hybridization and
wash conditions that minimize appreciable amounts of detectable binding to nonspecific
nucleic acids. High stringency conditions can be used to achieve selective hybridization
conditions as known in the art and discussed herein. Generally, the nucleic acid sequence
homology between the polyuucleotides, oligonucleotides, and fragments of the invention
and a nucleic acid sequence of interest will be at least 80%, and more typically with
preferably increasing homologies of at least 85%, 90%, 95%, 99%, and 100%. Two amino
acid sequences are homologous if there is a partial or complete identity between their
sequences. For example, 85% homology means that 85% of the amino acids are identical
when the two sequences are aligned for maximum matching. Gaps (in either of the two
30

WO 2006/109191 PCT/IB2006/001514
sequences being matched) are allowed in maximizing matching gap lengths of 5 or less are
preferred with 2 or less being more preferred. Alternatively and preferably, two protein
sequences (or polypeptide sequences derived from them of at least 30 amino acids in length)
are homologous, as this term is used herein, if they have an alignment score of at more than
5 (in standard deviation units) using the program ALIGN with the mutation data matrix and
a gap penalty of 6 or greater. See Dayhoff, M.O., in Atlas of Protein Sequence and
Structure, pp. 101-110 (Volume 5, National Biomedical Research Foundation (1972)) and
Supplement 2 to this volume, pp. 1-10. The two sequences or parts thereof are more
preferably homologous if their amino acids are greater than or equal to 50% identical when
optimally aligned using the ALIGN program. The term "corresponds to" is used herein to
mean that a polynucleotide sequence is homologous (i.e., is identical, not strictly
evolutionarily related) to all or a portion of a reference polynucleotide sequence, or that a
polypeptide sequence is identical to a reference polypept'de sequence. In contradistinction,
the term "complementary to" is used herein to mean that the complementary sequence is
homologous to all or a portion of a reference polynucleotide sequence. For illustration, the
nucleotide sequence "TATAC" corresponds to a reference sequence "TATAC" and is
complementary to a reference sequence "GTATA".
The following terms are used to describe the sequence relationships between two or
more polynucleotide or amino acid sequences: "reference sequence", "comparison window",
"sequence identity", "percentage of sequence identity", and "substantial identity". A
"reference sequence" is a defined sequence used as a basis for a sequence comparison a
reference sequence may be a subset of a larger sequence, for example, as a segment of a
full-length cDNA or gene sequence given in a sequence listing or may comprise a complete
cDNA or gene sequence. Generally, a reference sequence is at least 18 nucleotides or 6
amino acids in length, frequently at least 24 nucleotides or 8 amino acids in length, and
often at least 48 nucleotides or 16 amino acids in length. Since two polynucleotides or
amino acid sequences may each (1) comprise a sequence (i.e., a portion of the complete
polynucleotide or amino acid sequence) that is similar between the two molecules, and (2)
may further comprise a sequence that is divergent between the two polynucleotides or
amino acid sequences, sequence comparisons between two (or more) molecules are
typically performed by comparing sequences of the two molecules over a "comparison
window" to identify and compare local regions of sequence similarity. A "comparison
31

WO 2006/109191 PCT/IB2006/001514
window", as used herein, refers to a conceptual segment of at least 18 contiguous nucleotide
positions of 6 amino acids wherein a polynucleotide sequence or amino acid sequence may
be compared to a reference sequence of at least 18 contiguous nucleotides or 6 amino acid
sequences and wherein the portion of the polynucleotide sequence in the comparison
window may comprise additions, deletions, substitutions, and the like (i.e., gaps) of 20
percent or less as compared to the reference sequence (which does not comprise additions or
deletions) for optimal alignment of the two sequences. Optimal alignment of sequences for
aligning a comparison window may be conducted by the local homology algorithm of Smith
and Waterman Adv. AppL Math. 2:482 (1981), by the homology alignment algorithm of
Needleman and Wunsch J. Mol. Biol. 48:443 (1970), by the search for similarity method of
Pearson and Lipman Proc. Natl. Acad. Sci. (U.S.A.) 85:2444 (1988), by computerized
implementations of these algorithms (GAP, BESTFIT, FASTA, and TFASTA in the
Wisconsin Genetics Software Package Release 7.0, (Genetics Computer Group, 575 Science
Dr., Madison, Wis.), Geneworks, or Mac Vector software packages), or by inspection, and
the best alignment (i.e., resulting in the highest percentage of homology over the
comparison window) generated by the various methods is selected.
The term "sequence identity" means that two polynucleotide or ammo acid
sequences are identical (i.e., on a nucleotide-by-nucleotide or residue-by-residue basis) over
the comparison window. The term "percentage of sequence identity" is calculated by
comparing two optimally aligned sequences over the window of comparison, determining
the number of positions at which the identical nucleic acid base (e.g., A, T, C, G, U or I) or
residue occurs in both sequences to yield the number of matched positions, dividing the
number of matched positions by the total number of positions in the comparison window
(z. e., the window size), and multiplying the result by 100 to yield the percentage of sequence
identity. The terms "substantial identity" as used herein denotes a characteristic of a
polynucleotide or amino acid sequence, wherein the polynucleotide or amino acid
comprises a sequence that has at least 85 percent sequence identity, preferably at least 90 to
95 percent sequence identity, more usually at least 99 percent sequence identity as
compared to a reference sequence over a comparison window of at least 18 nucleotide (6
amino acid) positions, frequently over a window of at least 24-48 nucleotide (8-16 amino
acid) positions, wherein the percentage of sequence identity is calculated by comparing the
reference sequence to the sequence which may include deletions or additions which total 20
32

WO 2006/109191 PCT/IB2006/001514
percent or less of the reference sequence over the comparison window. The reference
sequence may be a subset of a larger sequence.
As used herein, the twenty conventional amino acids and their abbreviations follow
conventional usage. See Immunology - A Synthesis (2nd Edition, E.S. Golub and D.R.
Gren, Eds., Sinauer Associates, Sunderland Mass. (1991)). Stereoisomers (e.g., D- amino
acids) of the twenty conventional amino acids, unnatural amino acids such as a-, a-
disubstituted amino acids, N-alkyl amino acids, lactic acid, and other unconventional amino
acids may also be suitable components for polypeptides of the present invention. Examples
of unconventional amino acids include: 4 hydroxyproline, y-carboxyglutamate, e-N,N,N-
trimethyllysine, e -N-acetyllysine, O-phosphoserine, N- acetylserine, N-formylmethionine,
3-methylhistidine, 5-hydroxylysine, o-N-methylarginine, and other similar amino acids and
imino acids (e.g., 4- hydroxyproline). In the polypeptide notation used herein, the lefthand
direction is the amino terminal direction and the righthand direction is the carboxy-terminal
direction, in accordance with standard usage and convention.
Similarly, unless specified otherwise, the lefthand end of single- stranded
polynucleotide sequences is the 5' end the lefthand direction of double-stranded
polynucleotide sequences is referred to as the 51 direction. The direction of 5' to 3' addition
of nascent RNA transcripts is referred to as the transcription direction sequence regions on
the DNA strand having the same sequence as the RNA and which are 51 to the 5' end of the
RNA transcript are referred to as "upstream sequences", sequence regions on the DNA
strand having the same sequence as the RNA and which are 3' to the 3' end of the RNA
transcript are referred to as "downstream sequences".
As applied to polypeptides, the term "substantial identity" means that two peptide
sequences, when optimally aligned, such as by the programs GAP or BESTFIT using
default gap weights, share at least 80 percent sequence identity, preferably at least 90
percent sequence identity, more preferably at least 95 percent sequence identity, and most
preferably at least 99 percent sequence identity.
Preferably, residue positions which are not identical differ by conservative amino
acid substitutions.
Conservative amino acid substitutions refer to the interchangeability of residues
having similar side chains. For example, a group of amino acids having aliphatic side
chains is glycine, alanine, valine, leucine, and isoleucine; a group of amino acids having
33

WO 2006/109191 PCT/IB2006/001514
aliphatic-hydroxyl side chains is serine and threonine; a group of amino acids having amide-
containing side chains is asparagine and glutamine; a group of amino acids having aromatic
side chains is phenylalanine, tyrosine, and tryptophan; a group of amino acids having basic
side chains is lysine, arginine, and histidine; and a group of amino acids having sulfur-
containing side chains is cysteine and methionine. Preferred conservative amino acids
substitution groups are: valine-leucine-isoleucine, phenylalanine-tyrosine, lysine-arginine,
alanine valine, glutamic- aspartic, and asparagine-glutamine.
As discussed herein, minor variations in the amino acid sequences of antibodies or
immunoglobulin molecules are contemplated as being encompassed by the present
invention, providing that the variations in the amino acid sequence maintain at least 75%,
more preferably at least 80%, 90%, 95%, and most preferably 99%. In particular,
conservative amino acid replacements are contemplated. Conservative replacements are
. those that take place within a family of amino acids that are related in their side chains.
Genetically encoded amino acids are generally divided into families: (1) acidic amino acids
are aspartate, glutamate; (2) basic amino acids are lysine, arginine, histidine; (3) non-polar
amino acids are alanine, valine, leucine, isoleucine, proline, phenylalanine, methionine,
tryptophan, and (4) uncharged polar amino acids are glycine, asparagine, glutamine,
cysteine, serine, threonine, tyrosine. The hydrophilic amino acids include arginine,
asparagine, aspartate, glutamine, glutamate, histidine, lysine, serine, and threonine. The
hydrophobic amino acids include alanine, cysteine, isoleucine, leucine, methionine,
phenylalanine, proline, tryptophan, tyrosine and valine. Other families of amino acids
include (i) serine and threonine, which are the aliphatic-hydroxy family; (ii) asparagine and
glutamine, which are the amide containing family; (iii) alanine, valine, leucine and
isoleucine, which are the aliphatic family; and (iv) phenylalanine, tryptophan, and tyrosine,
which are the aromatic family. For example, it is reasonable to expect that an isolated
replacement of a leucine with an isoleucine or valine, an aspartate with a glutamate, a
threonine with a serine, or a similar replacement of an amino acid with a structurally related
amino acid will not have a major effect on the binding or properties of the resulting
molecule, especially if the replacement does not involve an amino acid within a framework
site. Whether an amino acid change results in a functional peptide can readily be
determined by assaying the specific activity of the polypeptide derivative. Assays are
described in detail herein. Fragments or analogs of antibodies or immunoglobulin
34

WO 2006/109191 PCT/IB2006/001514
molecules can be readily prepared by those of ordinary skill in the art. Preferred ammo- and
carboxy-termini of fragments or analogs occur near boundaries of functional domains.
Structural and functional domains can be identified by comparison of the nucleotide and/or
amino acid sequence data to public or proprietary sequence databases. Preferably,
computerized comparison methods are used to identify sequence motifs or predicted protein
conformation domains that OCCUT in other proteins of known structure and/or function.
Methods to identify protein sequences that fold into a known three-dimensional structure
are known. Bowies a/. Science 253:164 (1991). Thus, the foregoing examples
demonstrate that those of skill in the art can recognize sequence motifs and structural .
conformations that may be used to define structural and functional domains in accordance
with the invention.
Preferred amino acid substitutions are those which: (1) reduce susceptibility to
proteolysis, (2) reduce susceptibility to oxidation, (3) alter binding affinity for forming
protein complexes, (4) alter binding affinities, and (4) confer or modify other
pbysicochemical or functional properties of such analogs. Analogs can include various
muteins of a sequence other than the naturally-occurring peptide sequence. For example,
single or multiple amino acid substitutions (preferably conservative amino acid
substitutions) may be made in the naturally- occurring sequence (preferably in the portion of
the polypeptide outside the domain(s) forming intermolecular contacts. A conservative
amino acid substitution should not substantially change the structural characteristics of the
parent sequence (e.g., a replacement amino acid should not tend to break a helix that occurs
in tiie parent sequence, or disrupt other types of secondary structure that characterizes the
parent sequence). Examples of art-recognized polypeptide secondary and tertiary structures
are described in Proteins, Structures and Molecular Principles (Creighton, Ed., W. H.
Freeman and Company, New York (1984)); Introduction to Protein Structure (C. Branden
and J. Tooze, eds., Garland Publishing, New York, N.Y. (1991)); and Thornton et at
Nature 354:105 (1991).
The term "polypeptide fragment" as used herein refers to a polypeptide that has an
amino terminal and/or carboxy-terminal deletion, but where the remaining amino acid
sequence is identical to the corresponding positions in the naturally-occurring sequence
deduced, for example, from a full length cDNA sequence. Fragments typically are at least
5, 6, 8 or 10 amino acids long, preferably at least 14 amino acids long1 more preferably at
35

