Citations
- 379 F. Supp. 3d 53
Full opinion text
Hon. Patti B. Saris, Chief United States District Judge
TABLE OF CONTENTS
INTRODUCTION...60
FINDINGS OF FACT...60
I. Scientific Background...60
A. The Immune System and Receptor-Ligand Signaling...60
B. Experimental Methods...63
II. Discoveries of PD-1 and 292...64
A. Dr. Honjo Discovers the PD-1 Receptor...64
B. Dr. Honjo Asks for Help Identifying the Ligand for PD-1 and Begins to Collaborate with Dr. Wood in September 1998...65
C. Dr. Freeman Discovers the 292 Ligand in July 1998...65
D. Dr. Wood Connects the PD-1/PD-L1 Pathway in September 1999...68
III. October 25, 1999 Collaboration Meeting in Cambridge...69
IV. Developments Between the October 1999 and May 2000 Meetings...70
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...70
B. Dr. Freeman and Dr. Wood File a Provisional Patent Application in November 1999...71
C. Dr. Freeman, Dr. Wood, and Dr. Honjo Draft a Journal Article on the PD-1/PD-L1 Pathway in March and April 2000...71
D. Dr. Freeman Conducts Immunohistochemistry ("IHC") Experiments in the Winter of 2000...72
E. Dr. Freeman Discovers PD-L2 in the Fall of 1999...72
F. Dr. Freeman, Dr. Wood, and Dr. Minato Independently Develop Antibodies Throughout 1999 and 2000...73
G. Dr. Honjo and Dr. Wood's Meeting in March 2000...73
H. Dr. Iwai Begins In Vivo Tumor Model Studies in March 2000...74
V. May 13, 2000 Collaboration Meeting in Seattle...74
VI. Developments During the Summer of 2000...74
VII. September 8, 2000 Collaboration Meeting in Cambridge...75
VIII. Dr. Honjo and Dr. Iwai Conduct In Vivo Mouse Tumor Model Experiments and the Collaboration Ends...75
IX. Dr. Honjo and Ono File Patent Application in July 2002...76
X. BMS Develops Nivolumab with Exclusive License to the Honjo Patents...77
XI. Dana-Farber Initiates This Lawsuit...78
XII. Dr. Honjo Wins the Nobel Prize...78
EXPERT OPINIONS...78
I. Dana-Farber's Expert: Dr. Kenneth Murphy...79
II. Defendants' Expert: Dr. Mark Greene...80
CONCLUSIONS OF LAW...81
I. Joint Inventorship...81
A. Legal Standard...81
B. Claim Construction...83
C. Corroboration...84
D. The Collaboration of Dr. Freeman, Dr. Wood, and Dr. Honjo...86
E. Conception of the Honjo Patents...88
F. Dr. Freeman's and Dr. Wood's Contributions to Conception...89
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...89
2. Dr. Freeman's Discovery of the Expression of PD-L1 on Certain Tumors...92
3. Dr. Freeman and Dr. Wood's Discovery and Characterization of PD-L2...93
4. Method of Treating Cancer...94
5. Dr. Freeman's and Dr. Wood's Provision of Reagents...94
G. Significance of Dr. Freeman's and Dr. Wood's Contributions to the Claims in the Honjo Patents...95
1. Use of Anti-PD-1 or Anti-PD-L1 Antibodies to Treat Cancer...95
2. Expression or Over-Expression of PD-L1 or PD-L2...97
3. PD-L1 Expression by Specific Tumors...99
H. Conclusion...99
II. Laches...100
A. Legal Standard...100
B. Analysis...101
ORDER...102 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. 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 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
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.
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, B7-1 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.
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. 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 for publication 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 cells were mildly stimulated, suggesting that 292 does play a role in immune regulation. T3-35:6-23, 36:16-21.
Dana-Farber and GI had an existing oncology partnership, which included work on B7 ligands and related signaling molecules. T2-33:20-34:6; T3-21:6-19; Collins Depo. 17:3-6. Because of this existing collaboration and GI's expertise in making fusion proteins, Dr. Freeman thought GI could help with additional experiments on 292's biological function, including finding its receptor. T2-34:15-17; T3-38:4-13. In July 1999, he reached out to Dr. Mary Collins at GI and told her what he knew about 292. T2-34:12-15; T3-38:24-39:13; Collins Depo. 34:8-9; JTX-0480.0001. Dr. Collins agreed that GI could help, and Dr. Freeman sent GI the genetic materials encoding 292. T2-35:1-4; T3-39:14-18; JTX-0480.0001. Dr. Freeman and researchers at GI had a number of discussions over the next few months about Dr. Freeman's experiments. T3-41:19-42:2. Because 292 appeared to be a B7 ligand, they thought its receptor would be similar to CD28 and CTLA-4 (though Dr. Freeman had already shown that 292 did not bind to either receptor). T3-42:3-15.
