CELLECTIS

Patent Trials and Appeals BoardSep 15, 2021

2021001447 (P.T.A.B. Sep. 15, 2021)

UNITED STATES PATENT AND TRADEMARK OFFICE UNITED STATES DEPARTMENT OF COMMERCE United States Patent and Trademark Office Address: COMMISSIONER FOR PATENTS P.O. Box 1450 Alexandria, Virginia 22313-1450 www.uspto.gov APPLICATION NO. FILING DATE FIRST NAMED INVENTOR ATTORNEY DOCKET NO. CONFIRMATION NO. 14/889,686 11/06/2015 Roman GALETTO DI2013-18US2 3379 76392 7590 09/15/2021 ARRIGO, LEE, GUTTMAN & MOUTA-BELLUM LLP 2200 Pennsylvania Ave NW Suite 400E Washington, DC 20037 EXAMINER NGUYEN, QUANG ART UNIT PAPER NUMBER 1633 NOTIFICATION DATE DELIVERY MODE 09/15/2021 ELECTRONIC Please find below and/or attached an Office communication concerning this application or proceeding. The time period for reply, if any, is set in the attached communication. Notice of the Office communication was sent electronically on above-indicated "Notification Date" to the following e-mail address(es): SAL@ARRIGO.US legaladmin@arrigo.us scott@arrigo.us PTOL-90A (Rev. 04/07) UNITED STATES PATENT AND TRADEMARK OFFICE ____________ BEFORE THE PATENT TRIAL AND APPEAL BOARD ____________ Ex parte ROMAN GALETTO, AGNES GOUBLE, STEPHANIE GROSSE, CÉCILE SCHIFFER-MANNIOUI, LAURENT POIROT, ANDREW SCHARENBERG, and JULIANNE SMITH Appeal 2021-001447 Application 14/889,686 Technology Center 1600 ____________ Before RICHARD M. LEBOVITZ, JEFFREY N. FREDMAN, and ULRIKE W. JENKS, Administrative Patent Judges.1 LEBOVITZ, Administrative Patent Judge. DECISION ON APPEAL The Examiner rejected claims 29, 31, 35, 36, 38, and 52–55 under 35 U.S.C. § 103 as obvious and under nonstatutory obviousness-type double- patenting. Pursuant to 35 U.S.C. § 134(a), Appellant2 appeals from the 1 Administrative Patent Judge Eric B. Grimes participated in the Oral Hearing held July 20, 2021, but he is not available for this decision. Judge Fredman has replaced Judge Grimes on the merits panel. In re Bose Corp., 772 F.2d 866, 869 (Fed. Cir. 1985). 2 We use the word “Appellant” to refer to “applicant” as defined in 37 C.F.R. § 1.42. Appellant identifies the real party in interest as Cellectis. Appeal Br. 3. Appeal 2021-001447 Application 14/889,686 2 Examiner’s decision to reject the claims. We have jurisdiction under 35 U.S.C. § 6(b). We AFFIRM and set forth a new ground pursuant to 37 C.F.R. 41.50(b). STATEMENT OF THE CASE Claims 29, 31, 35, 36, 38, and 52–55 stand rejected by the Examiner in the Final Office Action as follows: 1. Claims 29 and 38 under 35 U.S.C. § 103 as obvious in view of Cooper et al (US 2014/0349402 A1, published Nov. 27, 2014) (“Cooper ’402”) and Gregory et al (US 2011/0136895, published Jun. 9, 2011) (“Gregory ’895”). Final Act. 3. 2. Claims 31, 35, 52 and 54 under 35 U.S.C. § 103 as obvious in view of Cooper ’402, Gregory ’895, Arthaud (US 2007/0286857 A1, published Dec. 13, 2007) (“Arthaud”), Barber et al. (J. lmmunol., 1998, 161:11-16) (“Barber), and Carrasco et al. (J. Exp. Med., 2001, 93:1045-1057) (“Carrasco”). Final Act. 8. 3. Claims 29, 31, 35, 36, 38, and 52–55 as provisionally rejected on the ground of nonstatutory obviousness-type double-patenting as obvious over claims 28, 29, 32, 34-37, 48, 49, 52, 54-56, 58, and 9 of co-pending Application No. 14/894,426 (“the ’426 application”). Final Act. 18. 4. Claims 29, 31, 36, 38, 52, and 53 as provisionally rejected on the ground of nonstatutory obviousness-type double-patenting as obvious over claims 26–30 of co-pending Application No. 16/027,629 (“the ’629 application”), Gregory et al (US 9,597,357 B2, issued Mar. 21, 2017, with the effective filing date of Oct. 10, 2013) (“Gregory ’357”), and Arthaud. Final Act. 22. Appeal 2021-001447 Application 14/889,686 3 5. Claims 35, 54, and 55 as provisionally rejected on the ground of nonstatutory obviousness-type double-patenting as obvious over 26–30 over the ’629 application, Gregory ’357, Arthaud, Barber, and Carrasco. Final Act. 26. Claim 29, the only independent claim on appeal, is reproduced below: 29. A population of isolated primary human T cells comprising at least 105 isolated primary human T cells that express a chimeric antigen receptor (CAR) with a 4-1 BB intracellular activation domain and have at least one PD1 allele inactivated; wherein the inactivation of the at least one PD1 allele enhances the anti-tumor activity of the population of isolated primary human T cells expressing the CAR. This appeal is related to Appeal 2020-001450, an appeal of the rejections in Application 14/894,426. An oral hearing was held July 20, 2021. A written transcript of the hearing has been entered into the record. CHIMERIC ANTIGEN RECEPTOR The claims are directed to human T-cells expressing a CAR and having an inactivated T-cell receptor and inactivated PD-1 gene. The claim requires that inactivation of the PD1 gene enhances the anti-tumor activity of the T-cells. A T-cell comprising a CAR, or chimeric antigen receptor, was known on the effective date of the application. The Specification explains: Novel specificities in T cells have been successfully generated through the genetic transfer of transgenic T cell receptors or chimeric antigen receptors (CARs) (Jena, Dotti et al. 2010). CARs are synthetic receptors consisting of a targeting moiety that is associated with one or more signaling domains [such as Appeal 2021-001447 Application 14/889,686 4 intracellular signal domains CD28, CD3zeta] in a single fusion molecule. In general, the binding moiety of a CAR consists of an antigen-binding domain of a single-chain antibody (scFv), comprising the light and variable fragments of a monoclonal antibody joined by a flexible linker. Spec. 1:24–30; see also 2:1–4. The Specification further discloses prior art in which “CARs have successfully allowed T cells to be redirected against antigens expressed at the surface of tumor cells from various