WO 2006/109191 PCT/IB2006/001514
least 20 amino acids long, usually at least 50 ammo acids long, and even more preferably at
least 70 amino acids long. The term "analog" as used herein refers to polypeptides which
are comprised of a segment of at least 25 amino acids that has substantial identity to a
portion of a deduced amino acid sequence and which has at least one of the following
properties: (1) specific binding to IFNy, under suitable binding conditions, (2) ability to
block appropriate IFNy binding, or (3) ability to inhibit IFNy-expressing cell growth in vitro
or in vivo. Typically, polypeptide analogs comprise a conservative amino acid substitution
(or addition or deletion) with respect to the naturally- occurring sequence. Analogs
typically are at least 20 amino acids long, preferably at least 50 amino acids long or longer,
and can often be as long as a full-length naturally-occurring polypeptide.
Peptide analogs are commonly used in the pharmaceutical industry as non-peptide
drugs with properties analogous to those of the template peptide. These types of non-
peptide compound are termed "peptide mimetics" or "peptidomimetics". Fauchere, J. Adv.
Drug Res. 15:29 (1986), Veber and Freidinger TINS p.392 (1985); and Evans et al. J. Med.
Chem. 30:1229 (1987). Such compounds are often developed with the aid of computerized
molecular modeling. Peptide mimetics that are structurally similar to therapeutically useful
peptides may be used to produce an equivalent therapeutic or prophylactic effect.
Generally, peptidomimetics are structurally similar to a paradigm polypeptide (i.e, a
polypeptide that has a biochemical property or pharmacological activity), such as human .
antibody, but have one or more peptide linkages optionally replaced by a linkage selected
from the group consisting of: - CH2NH-, ~CH2S-, -CH2-CH2-, -CH=CH~(cis and
trans), ~COCH2--, CH(OH)CH2~, and -CH2SO~, by methods well known in the art.
Systematic substitution of one or more amino acids of a consensus sequence with a D-
amino acid of the same type (e.g., D-lysine in place of L-lysine) may be used to generate
more stable peptides. In addition, constrained peptides comprising a consensus sequence or
a substantially identical consensus sequence variation may be generated by methods known
in the art (Rizo and Gierasch Ann. Rev. Biochem. 61:387 (1992)); for example, by adding
internal cysteine residues capable of forming intramolecular disulfide bridges which cyclize
the peptide.
The term "agent" is used herein to denote a chemical compound, a mixture of
chemical compounds, a biological macromolecule, or an extract made from biological
materials.
36

WO 2006/109191 PCT/IB2006/001514
As used herein, the terms "label" or "labeled" refers to incorporation of a detectable
marker, e.g., by incorporation of a radiolabeled amino acid or attachment to a polypeptide
of biorinyl moieties that can be detected by marked avidin (e.g., streptavidin containing a
fluorescent marker or enzymatic activity that can be detected by optical or calorimetric
methods). In certain situations, the label or marker can also be therapeutic. Various
methods of labeling polypeptides and glycoproteins are known in the art and may be used.
Examples of labels for polypeptides include, but are not limited to, the following:
radioisotopes or radionuclides (e.g., 3H, I4C, 15N, 35S, 90Y, 99Tc, 111ln, 1251,131I), fluorescent
labels (e.g., FITC, rhodarnine, lanthanide phosphors), enzymatic labels (e.g., horseradish
peroxidase, p-galactosidase, luciferase, alkaline phosphatase), chemiluminescent, biorinyl
groups, predetermined polypeptide epitopes recognized by a secondary reporter (e.g.,
leucine zipper pair sequences, binding sites for secondary antibodies, metal binding
domains, epitope tags). In some embodiments, labels are attached by spacer arms of various
lengths to reduce potential steric hindrance. The term "pharmaceutical agent or drug" as
used herein refers to a chemical compound or composition capable of inducing a desired
therapeutic effect when properly administered to a patient.
Other chemistry terms herein are used according to conventional usage in the art, as
exemplified by The McGraw-Hill Dictionary of Chemical Terms (Parker, S., Ed., McGraw-
Hill, San Francisco (1985)).
The term "antineoplastic agent" is used herein to refer to agents that have the
functional property of inhibiting a development or progression of a neoplasm in a human,
particularly a malignant (cancerous) lesion, such as a carcinoma, sarcoma, lymphoma, or
leukemia. Inhibition of metastasis is frequently a property of antineoplastic agents.
As used herein, "substantially pure" means an object species is the predominant
species present (i.e., on a molar basis it is more abundant than any other individual species
in the composition), and preferably a substantially purified fraction is a composition
wherein the object species comprises at least about 50 percent (on a molar basis) of all
macromolecular species present.
Generally, a substantially pure composition will comprise more than about 80
percent of all macromolecular species present in the composition, more preferably more
than about 85%, 90%, 95%, and 99%. Most preferably, the object species is purified to
essential homogeneity (contaminant species cannot be detected in the composition by
37

WO 2006/109191 PCT/IB2006/001514
conventional detection methods) wherein the composition consists essentially of a single
macromolecular species.
The term patient includes human and veterinary subjects. The term subject includes
humans and other mammals.
Human Antibodies and Humanization of Antibodies
A huIFNy antibody is generated, for example, using the procedures described in the
Examples provided below. An IgG hulFNy antibody is generated, for example, by .
converting a scFv clone an IgG format (see e.g., Example 6). Alternatively, such a huTFNy
antibody is developed, for example, using phase-display methods using antibodies
containing only human sequences. Such approaches are well-known in the art, e.g., in
WO92/01047 and U.S. Pat. No. 6,521,404, which are hereby incorporated by reference. In
this approach, a combinatorial library of phage carrying random pairs of light and heavy
chains are screened using natural or recombinant source of IFNy or fragments thereof.
A huIFNy antibody is produced by a process wherein at least one step of the process
includes immunizing a transgenic, non-human animal with human IFNy protein. Some of
the endogenous heavy and/or kappa light chain loci of this xenogenic non-human animal
have been disabled and are incapable of the rearrangement required to generate genes
encoding immunoglobulins in response to an antigen. In addition, at least one human heavy
chain locus and at least one human light chain locus have been stably transfected into the
animal. Thus, in response to an administered antigen, the human loci rearrange to provide
genes encoding human variable regions immunospecific for the antigen. Upon
immunization, therefore, the xenomouse produces B-cells that secrete fully human
immunoglobulins.
A variety of techniques are well-known in the art for producing xenogenic non-
human animals. For example, see U.S. Pat. No. 6,075,181 and No. 6,150,584. By one
strategy, the xenogeneic (human) heavy and light chain immunoglobulin genes are
introduced into the host germ line (e.g., sperm or oocytes) and, in separate steps, the
corresponding host genes are rendered non-functional by inactivation using homologous
recombination. Human heavy and light chain immunoglobulm genes are reconstructed in
an appropriate eukaryotic or prokaryotic microorganism, and the resulting DNA fragments
are introduced into the appropriate host, for example, the pronuclei of fertilized mouse
38

WO 2006/109191 PCT/IB2006/001514
oocytes or embryonic stem cells. Inactivation of the endogenous host immunoglobulin loci
is achieved by targeted disruption of the appropriate loci by homologous recombination in
the host cells, particularly embryonic stem cells or pronuclei of fertilized mouse oocytes.
The targeted disruption can involve introduction of a lesion or deletion in the target locus,
or deletion within the target locus accompanied by insertion into the locus, e.g., insertion of
a selectable marker, in the case of embryonic stem cells, chimeric animals are generated
which are derived in part from the modified embryonic stem cells and are capable of
transmitting the genetic modifications through the germ line. The mating of hosts with
introduced human immunoglobulin loci to strains with inactivated endogenous loci will
yield animals whose antibody production is purely xenogeneic, e.g., human.
In an alternative strategy, at least portions of the human heavy and light chain
immunoglobulin loci are used to replace directly the corresponding endogenous
immunoglobulin loci by homologous recombination in embryonic stem cells. This results in
simultaneous inactivation and replacement of the endogenous immunoglobulin. This is
followed by the generation of chimeric animals in which the embryonic stem cell-derived
cells can contribute to the germ lines.
For example, a B cell clone that expresses human anti-IFNy antibody is removed
from the xenogenic non-human animal and immortalized according to various methods
known within the art. Such B cells may be derived directly from the blood of the animal or
from lymphoid tissues, including but not restricted to spleen, tonsils, lymph nodes, and bone
marrow. The resultant, immortalized B cells may be expanded and cultured in vitro to
produce large, clinically applicable quantities of huIFNy antibody. Alternatively, genes
encoding the immunoglobulins with one or more human variable regions can be recovered
and expressed in a differing cell type, including but not restricted to a mammalian cell
culture system, in order to obtain the antibodies directly or individual chains thereof,
composed of single chain Fv molecules.
In addition, the entire set of fully human anti-IFNy antibodies generated by the
xenogenic non-human animal may be screened to identify one such clone with the optimal
characteristics. Such characteristics include, for example, binding affinity to the human
IFNy protein, stability of the interaction as well as the isotype of the fully human anti-IFNy
antibody. Clones from the entire set which have the desired characteristics men are used as
a source of nucleotide sequences encoding the desired variable regions, for further
39

