United States District Court, D. Massachusetts
FINDINGS OF FACT, CONCLUSIONS OF LAW, AND
ORDER
Hon.
Patti B. Saris Chief United States District Judge.
TABLE
OF CONTENTS
INTRODUCTION
................................................... 4
FINDINGS
OF FACT ...............................................
6
I.
Scientific Background
................................ 6
A. The
Immune System and Receptor-Ligand Signaling....6
B.
Experimental Methods ........................... 11
II.
Discoveries of PD-1 and 292
......................... 14
A. Dr.
Honjo Discovers the PD-1 Receptor .......... 14
B. Dr.
Honjo Asks for Help Identifying the Ligand for PD-1 and
Begins to Collaborate with Dr. Wood in September 1998
.............................. 17
C. Dr.
Freeman Discovers the 292 Ligand in July 1998
............................................... 20
D. Dr.
Wood Connects the PD-1/PD-L1 Pathway in September 1999
................................. 24
III.
October 25, 1999 Collaboration Meeting in Cambridge.
27 IV.
Developments Between the October 1999 and May 2000
Meetings
............................................ 29
A. Dr.
Freeman and Dr. Honjo Exchange Reagents, and Dr. Wood and Dr.
Honjo Run Experiments Confirming the Inhibitory Effect of the
PD-1/PD-L1 Pathway in November and December 1999
.................. 29
B. Dr.
Freeman and Dr. Wood File a Provisional Patent Application in
November 1999 ............ 31
C. Dr.
Freeman, Dr. Wood, and Dr. Honjo Draft a Journal Article on
the PD-1/PD-L1 Pathway in March and April 2000
........................... 32
D. Dr.
Freeman Conducts Immunohistochemistry (“IHC”)
Experiments in the Winter of 2000 .............. 34
E. Dr.
Freeman Discovers PD-L2 in the Fall of 1999 35
F. Dr.
Freeman, Dr. Wood, and Dr. Minato Independently Develop
Antibodies Throughout 1999 and 2000
....................................... 36
G. Dr.
Honjo and Dr. Wood's Meeting in March 2000. 37
H. Dr.
Iwai Begins In Vivo Tumor Model Studies in March 2000
..................................... 38
V.
May 13, 2000 Collaboration Meeting in Seattle
....... 39
VI.
Developments During the Summer of 2000
.............. 39
VII.
September 8, 2000 Collaboration Meeting in
Cambridge..
................................................... 41
VIII.
Dr. Honjo and Dr. Iwai Conduct In Vivo Mouse Tumor
Model Experiments and the Collaboration Ends
........ 43 IX. Dr. Honjo and Ono File Patent Application
in July 2002
.................................................... 45
X.
BMS Develops Nivolumab with Exclusive License to the
Honjo Patents ...................................... 47
XI.
Dana-Farber Initiates This Lawsuit
.................. 48
XII.
Dr. Honjo Wins the Nobel Prize
...................... 50
EXPERT
OPINIONS ...............................................
51
I.
Dana-Farber's Expert: Dr. Kenneth Murphy
............ 51
II.
Defendants' Expert: Dr. Mark Greene
................. 54
CONCLUSIONS
OF LAW ............................................ 58
I.
Joint Inventorship
.................................. 58
A.
Legal Standard ................................. 58
B.
Claim Construction ............................. 63
C.
Corroboration .................................. 64
D. The
Collaboration of Dr. Freeman, Dr. Wood, and Dr. Honjo
...................................... 70
E.
Conception of the Honjo Patents ................ 75
F. Dr.
Freeman's and Dr. Wood's Contributions to Conception
..................................... 78
1. Dr.
Freeman and Dr. Wood's Discovery of PD-L1 and Blocking
Antibodies and Dr. Wood's Discovery of the Inhibitory
Effect of the PD-1/PD-L1 Pathway ........................ 78
2. Dr.
Freeman's Discovery of the Expression of PD-L1 on Certain
Tumors ................... 86
3. Dr.
Freeman and Dr. Wood's Discovery and Characterization of
PD-L2 ................. 88
4.