malignancies including lymphomas and solid tumors.” Spec. 2:20–23. In other words, replacing the normal T- cell receptor antigen binding site with an antibody engineered to bind to antigens on tumors and cancers, allows the T-cell to be targeted to the tumor and cancer cells, and exert antitumor activity. PD-1, or the programmed cell death protein-1, was known to limit T- cell effector functions and antitumor activity. Spec. 2:21. PD-1 is a receptor on the surface on T-cells and its ligand is PD-L1 and PD-L2. Francisco3 2. “Engagement of PD-1 by either of its ligands during TCR signaling can block T-cell proliferation, cytokine production and cytolytic function, and impair T-cell survival.” Id. 4. Some tumors and cancers express PD-L1 ligand, “thereby augmenting the suppression of anti-tumor T-cell responses and allowing tumor progression.” Id. 20. The Specification discloses prior art in which a PD1 antibody was administered in a clinical trial to inhibit PD1 function in patients and tumour regression was observed in some cases. Spec. 2:23–26. 3 Francisco et al., 2010, Immunol. Rev., 236:219–242 (author manuscript available July 1, 2011). Appeal 2021-001447 Application 14/889,686 5 Example 3 of the Specification describes inactivating PD-1 in human primary T-cells and shows “restored cytotoxic activity against PDL-1 expressing HCT116 cells and improved cytotoxic activity against Daudi cells.” Spec. 78:9–11. OBVIOUSNESS REJECTIONS Both obviousness rejections are based on Cooper ’402 and Gregory ’895. Gregory ’895 describes inactivation of the PD1 gene in T-cells. Gregory ’895, ¶¶ 8, 52, claim 11. Claim 29 is directed to CAR T-cells in which the PD1 gene is inactivated. While Gregory ’895 does not describe CAR T-cells as required by claim 29, Gregory ’357 describes CAR T-cells and inactivation of PD1 gene in these cells (at 3:57–4:3, 48:25–60 (Example 3). Gregory ’357 is therefore closer prior art to the claim than Gregory ’895, yet it is only cited in the obviousness-type double-patenting rejection. During prosecution, claim 29 had been rejected under 35 U.S.C. § 102 as anticipated by Gregory ’357 and under 35 U.S.C. § 103 as obvious in view of Gregory ’895 and Cooper ’402. Non-Final Act. 3–4 (Aug. 30, 2017). The rejected claim 29 was directed to a CAR T-cell with an inactivated PD-1 gene. Claim amendment (Feb. 16, 2017). The claim was subsequently amended to a narrower embodiment of a cell population of 105 cells of TCR negative T-cells comprising an inactivated PD1 gene. Amendment (Feb. 27, 2018). The anticipation rejection was withdrawn Final Act. 2 (May 23, 2018). The obviousness rejection over Cooper ’402 and Gregory ’895 was maintained. Id. Gregory ’357 is closer prior art than Gregory ’895 because Gregory ’357 describes a CAR T-cell with inactive PD1, while Gregory ’895 only Appeal 2021-001447 Application 14/889,686 6 describes a T-cell with inactive PD1. For this reason, we find that an obviousness rejection based on Gregory ’357 is more appropriate. In addition to this, we also find an obviousness rejection based on Gregory ’357 is appropriate because the claims subsequently were amended to eliminate the requirement that the T-cells be TCR negative (claim amendment of Nov. 8, 2018), one of the reasons that Cooper ’402 had been cited. Accordingly, pursuant to 37 C.F.R. § 41.50(b), we set forth the following new grounds of rejection: Claims 29 and 38 under 35 U.S.C. § 103 as obvious in view of Gregory ’357. Claims 29, 31, 35, 38, 52, and 54 under 35 U.S.C. § 103 as obvious in view of Cooper ’402, Gregory ’357, Arthaud, Barber, and Carrasco. The obviousness rejections 1 and 2 based on Gregory ’895 are vacated. OBVIOUSNESS BASED ON GREGORY ’357 Gregory ’357 describes CAR T-cells engineered with an inactivated PD-1 gene as required by claim 29. Gregory ’357 identifies a problem with CAR T-cells: As useful as it is to develop a technology that will cause a T- cell to re-direct its attention to specific cells such as cancer cells [using CAR], there remains the issue that these target cells often express PD-1 ligand. As such, the PD1-PD-L1/PD-L2 interaction enables the tumor to escape action by the CAR- targeted T-cell by deactivating the T-cells and increasing apoptosis and cell exhaustion. Gregory ’357, 3:35–41. Gregory ’357 explains: Appeal 2021-001447 Application 14/889,686 7 Tumors have been found to express the PD1 ligand PD-L1 or, more rarely, the PD1 ligand PDL2 which, when combined with the up-regulation of PD1 in CTLs [cytotoxic lymphocytes], may be a contributory factor in the loss in T-cell functionality and the inability of CTLs to mediate an effective anti-tumor response. Gregory ’357, 2:6–11. The loss of T-cell functionality is also called T-cell exhaustion. Gregory ’357, 1:59–61 (“It is thought that PD1 up-regulation is somehow tied to T-cell exhaustion (defined as a progressive loss of key effector functions).)” Thus, binding of the PD-1 ligand to the PD-1 receptor on T- cells was known to produce T-cell exhaustion, which is a loss of T-cell effector function and cytotoxicity. Gregory ’357 describes inactivating or knocking out the PD-1 gene in CAR T-cells to avoid exhaustion: The use of a CAR in a cell that has also been, or will be, treated with PD1 and/or CTLA-4-specific nucleases or transcription factors, in which the PD1 or CTLA-4 gene(s) is(are) knocked out or otherwise similarly modulated, results in a T-cell expressing a CAR of interest that is resistant to the PD1 ligand produced by the cancer cell, and thus is not subject to PD-1 mediated T-cell exhaustion and/or resistant to CTLA-4 mediated T-cell inhibition. Gregory ’357, 16:38–45. Example 3 of Gregory ’357 describes generating “a T-cell population that expresses a CAR and in which PD1 and/or CTLA-4 are knocked out.” Gregory ’357, 48:33–35. Because PD-1 mediated T-cell exhaustion is