WO 2006/109191 PCT/IB2006/001514
manipulation to generate antibodies with the-se characteristics, in alternative cell systems,
using conventional recombinant or transgenic techniques.
This general strategy was demonstrated in connection with generation of the first
XenoMouse™ strains as published in 1994. See Green et al. Nature Genetics 7:13-21
(1994). This approach is further discussed and delineated in U.S. Patent Application Serial
Nos. 07/466,008, filed January 12,1990, 07/610,515, filed November 8,1990, 07/919,297,
filed July 24,1992, 07/922,649, filed July 30, 1992, filed 08/031,801, filed March 15,1993,
08/112,848, filed August 27, 1993, 08/234,145, ffled April 28,1994, 08/376,279, filed
January 20,1995,08/430, 938, April 27,1995,08/464,584, filed June 5,1995,08/464,582,
filed June 5,1995,08/463,191, filed June 5,1995,08/462,837, filed June 5,1995,
08/486,853, filed June 5,1995,08/486,857, filed June 5,1995,08/486,859, filed June 5,
1995, 08/462,513, filed June 5,1995, 08/724,752, filed October 2, 1996, and 08/759, 620,
filed December 3,1996 and U.S. Patent Nos. 6,162,963, 6,150,584, 6,114,598, 6,075,181,
and 5,939,598 and Japanese Patent Nos. 3 068 180 B2, 3 068 506 B2, and 3 068 507 B2.
See also Mendez et al. Nature Genetics 15:146-156 (1997) and Green and Jakobovits J.
Exp. Med.: 188:483-495 (1998). See also European Patent No., EP 0 463 151 Bl, grant
published June 12,1996, International Patent Application No., WO 94/02602, published
February 3,1994, International Patent Application No., WO 96/34096, published October
31,1996, WO 98/24893, published June 11,1998, WO 00/76310, published December
21,2000.
In an alternative approach, others have utilized a "minilocus" approach. In the
minilocus approach, an exogenous Ig locus is mimicked through the inclusion of pieces
(individual genes) from the Ig locus. Thus, one or more VH genes, one or more DH genes,
one or more JH genes, a mu constant region, and a second constant region (preferably a
gamma constant Tegion) are formed into a construct for insertion into an animal. This
approach is described in U.S. Patent No. 5,545,807 to Surani et al and U.S. Patent Nos.
5,545,806, 5,625,825, 5,625,126,5,633,425,5,661,016,5,770,429, 5,789,650, 5,814,318,
5,877,397, 5,874,299, and 6,255,458 each to Lonberg and Kay, U.S. Patent No. 5,591,669
and 6,023.010 to Krimpenfortand Berns, U.S. Patent Nos. 5,612,205, 5,721,367, and
5,789,215 to Berns et al, and U.S. Patent No. 5, 643,763 to Choi and Dunn, and GenPharm
International U.S. Patent Application Serial Nos. 07/574,748, filed August 29,1990,
07/575,962, filed August 31,1990,07/810,279, filed December 17,1991,07/853,408, filed
40

WO 2006/109191 PCT/IB2006/001514
March 18,1992, 07/904,068, filed June 23,1992,07/990,860, filed December 16,1992,
08/053,131, filed April 26,1993,08/096,762, filed July 22, 1993, 08/155,301, filed
November 18,1993, 081161,739, filed December 3,1993, 08/165,699, filed December 10,
1993, 08/209,741, filed March 9,1994. See also European Patent No. 0 546 073 Bl,
International Patent Application Nos. WO 92/03918, WO 92/22645, WO 92/22647, WO
92/22670, WO 93/12227, WO 94/00569, WO 94/25585, WO 96/14436, WO 97/13852, and
WO 98/24884 and U.S. Patent No. 5,981,175. See further Taylor et al., 1992, Chen et al,
1993, Tuaillon et al, 1993, Choi et al, 1993, Lonberg et al, (1994), Taylor et al, (1994),
and Tuaillon et al., (1995), Fishwild et al, (1996).
An advantage of the minilocus approach is the rapidity with which constructs
including portions of the Ig locus can be generated and introduced into animals.
Commensurately, however, a significant disadvantage of the minilocus approach is that, in
theory, insufficient diversity is introduced through the inclusion of small numbers of V, D,
and J genes. Indeed, the published work appears to support tins concern. B-cell
development and antibody production of animals produced through use of the minilocus
approach appear stunted. Therefore, research surrounding the present invention has
consistently been directed towards the introduction of large portions of the Ig locus in order
to achieve greater diversity and in an effort to reconstitute the immune repertoire of the
animals.
Generation of human antibodies from mice in which, through microcell fusion, large
pieces of chromosomes, or entire chromosomes, have been introduced, has also been
demonstrated. See European Patent Application Nos. 773 288 and 843 961.
Human anti-mouse antibody (HAMA) responses have led the industry to prepare
chimeric or otherwise humanized antibodies. While chimeric antibodies have a human
constant region and a immune variable region, it is expected that certain human anti-
chimeric antibody (HACA) responses will be observed, particularly in chronic or multi-dose
utilizations of the antibody. Thus, it would be desirable to provide fully human antibodies
against IFNy in order to vitiate concerns and/or effects of HAMA or HACA response.
The production of antibodies with reduced immunogenicity is also accomplished via
humanization and display techniques using appropriate libraries. It will be appreciated that
murine antibodies or antibodies from other species can be humanized or primatized using
techniques well known in the art. See e.g., Winter and Harris Immunol Today 14:43 46
41

WO 2006/109191 PCMB2006/001514
(1993) and Wright et al. Crit, Reviews in Immunol. 12125-168 (1992). The antibody of
interest may be engineered by recombinant DNA techniques to substitute the CHI, CH2,
CH3, hinge domains, and/or the framework domain with the corresponding human sequence
{See WO 92102190 and U.S. Patent Nos. 5,530,101, 5,585,089, 5,693,761, 5,693,792,
5,714,350, and 5,777,085). Also, the use of Ig cDNA for construction of chrmeric
imrnunoglobulin genes is known in the art (Liu et al. P.N.A.S. 84:3439 (1987) and J.
Immunol. 139:3521 (1987)). mRNA is isolated from a hybridoma or other cell producing
the antibody and used to produce cDNA. The cDNA of interest may be amplified by the
polymerase chain reaction using specific primers (U.S. Pat. Nos. 4,683,195 and 4,683,202).
Alternatively, a library is made and screened to isolate the sequence of interest. The DNA
sequence encoding the variable region of the antibody is then fused to human constant
region sequences. The sequences of human constant regions genes may be found in Kabat
et al. (1991) Sequences of Proteins of immunological Interest, N.I.H. publication no. 91-
3242. Human C region genes are readily available from known clones. The choice of
isotype will be guided by the desired effecter functions, such as complement fixation, or
activity in antibody-dependent cellular cytotoxicity. Preferred isotypes are IgGl, IgG3 and
IgG4. Either of the human light chain constant regions, kappa or lambda, may be used. The
chimeric, humanized antibody is then expressed by conventional methods.
Antibody fragments, such as Fv, F(ab')2 and Fab may be prepared by cleavage of the
intact protein, e.g., by protease or chemical cleavage. Alternatively, a truncated gene is
designed. For example, a chimeric gene encoding a portion of the F(ab')2 fragment would
include DNA sequences encoding the CHI domain and hinge region of the H chain,
followed by a translational stop codon to yield the truncated molecule.
Consensus sequences of H and L J regions may be used to design oligonucleotides
for use as priers to introduce useful restriction sites into the J region for subsequent linkage
of V region segments to human C region segments. C region cDNA can be modified by site
directed mutagenesis to place a restriction site at the analogous position in the human
sequence.
Expression vectors include plasmids, retrovinises, YACs, EBV derived episomes,
and the like. A convenient vector is one that encodes a functionally complete human CH or
CL immunoglobulin sequence, with appropriate restriction sites engineered so that any VH
or VL -31 sequence can be easily inserted and expressed. In such vectors, splicing usually
42

WO 2006/109191 PCT/IB2006/001514
occurs between the splice donor site in the inserted J region and the splice acceptor site
preceding the human C region, and also at the splice regions that occur within the human
CH exons. Polyadenylation and transcription termination occur at native chromosomal sites
downstream of the coding regions. The resulting chimeric antibody may be joined to any
strong promoter, including retroviral LTRs, e.g., SV-40 early promoter, (Okayama et al.
Mol. Cell. Bio. 3:280 (1983)), Rous sarcoma virus LTR (Gorman et al. P.N.A.S. 79:6777
(1982)), and moloney murine leukemia virus LTR (Grosschedl et al. Cell 41:885 (1985)).
Also, as will be appreciated, native Ig promoters and the like may be used.
Further, human antibodies or antibodies from other species can be generated through
display type technologies, including, without limitation, phage display, retroviral display,
ribosomal display, and other techniques, using techniques well known in the art and the
resulting molecules can be subjected to additional maturation, such as affinity maturation,
as such techniques are well known in the art. Wright and Harris, supra., Hanes and
Plucthau PEAS USA 94:4937-4942 (1997) (ribosomal display), Parmley and Smith Gene
73:305-318 (1988) (phage display), Scott TIBS 17:241-245 (1992), Cwirla et al. PNAS
USA 87:6378-6382 (1990), Russel et al Nucl. Acids Research 21:1081-1085 (1993),
Hoganboom et al. Immunol. Reviews 130:43-68 (1992), Chiswell and McCafferty
TIBTECH; 10-.80-8A (1992), and U.S. Patent No. 5,733,743. If display technologies are
utilized to produce antibodies that are not human, such antibodies can be humanized as
described above.
Using these techniques, antibodies can be generated to IFNy expressing cells, lFNy
itself, forms of IFNy, epitopes or peptides thereof, and expression libraries thereto {See e.g.,
U.S. Patent No. 5,703,057) which can thereafter be screened as described above for the
activities described above.
Design and Generation of Other Therapeutics *
In accordance with the present invention and based on the activity of the antibodies
that are produced and characterized herein with respect to IFNy, the design of other
therapeutic modalities beyond antibody moieties is facilitated. Such modalities include,
without limitation, advanced antibody therapeutics, such as bispecific antibodies,
immunotoxins, and radiolabeled therapeutics, generation of peptide therapeutics, gene
therapies, particularly intrabodies, antisense therapeutics, and small molecules.
43

WO 2006/109191 PCT/IB2006/001514
For example, in connection with bispecific antibodies, bispecific antibodies can be
generated that comprise (i) two antibodies one with a specificity to IFNy and another to a
second molecule that are conjugated together, (ii) a single antibody that has one chain
specific to IFNy and a second chain specific to a second molecule, or (iii) a single chain
antibody that has specificity to IFNy and the other molecule. Such bispecific antibodies are
generated using techniques that are well known for example, in connection with (i) and (ii)
See e.g., Fanger et al. Immunol Methods 4:72-81 (1994) and Wright and Harris, supra, and
in connection with (iii) See e.g., Traunecker et al. Int. J. Cancer (Suppl.) 7:51-52 (1992).
In connection with immunotoxins, antibodies can be modified to act as
immunotoxins utilizing techniques that are well known in the art See e.g., Vitetta Immunol
Today 14:252 (1993). See also U.S. Patent No. 5,194,594. In connection with the
preparation of Tadiolabeled antibodies, such modified antibodies can also be readily
prepared utilizing techniques that are well known in the art See e.g., Junghans et al. in
Cancer Chemotherapy and Biotherapy 655-686 (2d edition, Chaiher and Longo, eds.,
Lippincott Raven (1996)). See also U.S. Patent Nos. 4,681,581,4,735,210,
5,101,827,5,102,990 (RE 35,500), 5, 648,471, and 5,697,902. Each of immunotoxins and
radiolabeled molecules would be likely to kill cells expressing IFNy, and particularly those
cells in which the antibodies of the invention are effective.
hi connection with the generation of therapeutic peptides, through the utilization of
structural information related to IFNy and antibodies thereto, such as the antibodies of the
invention or screening of peptide libraries, therapeutic peptides can be generated that are
directed against IFNy. Design and screening of peptide therapeutics is discussed in
connection with Houghten et al. Biotechniques 13:412-421 (1992), HoughtenPNAS USA
82:5131-5135 (1985), Pinalla et al. Biotechniques 13:901-905 (1992), Blake and Lhzi-
Davis BioConjugate Chem. 3:510-513 (1992). Immunotoxins and radiolabeled molecules
can also be prepared, and in a similar manner, in connection with peptidic moieties as
discussed above in connection with antibodies. Assuming that the IFNy molecule (or a
form, such as a splice variant or alternate form) is functionally active in a disease process, it
will also be possible to design gene and antisense therapeutics thereto through conventional
techniques. Such modalities can be utilized for modulating the function of IFNy. In
connection therewith the antibodies of the present invention facilitate design and use of
functional assays related thereto. A design and strategy for antisense therapeutics is
44