On August 23, 1999, shortly after reaching out to GI, Dr. Freeman filed a provisional patent application. T3-39:22-24, 74:23-75:5; JTX-0043.0001. The application included his experimental results showing that 292 stimulated resting T cell activity. T3-75:22-78:21, 158:23-159:18; JTX-0043.0096, 108-109. Dr. Freeman hypothesized that 292, like B7-1 and B7-2, might have both inhibitory and stimulatory receptors. T3-154:6-17. Accordingly, the application listed embodiments in which anti-292 antibodies stimulate an immune response and others in which they inhibit an immune response. T3-154:6-156:24; JTX-0043.0008. The application identified the normal tissue cells on which Dr. Freeman had found 292 expression but did not mention that he discovered the molecule through ESTs from a human ovarian tumor. T3-157:17-158:22; JTX-0043.0095. The U.S. Patent and Trademark Office ("PTO") issued multiple patents to Dr. Freeman based on this application. T3-160:7-9. The claims of at least one patent were subsequently cancelled because, as discussed below, Dr. Lieping Chen at the Mayo Clinic discovered the amino acid sequence for the same molecule before Dr. Freeman. T3-161:2-23. Dr. Freeman did not know about Dr. Chen's discovery, which was not published until December 1999, at the time he made his own independent discovery. T3-161:12-23.
A few days after this application, Dr. Freeman and Dr. Vicki Boussiotis, a member of his laboratory, began an experiment to test the effect of 292 on activated T cells, which express certain receptors that resting T cells do not. T3-37:5-24, 78:22-79:5, 79:16-80:18; JTX-0229.0323, 346; JTX-0778.0038. Unlike the prior experiment with resting T cells, this experiment showed an inhibitory effect on the immune response. T3-37:25-38:2, 79:6-11, 85:20-22, 86:7-24, 163:9-21; JTX-0778.0040; JTX-0801.0021. Dr. Freeman concluded that 292 primarily inhibits activated T cells. T3-180:8-25.
D. Dr. Wood Connects the PD-1/PD-L1 Pathway in September 1999
During the summer of 1999, while Dr. Wood was searching for the ligand for PD-1 for Dr. Honjo, he became involved in GI's work with Dr. Freeman to study 292. T3-44:21-25. Because he thought that the ligand for PD-1 would be a B7 ligand and he knew from Dr. Freeman that 292 was a B7 ligand, he tested whether PD-1 and 292 bound together. T2-35:5-22; Collins Depo. 34:10-18. Dr. Wood's initial experiment showed that they did. T2-35:17-22; Collins Depo. 34:19-22.
Dr. Wood emailed Dr. Honjo about this preliminary result on September 7, 1999. JTX-0485.0001. He described his "significant progress" on the ligand search and his "encouraging" results. T2-40:19-41:10; T4-53:14-54:7; JTX-0485.0001. To facilitate additional confirmatory experiments, he asked Dr. Honjo for more PD-1 fusion protein, which Dr. Honjo provided. T2-40:19-41:10; T4-55:21-57:5; JTX-0485.0001. Around the same time, Dr. Wood told Dr. Freeman he had identified a receptor for 292 that came from Dr. Honjo. T2-45:7-14; T3-45:1-13.
To ensure his initial experiment did not show a false positive, Dr. Wood ran confirmatory experiments. T2-36:6-24. Dr. Wood followed up with another email to Dr. Honjo on October 4 to report that these experiments confirmed that he had identified the ligand for PD-1. T2-42:22-43:22; T4-57:9-16; JTX-0489.0001. Dr. Wood also told Dr. Honjo that the ligand came from Dr. Freeman. T2-42:24-43:22; JTX-0489.0001. Dr. Wood proposed that the three men meet during the upcoming SST collaboration meeting. T2-42:22-43:22; JTX-0489.0001.
Dr. Honjo responded with excitement at Dr. Wood's discovery and agreed to the upcoming meeting. T2-44:6-19; JTX-0492.0001.
After identifying 292, which the three scientists began to call "PD-L1," Dr. Wood ran experiments to test the immunological effect of PD-L1. T2-47:14-49:15; JTX-0501.0003. These experiments confirmed Dr. Wood's hypothesis that PD-L1 inhibits the immune response. T2-47:14-48:14; JTX-0501.0003. He conveyed these results via email to Dr. Honjo on October 12. T2-47:10-22; JTX-0501.0003. In his email, Dr. Wood also laid out an outline for a journal article he, Dr. Freeman, and Dr. Honjo could write about the discovery of PD-L1. T2-49:16-50:4; JTX-0501.0003. Finally, Dr. Wood asked Dr. Honjo to send him his anti-PD-1 antibodies so that he could test blocking of the PD-1/PD-L1 pathway. T2-147:4-25; JTX-0501.0003-4. In response, Dr. Honjo noted that he "appreciate[d] [Dr. Wood's] strong collaboration without which this work had not been accomplished so soon" and agreed to send Dr. Wood his antibodies. T2-55:9-16, 148:19-25; JTX-0501.0001, 7. Dr. Wood performed preliminary experiments that showed that the human and mouse antibodies bound strongly to human and mouse PD-1, respectively, and that the mouse antibody blocked the interaction between PD-1 and PD-L1. T2-61:10-63:5, 156:22-157:14; JTX-0086.0017.