eliminated, it would have been expected that such cells would not experience the progressive loss of effector function and would show enhanced anti-tumor activity. See Gregory Appeal 2021-001447 Application 14/889,686 8 ’357, 2:6-11 (reproduced above); 3:35–41 (reproduced above); 16:33–46.4 Thus, knocking out the PD1 gene in CAR T-cells would have been expected to result in the enhancement of “the anti-tumor activity of the population of isolated primary human T cells expressing the CAR” as required by claim 29. Example 3 does not disclose that the CAR has the claimed 4-1 BB intracellular activation domain. However, Gregory ’357 discloses that such domain can be a part of the CAR: In some instances, CAR can comprise an extracellular hinge domain, transmembrane domain, and optionally, an intracellular hinge domain comprising CD8 and an intracellular T-cell receptor signaling domain comprising CD28; 4-1BB, and CD3.zeta. Gregory ’357, 15:36–40. The intercellular signaling domains can be derived from TCR chains such as zeta and other members of the CD3 complex such as the γ and ε chains. In some cases, the CARs may comprise additional co-stimulator domains such as the intercellular domains from CD28, CD137 (also known as 4- 1BB) or CD134. In still further cases, two types of co- stimulator domains may be used simultaneously (i.e. CD3 zeta used with CD28+CD137). Gregory ’357, 26:14–22. 4 “Thus, the invention contemplates, for example, methods in which a CAR that specifically targets a protein or non-protein tumor antigen is introduced into a T-cell such that the T-cell bearing such a CAR will become activated in the presence of the antigen. The use of a CAR in a cell that has also been, or will be, treated with PD1- or CTLA-4-specific nucleases or transcription factors, in which the PD1 or CTLA-4 gene(s) is(are) knocked out or otherwise similarly modulated, results in a T-cell expressing a CAR of interest that is resistant to the PD1 ligand produced by the cancer cell, and thus is not subject to PD-1 mediated T-cell exhaustion and/or resistant to CTLA-4 mediated T-cell inhibition.” Appeal 2021-001447 Application 14/889,686 9 Gregory ’357 therefore expressly teaches that the recited 4-1BB domain can be part of the CAR. While Gregory ’357 describes a population of CAR T-cell with the 4- 1BB domain and inactivated PD-1 as required by claim 29, Gregory ’357 does not disclose the number of cells in the population, such as 105 cells as recited by the claim. However, such value would have been obvious to provide a patient with an effective amount of cells to achieve an anti-tumor effect, the purpose for which the cells are engineered. There is no evidence before us that the value of 105 cells is critical. For the foregoing reason, claim 29 is rejected as obvious in view of Gregory ’357. Dependent claim 38 further limits claim 29 by reciting that “the CAR is directed against CD19 antigen.” Gregory ’357 discloses that CAR can be engineered to target the CD19 antigen. Gregory ’357, 3:6–7, 15–16 (Table 1); 39:3–5. Thus, claim 38 is also obvious based on Gregory ’357 alone. OBVIOUSNESS BASED ON COOPER ’402, GREGORY ’357, ARTHAUD, BARBER, CARRASCO The Examiner rejected dependent claims 31, 35, 52, and 54 over Cooper ’402, Gregory ’895, Arthaud, Barber, and Carrasco. Final Act. 8–10. These dependent claims are drawn to T-cells having TCR and CD52 alleles inactivated (claim 31), a fragment of preTalpha to support CD3 surface expression (claim 35), and further dependent claims reciting that the CAR is directed again C19 antigen. For the reasons already explained, the rejection based on Gregory ’895 is vacated and a new ground is set forth relying instead on Gregory ’357. Appeal 2021-001447 Application 14/889,686 10 Cooper ’402 was cited by the Examiner to address the TCR inactivation in the CAR T-cells. Cooper ’402 describes T-cells engineered to express an antigen-specific chimeric antigen receptor (CAR) and to eliminate expression of endogenous alpha/beta T-cell receptor (TCR). Cooper ’402, ¶¶ 6, 8. The Specification acknowledges that CAR T-cells were known prior to the application’s filing date. Spec. 1–2 (“Background of the Invention”). The Specification also discloses that CAR T-cells comprising a CAR with a 4-1BB signal domain had been engineered into CAR, the same signaling domain which is claimed. Spec. 2:8–11. Cooper ’402 also discloses that CAR can comprises the 4-1BB signaling domain. Cooper ’402, ¶¶ 83, 88. The difference between Cooper ’402 and claim 29 is that Cooper ’402 does not describe a CAR T-cell with inactivated PD-1, the latter which is made up by Gregory ’357 as described above. Appellant did not provide arguments in the Appeal Brief on any of these additionally cited publications as they pertain to the dependent claims, except to assert they do not describe CAR or PD-1. Appeal Br. 24. However, the publications were not cited for their description of either CAR or PD-1. Thus, we affirm the rejection of these dependent claims for the reasons discussed by the Examiner. We also include claims 29 and 38 in the rejection to further address the limitation in claim 29 of at least 105 cells. Cooper ’402 shows experiments using more than 106 T-cells and explains that such numbers are useful “to achieve high enough cell numbers for a single donor-derived, modified T cell pool to be sufficient for subsequent infusion into multiple recipients, as the need arises.” Cooper ’402, 189, Fig. 6. Thus, Cooper ’402 Appeal 2021-001447 Application 14/889,686 11 provides reason to have made at least 105 cells of the T-cell population described by Gregory ’357. Declaration by Laurent Poirot To rebut the Examiner’s rejection, Appellant provides a declaration under 37 C.F.R. § 1.132 by Laurent Poirot, a co-inventor of the ’686 application (“Poirot Decl.”) (“Dr. Poirot”). The declaration is the same