WO 2006/109191 PCT/IB2006/001514
discussed in detail in Internationa] Patent Application No. WO 94/29444. Design and
strategies for gene therapy are well known. However, in particular, the use of gene
therapeutic techniques involving intrabodies could prove to be particularly advantageous.
See e.g., Chen et al. Human Gene Therapy 5:595-601 (1994) and Marasco Gene Therapy
4:11-15 (1997). General design of and considerations related to gene therapeutics is also
discussed in International Patent Application No. WO 97/38137.
Knowledge gleaned from the structure of the IFNy molecule and its interactions with
other molecules in accordance with the present invention, such as the antibodies of the
invention, and others can be utilized to rationally design additional therapeutic modalities.
In this regard, rational drug design techniques such as X-ray crystallography, computer-
aided (or assisted) molecular modeling (CAMM), quantitative or qualitative structure-
activity relationship (QSAR), and similar technologies can be utilized to focus drug
discovery efforts. Rational design allows prediction of protein or synthetic structures which
can interact with the molecule or specific forms thereof which can be used to modify or
modulate the activity of IFNy. Such structures can be synthesized chemically or expressed
in biological systems. This approach has been reviewed in Capsey et al. Genetically
Engineered Human Therapeutic Drugs (Stockton Press, NY (1988)). Further, combinatorial
libraries can be designed and synthesized and used in screening programs, such as high
throughput screening efforts.
Therapeutic Administration and Formulations
It will be appreciated that administration of therapeutic entities in accordance with
the invention will be administered with suitable carriers, excipients, and other agents that
are incorporated into formulations to provide improved transfer, delivery, tolerance, and the
like. A multitude of appropriate formulations can be found in the formulary known to all
pharmaceutical chemists: Remington's Pharmaceutical Sciences (15th ed, Mack Publishing
Company, Easton, PA (1975)), particularly Chapter 87 by Blaug, Seymour, therein. These
formulations include, for example, powders, pastes, ointments, jellies, waxes, oils, lipids,
lipid (cationic or anionic) containing vesicles (such as Lipofectin™), DNA conjugates,
anhydrous absorption pastes, oil-in-water and water-in-oil emulsions, emulsions carbowax
(polyethylene glycols of various molecular weights), semi-solid gels, and semi-solid
mixtures containing carbowax. Any of the foregoing mixtures may be appropriate in
45

WO 2006/109191 PCT/IB2006/001514
treatments and therapies in accordance with the present invention, provided that the active
ingredient in the formulation is not inactivated by the formulation and the formulation is
physiologically compatible and tolerable with the route of administration. See also Baldrick
P. "Pharmaceutical excipient development: the need for preclinical guidance." Regul.
Toxicol Pharmacol. 32(2):210-8 (2000), Wang W. "Lyopbilization and development of
solid protein Pharmaceuticals." Int. I Pharm. 203(1-2): 1-60 (2000), Charman WN "Lipids,
lipophilic drugs, and oral drug delivery-some emerging concepts." J Pharm Sci.89(8):967-
78 (2000), Powell et al. "Compendium of excipients for parenteral formulations" PDA J
Pharm Sci Technol. 52:238-311 (1998) and the citations therein for additional information
related to formulations, excipients and carriers well known to pharmaceutical chemists.
Therapeutic formulations of the invention, which include a huIFNy antibody of the
invention, are used to treat or alleviate a symptom associated with an immune-related
disorder, such as, for example, an autoimmune disease or an inflammatory disorder.
For example, administering a huIFNy antibody to a subject suffering from Crohn's
Disease (CD) can act directly on the disease-causing immune cells, thereby providing rapid
intervention with minimal suppression of the immune system. Administering a huIFNy
antibody to a subject suffering from Systemic Lupus Erythematosus is another medical
indication that provides an opportunity to modify the immune cells responsible for the
disease. Administering an huIFNy antibody, a fully human protein, to a subject suffering
from psoriasis avoids the need to treat patients wife more aggressive medications (e.g.,
Methotrexate) that have well documented unwanted side effects (e.g., liver damage).
Administering a huIFNy antibody to a subject suffering from rheumatoid arthritis is another
medical indication that provides the opportunity to modulate the upstream generation and
function of disease-inducing Thl-mediated response.
Autoimmune diseases include, for example, Acquired Immunodeficiency Syndrome
(AIDS, which is a viral disease with an autoimmune component), alopecia areata,
ankylosing spondylitis, antiphospholipid syndrome, autoimmune Addison's disease,
autoimmune hemolytic anemia, autoimmune hepatitis, autoimmune inner ear disease
(AIED), autoimmune lymphoproliferative syndrome (ALPS), autoimmune
thrombocytopenic purpura (ATP), Behcet's disease, cardiomyopathy, celiac sprue-
dermatitis hepetiformis; chronic fatigue immune dysfunction syndrome (CFIDS), chronic
inflammatory demyelinating polyneuropathy (CIPD), cicatricial pemphigold, cold
46

WO 2006/109191 PCT/IB2006/001514
agglutinin disease, crest syndrome, Crohn's disease, Degos' disease, dermatomyositis-
juvenile, discoid lupus, essential mixed cryoglobulinemia, fibromyalgia-fibromyositis,
Graves' disease, Guillain-Barr6 syndrome, Hashimoto's thyroiditis, idiopathic pulmonary
fibrosis, idiopathic thrombocytopenia purpura (ITP), IgA nephropathy, insulin-dependent
diabetes mellitus, juvenile chronic arthritis (Still's disease), juvenile rheumatoid arthritis,
Meniere's disease, mixed connective tissue disease, multiple sclerosis, myasthenia gravis,
pernacious anemia, polyarteritis nodosa, polychondritis, polyglandular syndromes,
polymyalgia rheumatica, polymyositis and dermatomyositis, primary agammaglobulinemia,
primaiy biliary cirrhosis, psoriasis, psoriatic arthritis, Raynaud's phenomena, Reiter's
syndrome, rheumatic fever, rheumatoid arthritis, sarcoidosis, scleroderma (progressive
systemic sclerosis (PSS), also known as systemic sclerosis (SS)), SjOgren's syndrome, stiff-
man syndrome, systemic lupus erythematosus, Takayasu arteritis, temporal arteritis/giant
cell arteritis, ulcerative colitis, uveitis, vitiligo and Wegener's granulomatosis.
Inflammatory disorders include, for example, chronic and acute inflammatory
disorders. Examples of inflammatory disorders include Alzheimer's disease, asthma, atopic
allergy, allergy, atherosclerosis, bronchial asthma, eczema, glomerulonephritis, graft vs.
host disease, hemolytic anemias, osteoarthritis, sepsis, stroke, transplantation of tissue and
organs, vasculitis, diabetic retinopathy and ventilator induced lung injury.
The huIFNy antibodies modulate an immune response in a subject, e.g., in a human
subject. For example, the huIFNy antibodies described herein modulate, e.g., reduce, inhibit
or prevent an exaggerated Thl-mediated immune response, such as an exaggerated Thl-
mediated immune response associated with an autoimmune or inflammatory disorder such
as, for example, Crohn's disease, system lupus erythematosus, psoriasis, sarcoidosis,
rheumatoid arthritis, vasculitis, atopic dermatitis and secondary progressive multiple
sclerosis. In an exaggerated Thl-mediated immune response, Thl cytokine(s), such as IL-2,
IL-3, TNF-alpha (TNFa) and IFNy, are presented in a subject at level that is higher than the
level of Thl cytokine production in a subject not suffering from a disease or disorder
associated with an exaggerated Th-1 immune response. To classify a Thl-mediated
immune response as an exaggerated response, the level of a Thl cytolcine production
response is evaluated, e.g., by measuring and analyzing the level of secreted cytokines using
an ELISA or other assay.
47

WO 2006/109191 PCT/IB2006/001514
The huIFNy antibodies described herein are also used to modulate, e.g., inhibit,
reduce or prevent, class switching to an IgG isotype, such as IFNy-induced class switching.
These huIFNy antibodies modulate, e.g., inhibit, prevent or reduce a Till-mediated response
and consequently decrease IFNY-induced switching.
In one embodiment, the huIFNy antibody compositions used to treat an immune-
related disorder are administered in combination with any of a variety of anti-cytokine
agents or anti-chemokine agents. Suitable anti-cytokine or anti-chemokme reagents
recognize, for example, cytokines such as interleukin 1 (IL-1), IL-2, EL-4, IL-6, EL-12, IL-
13, IL-15, IL-17, IL-18, IL-20, IL-21, IL-22, IL-23, IL-27 and IL-31, and/or chemokines
such as MIP1 alpha, MEP1 beta, RANTES, MCP1, IP-10, ITAC, MIG, SDF and fractalkine.
The present invention also provides methods of treating or alleviating a symptom
associated with an immune-related disorder. For example, the compositions of the
invention are used to treat or alleviate a symptom of any of the autoimmune diseases and
inflammatory disorders described herein. Symptoms associated with immune-related
disorders include, for example, inflammation, fever, loss of appetite, weight loss, abdominal
symptoms such as, for example, abdominal pain, diarrhea or constipation, joint pain or
aches (arthralgia), fatigue, rash, anemia, extreme sensitivity to cold (Raynaud's
phenomenon), muscle weakness, muscle fatigue, changes in skin or tissue tone, shortness of
breath or other abnormal breathing patterns, chest pain or constriction of the chest muscles,
abnormal heart rate (e.g., elevated or lowered), light sensitivity, blurry or otherwise
abnormal vision, and reduced organ function.
The therapeutic formulations of huIFNy antibody are administered to a subject
suffering from an immune-related disorder, such as an autoimmune disease or an
inflammatory disorder. A subject suffering from an autoimmune disease or an
inflarnmatory disorder is identified by methods known in the art. For example, subjects
suffering from an autoimmune disease such as Crohn's disease, lupus or psoriasis, are
dentified using any of a variety of clinical and/or laboratory tests such as, physical
;xamination, radiologic examination and blood, urine and stool analysis to evaluate immune
status. For example, patients suffering from lupus are identified, e.g., by using the anti-
nuclear antibody test (ANA) to determine if auto-antibodies to cell nuclei are present in the
blood. Patients suffering from Crohn's are identified, e.g., using an upper gastrointestinal
GI) series and/or a colonoscopy to evaluate the small and large intestines, respectively.
48

WO 2006/109191 PCT/IB2006/001514
Patients suffering from psoriasis are identified, e.g., using microscopic examination of
tissue taken from the affected skin patch, while patients suffering from rheumatoid arthritis
are identified using, e.g., blood tests and/or x-ray or other imaging evaluation.
Administration of a huIFNy antibody to a patient suffering from an immune-related
disorder such as an autoimmune disease or an inflammatory disorder if any of a variety of
laboratory or clinical results is achieved. For example, administration of a huIFNy antibody
to a patient suffering from an immune-related disorder such as an autoimmune disease or an
inflammatory disorder is considered successful one or more of the symptoms associated
with the disorder is alleviated, reduced, inhibited or does not progress to a further, i.e.,
worse, state. Administration of a huIFNy antibody to a patient suffering from an immune-
related disorder such as an autoimmune disease or an inflammatory disorder is considered
successful if the disorder, e.g., an autoimmune disorder, enters remission or does not
progress to a further, i.e., worse, state.
Diagnostic and Prophylactic Formulations
The fully human anti-IFNy MAbs of the invention are used in diagnostic and
prophylactic formulations. In one embodiment, a huIFNy MAb of the invention is
administered to patients that are at risk of developing one of the aforementioned
autoimmune diseases. A patient's predisposition to one or more of the aforementioned
autoimmune diseases can be determined using genotypic, serological or biochemical
markers.
In another embodiment of the invention, a huIFNy antibody is administered to
human individuals diagnosed with one or more of the aforementioned autoimmune diseases.
Upon diagnosis, a huIFNy antibody is administered to mitigate or reverse the effects of
autoimmuniry.
Antibodies of the invention are also useful in the detection of IFNy in patient
samples and accordingly are useful as diagnostics. For example, the huIFNy antibodies of
the invention are used in in vitro assays, e.g., ELISA, to detect IFNy levels in a patient
sample.
In one embodiment, a huIFNy antibody of the invention is immobilized on a solid
support {e.g., the well(s) of a microtiter plate). The immobilized antibody serves as a
capture antibody for any IFNy that may be present in a test sample. Prior to contacting the
49