Method of Treating Cancer ................. 89
5. Dr.
Freeman's and Dr. Wood's Provision of Reagents
.................................. 91
G.
Significance of Dr. Freeman's and Dr. Wood's
Contributions to the Claims in the Honjo Patents
............................................... 92
1. Use
of Anti-PD-1 or Anti-PD-L1 Antibodies to Treat Cancer
.............................. 93
2.
Expression or Over-Expression of PD-L1 or PD-L2
..................................... 99
3.
PD-L1 Expression by Specific Tumors ...... 102
H.
Conclusion .................................... 103
II.
Laches
.............................................. 104
A.
Legal Standard ................................ 105
B.
Analysis ....................................... 107
ORDER
........................................................ 110
INTRODUCTION
Plaintiff
Dana-Farber Cancer Institute, Inc.
(“Dana-Farber”) brings this civil action to
correct inventorship of six disputed patents (“the
Honjo patents”) against Defendants Ono Pharmaceuticals
Co., Ltd. (“Ono”); Dr. Tasuku Honjo; E.R. Squibb
& Sons, L.L.C.; and Bristol-Myers Squibb, Co.
(“BMS”). The Honjo patents claim methods of
cancer immunotherapy. Dr. Honjo is the named inventor on
these patents together with two colleagues from Kyoto
University and a researcher at Ono. Dana-Farber contends that
Dr. Gordon Freeman, one of its professors, and Dr. Clive
Wood, formerly of the Genetics Institute (“GI”),
made significant contributions to the conception of the
inventions in the Honjo patents through, among other things,
the discovery and characterization of the PD-L1 and PD-L2
ligands, the discovery that the interaction between PD-1 and
PD-L1 (“the PD-1/PD-L1 pathway”) is inhibitory
and could be blocked by antibodies, and the discovery that
PD-L1 is expressed in human tumors.[1] Dana-Farber seeks to add Dr.
Freeman and Dr. Wood as joint inventors on the Honjo patents.
Defendants argue that Dr. Freeman's and Dr. Wood's
contributions to the inventions are not significant enough to
make them joint inventors.
After a
bench trial, I find Dana-Farber has presented clear and
convincing evidence that Dr. Freeman and Dr. Wood are joint
inventors of the six Honjo patents. Dr. Honjo collaborated
extensively with both Dr. Freeman and Dr. Wood from at least
October 1999[2] until at least September 2000 through
numerous meetings, joint authorship of scientific journal
articles, written collaboration agreements, and sharing of
experimental results and ideas. Indeed, Dr. Honjo himself
referred to his work with Dr. Freeman and Dr. Wood as a
collaboration on at least six occasions. While the
relationship among these three brilliant scientists
eventually soured, all three made significant contributions
to the inventions. After a review of the extensive record and
evaluation of the credibility of the witnesses, I conclude
that both Dr. Freeman's and Dr. Wood's contributions
were significant in light of the dimension of the full
inventions claimed in the six Honjo patents, which are all
premised on blocking the inhibitory interaction of the
PD-1/PD-L1 pathway to treat tumors that express PD-L1 or
PD-L2. Judgment shall enter for Dana-Farber.
FINDINGS
OF FACT
I.
Scientific Background [3]
A.
The Immune System and Receptor-Ligand Signaling
The
immune system is the body's defense against foreign
invaders, such as viruses, bacteria, and other pathogens. The
immune system works through a network of different types of
cells, each with a specific function. Dendritic cells, for
example, detect the presence of pathogens and alert the rest
of immune system. B cells respond by producing proteins
called antibodies that bind to pathogens and neutralize them.
The most important immune cells for the purposes of this
dispute are T cells. T cells either coordinate the immune
system's response to pathogens (“helper” T
cells) or eliminate infected or abnormal cells from the body
(“killer” or “cytotoxic” T cells).
Killer T cells can help prevent cancer from growing in the
body. Once the immune system recognizes cancer cells as
abnormal, T cells attack the cancer cells in the same way
they attack cells infected with viruses and bacteria.