declaration filed in the ’426 application, which was addressed in detail in the related appeal, 2021-001450. The rejection in the 2021-001450 appeal that was addressed by Dr. Poirot was based on Gregory ’357. The rejections in this appeal are based on Gregory ’895, but we have vacated these rejections and relied on Gregory ’357, instead. The main issue addressed in the declaration by Dr. Poirot was the expectation of success of knocking out a PD-1 gene in CAR T-cells as described by Gregory ’357. Because we have made a new rejection over Gregory ’357, the arguments made by Dr. Poirot in the declaration, and our response to them in the ’426 application, are relevant here. For consistency between the two appeals which have the same issue with respect to Gregory ’357, the response to Dr. Poirot’s declaration from the ’426 application is substantially copied below. Summary of Dr. Poirot’s arguments To rebut the Examiner’s rejection, Appellant provides a declaration under 37 C.F.R. § 1.132 by Laurent Poirot, a co-inventor of the ’426 application (“Poirot Decl.”) (“Dr. Poirot”). Dr. Poirot’s principal argument is that one of ordinary skill in the art would not have reasonably expected on the effective date of the application that PD-1 gene inactivation in a CAR T-cell as claimed would enhance its Appeal 2021-001447 Application 14/889,686 12 tumor activity. Thus, despite the extensive statements in Gregory ’357 about inactivating PD-1 in CAR T-cells, Dr. Poirot opines that the skilled worker would not have believed that such approach would result in the successful enhancement of the anti-tumor activity of CAR T-cells until experiments had actually been performed in which a CAR T-cell with a knocked out and inactivated PD-1 was made and tested against tumor cells. Poirot Decl. ¶ 13. Dr. Poirot argues that this lack of an expectation of success is because “of the well-known differences between exhausted T cells that have been repeatedly and continuously exposed to their specific antigen (such as in chronic infection) and CAR T cells.” Poirot Decl. ¶ 8. Dr. Poirot identifies various difference between the two cell types throughout the declaration, including differences in the receptor affinity for the antigen, the alleged ability of CAR T-cells to bypass certain escape mechanisms through which tumors avoid T-cell recognition, MHC independence, and PD1 sensitivity. We address each of these arguments below to determine whether they establish a lack of an expectation of success that PD-1 inactivation in CAR T-cells would enhance anti-tumor activity. Appellant contends that the Examiner misunderstood the differences between exhausted T-cells and CAR T-cells. Appeal Br. 20. Appellant states it is “indisputable” that Gregory ’357 “doesn’t show any results with CAR T cells” and “can’t teach that PD-1 immunosuppression even exists in CART cells.” Id. at 21. Appeal 2021-001447 Application 14/889,686 13 Differences between native and CAR T-cells To illustrate the differences between a native T-cell and a CAR T-cell, Figure 1 of Chmielewski5 is copied below: Figure 1, reproduced above, shows that CAR is a one-chain protein that comprises the zeta (ζ) (red) and CD28 (pink) domains that are part of the T-cell receptor. The figure shows that CAR attempts to mimic the TCR, and reconstitute its function, by placing certain effector components of the TCR synapse on the same protein chain in CAR. 5 Chmielewski et al., 2013, Frontiers in Immunology, 2013, 4(371):1–7. This reference was published after the effective date of the ’426 application, but is relied upon to establish the state of the art on the application’s effective date. Appeal 2021-001447 Application 14/889,686 14 Post-filing evidence The claims require a CAR T-cell with an inactivated PD-1 gene. Dr. Poirot cites to the Beatty6 and Long7 references, published after the effective date of the ’686 application, as evidence that it was not known as of the effective filing date that PD-1 plays a role in limiting CAR T-cell efficacy. Poirot Dec. ¶¶ 17–23. Specifically, Dr. Poirot testified that Long8 and Beatty establish that T-cell exhaustion had not been studied prior to the effective date of the application. Based on this evidence, Dr. Poirot concluded, that despite the disclosure in Gregory ’357, it would not have been reasonably expected that inactivating the PD-1 gene would enhance the anti-tumor activity of the CAR T-cells. Id. While it is true that there is no evidence before us of actual experiments studying CAR T-cell exhaustion and PD-1 inactivation, Gregory ’357, before the application’s effective filing date, describes inactivating the PD-1 gene in CAR T-cells to make them resistant to T-cell exhaustion. Gregory ’357, 16: 31–46. A prophetic example of this activation is disclosed, but was not actually carried out. Id. at 48: 25–50 (Example 3). 6 Beatty et al., 2014, Oncolmmunology, 3:11, e970027. This reference was published after the effective date of the ’426 application, but is relied upon to establish the state of the art on the application’s effective date. 7 Long et al., 2015, Nat Med., 21(6): 581−590. This reference was published after the effective date of the ’426 application, but is relied upon to establish the state of the art on the application’s effective date. 8 “Exhausted T cells have low proliferative and cytokine producing capacities, high rates of apoptosis, and express high levels of inhibitory receptors such as PD-1, TIM-3, and LAG-3. Whether exhaustion plays a significant role in limiting CAR efficacy, and how CAR structural design impacts the development of exhaustion, has not been previously studied.” Long 2 (Introduction) (footnotes omitted). Appeal 2021-001447 Application 14/889,686 15 Gregory ’357 did not actually test whether PD-1 inactivation would enhance CAR T-cell activity, but that was the purpose