WO 2006/109191 PCT/IB2006/001514
immobilized antibody with a patient sample, the solid support is rinsed and treated with a
blocking agent such as mink protein or albumin to prevent nonspecific adsorption of the
analyte.
Subsequently the wells are treated with a test sample suspected of containing the
antigen, or with a solution containing a standard amount of the antigen. Such a sample is,
e.g., a serum sample from a subject suspected of having levels of circulating antigen
considered to be diagnostic of a pathology. After rinsing away the test sample or standard,
the solid support is treated with a second antibody that is detectably labeled. The labeled
second antibody serves as a detecting antibody. The level of detectable label is measured,
and the concentration of IFNy antigen in the test sample is determined by comparison with a
standard curve developed from the standard samples.
It will be appreciated that based on the results obtained using the huIFNy antibodies
of the invention in an in vitro diagnostic assay, it is possible to stage a disease {e.g., an
autoimmune or inflammatory disorder) in a subject based on expression levels of the IFNy
antigen. For a given disease, samples of blood are taken from subjects diagnosed as being
at various stages in the progression of the disease, and/or at various points in the therapeutic
treatment of the disease. Using a population of samples that provides statistically
significant results for each stage of progression or therapy, a range of concentrations of the
antigen that may be considered characteristic of each stage is designated.
All publications and patent documents cited herein are incorporated herein by
reference as if each such publication or document was specifically and individually
indicated to be incorporated herein by reference. Citation of publications and patent
documents is not intended as an admission that any is pertinent prior art, nor does it
constitute any admission as to the contents or date of the same. The invention having now
been described by way of written description, those of skill in the art will recognize that the
invention can be practiced in a variety of embodiments and that the foregoing description
and examples below are for purposes of illustration and not limitation of the claims that
follow.
50

WO 2006/109191 PCT/IB2006/001514
EXAMPLES
The following examples, including the experiments conducted and results achieved
are provided for illustrative purposes only and are not to be construed as limiting upon the
present invention.
EXAMPLE 1: Cloning, Expression and Purification of Human Interferon Gamma
Cloning.
The sequence corresponding to the mature sequence of human interferon gamma
(hlFNy, huIFNy) was amplified from human cDNA by polymerase chain reaction (PCR)
using specific oligonucleotides. The amplification production was gel-purified and cloned
into the pET41c expression vector (Novagen, San Diego CA). The vector was further
modified to introduce an Avitag™ (Avidity, Denver CO) and an octa-histidine tag at the C-
terminus of hEFNy allowing for in vivo biotinylation of the protein and purification by
IMAC (Immobilized Metal Ion Affinity Chromatography).
Expression.
E. coli BL21 cells were co-transformed with the pET41c-MFNy and a pACYCl 84-
BirA vector, which encodes the BirA enzyme required for the in vivo biotinylation of the
Avitag™ sequence. Single colonies resistant to Kanamycin (50 ng/ml) and
Chloramphenicol (10 fig/ml) were selected and used to inoculate a starter culture in LB
(Kan 50 mg/ml/Cm 10 jig/ml) and grown overnight at 37 °C.
The next day, the culture was used to inoculate (1:100 dilution) a 400 ml culture of
LB (Kan 50 mg/ml/Cm 10 mg/ml) supplemented with 50 mM biotin. The culture was grown
at 37 °C with shaking (240 rpra) until an ODMO of 0.6 was reached. At that point,
isopropyl-beta-D-thiogalactopyranoside (IPTG) was added to a final concentration of
1 mM, and the culture was further incubated for 3h under the same conditions. Cells were
centrifuged at 4000 rpm for 20 minutes, and the pellet was frozen at -20°C. Under these
conditions essentially all of the hlFNy was insoluble and found in inclusion bodies.
Purification.
Bacterial pellets were thawed and resuspended in 8 ml of Bugbuster reagent
containing 8 p.1 of Benzonaze (Novagen) and incubated at room temperature for 30 minutes.
51

WO 2006/109191 PCT/IB2006/001514
The solution was centrifuged for 30 minutes at 15'000g at 4 °C. The pellet containing the
inclusion bodies was resuspended in 7 ml of solubilization buffer (50 mM Tris-HCL pH 7.4,
300 mM NaCl, 20 mM Imidazole, 5 mM p-mercaptoethanol, 6M Guanidin-HCl). The
resuspended material was centrifuged at 4 °C for 30 minutes at 15'000g.
Two 5 ml Hi Trap Chelating column (Amersham, Buckinghamshire, England),
loaded with NiSO4 and equilibrated witli solubilization buffer, were connected together
according to manufacturer's instructions. The supernatant after the centrifugation step was
filter on a 0.45 pm membrane and loaded on the column with the help of peristaltic pump at
1 ml/min. The columns weTe then placed on an AKTA prime chromatography system for on
column protein refolding and elution. The immobilized protein was washed with 35 ml of
solubilization buffer at 1 ml/min. A linear gradient of solubilization buffer with increasing
concentration of refolding buffer (50 mM Tris-HCL pH 7.4,300 mM NaCl) was applied at
1 ml/min. for 1 hour until 100% refolding buffer was reached. The column was then further
washed with 25 ml of refolding buffer. The refolded protein was then eluted from the
column with elution buffer (50 mM Tris-HCl, 300 mM NaCl, 400 mM Imidazole). Protein
containing fractions were pooled and desalted onPDIO columns (Amersham) equilibrated
with PBS. The desalted protein was then aliquoted and stored at -80 °C.
EXAMPLE 2: Cells Expressing Interferon Gamma on Cell Surface
Chinese hamster ovary (CHO) cells (available from ATCC) were stably transfected
with c-myc-tagged human IFNy cDNA. cDNAs were subcloned into pCDNA 3.1 plasmids
(Invitrogen, Carlsbad CA) containing neomycin resistance genes. Transfectants were
selected by using this antibiotic, and successive cell sorting was accomplished by flow
cytometry using an anti-6xHis (Sigma) antibody. Surface expression of human IFNy was
confirmed via flow cytometry using an anti-IFNy mAb (clone B27, Becton Dickinson,
Franklin Lakes NJ).
EXAMPLE 3: Screening of human scFv libraries
General procedures for construction and handling of human scFv libraries are
described in Vaughan et al., (Nat. Biotech. 1996,14:309-314), hereby incorporated by
reference in its entirety. Libraries of human scFv were screened against hlFNy according to
the following procedure.
52

WO 2006/109191 PCT/IB2006/001514
Liquid phase selections.
Aliquots of scFvphage libraries (1012 Pfu) obtained from Cambridge Antibody
Technology (Cambridge, UK) were blocked with PBS containing 3% (w/v) skimmed milk
for one hour at room temperature on a rotary mixer. Blocked phage was then deselected on
streptavidin magnetic beads (Dynal M-280) for one hour at room temperature on a rotary
mixer. Deselected phage was then incubated with in vivo biorinylated hEFNy (100 nM) for
two hours at room temperature on a rotary mixer. Beads were captured using a magnetic
stand followed by four washes with PBS/0.1% Tween 20 and 3 washes with PBS. Beads
were then directly added to 10 ml of exponentially growing TGI cells and incubated for one
hour at 37 °C with slow shaking (100 rpm). An aliquot of the infected TGI was serial
diluted to titer the selection output. The remaining infected TGI were spun at 3000 rpm for
15 minutes and re-suspended in 0.5 ml 2xTY-AG (2xTY media containing 100 mg/ml
ampicilin and 2% glucose) and spread on 2xTYAG agar Bioassay plates. After overnight
incubation at 30 °C 10 ml of 2xTYAG was added to the plates and the cells were scraped
. form the surface and transferred to a 50 ml polypropylene tube. 2xTYAG containing 50%
glycerol was added to the cell suspension to obtain a final concentration of 17% glycerol.
Aliquots of the selection round were kept at-80 °C.
Cell surface selections.
Aliquots of scFv phage libraries (1012 Pfu) obtained from Cambridge Antibody
Technology (Cambridge, UK) were blocked with PBS containing 3% (w/v) skimmed milk
for one hour at room temperature on a rotary mixer. Blocked phage was then deselected for
one hour at 37 °C/5% CO2 on CHO cells transfected with an empty pDisplay vector (in a
T75 flask 80% confluence) and that had been previously blocked with PBS containing 2%
(w/v) skimmed milk. Deselected phage was then incubated CHO-pDisplay-hlFNy cells for
one hour at room temperature with gentle shaking. Cells were then washed ten times with
PBS. Bound phage was eluted by adding directly 10 ml of exponentially growing TGI to
the T75 flask and incubating for one hour at 37 °C with slow shaking. An aliquot of the
infected TGI was serial diluted to titer the selection output. Infected TGI were spun at 3000
rpm for 15 minutes and re-suspended in 0.5 ml 2xTY-AG (2xTY media containing 100
mg/ml ampicilin and 2% glucose) and spread on 2xTYAG agar Bioassay plates. After
overnight incubation at 30°C 10 ml of 2xTYAG was added to the plates and the cells were
53

WO 2006/109191 PCT/IB2006/001514
scraped form the surface and transferred to a 50 ml polypropylene tube. 2xTYAG
containing 50% glycetol was added to the cell suspension to obtain a final concentration of
17% glycerol. Aliquots of the selection round were kept at ~80°C.
Phage rescue.
100 f.il of cell suspension obtained from previous selection rounds were added to 20
ml of 2xTYAG and grown at 37 °C with agitation (240 rpm) until an OD60o of 0.3 to 0.5
was reached. The culture was then super-infected with 3.3 x 1010 MK13K07 helper phage
and incubated for one hour at 37 °C (150 rpm). The medium was then changed by
centrifugating the cells at 2000 rpm for 10 minutes, removing the medium and resuspending
the pellet in 20 ml of 2xTY-AK (lOOjig/ml ampicilin; 50 mg/ml kanamycin). The culture
was then grown overnight at 30 °C (240 rpm).
Monoclonal phage rescue for ELISA.
Single clones were picked into a microtiter plate containing 150ul of 2xTYAG
media (2% glucose) per well and grown at 37°C (100-120 rpm) for 5-6h. M13KO7 helper
phage was added to each well to obtain a multiplicity of infection (MOI) of 10 (i.e., 10
phage for each cell in the culture) and incubated at 37°C (100 rpm) for Ih. Following
growth, plates weTe.centrifuged at 3,200 rpm for 10 min. Supernatant was carefully
removed, cells re-suspended in 150 u.12xTYAK. medium and grown overnight at 30 °C (120
rpm). For the ELISA, the phage are blocked by adding 150ml of 2x concentration PBS
containing 5% skimmed milk powder followed by one hour incubation at room temperature.
The plates were then centrifuged 10 minutes at 3000 rpm and the phage containing
supernatant used for the ELISA.
Phage ELISA.
ELISA plates (Maxisorb, NUNC) were coated overnight with 2 jig/ml HFNy in
PBS. Control plates were coated with 2mg/ml BSA. Plates were then blocked with 3%
ikimmed milk / PBS at room temperature for lh. Plates were washed 3 times with PBS
(.05% Tween 20 before transferring the pre-blocked phage supernatants and incubation for
me hour at room temperature. Plates were then washed 3 times with PBS 0.05% Tween 20.
50ml of 3% skimmed milk/ PBS containing (HRP)-conjugated anti-Ml3 antibody
Amersham, diluted 1:10,000) to each well. Following incubation at room temperature for
1. hr, the plates were washed 5 times with PBS 0.05% Tween 20. The ELISA was then
54