Dr. Freeman emailed Dr. Honjo on October 22, three days before their scheduled meeting. T3-46:24-47:6; JTX-0505.0001. Dr. Freeman expressed his excitement about the possibility of a research collaboration on the PD-1/PD-L1 pathway. T3-47:7-17; JTX-0505.0001. Dr. Honjo responded that he was looking forward to their meeting. T3-48:3-12; JTX-0507.0001. These emails were the first communication between the two. T3-48:6-8.
III. October 25, 1999 Collaboration Meeting in Cambridge
Dr. Freeman, Dr. Wood, and Dr. Honjo, along with representatives from Ono and GI, met as planned on October 25, 1999 during the prescheduled SST collaboration meeting in Cambridge, Massachusetts. T2-55:17-19, 56:2-13; T3-48:13-22; T4-58:3-5; JTX-0090.0001. Dr. Wood began the meeting by summarizing what he knew about PD-1 from Dr. Honjo's research. T2-156:8-21; T4-67:19-23; JTX-0086.0002. He then described how the similarities in the structure of PD-1 and CTLA-4 triggered his hypothesis that PD-1's ligand would be a B7 ligand. T2-57:2-23; Shibayama Depo. 106:19-107:12; JTX-0086.0003-4; JTX-0097.0003. He shared experimental results demonstrating that PD-L1 binds to PD-1 but not to CTLA-4. T2-57:2-23, 58:16-22; JTX-0086.0005-9; JTX-0097.0004. He ended with graphs showing his newest data on the inhibitory effect of PD-L1 and the successful blocking of the pathway with Dr. Honjo's antibodies. T2-59:12-63:5; T3-51:17-23, 53:7-55:6; JTX-0086.0013-17.
Dr. Freeman presented next. T2-64:11-13; T3-55:7-8; JTX-0090.0001. He shared that the 292 ESTs came from a human ovarian tumor. T2-64:4-10; T3-58:1-7; JTX-0095.0001; JTX-0456.0003. He explained that PD-L1 shares around 20% of its amino acid sequence, which he provided, with B7-1 and B7-2 but does not bind to either CD28 or CTLA-4. T3-59:22-61:21; JTX-0095.0003-6; JTX-0456.0003. Finally, he noted that 292 is expressed in certain types of cells, such as placenta, lung, and heart cells, but not in certain tumor cells. T4-66:10-67:7; JTX-0095.0009.
Dr. Honjo presented last of the three. T2-64:14-15; T3-61:22-62:1; JTX-0090.0001. He described his recently published data showing autoimmune-like symptoms in PD-1 knockout mice. T2-64:22-65:2; T3-62:2-8; T4-58:20-59:8; JTX-0091.0001. He presented unpublished knockout mouse data that also suggested PD-1 inhibits the immune response. T2-152:7-15; T4-59:13-60:15; JTX-0091.0012-14; JTX-0097.0004. He did not mention cancer during his presentation. T2-64:22-65:2; T3-63:7-9.
During the meeting and at dinner, Dr. Freeman, Dr. Wood, and Dr. Honjo agreed to continue to collaborate to study the PD-1/PD-L1 pathway. T2-65:12-24; T3-65:12-19. They discussed developing further tools to study the pathway, such as new fusion proteins and antibodies, and conducting additional experiments, including more knockout mouse studies. T3-63:10-18.
IV. Developments Between the October 1999 and May 2000 Meetings
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
Immediately after the October 25, 1999 meeting in Cambridge, Dr. Freeman and Dr. Honjo began the process of exchanging reagents. T3-67:1-16; JTX-0508.0001; JTX-0510.0001; JTX-0517.0001. They executed a Material Transfer Agreement in which Dr. Freeman agreed to send Dr. Honjo mouse and human PD-L1 cDNA and transfected cells for use solely in their "collaborative efforts." T3-68:7-70:2, 71:16-20; T4-82:18-84:5; Honjo Depo. 91:18-92:25; JTX-0159.0001. In a subsequent email to Dr. Freeman, Dr. Honjo expressed his pleasure that they had "reached at least a tentative agreement to push [their] collaboration as soon as possible." JTX-0517.0001. Dr. Freeman sent his own reagents to Dr. Honjo in November 1999. T3-71:21-72:3; Honjo Depo. 99:24-100:14; JTX-0522.0001; JTX-526.0001. Dr. Honjo sent his PD-1 reagents to Dr. Freeman pursuant to a separate agreement. T3-70:3-14; JTX-0517.0001.
Meanwhile, Dr. Wood continued to run experiments exploring the function of the PD-1/PD-L1 pathway. JTX-0433.0026. On November 25, he reported to Dr. Honjo that he was getting "confusing" results with no "clearly reproducible effects." Id. A week later, the December issue of Nature Medicine was released. JTX-0433.0027. It included an article by Dr. Lieping Chen at the Mayo Clinic reporting the sequence for a molecule ("B7-H1") that was molecularly identical to PD-L1. T2-66:21-67:17; T4-75:10-25; JTX-0433.0027. In the article, Dr. Chen did not identify B7-H1's receptor, and he reported that B7-H1 has a stimulatory effect on the immune system. T2-66:21-67:17; T4-88:10-13; JTX-0433.0027. Dr. Wood emailed Dr. Honjo about the Chen article the day it came out. T2-66:21-25; JTX-0433.0027. He expressed surprise that Dr. Chen had found that B7-H1 has a stimulatory effect because the data he and Dr. Honjo had generated showed that PD-L1 is inhibitory. T2-67:4-9; JTX-0433.0027. Dr. Wood suggested that the existence of a second, stimulatory receptor could explain Dr. Chen's results and some data of his own showing stimulation. T2-67:14-17; T4-76:4-11; JTX-0433.0027.