of describing a CAR T-cell with the PD-1 gene knocked out. The question is whether one of ordinary skill in the art required actual experiments and experimental proof, as asserted by Dr. Poirot, before it would have been believed that exhaustion and PD-1 inhibition were involved in CAR T-cell efficacy? Poirot Decl. ¶¶ 23, 24. To establish obviousness under 35 U.S.C. § 103, one of ordinary skill in the art must have a reasonable expectation that the prior art, when combined, would succeed in making the claimed invention, which here is enhanced anti-tumor activity due to inactivation of the PD-1 gene. In re Cyclobenzaprine Hydrochloride Extended–Release Capsule Patent Litig., 676 F.3d 1063, 1068–69 (Fed. Cir. 2012). However, “[c]onclusive proof of efficacy is not necessary to show obviousness.” Accorda Therapeutics, Inc. v. Roxane Laboratories, Inc., 903 F.3d 1310, 1333 (Fed. Cir. 2018) (quoting from Hoffmann-La Roche Inc. v. Apotex Inc., 748 F.3d 1326, 1331 (Fed. Cir. 2014); see also Pfizer, Inc. v. Apotex, Inc., 480 F.3d 1348, 1364, 1367–68 (Fed. Cir. 2007) (reasoning that “the expectation of success need only be reasonable, not absolute”). Thus, the absence of actual experimental data, and the fact that exhaustion had not been studied in CAR T-cells, is not dispositive on the issue of whether the skilled worker would have reasonably expected PD-1 inactivation to enhance anti-tumor efficacy as required by claim 29. Rather, we must look closely at the evidence provided by Dr. Poirot to determine whether it upends the strong evidence in Gregory ’357 of using PD-1 inactivation to enhance the anti-tumor activity of CAR T-cells. Appeal 2021-001447 Application 14/889,686 16 Receptor affinity Dr. Poirot argues that CAR T-cells have a stronger affinity for the tumor antigen than native TCR, and thus the skilled worker would not have been able to predict what effect PD-1 knockout would have on cells. Poirot Decl. ¶ 52. Specifically, Dr. Poirot states that “it was thought . . . that the extent of PD-1 inhibition depended on strength of TCR signal, with more inhibition at lower levels of TCR stimulation.” Id. (citing Francisco and Freeman9). Dr. Poirot cited the following disclosure from Francisco to support his argument: Engagement of PD-1 by either of its ligands during TCR signaling can block T-cell proliferation, cytokine production and cytolytic function, and impair T-cell survival (19). The extent of PD-1 mediated inhibition depends on the strength of the TCR signal, with more inhibition occurring at lower levels of TCR stimulation. PD-1 often inhibits cytokine production to a greater extent than cell proliferation. CD28 costimulation (31) or IL-2 (43) can override PD-1-mediated inhibition. Francisco 4 (emphasis added). Freeman teaches: We have demonstrated that PD-L1 signaling can inhibit the TCR-mediated proliferation of T cells. The capacity of the PD- 1–PD-L1 interaction to downregulate a CD3/CD28-stimulated response shows that PD-1 engagement results in the delivery of a strong inhibitory signal. However, the functional consequences of the PD-1–PD-L1 interaction are dependent on the relative strength of signals delivered via the TCR and CD28. Increasing levels of TCR or CD28 signaling can circumvent the inhibitory effects of PD-1 ligation at the activation stage. 9 Freeman et al., 2006, JEM, 203(10): 2223–2227. Appeal 2021-001447 Application 14/889,686 17 Freeman 1033 (emphasis added). Dr. Poirot, citing Sadelain (2013),10 states that because “CARs were initially designed to maximally activate T-cells without any intent of regulation and using antibodies selected to display high affinity,” he would not have expected “in May of 2014 that CAR T cells would have been subject to natural inhibitory loops in general and by PD-1 in particular.” Poirot Decl. ¶ 54. He cited evidence that “the affinities of TCR interactions with MHC-peptide complexes is in the micromolar range,” but in contrast “the affinity between a CAR and its antigen is in the nanomolar range or less . . . indicating thousand fold stronger affinity of the CAR.” Id. at ¶ 55. For this reason. Dr. Poirot concluded that “PD1 inactivation in CAR T cells was generally regarded as unnecessary or superfluous.” Id. at ¶ 56. This argument does not persuade us that the skilled worker would have been dissuaded from following Gregory ’357’s disclosure of knocking out PD1 in CAR T-cells. Dr. Poirot states that the CAR T-cells would be designed with high affinity to the antigen to avoid PD1 activation. However, Sadelain (2013) is not entirely consistent with Dr. Poirot’s opinion. First, Sadelain discloses that the “optimal affinity of CARs is . . . little defined” and that it is “uncertain whether CARs are as exquisitely sensitive as TCRs.” Sadelain (2013) 2 (“CAR Targeting”). Second, Sadelain (2013) also discloses that “the design of T cells that are effective, highly tumor-specific, and regulated in their maximal accumulation and activation (so as to prelude toxic cytokine elevation), will represent a valuable advance for the use of CARs.” Sadelain (2013) 7. In other words, despite Dr. Poirot’s testimony, Sadelain 10 Sadelain et al., 2013 April, Cancer Disc., 3(4): 388–398. Appeal 2021-001447 Application 14/889,686 18 (2013) indicates that maximal activation of the CAR T-cells may not be desirable because it could cause deleterious effects. Therefore, CAR is not necessarily designed, as asserted by Dr. Poirot, to “maximally activate T- cells without any intent of regulation.” Poirot ¶ 55. We have not been guided to a teaching that would direct the skilled worker to engineer a CAR with an affinity that would maximally stimulate the T-cell to avoid PD-1 inhibition, when other deleterious effects, as discussed by Sadelain (2013) (“regulated . . . to prelude toxic cytokine elevation”), might be encountered at such levels. Even