WO 2006/109191 PCT/IB2006/001514
revealed by adding 50ml of 1MB (Sigma) and 50ml of 2N H2SO4 to stop the reaction.
Absorption intensity was read at 450nm.
Phage clone sequencing
Single clones were placed in a microtiter plate containing 150ul of 2xTYAG media
(2% glucose) per well and grown at 30 °C (120 rpm) overnight. The next day 5 ml of culture
was transferred into another plate containing 45 mlof dH2O and mixed. The plates was then
frozen at-20 °C. After thawing, 1m l of this suspension was used for PCR amplification
using standard PCR protocols with primer specific for pCANTAB6: mycseq, 5'-
CTCTTCTGAGATGAGTTTTTG-3' (SEQ ID NO: 100) and gene3leader, 5'-
TTATTATTCGCAATTCCTTTAGTTGTTCCT-3' (SEQ IDNO:101).
The PCR reactions were purified in 96 well format using the Montage PCRf.i96
system (Millipore). 5 ml of the eluted DNA was sequencing using the mycseq and
gene31eader primers.
ScFv periplasmic preparation for functional tests.
Individual clones were inoculated into a deep well microtiter plate containing 0.9 ml
of 2xTYAG media (0.1% glucose) per well and grown at 37 °C for 5-6h (250 rpm). l00ml
per well of 0.2 mM IPTG in 2xTY medium were then added to give a final concentration of
0.02 mM IPTG. Plates were then incubated overnight at 30 °C with shaking at 250 rpm.
The deep-well plates were centrifuged at 2,500 rpm for 10 min and the supernatant carefully
removed. The pellets were re-suspended in 150ml TES buffer (50 mM Tris / HC1 (pH 8), 1
mM EDTA (pH 8), 20% sucrose, complemented with Complete protease inhibitor, Roche).
A hypotonic shock was produced by adding 150 ml of diluted TES buffer (1:5 TES:water
dilution) and incubation on ice for 30 min. Plates were then centrifuged at 4000 rpm for 10
minutes to remove cells and debris. The supernatants were carefully transferred into
another microtiter plate and kept on ice for immediate testing in functional assays or
ELISAs.
Large scale scFv purification
A starter culture of 1 ml of 2xTYAG was inoculated with a single colony from a
freshly streaked 2xTYAG agar plate and incubated with shaking (240 rpm) at 37 °C for 5
hours. 0.9 ml of this culture was used to inoculate a 400 ml culture of the same media and
was grown overnight at 30 °C with vigorous shaking (300 rpm).
55

WO 2006/109191 PCT/IB2006/001514
The next day the culture was induced by adding 400 m1 of 1M IPTG and incubation
was continued for an additional 3 hours. The cells were collected by centrifugation at 5,000
rpm for 10 minutes at 4 °C. Pelleted cells were resuspended in 10 ml of ice-cold TES buffer
complemented with protease inhibitors as described above. Osmotic shock was achieved by
adding 15 ml of 1:5 diluted TES buffer and incubation for 1 hour on ice. Cells were
centrifuged at 10,000 rpm for 20 minutes at 4 °C to pellet cell debris. The supernatant was
carefully transferred to a fresh tube. Imidazole was added to the supernatant to a final
concentration of 10 mM. 1 ml of Ni-NTA resin (Qiagen), equilibrated in PBS was added to
each tube and incubated on a rotary mixer at 4 °C (20 rpm) for 1 hour.
The tubes were centrifuged at 2,000 rpm for 5 minutes and the supernatant carefully
removed. The pelleted resin was resuspended in 10 ml of cold (4 °C) Wash buffer 1 (50
mM NaH2PO4, 300 mM NaCl, 10 mM imidazole, pH to 8.0). The suspension was added to
a polyprep column (Biorad). 8 ml of cold Wash Buffer 2 (50 mM NaH2PO4,300 mM NaCl,
20 mM imidazole, pH to 8.0) were used to wash the column by gravity flow. The scFv were
eluted from the column with 2 ml of Elution buffer (50 mM NaH2PO4, 300 mM NaCl, 250
mM imidazole, pH to 8.0). Fractions were analyzed by absorption at 280 nm and protein
containing fractions were pooled before buffer exchange on a PD10 desalting column
(Amersham) equilibrated with PBS. The scFv in PBS were analyzed by SDS-PAGE and
quantified by absorption at 280 nm. The purified scFv were aliquoted and stored at -20°C
and at 4°C.
EXAMPLE 4: scFv Extract Inhibition of Interferon Gamma-Induced Reporter Gene
Expression
Periplasmic scFv extracts of various huIFNy antibodies were produced as described
above. A high through-put screen cell-based assay was used for the identification of single
chain variable fragment (scFv) blockers of IFNy activity. A reporter gene (firefly
luciferase), driven by the IFNy-inducible GBP1 promoter, was transfected into the human
melanoma cell line, Me67.8. Both scFv and IFNy were added to the cell culture
concomitantly. Following a 6 hour incubation time, the luciferase reporter assay was
performed. The scFv found to inhibit the induction of firefly luciferase were retained for
further validation.
56

WO 2006/109191PCT/IB2006/001514



Several scFv extracts inhibited the IFNy-induced reporter gene in a dose dependant
fashion (Figure 15). For each scFv clone shown in Figure 15, various concentrations (2.7,
0.68, 0.17,0.043 and 0.011 nM) were tested as shown by the columns above each clone
name (descending concentration from left to right). The percentage inhibition exhibited by
each scFv extract at these various concentrations is shown in Table 3 below.
Table 3: Percentage inhibition of IFNy-induced reporter gene expression by
periplasmic scFV extracts

IscFv) nM AS HS A8 D8 CIO B4 R9 F9 A4 El C» G7 G10 D6 C6 G9 D3 FS
2.7 82 80 85 60 63 63 62 68 36 43 56 75 47 82 73 52 69 64
0.68 92 75 86 60 50 49 53 32 1 68 67 73 44 73 66 12 55 64
0.17 100 65 87 40 53 21 56 3 0 38 58 24 0 31 25 0 36 48
0.O43 87 26 65 10 34 5 0 0 0 10 33 38 0 11 O 0 28 O
0.011 0 0 13 0 19 O 0 0 0 0 0 4 0 0 0 0 20 0
EXAMPLE 5: scFv Inhibition of Interferon Gamma-Induced MHC Class II
Expression
0 A flow cytometric assay was implemented to identify fully human IgG antibodies, or
fragments thereof, capable of blocking the expression of IFNy-induced MHC class II
molecules. Following the plating of Me67.8 cells, 5 ng/ml recombinant human IFNy was
added to cultures in the presence of various concentrations of candidate fully human anti-
IFNy monoclonal antibodies. Following 48 h in culture, cells were stained with
5 fluorescently labeled anti-human MHC class II antibody (HLA-DR) and analyzed using a
FACSCalibur®. Thus, the IC50 (where 50% of the IFNy-induced MHC class II expression is
inhibited, i.e,, 50% inhibitory concentration), for each candidate antibody is measured.
Purified fully human scFv were produced as described above in Example 1. The
effect of the scFv on IFNy-induced MHC class II expression on melanoma cells was
[) evaluated using the flow cytometric cell-based assay described above. These scFv inhibited
IFNy-induced MHC II expression on melanoma cells. (Figure 16, Panels 1-12). The ability
of these scFv clones to inhibit IFNy-induced MHC II expression on melanoma cells was
compared to a mouse anti-human IFNy mAb referred to herein as 16C3. scFv clones (—)
and the mouse anti-human IFNy mAb 16C3 (—) are depicted in Figure 16.
57

WO 2006/109191 PCT/IB2006/001514
EXAMPLE 6: Reformatting scFv into IgG Format
Purified fully human scFv were produced as described above in Example 1. The VH
and VL. sequence of selected scFv were amplified with specific oligonucleotides introducing
a leader sequence and a HindlTl restriction site at the 5' end. An Apal or an Avrll site was
introduced at the 3' end of the heavy and light chain sequence, respectively. The amplified
VH sequences were digested HindlH/Apal and cloned into the pCon_gammal expression
vector (LONZA, Basel, Switzerland). The amplified VL sequences were digested HindlD/
Avrll and cloned into the pCon_lambda2 expression vector (LONZA). The constructions
were verified by sequencing before transfection into mammalian cells.
The VH and VL CDNA sequences in their appropriate expression vectors were
transfected into mammalian cells using the Fugene 6 Transfection Reagent (Roche, Basel,
Switzerland). Briefly, Peak cells were cultured in 6-well plates at a concentration of 6 x 105
cells per well in 2 ml culture media containing fetal bovine serum. The expression vectors,
encoding the candidate VH and VL sequences, were co-transfected into the cells using the
Fugene 6 Transfection Reagent according to manufacturer's instructions. One day
following transfection, the culture media was aspirated, and 3 ml of fresh serum-free media
was added to cells and cultured for three days at 37 °C. Following three days culture period,
the supernatant was harvested for IgG purified on protein G columns.
Reformatted fully IgG was purified from serum-free supernatants from transfected
cells using Protein G-Sepharose 4B fast flow columns (Sigma, St. Louis, MO) according to
manufacturer's instructions. Briefly, supernatants from transfected cells were incubated
overnight at 4 °C with ImmunoPure (G) IgG binding buffer (Pierce, Rockford IL). Samples
were then passed over Protein G-Sepharose 4B fast flow columns and the IgG consequently
purified using elution buffer. The eluted IgG fraction was then dialyzed against PBS and
the IgG content quantified by absorption at 280 nm. Purity and IgG integrity were verified
by SDS-PAGE.
EXAMPLE 7: Inhibition of Interferon Gamma-Induced MHC Class II Expression by
Reformatted scFv
scFv were reformatted into an IgG format as described above. The effect of the IgG
clones on IFNy-induced MHC class II expression on melanoma cells was evaluated using
the flow cytometric cell-based assay described above in Example 2. As shown in Figure 17,
58

WO 2006/109191PCT/IB2006/001514



Panels 1-7, these IgG clones inhibited IFNy-induced MHCII expression on melanoma cells.
The ability of these IgG clones to inhibit IFNy-induced MHC II expression on melanoma
cells was compared to the mouse anti-human IFNy mAb 16C3 and the R&D Systems mouse
anti-human EFNy antibody MAB285. Fully IgG clones
(-X-), the mouse anti-human IFNy mAb 16C3 (-A-), and the R&D Systems,-Inc.
(Minneapolis, MN) mouse anti-human IFNy MAB285 (-•-) are depicted.
The IC50 values for these IgG clones are shown below in Table 4.
Table 4. JCso analysis of fully human anti-IFNy monoclonal antibodies.