Once he received Dr. Freeman's PD-L1 reagents, Dr. Honjo ran his own in vitro experiments on the function of the PD-1/PD-L1 pathway. T4-77:1-9. These experiments showed that the pathway inhibited the immune response. Id. Unlike in Dr. Wood's experiments, Dr. Honjo used cells derived from a PD-1 knockout mouse as a control, which allowed him to attribute the inhibitory effect specifically to the PD-1/PD-L1 pathway. T4-77:3-12. He reported these results to Dr. Wood via email on December 6 and sent the underlying data on December 11. JTX-0433.0028; JTX-0535.0001-2. Dr. Wood responded with excitement at Dr. Honjo's "outstandingly good result." T4-79:13-80:8; JTX-0433.0029. He noted that he had just run some experiments that also showed inhibition, but he called Dr. Honjo's data "unquestionably the most convincing." JTX-0433.0029.
B. Dr. Freeman and Dr. Wood File a Provisional Patent Application in November 1999
On November 10, 1999, about two weeks after the meeting in Cambridge, Dr. Freeman and Dr. Wood filed a provisional patent application. T3-164:15-24; JTX-0045.0004. The application listed only the two as co-inventors. JTX-0045.0006. Dr. Freeman and Dr. Wood did not tell Dr. Honjo about this application at the meeting. T2-125:17-21; T3-166:7-11.
The application claimed methods of modulating the immune response via activating or blocking the PD-1/PD-L1 pathway. JTX-0045.117-119. It explained that the PD-1/PD-L1 interaction inhibits an immune response. T2-219:16-220:5; T3-205:16-206:4; JTX-0045.0017. Because Dr. Freeman and Dr. Wood theorized that PD-L1, like B7-1 and B7-2, might have a second receptor, the application contained experimental results that show stimulation of T cells in the presence of PD-L1 and disclosed that PD-L1 could have both a stimulatory and inhibitory effect. T3-167:11-24, 169:15-170:9; JTX-0045.0114. The application included a claim in which PD-1 signaling is inhibited to upregulate the immune response to a tumor. JTX-0045.0118. It also listed an embodiment in which PD-L1 levels are increased in tumor cells to enhance the co-stimulatory interaction with PD-L1's second receptor to treat cancer. T3-168:4-169:3; JTX-0045.0084. Dr. Wood and Dr. Freeman submitted a corresponding international application in August 2000. JTX-0073.0001. The PTO issued three patents based on this application beginning in 2004. T3-199:16-200:5; JTX-0008; JTX-0011; JTX-0015.
C. Dr. Freeman, Dr. Wood, and Dr. Honjo Draft a Journal Article on the PD-1/PD-L1 Pathway in March and April 2000
Dr. Freeman, Dr. Wood, and Dr. Honjo agreed to write a journal article about the discovery of PD-L1. T4-97:13-98:1. Dr. Wood did the majority of the writing, though he solicited data and coordinated edits from Dr. Freeman and Dr. Honjo. T2-68:12-21; T3-92:22-93:1; T4-108:3-7. The article explained Dr. Honjo's discovery of PD-1, the need to find its ligand to further understand its function, Dr. Wood's hypothesis about the similarities between PD-L1 and the known B7 ligands, Dr. Freeman's discovery of 292 via a BLAST search, and the results of experiments from Dr. Wood's and Dr. Honjo's laboratories showing that the PD-1/PD-L1 pathway inhibits the immune response. T2-69:8-22, 192:20-193:11; JTX-0305. All three scientists contributed data to the article. T3-94:25-96:9. The authors noted Dr. Chen's seemingly inconsistent results and explained their hypothesis that PD-L1 could have a second receptor. JTX-0305.0007.
Over two rounds of edits on March 19 and April 7, 2000, Dr. Freeman added the following two sentences to the last paragraph of the article: "PD-L1 is also expressed in some cancers, as three ESTs are from human ovarian tumors. This raises the possibility that some tumors may use PD-LI to inhibit an antitumor immune response." T2-69:23-70:12; T3-91:18-92:14, 100:20-102:22; T4-99:17-100:5; JTX-0305.0007; JTX-0806.0014; JTX-0807.0014. Dr. Honjo did not receive a draft of the article containing Dr. Freeman's addition until April 8. T4-107:20-110:22; JTX-0420.0014; JTX-0568.0008, 11; JTX-0589.0014. The article was published in the Journal of Experimental Medicine on October 2, 2000. T2-68:4-11; JTX-0305.0001.