assuming that the antibody has a higher affinity for the antigen than the native TCR, Appellant did not provide evidence that a CAR with high affinity would suppress PD- 1. We are not ignoring the evidence that CAR has a higher affinity for the antigen as compared to a TCR. However, while the evidence does show that strength of the binding determines “the functional consequences of the PD-1–PD-L1 interaction” (Freeman 1033), the evidence does not show that the high affinity of a CAR would completely abolish PD-1 activity, particularly in the context of tumor cells producing the PD-1 ligand11 which engage PD-1 and therefore could stimulate PD-1 and cause exhaustion,12 and the lack of evidence provided by Appellant of how much CAR activation would result when stimulated. Obviousness does not require absolute predictability of success. In re Kubin, 561 F.3d 1351, 1360 (Fed. Cir. 2009). 11 “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-L1 to inhibit an antitumor immune response.” Freeman 1033. 12 Gregory ‘357, 2:6–11 (see supra, at 6). Appeal 2021-001447 Application 14/889,686 19 In our view, the teachings in Freeman, Francisco, and Sadelain (2013) do not rise to a “teaching way” which would have dissuaded the skill worker from knocking out the PD-1 receptor. As explained in In re Gurley, 27 F.3d 551, 553 (Fed. Cir. 1994): A reference may be said to teach away when a person of ordinary skill, upon reading the reference, would be discouraged from following the path set out in the reference, or would be led in a direction divergent from the path that was taken by the applicant. The degree of teaching away will of course depend on the particular facts; in general, a reference will teach away if it suggests that the line of development flowing from the reference’s disclosure is unlikely to be productive of the result sought by the applicant. We have not been pointed to any persuasive evidence in Francisco Freeman, and Sadelain (2013), when taken as a whole in in the context of Gregory ’357, that would have discouraged the skilled worker from following the guidance of Gregory ’357 in inactivating the PD-1 gene. Dr. Poirot asserted that the high affinity would have led the skill worker to believe that PD-1 would not be an issue, but as discussed above, Sadelain (2013) discusses the affinity for CAR T-cells and does not establish that high affinity was necessarily believed to be a goal in the CAR design, a basis for Dr. Poirot’s opinion. In our view, Dr. Poirot’s opinion is speculative and not enough to undermine the express teaching of Gregory ’357. Bypass escape mechanism In making his argument that the skilled worker would not have had a reasonable expectation that inactivating PD1 would enhance tumor activity, Dr. Poirot asserted that “chimeric receptor approach was thought to be able to bypass many of the mechanisms by which tumors avoid Appeal 2021-001447 Application 14/889,686 20 immunorecognition, such as MHC down-regulation, lack of expression of costimulatory molecules, CTL resistance, and induction of T cell suppression.” Poirot Decl. ¶ 43 (citing Finney13). This argument does not persuade us that the skilled worker would not have followed the teaching by Gregory ’357 to inactivate PD-1. Finney, as cited by Dr. Poirot has the following disclosure: This chimeric receptor approach is especially suited to immunotherapy of cancer, being able to bypass many of the mechanisms by which tumors avoid immunorecognition, such as MHC down-regulation, lack of expression of costimulatory molecules, CTL resistance, and induction of T cell suppression (3). Finney 104. Finney’s actual experiments involved including “CD28 signaling in series with TCR in the same receptor have been demonstrated to activate prestimulated human primary T cells more efficiently than a receptor providing TCC[zeta]signaling alone.” Finney 104 (Abstract). While Finney mentioned “T cell suppression” in its introduction, there is no further discussion of it in the publication.14 13 Finney et al., 2004, J. Immunol., 172:104–113. 14 Finney references publication “(3)” for T cell suppression. Publication (3) is Sadelain et al., Jan. 2003, Nature Reviews, 3:35–45. Sadelain (2003) is a review article. Sadelain (2003) discusses T cell engineering “to enhance their antitumoral activities. This might be accomplished on different levels, such as by increasing T-cell expansion, offsetting anergizing or pro- apoptotic signals, expanding the range of tumoricidal functions and protecting T cells against the suppressive effects of the tumour microenvironment.” Sadelain (2003) 43. Sadelain (2003) does not indicate that CAR would avoid T-cell suppression, but rather proposed engineering T-cells to avoid suppression, consistent with Gregory ’357’s disclosure of engineering a CAR T-cell by inactivating PD1. Sadelain (2003) is newly Appeal 2021-001447 Application 14/889,686 21 Dr. Poirot also made the same assertion about Sadelain (2013), stating that “T cells had been designed to circumvent some immune escape pathways.” Poirot Decl. ¶ 42. Dr. Poirot did not identify the passage in Sadelain (2013) for this statement. We believe that Dr. Poirot is referring to the following statement in Sadelain (2013): Furthermore, CARs can target tumor cells that have downregulated HLA expression or proteasomal antigen processing, two mechanisms that contribute to tumor escape from TCR-mediated immunity. Sadelain (2013) 2. This statement refers to HLA expression and antigen processing, not to PD-1. Dr. Poirot did not explain how these “escape” mechanisms involving pathways different from PD-1 would have led one of ordinary skill in the art to lack a reasonable expectation of success that inactivating PD-1 would enhance antitumor efficacy of a CAR T-cell. In sum, there is no evidence that CAR T-cells were expected to by- pass escape