In a
healthy person, the immune system activates to fight
pathogens and then deactivates to protect healthy cells from
immune attack. Disorders of the immune system come in two
forms. An individual with a suppressed immune response, such
as someone with AIDS, is highly susceptible to infections and
other diseases. An overactive immune response, on the other
hand, can lead to autoimmune diseases in which the immune
system attacks healthy cells.
To
maintain a healthy balance, the immune system relies on
communication among immune cells and between immune cells and
other cells found in the body. Cells can communicate through
receptor-ligand interactions. A receptor is a protein located
on the cellular membrane that allows the cell to detect and
respond to its environment. The receptor receives a signal
from outside the cell and then transmits the signal to the
internal components of the cell to trigger a response.
Ligands are proteins that bind to receptors to initiate
signaling. Ligands can be secreted by cells
(“cytokines”) or found on the cell surface. When
a ligand binds to its receptor, it activates the
intracellular signaling pathway that tells the cell with the
receptor how to respond.
Receptor-ligand
interactions play a critical role in regulating the immune
system. In the presence of pathogens, some receptors act as
accelerators that “upregulate” or
“stimulate” immune cells to increase the immune
response. To prevent activated immune cells from damaging
healthy cells, other receptors act as brakes to
“downregulate” or “inhibit” the
immune response. The immune system maintains a balance via
the "on-off switches" of receptor-ligand signaling
by upregulating when it detects infected or abnormal cells
and downregulating once those cells are eliminated.
(Image
Omitted.)
The
primary receptor on a T cell is known as the T cell receptor
("TCR"). The TCR binds to foreign proteins known as
antigens, which come from viruses, bacteria, or cancers. In
combination with other signals, binding between the TCR and
antigen activates the T cell to attack the pathogen.
T cells
also have other receptors on their surface. For example, a
signal sent to the TCR does not activate a T cell unless a
ligand binds to one of its co-stimulatory receptors. An
important co-stimulatory receptor is called CD28. CD28's
two ligands, B7-l and B7-2, are expressed on dendritic cells
that have detected infection or cancer. In order for a T cell
to activate, an antigen on the dendritic cell must bind to
the TCR on the T cell and a B7 ligand on the dendritic cell
must also bind to the CD28 receptor on the T cell. In the
absence of an infection or cancer, the dendritic cell will
not express a B7 ligand on its surface; if the TCR on the T
cell interacts with the dendritic cell but does not receive a
signal through CD28, the T cell will not activate. This
requirement for co-stimulation ensures the immune system does
not activate unless pathogens are present.
The B7
ligands also bind to an inhibitory receptor called CTLA-4,
which is only expressed on highly activated T cells. The B7
ligands bind more tightly to CTLA-4 than CD28. Thus, when a T
cell expresses both CD28 and CTLA-4, CTLA-4 prevents the B7
ligands from activating the T cell through the CD28 receptor.
CTLA-4 thereby ensures the immune system does not run out of
control and harm healthy cells.
The
Honjo patents target another inhibitory receptor on T cells
known as PD-1. When PD-1 binds to one of its ligands, PD-L1
or PD-L2, the T cell receives an inhibitory signal that
prevents it from attacking the cell expressing PD-L1 or
PD-L2. Expression of PD-L1 or PD-L2 on healthy cells protects
the cells from immune attack. Some tumor cells also express
PD-L1 or PD-L2, allowing them to masquerade as healthy cells
by activating PD-1 to send an inhibitory signal to T cells.
(Image
Omitted.)
Because
of their importance in the immune system, receptor-ligand
interactions are an attractive target for research and
therapy. For example, scientists can develop monoclonal
antibodies that bind to a specific receptor or ligand.
Antibodies are named according to the target protein to which
they bind (e.g., anti-PD-1 antibodies). A monoclonal antibody
can be designed to trigger a receptor's signal
(“agonist”) or block a signal either by binding
to the ligand or the receptor (“antagonist”). If
the receptor-ligand interaction stimulates immune cells, an
antagonistic monoclonal antibody decreases the immune
response by blocking the stimulation. This can be useful for
treating autoimmune diseases. By contrast, if the
receptor-ligand interaction inhibits immune cells, an
antagonistic monoclonal antibody increases the immune
response by blocking the inhibition. This can be useful for
treating viruses or cancer.