D. Dr. Freeman Conducts Immunohistochemistry ("IHC") Experiments in the Winter of 2000
In January 2000, Dr. Freeman began IHC experiments to determine which human tissues express PD-L1. T2-83:5-84:6; T3-112:11-13; T6-10:4-11. He conducted this work with Dr. David Dorfman, a pathologist at the Brigham and Women's Hospital, and Dr. Julia Brown, a new postdoctoral researcher in his own laboratory. T3-111:20-112:2; T6-8:8-10, 10:18-11:1. Dr. Freeman asked Dr. Dorfman to test both normal and tumor tissues, but he was particularly interested to know whether PD-L1 was expressed in tumors given the pathway's inhibitory function and his discovery of PD-L1 from ovarian tumor ESTs. T2-83:5-6; T3-112:3-10, 112:25-113:5; T6-11:2-7.
Dr. Dorfman shared preliminary results with Dr. Freeman in February and final results in March and April. T3-114:7-12; T6-12:10-12. He found that PD-L1 was highly expressed in placenta and endothelial cells in the heart and on various tumors, including squamous cell carcinoma of the tongue, breast lobular carcinoma, lung and colon adenocarcinoma, and anaplastic large cell lymphoma. T3-113:9-21, 114:13-119:25; JTX-0808-0813. Based on these results and other experiments Dr. Freeman and Dr. Brown conducted between December 1999 and August 2000 that showed PD-L1 expression on mouse and human tumor cells, Dr. Freeman hypothesized that some tumors use the PD-1/PD-L1 pathway to inhibit an immune response. T3-108:5-110:1, 113:22-114:3; T6-11:21-12:24, 34:14-35:20; JTX-0332.0003. Dr. Freeman, Dr. Dorfman, and Dr. Brown did not publish the IHC results until 2003. T3-120:1-11; T6-13:3-12; JTX-0282.0008.
On March 14, 2000, Dr. Dorfman emailed Dr. Honjo explaining that he was working with Dr. Freeman to study staining of PD-L1 in both normal and cancerous human tissue. T5-10:4-22; JTX-0571.0001. He asked whether Dr. Honjo was interested in collaborating to study PD-1 expression in tumors. JTX-0571.0001. There is no evidence Dr. Honjo responded to Dr. Dorfman's email.
E. Dr. Freeman Discovers PD-L2 in the Fall of 1999
Soon after Dr. Wood discovered that 292 binds to PD-1, Dr. Freeman conducted a second BLAST search for molecules similar to 292. T3-102:24-103:15; T4-89:7-15; JTX-0332.0002. He identified another B7-like molecule that shares 38% of its amino acids with PD-L1. T2-75:10-15; T3-102:24-103:7; JTX-0332.0002. Dr. Freeman and Dr. Wood discovered that, like PD-L1, this molecule binds to PD-1 and its interaction with PD-1 inhibits the immune response. T2-75:10-15; T3-103:16-104:8. Between December 1999 and August 2000, Dr. Freeman ran a number of experiments showing that this ligand, which they called "PD-L2," was expressed on mouse tumor cells. T3-108:5-109:17; JTX-0332.0003.
On March 24, 2000, Dr. Freeman emailed Dr. Honjo to tell him about PD-L2. T3-104:25-105:13; JTX-0578.0001. A month and a half later, Dr. Freeman sent the PD-L2 cDNA and its sequence to Dr. Honjo. T3-106:3-22; Honjo Depo. 129:15-130:8; JTX-0599.0001. Dr. Honjo never himself conducted any experiments involving PD-L2. T2-75:16-19; T3-105:23-25; T4-117:22-23.
F. Dr. Freeman, Dr. Wood, and Dr. Minato Independently Develop Antibodies Throughout 1999 and 2000
Dr. Freeman, Dr. Wood, and Dr. Minato all separately worked to develop antibodies. Dr. Freeman began just before the October 1999 meeting, and he had a set of anti-PD-L1 antibody candidates by January 2000. T3-87:8-16; T6-9:7-10. Dr. Freeman and Dr. Brown tested how well these candidates bound to PD-L1 and blocked the PD-1/PD-L1 pathway to figure out which antibodies had the most promise for further research. T3-87:17-91:11; T6-9:11-23; JTX-0227.0525-526, 536. They had functional antibodies to use for in vitro experiments by February 2000. T6-9:24-10:3.
Dr. Wood developed anti-PD-1 and anti-PD-L1 antibodies through GI's collaboration with CAT. T2-78:8-18, 91:9-23. Through in vitro testing, they narrowed the pool of almost 150 antibody fragments to 26 unique PD-1 antibodies and 24 unique PD-L1 antibodies. T2-78:8-18, 91:9-94:3; JTX-0108.0026-32. Additional testing demonstrated that some of these antibodies blocked the inhibitory PD-1/PD-L1 interaction and increased the proliferation of T cells. T2-94:6-97:25; JTX-0108.0046.