mechanisms, such as exhaustion caused by PD-1 (see especially fn. 11). MHC One of the differences between native T-cells and CAR T-cells identified by Dr. Poirot is in the MHC (major histocompatibility complex). Poirot Dec. ¶¶ 33, 35. Native T-cells, using a TCR with an antigen-binding site, recognize the antigen in the context of MHC loaded with the processed antigen peptide. See Chmielewski. CAR T-cells, however, are engineered cited in response to Dr. Poirot’s reference to Finney, which referenced Sadelain (2003) for the fact relied upon by Dr. Poirot. Appeal 2021-001447 Application 14/889,686 22 with a chimeric receptor that binds directly to the antigen without requiring an interaction with MHC. It is independent of MHC. Id. This is a well- known difference between native T-cells and CAR T-cells. Dr. Poirot did not explain how this difference in antigen recognition by the T-cell has any relationship to the question of whether it would have been reasonably expected that a CAR T-cell would experience T-cell exhaustion. Based on Beatty, Dr. Poirot further testified that on the effective date of the application “little was known regarding whether PD-1 inhibition was involved in CAR efficacy since it was thought that ‘T cells genetically modified to express a CAR that recognizes a tumor associated antigen are unaffected by tumor escape mechanisms involving the loss or downregulation of major histocompatibility molecules.’” Poirot Decl. ¶¶ 20– 21. Again, Dr. Poirot did not explain how MHC-independence would suggest lack of enhanced CAR efficacy caused by PD-1 inhibition. Dr. Poirot also argued that the affinity difference between antigen recognition by a CAR T-cell using the chimeric receptor and the native T- cell using MHC. Poirot ¶¶ 33–37. This difference has been addressed above (see “Affinity” supra.). PD-1 Dr. Poirot states, citing Francisco, that it was known that “PD-1 expression is consequence of activation through TCR or BCR (B-cell receptor) signaling.” Poirot Decl. ¶ 38. For this reason, Dr. Poirot concludes that because “CAR T cells signal through a CAR, and not TCR, the skilled artisan would not have known whether any PD-1 expression would occur in CAR T cells. Id. at ¶ 39. Appeal 2021-001447 Application 14/889,686 23 This argument does not persuade us that it would not be reasonably expected that CAR T-cells would engage PD-1. Dr. Poirot states that he considered Rolland. Poirot Decl. ¶¶ 64-68. Rolland, as indicated by the Examiner (Final Act. 19) describes the interaction of PD-1 with T-cells. Rolland explains: CD28, also expressed by T cells, likewise binds to CD80 and CD86, however this binding leads to the opposite effect, the generation of a T cell activation signal. . . . Engagement of PD- 1 by PD-L1 or PD-L2 negatively regulates immune responses in a manner similar to but distinct from that produced following CTLA-4 binding to CD80 or CD86 (in part based on distinct expression patterns between these molecules). Like CTLA-4, PD-L1 is also capable of binding CD80, and therefore through competition for CD80 binding PD-L1 may also reduce CD28- mediated costimulatory signals. Rolland ¶ 45. Rolland therefore teaches the PD-1 inhibition may result from interactions with CD80 and CD28. The CAR receptor described in Gregory ’357 can contain CD28 (Gregory ’357, 15:14–17; 15:36–16:2). Thus, contrary to Dr. Poirot’s opinion, there is evidence that the CAR receptor would be subject to inhibition by PD1 because it contains CD28, in addition to other molecules, such as CD28 normally expressed in the T-cell. Francisco, cited by Dr. Poirot, is not inconsistent with Rolland because Francisco did not address the mechanism of PD-1 inhibition and Francisco describes the interaction of PD-1 with the native T-cell receptor, not CAR comprising the CD28 signaling domain on the receptor itself. Appeal 2021-001447 Application 14/889,686 24 Co-stimulatory signaling regions Both Finney and Imai15 are cited in Dr. Poirot’s declaration as describing CAR having costimulatory domains that enabled the engineered T-cells “to survive and proliferate in response to AG” and exert “powerful and specific cytotoxicity against ALL cells,” respectively. Poirot Decl. ¶¶ 45–47. Similarly, Dr. Poirot cited Milone16 for showing the efficacy of CAR T-cells having a receptor with a costimulatory domain. Poirot Decl. ¶¶ 48– 49. Dr. Poirot did not explain the relevance of these disclosures to the expectation of success that knocking out PD-1 would increase CAR efficacy. Presumably, Dr. Poirot’s unstated point is that efficacy, and even superiority was observed with T-cells comprising signaling domains in CAR cells, raising the question of whether it was necessary to inactivate PD-1. This evidence is not persuasive. First, as explained in Gregory ’357, T-cell exhaustion in response to PD-1 up-regulation is “defined as a progressive loss of key effector function.” Gregory ’357, 1:60-62. Thus, while efficacy might be observed, this does not rule out that effector function could be lost progressively over time. Second, Sadelain (2013) disclose there was antitumor efficacy with T- cells comprising CAR comprising stimulatory domains, yet Sadelain (2013) still considered that T-cell function and survival could be improved, and even mentioned exhaustion: 15 Imai et al., 2004, Leukemia, 18:674–684. 