The
Honjo patents claim methods of treating cancer by using the
body's immune system to attack tumor cells, a type of
treatment known as cancer immunotherapy. Specifically, the
methods involve administering antagonistic monoclonal
antibodies that bind to PD-1 or PD-L1 and block the
inhibitory interaction between PD-1 and PD-L1/PD-L2. By
blocking the signaling pathway, the methods aim to stimulate
the immune system to attack the tumor cells.
B.
Experimental Methods
This
case also requires understanding how scientists study genes,
proteins, and pathways. The Basic Local Alignment Search Tool
(“BLAST”), a public database managed by the
National Center for Biotechnology Information, contains
millions of DNA sequences. Many of these sequences are short
fragments of genetic material called “Expressed
Sequence Tags” (“ESTs”) whose identity,
complete sequence, and function are not known. A search
through the BLAST database allows scientists to identify new
DNA sequences and proteins to study. For example, a scientist
can input a reference DNA sequence that encodes a known
protein with a known function, and the BLAST search will show
ESTs that share similar sequences with the reference DNA.
After identifying the full-length sequences, she can then
determine if they encode proteins with similar functions to
the known proteins.
Having
identified a gene or protein of interest, she can use
complementary DNA (“cDNA”) and “Fc-fusion
proteins” to further study it. cDNA is a DNA sequence
that contains only the parts of a gene necessary for encoding
a protein. By inserting cDNA into a vector, scientists can
cause a wide variety of cells to express a specific protein
and then use those cells in experiments. An “Fc-fusion
protein” contains a generic “handle” (the
“Fc” region) that allows the protein to be easily
manipulated and studied apart from the cell. The relevant
portion of the amino acid sequence of the protein of interest
is attached to the handle. For example, PD-1 fusion protein
contains the binding portion of the PD-1 receptor attached to
a generic protein handle. The fusion protein can then be used
to test whether PD-1 binds to various molecules and whether
the expression of PD-1 has an effect on the immune response.
To
explore the function and structure of proteins, scientists
conduct both in vitro and in vivo experiments. In vitro
experiments occur outside of a living organism in test tubes,
flasks, and other controlled environments. They allow
scientists to learn about a protein without worrying about
confounding effects from other molecules within a living
organism. For example, mixing T cells expressing a receptor
with cells expressing the receptor's ligand and then
observing the number of T cells shows whether the signaling
pathway stimulates or inhibits the immune response. Another
in vitro experiment, known as immunohistochemistry
(“IHC”), involves administering a monoclonal
antibody to thin sections of tissue to determine whether the
molecule to which the antibody binds is present.
In vivo
experiments are conducted using living organisms. Scientists
use in vivo experiments to study proteins in their biological
context. “Knockout mouse” studies are one type of
in vivo experiment. A “knockout mouse” is a mouse
without the gene that encodes a particular protein and
therefore is unable to make the protein. Observing the
characteristics of the knockout mouse reveals the role the
protein plays in the organism. For example, if knocking out a
gene leads the mouse to have an abnormally active immune
system, the protein encoded by that gene likely has an
inhibitory effect on the immune system. Mouse tumor models
are another type of in vivo experiment used to study cancer.
In these experiments, mice are inoculated with tumor cells,
and specific signaling pathways or proteins are then blocked
in some of the mice. If the tumors grow more or less quickly
in the altered mice than in normal mice, the tumor model
suggests that the pathway or protein has an effect on tumor
growth.
II.
Discoveries of PD-1 and 292
A.
Dr. Honjo Discovers the PD-1 Receptor
Dr.
Tasuku Honjo is a professor at the medical school at Kyoto
University. T4-8:22-23, 12:24-25.[4] After receiving his medical
degree and PhD in biochemistry in Japan, he came to the
United States to work at the Carnegie Institution of
Washington in Baltimore, Maryland where he began to study
immunology. T4-10:6-24. He then worked at the National
Institutes of Health before returning to Japan. T4-11:5-23.
He has been a professor at Kyoto University since 1984.