As soon as Dr. Honjo received Dr. Freeman's PD-L1 cDNA in late 1999, Dr. Minato started to make anti-PD-L1 antibodies. T6-100:6-17, 101:4-8. By April 2000, he created two mouse anti-PD-L1 antibodies. T6-102:13-22, 103:15-16, 136:25-137:6. He used these antibodies to test for expression of PD-L1 in normal and tumor cell lines in mice. T6-102:4-12, 105:3-9; JTX-0663.0001. The results, presented at his laboratory meeting on September 29, 2000, showed that PD-L1 was expressed on some of the tested cell lines. T6-102:1-3, 105:3-9, 138:12-139:4; JTX-0663.0001.
G. Dr. Honjo and Dr. Wood's Meeting in March 2000
On March 27, 2000, Dr. Honjo and Dr. Wood met again at the next SST collaboration meeting in Kyoto, Japan. T2-71:2-25; JTX-0101.0001. Dr. Freeman did not attend this meeting. T2-79:2-9. The attendees discussed the PD-1/PD-L1 collaboration for much of the meeting. Shibayama Depo. 141:21-142:15; JTX-0105.0003. Dr. Taku Okazaki, a graduate student in Dr. Honjo's laboratory, presented his work on PD-1 and autoimmune diseases. T4-94:21-95:24; JTX-0103.0015; JTX-0105.0003-4. Dr. Wood shared his and Dr. Freeman's discovery of PD-L2. T2-74:19-75:6. Dr. Wood also discussed the therapeutic possibilities of the PD-1/PD-L1 pathway, including using antagonistic anti-PD-1 antibodies to block the pathway and enhance the immune response. T2-75:20-76:9; T4-96:13-21; JTX-0782.0019. He specifically described the possibility of using this technique to treat cancer. T2-76:10-12, 185:7-13, 186:25-187:6; JTX-0105.0004. As part of this discussion, he mentioned his collaboration with CAT to develop antibodies. T2-78:8-18;
JTX-0105.0004. The participants in the meeting agreed that there were promising pharmaceutical applications for anti-PD-1 and anti-PD-L1 antibodies. Shibayama Depo. 142:17-22; JTX-0105.0003.
H. Dr. Iwai Begins In Vivo Tumor Model Studies in March 2000
Upon her return to Dr. Honjo's laboratory after her leave of absence in early 2000, Dr. Iwai resumed her work on PD-1. Iwai Depo. 83:05-20; JTX-0429.0027. By March 16, 2000, two days after Dr. Dorfman emailed Dr. Honjo about his work with Dr. Freeman, she began a series of experiments to study the effect of the PD-1/PD-L1 pathway on the immune response to tumors. T4-92:17-94:4; JTX-0573.0001, 3. She planned to introduce PD-L1 derived from Dr. Freeman's cDNA into mouse tumors to see whether PD-L1 had any effect on the tumor's growth. T4-90:14-91:1; T5-23:11-14; JTX-0125.0032. She presented her plan at the March 31, 2000 laboratory meeting. T4-90:7-17; JTX-0125.0032.
V. May 13, 2000 Collaboration Meeting in Seattle
Dr. Freeman, Dr. Wood, and Dr. Honjo all attended the American Association of Immunologists ("AAI") conference in Seattle, Washington in May 2000, so they decided to meet to update each other about their ongoing PD-L1/PD-L1 work. T2-84:12-18, 85:2-4; T3-106:3-16, 120:18-25, 121:19-122:6; Carreno Depo. 189:16-190:9. Dr. Freeman explained his IHC results showing expression of PD-L1 on a number of normal and tumor cells. T2-84:7-11, 19-23; T3-125:8-25; JTX-0815.0006. He also shared information about PD-L2. T3-123:17-22. Finally, he discussed his development of anti-PD-L1 antibodies and mentioned that he had seven that blocked the binding of PD-1 and PD-L1. T3-91:12-17, 124:21-125:3; JTX-0815.0004. The three scientists discussed the therapeutic possibilities of using antibodies to target the PD-1/PD-L1 pathway to treat cancer. T3-126:6-127:1.
VI. Developments During the Summer of 2000
In June 2000, Dr. Honjo found out about the provisional patent application Dr. Freeman and Dr. Wood filed in November 1999. T4-183:2-11, 183:22-184:9; JTX-0616.0001; JTX-0617.0001. Dr. Honjo wrote to both Dr. Wood and Dr. Clark at GI to explain that he should be a joint inventor on the application because he proposed the PD-L1 project based on his prior work on PD-1. T4-183:22-184:9, 190:17-191:2; JTX-0616.0001; JTX-0617.0001. In his email to Dr. Clark, he also noted that he was "very pleased with [the] recent productive collaboration on PD-1 and PD-L1" and felt that it was "coming close to drug development." JTX-0617.0001. GI hired a lawyer to represent Dr. Honjo, and GI and Dr. Honjo began two years of discussions about his inventorship claim. T2-124:7-14; T4-123:16-24, 124:16-17, 188:4-8, 189:3-8, 190:2-16; JTX-0727.0001; JTX-0820.0001. As discussed below, GI ultimately decided not to add Dr. Honjo as a joint inventor on the patent application. Dr. Honjo never discussed this issue with Dr. Freeman. T4-188:9-15.