IgG mAb MHC H InhibitionCell-Based AssayIC50
16C3 lOOpM
MAB285 400pM
AC1.2R3P2_A6 41pM
AD14R4P1_B9 322pM
AC1.4R4P2_C10 203pM
AC1.2R3P2JD8 708pM
AD1.3R3P5JF8 1525pM
AD1.3R3P6JF9 185pM
AD14R4P2_G7 233pM
EXAMPLE 8: Back-Mutation of huIFNy Antibody Clone to Germline Sequence
In the studies described herein, the nucleotides and amino acid residues in the
nucleic acid and amino acid sequence of the A6 clone were mutated to correspond to the
nucleotide or amino acid residue found in the germline sequence. This process is referred to
herein as "back-mutation".
A6 heavy chain: The immunoglobulin heavy variable gene of antibody A6 had a
100% homology to the human germ line DP-47 or IGHV3-23 (GenBank Accession number
M99660). The immunoglobulin heavy joining (IGHJ) region of A6 was compared to the
six human functional IGHJ regions. The IGHJ region of A6 was identified as IGHJ2 (Table
5A below), but had a better overall homology with IGHJ5-02 (Table 5B below). The
59

original IGHJ region of A6 was therefore mutated to correspond to the sequence of IGHJ5-
02, but only for the sequence outside the CDR3. Mutated nucleotides and amino acid
residues are shown in boxes in Tables 5A and 5B, and the CDR regions are underlined.

A6 light chain: The immunoglobulin lambda variable gene (VL) of antibody A6
belongs to the IGLV6-57 or VI-22 subgroup (GenBank Accession Number Z73673). A6-
VL has 7 mutations compared to IGLV6-57, three in the CDRs and four in the frameworks
(Table 6 below). The mutated nucleotides and amino acid residues are shown in boxes in
Table 6, and the CDR regions are underlined.
The four mutations in framework regions are: Ser to Ala in framework 2 region at
Kabat position 43; Ser to Thr in framework 3 region at Kabat position 72; Lys to Glu and
Thr to Ala in framework 3 region at Kabat positions 79 and 80, respectively. The four
mutations in the framework regions were changed first individually, then all together back
to the corresponding human germ line residue. The mutations of these four residues back to
the corresponding human germ line amino acid did not alter in any way the binding affinity
of the NI-0501 antibody, also referred to herein as "backmutated A6", to its target antigen
as compared to the A6 antibody. The mutations from the A6 VL sequence to the
corresponding germ line residue in CDRl (Ala to Val) and CDR2 (Gin to Arg) were carried
out and were shown not to modify the overall affinity for huIFNy of the NI-0501 antibody
(backmutated A6) as compared to the A6 antibody.

Table 6: Comparison between A6 and human functional IGHV6-57 gene

The complete sequences of the NI-0501 heavy and light chains are set forth in
Figures 1A-1D. The nucleotides and amino acid residues that were backrautated to produce
the NI-0501 antibody (i.e., those nucleotides and residues that were changed from the
original A6 sequence) are underlined and italicized in Figures 1A and 1C.
EXAMPLE 9: Affinity and Binding Kinetics of huIFNy Antibody
The affinity and binding kinetics of the NI-0501 huIFNy antibody were
characterized on a Biacore 2000 instrument (Biacore AB, Uppsala, Sweden). 200 RU of
NI-0501 were immobilized by EDC/NHS chemistry on a Cl Biacore chip. Binding was
measured by passing hlFNy (R&D Systems) in HBS-EP buffer at concentrations between
200 nM and 1 nM. The flow rate was 100 PCT/IB2006/001514I/minute and the temperature set at 25 °C. The
data was fitted according to 1:1 Langmuir model and the Kon, KofTand KD values
determined (Figure 18).
EXAMPLE 10: Activity of huIFNy Antibody
The activity of the NI-0501 huIFNy antibody was compared to the activity of the
antibody produced by the clone A6 (i.e., the A6 huIFNy antibody). In this study, the ability
of each huIFNy antibody to inhibit recombinant human IFNy (rhuIFNy)-induced MHC class
II up-regulation on the human melanoma cell line, Me67.8 was evaluated. Briefly, Me67.8
melanoma cells were incubated with rhuIFNy, in the presence of NI-0501 or the A6 huIFNy
antibody for 48-72 h. MHC class II upregulation was measured as described above in
Example 5. The two antibodies presented a similar activity, which demonstrates that the
**1

WO 2006/109191 PCT/IB2006/001514
backmutations in the NI-0501 huIFNy antibody did not modify the activity of the antibody
(Figure 19).
The activity of the NI-0501 huIFNy antibody was then tested on native IFNy. In this
study, human peripheral blood mononuclear cells (PBMCs) were activated with 1 mg/ml of
the mitogen PHA for 48 h, and supernatants were tested via ELISA for the presence of
native IFNy. This supernatant was then used to stimulate the MHC class II upregulation on
Me67.8 cells. NI-0501 was able to neutralize the MHC class II upregulation induced by
native human IFNy (Figure 20).
EXAMPLE 11: Cross-Reactivity of huIFNy Antibody
Binding assay: NI-0501 was tested for its ability to bind to IFNy using a Sandwich
ELISA format assay. Briefly, IFNy from the species mentioned in the title of each graph
shown in Figure 21 was captured with pre-coated NI-0501 (- A-) or the control anti-species
IFNy mAb (-■-). The IFNy from each species was detected using a polyclonal antibody
specific for the IFNy in that assay. As seen in Figure 21, NI-0501 binding to rat IFNy is
similar to the control antibody, but not for the other species, excluding cynomolgus
monkey.
Neutralization of IFNy activity: The antibody NI-0501 was tested for its ability to
neutralize or inhibit recombinant IFNy proteins from several different species. Briefly,
recombinant IFNy from the various tested species was placed in culture with Me67.8 cells
in the presence or absence of NI-0501 for 48-72 h. MHC class II upregulation was
measured as described above in Example 5. The cross-reactivity to, and neutralization of,
cynomolgus IFNy was demonstrated by inhibiting the MHC class II upregulation on the
human melanoma cell line, Me67.8 (Figure 21). NI-0501 was able to inhibit IFNy from
cynomolgus monkey but could not neutralize IFNy from the other tested species,
demonstrating no cross reactivity the antibody with these species (Table 7).
62

WO 2006/109191

PCT/IB2006/001514

Table 7: Cross Reactivity of NI-0501

Nl-0501 nhuIFNy rbulFNf ncylFNy rcylFNy rdlFNy rcIFNr irlFNy rmrFNy
Binding + + + + - - - -
Neutralization + + + * * * *
nhu = native human IFNy
rhu = recombinant human IFNy
ncy = native cynomolgus IFNy
rcy = recombinant cynomolgus IFNy
rd = recombinant dog IFNy
re = recombinant cat IFNy
rr = recombinant rat IFNy
rm = recombinant mouse IFNy
+ = cross-react
- = do not cross-react
* = not tested
In addition, cynomolgus PBMCs were activated with 1 jig/ml of the mitogen PHA
for 48 h, and supernatants were tested via ELISA for the presence of native IFNy. This
supernatant was then used to stimulate the MHC class II upregulation on Me67.8. NI-0501
was able to neutralize the MHC class II upregulation induced by native cynomolgus TFNy
(Figure 22).
EXAMPLE 12: Biological Activity of huIFNy Antibody
The studies described herein were designed to test the biological activity of the NI-
0501 huIFNy antibody upon administration to cynomolgus monkeys. NI-0501 was chosen
for the safety and pharmacokinerics (PK) studies described herein because this huIFNy
antibody was found to cross-react with the IFNy from cynomolgus monkeys, as described
above. To evaluate adverse clinical effects after multiple intravenous infusions, monkeys
are infused with the following doses: 30 mg/kg, 100 mg/kg and 200 mg/kg.
In mice with a disrupted IFNy gene, decreased levels of IgG2a and increased levels
of IgGl were observed in response to KLH immunization, demonstrating the correlation
between IFNy and the IgG response. During the 13 week main toxicology study, monkeys
are immunized with KLH in Incomplete Freund's Adjuvant (IFA). A typical immune
response to KLH/TFA in monkeys, co-treated with placebo, elicits a KLH-specific IgM and
IgG response detectable in the serum. These studies are designed to evaluate whether
neutralizing IFNy in NI-0501-treated monkeys that were immunized with KLH in IF A,
alters the KLH-specific IgG titer.
63

WO 2006/109191 PCT/1B2006/0015I4
EXAMPLE 13: Modulation of EFNy Activity Using huIFNy Antibodies
The production of the chemokine IP-10 is up-regiilated by IFNy in several different
cell lines. Based on this observation a whole blood assay was developed. In flu's whole
blood assay, whole blood samples from several donors were mixed with a fixed
concentration of IFNy and different concentrations of NI-0501. After incubation, IP-10
levels were measured by ELISA as a means for evaluating the efficacy of the anti-IFNy
antibody to block the production of IP-10 (Figure 23).
Other Embodiments
While the invention has been described in conjunction with the detailed description
thereof, the foregoing description is intended to illustrate and not limit the scope of the
invention, which is defined by the scope of the appended claims. Other aspects, advantages,
and modifications are within the scope of the following claims.
64

WO 2006/109191 PCT/IB2006/001514
What is claimed is:
1. An isolated fully human monoclonal anti-IFNy antibody or fragment thereof,
wherein said antibody comprises:
(a) a VH CDR1 region comprising the amino acid sequence SYAMS (SEQ ID
NO:3) or SNAMS (SEQ ED NO:43);
(b) a VH CDR2 region comprising the amino acid sequence
AISGSGGSTYYADSVKG (SEQ ID NO:4) or TLTGSGGTAYYADSVEG
(SEQroNO:44),and
(c) a VH CDR3 region comprising an amino acid sequence selected from the
group consisting of DGSSGWYVPHWFDP (SEQ ID NO:5);
DHSSGWYVISGMDV (SEQ ID NO: 13); DLTVGGPWYYFDY (SEQ ID
NO:21); DGWNALGWLES (SEQ ID NO:29); GTELVGGGLDN (SEQ ID
NO:45); RSFDSGGSFEY (SEQ IDNO:64); VGSWYLEDFDI (SEQ ID
NO:69); GGNYGDYFDYFDY (SEQ ID NO:76); and DFWVITSGNDY
(SEQ ID NO:89),
wherein said antibody binds IFNy.
The antibody of claim 1, wherein said antibody further comprises:
(d) a VL CDR1 region comprising an amino acid sequence selected from the
group consisting of TRSSGSIASNYVQ (SEQ ID NO:8);
TRSSGSIASNYVQ (SEQ ID NO: 16); TRSGGSIGSYYVQ (SEQ ID
NO:32); TRSSGTIASNYVQ (SEQ ID NO:39); TGSGGSIATNYVQ (SEQ
ID NO:48); TGSSGSIASNYVQ (SEQ ID NO:55); TRSSGSIASNYVH
(SEQ ID N0.72); TGRNGNIASNYVQ (SEQ ID NO:84);
AGSSGSIASNYVQ (SEQ ID NO:97) and TRSSGSIVSNYVQ (SEQ ID
NO: 106);
(e) a VL CDR2 region comprising an amino acid sequence selected from the
group consisting of EDNQRPS (SEQ ID NO:9); EDNQRPS (SEQ ID
NO:17); DDDQRPS (SEQ ID NO:25); DDKKRPS (SEQ ID NO:33);
EDTQRPS (SEQ ED NO:85) and EDNRRPS (SEQ ID NO:107); and
65