T4-12:16-25.
In the
early 1990s, Dr. Honjo discovered a new receptor expressed on
certain mouse immune cells. T4-14:19-21, 19:10-15;
JTX-0320.0001. He named the molecule “PD-1”
because he believed the receptor was involved in programmed
cell death, a process by which the body kills off old cells
when new cells generate. T4-16:10-17:6. He published his
discovery in 1992. T4-16:1-9; JTX-0320.0001. Dr. Honjo
isolated the human DNA sequence for the gene that encodes
PD-1 and, along with researchers from another Japanese
University, developed antibodies against both mouse and human
PD-1 to help study its function. T4-20:15-21:1, 22:2-23:5;
Iwai Depo. 41:25-43:3; JTX-0272.0001; JTX-0373.0001;
JTX-0429.0011. In 1996, he published another article
describing the expression of PD-1 in mouse cells and the PD-1
fusion protein he was using to study the molecule.
T4-22:2-11, 131:12-132:7; JTX-0272.0001-2. His early
experiments demonstrated that PD-1 was not, in fact, involved
in programmed cell death. T4-17:7-14.
To
learn more about PD-1's function, Dr. Honjo and Dr.
Nagahiro Minato, a colleague studying tumor immunology, began
experiments with PD-1 knockout mice. T4-14:1-18, 23:21-25,
29:3-7; T6-89:18-24; JTX-0354.0001. They discovered that mice
without the gene encoding PD-1 showed symptoms typical of
autoimmune disease, suggesting that PD-1 is involved in
inhibiting the immune response. T4-26:11-16; T6-93:12-94:12;
JTX-0354.0001. Dr. Honjo and Dr. Minato submitted these
results on April 12, 1999. T2-136:18-137:8; JTX-0354.0010.
Their article was published in Immunity in August
1999 and described PD-1 as “a negative regulator of
immune responses.” JTX-0354.0001.
Once
Dr. Honjo and Dr. Minato discovered that PD-1 inhibited the
immune system through their knockout mouse experiments, they
discussed the possibility that altering the PD-1 signal could
have therapeutic applications for autoimmune diseases,
infectious diseases, organ transplantation, and cancer.
T4-29:23-30:8; T6-129:19-25; Okazaki Depo. 50:25-51:13. They
planned to conduct experiments involving tumors but did not
do so at the time due to the limited manpower in their
laboratories. T4-30:9-17; T6-98:22-99:8.
Based
on its structure, Dr. Honjo knew PD-1 was in the same family
of proteins as CTLA-4, another inhibitory receptor.
T4-31:6-9. But he did not fully understand the molecular
mechanism through which PD-1 had its inhibitory effect
because he had not identified its ligand. T4-28:3-24,
32:16-25, 141:12-142:6; JTX-0354.0008. Multiple students in
his laboratory tried and failed to find PD-1's ligand.
T4-143:8-13.
In
mid-1998, Dr. Honjo tasked a new graduate student, Dr.
Yoshiko Iwai, with the ligand search. T4-38:8-24, 144:5-13;
Iwai Depo. 12:2-25. At the May 21, 1999 meeting of Dr.
Honjo's laboratory, Dr. Iwai reported her preliminary
results. T4-42:23-43:3; JTX-0125.0021. She identified binding
of various strengths with human and mouse PD-1 fusion protein
in a number of mouse cells she had tested, including cells
derived from mouse white blood cell tumor lines.
T4-44:24-45:5, 147:8-149:4; Iwai Depo. 14:2-24;
JTX-0125.0021. She also reported weak binding with PD-1 in
one human B cell cancer line called Daudi. T4-47:17-48:1,
157:3-18; JTX-0125.0021.
Although
these results showed binding with the PD-1 fusion protein,
they did not identify what molecule the protein was binding
to. T4-146:10-147:7; Iwai Depo. 14:10-24, 15:5-12, 68:20-25,
70:9-17; Honjo Depo. 40:17-25. Dr. Iwai recognized that her
experiment could have shown “false positives”
because of the type of fusion protein she used. T4-48:2-19;
JTX-0125.0022. About a month after disclosing her results,
she reported at another laboratory meeting that PD-1's
“[l]igand may express on B cell lines?!”