On August 23, Dr. Freeman emailed Dr. Honjo seeking feedback on an abstract about PD-L1 for the American Society of Hematology meeting in December. T3-127:23-128:6; T5-25:18-26:4; JTX-0647.0001. In the draft, Dr. Freeman wrote that "PD-L1 is also expressed on some tumors including many lung and breast malignancies and may have a role in attenuating immune attack against these tumors." T3-128:7-12; T5-26:9-24; JTX-0647.0001. Dr. Honjo approved the abstract. T3-128:21-129:2; JTX-0648.0001.
On September 1, Dr. Iwai reported results from her first tumor model experiment at a Honjo laboratory meeting. JTX-0626.0003. In this experiment, she injected PD-L1-expressing melanoma tumors into some mice and non-PD-L1-expressing melanoma tumors into others. Id. The PD-L1-expressing tumors grew faster than the non-PD-L1-expressing tumors. Id.
Dr. Freeman sent Dr. Honjo a draft of the article he and Dr. Wood were writing on PD-L2 on September 6. T3-107:14-19; JTX-0656.0001. This article, which included Dr. Honjo as a co-author, was published in March 2001 and discussed the possibility of targeting the PD-1/PD-L1 pathway as method of treating cancer. T3-110:2-23; JTX-0332.0001, 6. The article also included experimental data from Dr. Freeman's laboratory showing PD-L1 expression in a number of mouse tumor cell lines, including sarcoma, neuroma, and leukemia lines. T3-108:8-109:13, 135:11-18; JTX-0332.0003.
VII. September 8, 2000 Collaboration Meeting in Cambridge
On September 8, 2000, Dr. Freeman, Dr. Wood, and Dr. Honjo met again during the next SST collaboration meeting in Cambridge, Massachusetts. T2-85:5-15; T3-129:3-7; JTX-0108.0001-2; JTX-0111.0003. The main topic of the meeting was the PD-1/PD-L1 project. JTX-0111.0003. The meeting began with presentations from a number of GI scientists who worked with Dr. Wood. T3-130:7-12; JTX-0108.0002. They presented data showing that the PD-1/PD-L1 pathway inhibits both helper and killer T cells and that both PD-L1 and PD-L2 inhibit cytokine production. T2-86:23-87:25, 88:19-89:9; JTX-0108.0004, 7, 17. They also explained the results of an in vivo mouse study showing that the presence of antagonistic antibodies to block the inhibitory PD-1/PD-L1 interaction leads to the proliferation of T cells. T2-94:6-97:25; JTX-0108.0046
Dr. Freeman presented the same slides he used at the May 2000 meeting in Seattle. T3-129:13-130:6. He shared information on gene structures of PD-L1 and PD-L2. T2-98:17-20. He reported that he had found PD-L2 expression on dendritic cells, suggesting that it plays a role in immune inhibition. T2-98:21-99:9; JTX-0113.0001. Finally, he showed the IHC staining slides he received from Dr. Dorfman showing expression of PD-L1 on certain normal and tumor tissues. T2-99:10-20; T3-126:1-3, 132:23-133:15; T4-113:2-21; JTX-0100.0108-109; JTX-0113.0001. Dr. Freeman explained that he found PD-L1 expressed on all thymomas, some lung carcinomas, some tongue squamous cell carcinomas, and some T cell neoplasms, primarily anaplastic large cell lymphoma. T2-101:12-103:1; JTX-0100.0108-109; JTX-0113.0002.
Dr. Honjo was not scheduled to speak, but he shared an update after one of his graduate students gave a presentation. T2-103:5-11; JTX-0108.0002; JTX-0113.0002. As part of his update, Dr. Honjo presented the data from Dr. Iwai's tumor model experiment that she had generated a week earlier. T2-103:11-15, 104:6-23; T4-114:18-115:17; JTX-0116.0004.
VIII. Dr. Honjo and Dr. Iwai Conduct In Vivo Mouse Tumor Model Experiments and the Collaboration Ends
On September 26, 2000, Dr. Honjo emailed Dr. Freeman to ask for his human anti-PD-L1 monoclonal antibodies for use in his experiments. JTX-0661.0001. He added that, "Needless to say, we will do [the experiments] as collaboration." Id. As requested, Dr. Freeman sent Dr. Honjo some of his antibodies pursuant to a new Material Transfer Agreement. Honjo Depo. 181:23-183:11; JTX-0170.0001. Dr. Wood also provided Dr. Honjo with his own human anti-PD-L1 antibodies in October 2000. Honjo Depo. 445:15-446:4; JTX-0637.0013.
On October 27, 2000, Dr. Iwai reported the results of additional mouse tumor model experiments at another laboratory meeting in Japan. T4-115:18-116:20; JTX-0662.0003. The experiments confirmed the results she presented in September that PD-L1-expressing melanoma tumors grew faster in mice than non-PD-L1-expressing melanoma tumors. JTX-0662.0003. She also showed that PD-L1-expressing tumors grew less quickly in PD-1 knockout mice than in mice that expressed PD-1. T4-116:14-20; JTX-0662.0003. These results indicated to Dr. Iwai and Dr. Honjo that blocking PD-1 can suppress tumor growth. T4-116:21-24. Dr. Honjo, Dr. Minato, and Dr. Iwai began discussing using antibodies to block the PD-1/PD-L1 pathway as a method of treating cancer. T4-116:25-117:4, 118:13-18; T6-107:7-12; Honjo Depo. 29:8-30:6; JTX-0662.0003. Defendants take the position that they conceived of the inventions in the Honjo patents at this point in October 2000.