WO 2006/109191 PCT/IB2006/001514
(f) a VL CDR3 region comprising an amino acid sequence selected from the
group consisting of QSYDGSNRWM (SEQ ID NO: 10); QSNDSDNW
(SEQ ID NO:18); QSYDSSNW (SEQ ID NO:26); QSYDSNNLW (SEQ
ID NO:34); QSYDNSNHWV (SEQ ID NO:40); QSYDSDNHHW (SEQ ID
NO:49); QSYDSSNQEW (SEQ ID NO:56); QSYDSNNFWV (SEQ ID
NO:61); QSSDTTYHGGW (SEQ ID NO:73); QSYEGF (SEQ ID NO:79);
QSSDSNRVL (SEQ ID NO:86); QSFDSTNLVV (SEQ ID NO:92); and
QSYSYNNQW (SEQ ID NO: 98).
3. The antibody of claim 1, wherein said antibody is an IgG isotype.
4. The antibody of claim 2, wherein said antibody comprises a VH CDR1 region
comprising the amino acid sequence SYAMS (SEQ ID NO:3); a VH CDR2 region
comprising the amino acid sequence AISGSGGSTYYADSVKG (SEQ ID NO:4), a VH
CDR3 region comprising the amino acid sequence DGSSGWYVPHWFDP (SEQ ID NO:5);
a VL CDR1 region comprising the amino acid sequence TRSSGSIASNYVQ (SEQ ID
NO:8); a VL CDR2 region comprising the amino acid sequence EDNQRPS (SEQ ID NO:9);
and a VL CDR3 region comprising an amino acid sequence QSYDGSNRWM (SEQ ID
NO: 10).
5. The antibody of claim 1, wherein said antibody is NI-0501.
6. An isolated fully human monoclonal antibody, wherein said antibody comprises a
heavy chain variable amino acid sequence selected from the group consisting of SEQ ID
NOS: 2,12,20,28, 36,42, 51,58,63, 68,75, 81, 88, 94 or 103, wherein said antibody
binds IFNy.
7. The antibody of claim 6, wherein said antibody further comprises a light chain
variable amino acid sequence selected from the group consisting of SEQ ID NOS: 7,15,23,
31,38,47, 54, 60, 66,71,78, 83,91,96 or 105, wherein said antibody binds IFNy.
66


WO 2006/109191 PCT/IB2006/001514
8. The antibody of claim 7, wherein said antibody comprises a VH CDR1 region
comprising the amino acid sequence SYAMS (SEQ ID NO:3); a VH CDR2 region
comprising the amino acid sequence AISGSGGSTYYADSVKG (SEQ ID NO:4), a VH
CDR3 region comprising the amino acid sequence DGSSGWYVPHWFDP (SEQ ID NO:5);
a VL CDR1 region comprising the amino acid sequence TRSSGSIASNYVQ (SEQ ID
NO: 8); a VL CDR2 region comprising the amino acid sequence EDNQRPS (SEQ ID NO:9);
and a VL CDR3 region comprising an amino acid sequence QSYDGSNRWM (SEQ ED
NO: 10).
9. The antibody of claim 4, wherein said antibody is an IgG isotype.
10. A pharmaceutical composition comprising an antibody of claim 1 and a carrier.
11. A pharmaceutical composition comprising an antibody of claim 4 and a carrier.
12. A method of alleviating a symptom of an autoimmune disease or inflammatory
disorder, the method comprising administering an antibody of claim 1 to a subject in need
thereof in an amount sufficient to alleviate the symptom of the autoimmune disease or
inflammatory disorder in the subject
13. The method of claim 12, wherein said subject is a human.
14. The method of claim 12, wherein said antibody comprises a VH CDR1 region
comprising the amino acid sequence SYAMS (SEQ ID NO:3); a VH CDR2 region
comprising the amino acid sequence AISGSGGSTYYADSVKG (SEQ ID NO:4), a VH
CDR3 region comprising the amino acid sequence DGSSGWYVPHWFDP (SEQ ID NO:5);
a VL CDR1 region comprising the amino acid sequence TRSSGSIASNYVQ (SEQ LD
NO:8); a VL CDR2 region comprising the amino acid sequence EDNQRPS (SEQ ID NO:9);
and a VL CDR3 region comprising an amino acid sequence QSYDGSNRWM (SEQ ID
NO:10).
15. The method of claim 14, wherein said antibody is NI-0501.
67

WO 2006/109191 PCT/IB2006/001514
16. The method of claim 12, wherein said autoimmune disease or inflammatory disorder
is selected from the group consisting of Crohn's Disease, systemic lupus erythematosus,
psoriasis, rheumatoid arthritis, vasculitis, atopic dermatitis and secondary progressive
multiple sclerosis.
17. The method of claim 12, wherein said antibody is administered intravenously.
18. The method of claim 12, wherein said antibody is co-administered with an second
agent selected from the group consisting of:
(a) an anti-cytokine that recognizes one or more cytokines selected from
interleukin 1 (IL-1), IL-2, IL-4, IL-6, IL-12, IL-13, EL-15, IL-17, IL-18; IL-
20, IL-21, DL-22, IL-23, IL-27 and IL-31;
(b) an anti-chemokine reagent that recognizes one or more cytokines selected
from IL-1, IL-2, BL-4, IL-6, IL-12, IL-13, EL-15, IL-17, IL-18, EL-20, IL-21,
IL-22, IL-23, IL-27 and IL-31;
(c) a chemokines selected from MIP1 alpha, MIP1 beta, RANTES, MCP1, IP-
10, ITAC, MIG, SDF and fractalkine.
1.9. A method of reducing MHC class II expression on a cell, the method comprising
contacting a cell with an antibody of claim 1 in an amount sufficient to reduce MHC class II
expression on said cell.
20. The method of claim 19, wherein said cell is a human melanoma cell.
21. The method of claim 19, wherein said antibody comprises a VH CDR1 region
comprising the amino acid sequence SYAMS (SEQ ID NO:3); a VH CDR2 region
comprising the amino acid sequence AISGSGGSTYYADSVKG (SEQ ID NO:4), a VH
CDR3 region comprising the amino acid sequence DGSSGWYYPHWFDP (SEQ ID NO:5);
a VL CDR1 region comprising the amino acid sequence TRSSGSIASNYVQ (SEQ ID
NO:8); a VL CDR2 region comprising the amino acid sequence EDNQRPS (SEQ ID NO:9);
68

WO 2006/109191 PCT/IB2006/001514
and a VL CDR3 region comprising an amino acid sequence QSYDGSNRWM (SEQ ID
NO:10).
22. The method of claim 21, wherein said antibody is NI-05 01.
23. The method of claim 19, wherein said cell is contacted with a second agent selected
from the group consisting of:
(a) an anti-cytokine that recognizes one or more cytokines selected from
interleukin 1 (IL-1), IL-2, EL-4, IL-6, IL-12, IL-13, IL-15, IL-17, EL-18, IL-
20, IL-21, IL-22, IL-23, IL-27 and IL-31;
(b) an anti-chemokine reagent that recognizes one or more cytokines selected
from IL-1, IL-2, IL-4, IL-6, IL-12, EL-13, IL-15, IL-17, IL-18, IL-20, IL-21,
IL-22, IL-23, IL-27 and IL-31;
(c) a chemokines selected from MIP1 alpha, MIP1 beta, RANTES, MCP1, IP-
10, ITAC, MIG, SDF and fractalkine.
69

The invention relates to fully
human antibodies, and fragments thereof,
that bind to human interferon gamma
(hIFNγ), thereby modulating the interaction
between IFNγ and its receptor, IFNγ-R,
and/or modulating the biological activities of
IFNγ. The invention also relates to the use of
such anti-IFNγ antibodies in the prevention
or treatment of immune- related disorders
and in the amelioration of a symptom
associated with an immune-related disorder.

Documents:

02836-kolnp-2007-abstract.pdf

02836-kolnp-2007-claims.pdf

02836-kolnp-2007-correspondence others.pdf

02836-kolnp-2007-description complete.pdf

02836-kolnp-2007-drawings.pdf

02836-kolnp-2007-form 1.pdf

02836-kolnp-2007-form 3.pdf

02836-kolnp-2007-form 5.pdf

02836-kolnp-2007-international publication.pdf

02836-kolnp-2007-international search report.pdf

02836-kolnp-2007-pct request form.pdf

02836-kolnp-2007-priority document.pdf

02836-kolnp-2007-sequence listing.pdf

2836-KOLNP-2007-(01-05-2014)-CORRESPONDENCE.pdf

2836-KOLNP-2007-(07-05-2012)-ABSTRACT.pdf

2836-KOLNP-2007-(07-05-2012)-AMANDED CLAIMS.pdf

2836-KOLNP-2007-(07-05-2012)-DESCRIPTION (COMPLETE).pdf

2836-KOLNP-2007-(07-05-2012)-DRAWINGS.pdf

2836-KOLNP-2007-(07-05-2012)-EXAMINATION REPORT REPLY RECEIVED.pdf

2836-KOLNP-2007-(07-05-2012)-FORM-1.pdf

2836-KOLNP-2007-(07-05-2012)-FORM-13.pdf

2836-KOLNP-2007-(07-05-2012)-FORM-2.pdf

2836-KOLNP-2007-(07-05-2012)-FORM-3.pdf

2836-KOLNP-2007-(07-05-2012)-OTHERS.pdf

2836-KOLNP-2007-(07-05-2012)-PA-CERTIFIED COPIES.pdf

2836-KOLNP-2007-(07-05-2012)-PETITION UNDER RULE 137.pdf

2836-KOLNP-2007-(07-05-2012)-SEQUENCE LISTING.pdf

2836-KOLNP-2007-(17-02-2014)-ANNEXURE TO FORM 3.pdf

2836-KOLNP-2007-(17-02-2014)-CORRESPONDENCE.pdf

2836-KOLNP-2007-(18-03-2013)-CORRESPONDENCE.pdf

2836-KOLNP-2007-(18-03-2013)-FORM 3.pdf

2836-KOLNP-2007-(23-07-2013)-CORRESPONDENCE.pdf

2836-KOLNP-2007-(28-11-2014)-CLAIMS.pdf

2836-KOLNP-2007-(28-11-2014)-CORRESPONDENCE.pdf

2836-KOLNP-2007-(28-11-2014)-OTHERS.pdf

2836-KOLNP-2007-(29-08-2013)-ANNEXURE TO FORM 3.pdf

2836-KOLNP-2007-(29-08-2013)-CORRESPONDENCE.pdf

2836-KOLNP-2007-ASSIGNMENT.pdf

2836-KOLNP-2007-CORRESPONDENCE OTHERS 1.1.pdf

2836-kolnp-2007-form 18.pdf

abstract-02836-kolnp-2007.jpg


Patent Number 265029
Indian Patent Application Number 2836/KOLNP/2007
PG Journal Number 06/2015
Publication Date 06-Feb-2015
Grant Date 02-Feb-2015
Date of Filing 02-Aug-2007
Name of Patentee NOVIMMUNE S.A.
Applicant Address 64, AVENUE DE LA ROSERAIE CH-1211, GENEVA
Inventors:
# Inventor's Name Inventor's Address
1 FERLIN, WALTER VILLA DE L'ARCHET, 217 RUE DE LARCHET, F-74140 SAINT CERGUES
2 ELSON, GREG 222, ROUTE DE BOSSEY, F-74160, COLLONGES SOUS SALEVE
3 LEGER, OLIVIER 603 ROUTE DES LUCHES, F-74800 ST. SIXT
4 FISCHER, NICOLAS 16, CHEMIN DES OUCHES, CH-1203, GENEVA
PCT International Classification Number C07K 16/24
PCT International Application Number PCT/IB06/001514
PCT International Filing date 2006-01-27
PCT Conventions:
# PCT Application Number Date of Convention Priority Country
1 60/648219 2005-01-27 U.S.A.