JTX-0125.0024. She planned to conduct additional experiments
using different fusion proteins to identify the ligand, but
she had to take a leave of absence at the end of the summer
due to illness. T4-49:2-8, 50:12-22, 51:11-18, 161:16-162:15;
Iwai Depo. 13:13-14:5, 72:15-73:3, 82:7-19. The results of
Dr. Iwai's experiments were never published. T4-51:1-9,
164:10-12.
B.
Dr. Honjo Asks for Help Identifying the Ligand for PD-1 and
Begins to Collaborate with Dr. Wood in September
1998
In
September 1998, as Dr. Iwai was beginning her experiments to
identify the ligand for PD-1, Dr. Honjo flew to Cambridge,
Massachusetts for a meeting with representatives from Ono, a
Japanese pharmaceutical company, and GI, a Cambridge
biotechnology research and development company. T2-8:23-9:2,
20:3-6; T4-32:2-12; JTX-0432.0001. This meeting was part of a
three-way research collaboration among GI, Dr. Honjo, and Ono
that had been established in the mid-1990s. T2-18:6-19:7;
JTX-0140; JTX-0142; Dkt. No. 314-1 ¶ 7
(“Stip.”). This “signal sequence
trap” (“SST”) collaboration involved using
yeast-based traps to identify signaling proteins secreted by
cells that could then be studied as potential targets for new
drug candidates. T2-17:1-18:5; JTX-0140.0001-2. The ultimate
goal of the collaboration was “the discovery,
development and commercialization of novel pharmaceutical
products.” JTX-0142.0007. GI, Dr. Honjo, and Ono held
core collaboration meetings biannually, which alternated
between Cambridge and Japan. T2-19:13-21.
While
in Cambridge, Dr. Honjo asked Dr. Steve Clark, the
coordinator at GI for the SST collaboration, if he had any
ideas for how to identify the PD-1 ligand. T4-32:7-19. Dr.
Clark proposed using GI's newly acquired Biacore machine,
which would allow for quick screening of many ligand
candidates. T4-34:4-12, 35:9-11. Because Dr. Honjo did not
have access to a Biacore machine at Kyoto University, he
agreed. T4-35:7-8.
To
facilitate this collaboration, Dr. Clark introduced Dr. Honjo
to Dr. Clive Wood, the director of molecular immunology at
GI, who also participated in the collaboration meeting that
day. T2-13:13-15, 20:2-6; T4-36:18-22; JTX-0792.0004. Dr.
Wood earned a PhD in biochemistry from Imperial College
London. T2-8:2-6. He began working at GI in 1986 as a staff
scientist. T2-8:19-22. In 1998, he was promoted to serve as
the director of molecular immunology. JTX-0792.0004. He left
GI in the early 2000s and now works as a corporate senior
vice president responsible for global research activities for
Boehringer Ingelheim. T2-7:10-14; JTX-0792.0004.
Dr.
Wood and Dr. Honjo had dinner the night of the September 1998
meeting and discussed Dr. Honjo's work on PD-1.
T2-20:6-10; JTX-0432.0001. Dr. Honjo explained that he had
discovered PD-1 and its inhibitory function but had not been
able to find its ligand. T2-134:16-135:3. Dr. Wood agreed to
collaborate with him to identify the ligand. T2-129:4-24.
On
September 22, about a week after the meeting, Dr. Honjo sent
Dr. Wood a letter with more details about their
collaboration. JTX-0432.0001. Dr. Wood responded on September
28 confirming his interest. T2-22:6-14; JTX-0436.0001. He
also told Dr. Honjo that he thought the PD-1 receptor could
be a candidate for a collaboration GI was establishing with
Cambridge Antibody Technology (“CAT”) to develop
antibodies as potential therapeutics. T2:22:21-23:6;
JTX-0436.0001. The following day, Dr. Wood submitted a form
to GI seeking approval for the PD-1 project and permission to
exchange materials with Dr. Honjo. T2-23:14-24:6;
JTX-0437.0001. Dr. Honjo sent PD-1 fusion proteins and cDNA
developed in his laboratory to Dr. Wood to use in experiments
to identify the ligand. T2-130:18-25; T4-36:23-37:2. Soon
after their collaboration began, Dr. Honjo provided Dr. Wood
with a confidential draft of his Immunity article
that described his PD-1 knockout mouse experiments.