Building off Dr. Iwai's results, Dr. Honjo and Dr. Minato conducted other experiments over the next two years to study the effect of the PD-1/PD-L1 pathway on tumors. Dr. Minato's laboratory examined the expression of PD-L1 on tumor and normal cells and how PD-L1 interacts with PD-1 on T cells. T6-110:13-15. Dr. Honjo's laboratory used knockout mice to investigate further how tumors grow in the presence or absence of PD-1 and PD-L1. T6-110:10-13; Iwai Depo. 92:24-94:3; JTX-0691.0001. Dr. Honjo also conducted experiments that showed less tumor growth after administration of anti-PD-1 antibodies. Iwai Depo. 144:24-145:12; JTX-0739.0005. The results of these experiments were not shared with Dr. Freeman and Dr. Wood.
Dr. Wood, Dr. Honjo, and others from Ono and GI discussed the PD-1/PD-L1 pathway one last time at an SST collaboration meeting on April 2, 2001. JTX-0118.0001. Dr. Beatriz Carreno from GI talked specifically about upregulating T cells to treat tumors. T2-110:2-11; JTX-0119.0001. Because there is no evidence of additional meetings, data sharing, or the like after this date, it appears the collaboration effectively ended.
IX. Dr. Honjo and Ono File Patent Application in July 2002
Meanwhile, attorneys for GI and Dr. Honjo were still discussing Dr. Honjo's inventorship claim for the November 1999 patent application. On April 12, 2002, Dr. Honjo sent a letter to Dr. Clark at GI expressing his belief that GI was not responding to his claim "faithfully." JTX-0820.0001. He told Dr. Clark that he felt "obliged to fight against [the] unfair and unfaithful attitude of the G.I. management." Id. Four days later, an attorney for GI wrote to Dr. Honjo's attorney explaining why GI would not list Dr. Honjo as a joint inventor. JTX-0727.0001. He stated that GI intended to allow the PTO examiner to make the final inventorship determination and encouraged Dr. Honjo to participate in the process. JTX-0727.0001-2.
In the wake of this angry exchange, Dr. Honjo and Ono filed their own Japanese patent application on July 3, 2002 claiming methods of treating cancer by blocking the PD-1/PD-L1 pathway. T4-119:5-13; JTX-0076.0001. The application contained the results of the experiments Dr. Honjo, Dr. Iwai, and Dr. Minato conducted beginning in 2000. T4-119:14-17. It named only the three as inventors, thereby excluding Dr. Freeman and Dr. Wood. T4-119:5-13; JTX-0076.0001. Dr. Honjo, Dr. Iwai, and Dr. Minato subsequently published the results of their in vivo tumor model experiments on September 17, 2002 in PNAS. T4-119:18-24; JTX-0322.0001.
A year later, Dr. Honjo and Ono filed an international patent application claiming methods of treating cancer by administering antibodies to block the PD-1/PD-L1 pathway. JTX-0001.0002. In addition to Dr. Honjo, Dr. Minato, and Dr. Iwai, this application named Dr. Shiro Shibayama, an Ono scientist, as an inventor. T4-120:25-121:2; JTX-0001.0002. Dr. Shibayama attended collaboration meetings in 1999 and 2000. JTX-0090.0001; JTX-0108.0002. He also conducted one in vitro experiment in February 2003, the results of which were included in the patent application. T4-121:3-8; T5-17:23-18:13; Shibayama Depo. 13:7-18, 30:25-31:2, 46:22-47:3; JTX-0001.0019.
The PTO issued six patents from 2009 to 2016: Patent No. 7,595,048 on September 29, 2009 ("the '048 Patent"); Patent No. 8,168,179 on May 1, 2012 ("the '179 Patent"); Patent No. 8,728,474 on May 20, 2014 ("the '474 Patent"); Patent No. 9,067,999 on June 30, 2015 ("the '999 Patent"); Patent No. 9,073,994 on July 7, 2015 ("the '994 Patent"); and Patent No. 9,402,899 on August 2, 2016 ("the '899 Patent"). JTX-0001.0002; JTX-0002.0002; JTX-0003.0002; JTX-0004.0002; JTX-0005.0002; JTX-0006.0001. The six Honjo patents list Dr. Honjo, Dr. Minato, Dr. Iwai, and Dr. Shibayama as inventors. Id.
X. BMS Develops Nivolumab with Exclusive License to the Honjo Patents
In the mid-2000s, Medarex, an American biotechnology company, negotiated with Ono to secure an exclusive license to the Honjo patents. T6-43:12-15, 44:21-45:1. Medarex began clinical trials on nivolumab, an anti-PD-1 monoclon