T2-135:12-136:22; T4-191:9-192:8. As part of these
preliminary discussions, Dr. Wood and Dr. Honjo decided to
add the PD-1 project to the existing SST collaboration, which
GI, Dr. Honjo, and Ono formally agreed to in March 1999.
T2-21:9-13, 26:21-27:10; Shibayama Depo. 82:16-19,
84:18-85:8; JTX-0450.0003; JTX-0471.0001.
When he
started work on the project, Dr. Wood recognized that the
PD-1 receptor looked like the CTLA-4 receptor found on T
cells. T2-28:6-9. Accordingly, because B7-1 and B7-2 were
ligands for CTLA-4, he hypothesized that the ligand for PD-1
would also be a member of the B7 family. T2-28:10-14,
29:11-12, 31:3-7, 69:8-16; JTX-0305.0002. And since the
interaction between CTLA-4 and the B7 ligands inhibits T
cells, he suspected that the interaction between PD-1 and its
ligand would also be inhibitory. T2-29:12-14. However, his
initial experiments failed to identify a B7 ligand that bound
to PD-1. T2-35:14-17.
C.
Dr. Freeman Discovers the 292 Ligand in July 1998
Dr.
Gordon Freeman is a professor of medicine in the department
of medical oncology at Dana-Farber and Harvard Medical
School. T3:10:20-24, 11:18-22. Dana-Farber is a nonprofit
cancer treatment and research center located in Boston,
Massachusetts. Stip. ¶¶ 1, 26. Dr. Freeman earned a
PhD from Harvard University in microbiology and molecular
genetics in 1979. T3-9:8-13. He then began a postdoctoral
fellowship at Dana-Farber working on tumor immunology.
T3-9:14-17, 11:23-12:3. He became an assistant professor in
1994. T3-12:12-15.
In July
1998, shortly before Dr. Honjo and Dr. Wood's meeting in
Cambridge, Dr. Freeman began a search for novel B7 ligands.
T3-22:14-23:1. Dr. Freeman's work had focused for almost
fifteen years on B7 ligands, and he had discovered B7-2 and
its role in immune regulation. T3-12:16-21, 17:21-18:11,
19:1-12, 20:22-21:1. Given the important interactions between
the B7-1 and B7-2 ligands and the CD28 and CTLA-4 receptors,
he suspected there might be similar ligands with
immunological activity. T3-22:18-24. On July 27, 1998, Dr.
Freeman ran a BLAST search with a sequence of 208 amino acids
that forms part of binding portion of the B7-1 molecule.
T3-25:25-26:18, 27:16-18, 150:13-21; JTX-0305.0002. The
search produced a list of twelve ESTs that resembled the B7-1
sequence. T3-26:9-12, 151:11-14; JTX-0431.0001. Two of these
twelve ESTs were part of the same sequence and came from a
human ovarian tumor, which Dr. Freeman found interesting
because the known B7 molecules were only expressed in immune
cells, not in solid tumors. T3-28:9-24, 151:15-17;
JTX-0431.0001. He decided to investigate this new sequence,
which he called “292” after its label in the
database. T3-28:24, 31:3-5. He generated the full human cDNA
sequence for the 292 protein. T3-30:25-31:1. Through work on
similar mouse DNA sequences found in the BLAST database, he
also identified the full-length sequence for mouse 292.
T3-33:23-34:7.
In
early 1999, Dr. Freeman investigated 292's expression and
immunologic activity. T3-32:13-20. Although the ESTs came
from a human ovarian tumor, his experiments showed that
immune cells also express 292. T3-33:6-17. Given the
similarities with B7-1 and B7-2, he thought 292 might affect
the immune response. T3-33:18-22. When he exposed resting T
cells to cells expressing the 292 protein, the T ...