16 Milone et al., 2009, Molecular Therapy, 17(8):1453–1464. Appeal 2021-001447 Application 14/889,686 25 A first clinical study utilizing a CD20-specific CD28/4- 1BB/CD3[zeta]did not shown dramatic responses, (31) but this early result should not in anyway detract from the potential value of these “triple-decker” CARs. Overall, more investigation is needed to attain a better understanding of optimal CAR signaling to promote sustained T cell function and survival, preventing premature death, rapid exhaustion or undue proliferation. Sadelain (2013) 3. Thus, co-stimulation did not lead to sustained T cell function and survival, even when costimulatory domains were present. Experimental evidence Experiments are described in the Specification (Spec. ¶¶ 80–81) in which a TALEN nuclease was introduced into T-cells to knock out the PD-1 gene, and then a week later, CAR mRNA was introduced into the same cells to produce a final cell population of T-cells comprising CAR and an inactivated PD-1 gene. Poirot Decl. ¶¶ 81–82. The CAR comprised a signal peptide, an anti-CD19 scFv, a CD8a hinge, a 4-1BB co-stimulatory domain and a CD3ζ signaling domain. Id. at ¶ 82. According to Dr. Poirot, the “antitumor activity” of the cells “was measured in [a] cellular cytotoxicity assay using CD19+ Daudi cells (vs. K562 as control) or HCT116 cells, which express PD1 ligand 1 (PDL 1) transduced with CD19 expression vector (vs. parental HCT116 cells as control).” Poirot Decl. ¶ 83. “PD1 TALEN transfection restored cytotoxic activity against PDL1-expressing HCT116 cells and improved cytotoxic activity against Daudi cells.” Spec. 81:1–4. We address these results below in the next section. Appeal 2021-001447 Application 14/889,686 26 Obvious to try “When there is a design need or market pressure to solve a problem and there are a finite number of identified, predictable solutions, a person of ordinary skill has good reason to pursue the known options within his or her technical grasp.” KSR Int’l Co. v. Teleflex Inc., 550 U.S. 398, 421, 127 S.Ct. 1727, 167 L.Ed.2d 705 (2007). If one of these “predictable solutions” leads to the “anticipated success,” the combination was obvious to try. Id. Our reviewing court has “identified two categories of impermissible ‘obvious to try’ analyses that run afoul of KSR and § 103: when what was ‘obvious to try’ was (a) to vary all parameters or try every available option until one succeeds, where the prior art gave no indication of critical parameters and no direction as to which of many possibilities is likely to be successful; or (b) to explore a new technology or general approach in a seemingly promising field of experimentation, where the prior art gave only general guidance as to the particular form or method of achieving the claimed invention. See In re Kubin, 561 F.3d 1351, 1359 (Fed. Cir. 2009) (quoting In re O’Farrell, 853 F.2d 894, 903 (Fed. Cir. 1988)). In re Copaxone Consolidated Cases, 906 F.3d 1013, 1025 (Fed. Cir. 2018) This appeal falls into neither of the two impermissible categories. To begin, Gregory ’357 provides an expectation of “anticipated success” that inactivating the PD-1 gene would prevent T-cell exhaustion and result in enhanced anti-tumor activity because it teaches exactly that in its disclosure, albeit with a prophetic example of such solution to the problem of T-cell exhaustion. We have reviewed all the evidence provided by Appellant to challenge the anticipated success of Gregory ’357’s disclosure and prophetic example, but as explained in detail above, we do not find the evidence persuasively negated the anticipated success of applying Gregory ’357’s Appeal 2021-001447 Application 14/889,686 27 disclosure to Cooper ’403’s CAR T-cells. We acknowledge the differences between a native T-cell and a CAR T-cell, but Appellant did not establish, in view of Gregory ’357, that the skilled would have lacked a reasonable expectation that PD-1 inactivation would lead to an enhancement of the CAR T-cell’s effector functions. For example, Sadelain (2013)(at p. 4) mentions exhaustion as something to be prevented in CAR T-cells and Rolland provides a mechanism for PD-1 suppression involving CD28 which is described by Gregory ’357 as present in its CAR. There is evidence that CAR has a higher affinity for the antigen than the native TCR, and evidence that the extent of PD-1 mediated inhibition depends on the strength of the TCR signal, with more inhibition occurring at lower levels of TCR stimulation. However, Appellant did not provide evidence that the stronger binding to antigen observed with CAR would necessarily lead to high levels of receptor stimulation and overcome PD-1 inhibition. In fact, the evidence discussed by Sadelain (2013) about the lack of “dramatic responses” which could be explained by T-cell inhibition, such as exhaustion, further indicates the obviousness of using PD-1 inactivation to enhance antitumor activity as disclosed by Gregory ’357. Overall, Dr. Poirot’s opinion is speculative. Appellant also did not provide evidence that experimental approach disclosed in the Specification, as described above, did anything different than follow the guidance in the cited publications in accordance with the level of ordinary skill in the art. Dr. Poirot, in describing the experiments, did not identify a lack of direction in the prior art or a deficiency in the guidance provided by Gregory ’357 and Cooper ’403. In our view, when the reference tells a scientist how to engineer the cell to get a better antitumor response (Gregory ’357, 2:6–11), and the scientist does just what it says, Appeal 2021-001447 Application 14/889,686 28 without having to invoke anything beyond routine technical skill to achieve a successful result, that invention is obvious. See also Pharma Stem Therpeutic, Inc. v. ViaCell, Inc., 491 F.3d 1342, 1363–1364 (2007) (“Scientific confirmation of what was already believed to be true may be a valuable contribution, but it does not give rise to a patentable invention.” The obviousness of claim 28 is affirmed. Claims 29, 32, 34, 36, 37, 48, 49, 52, 54, 56, 58, and 59 were not argued separately and therefore fall with claim 28. 37 C.F.R. § 41.37(c)(1)(iv). OBVIOUSNESS-TYPE DOUBLE-PATENTING REJECTIONS There are three provisional obviousness-type double-patenting rejections over co-pending applications No. 14/894,426 and No. 16/027,629. Appellant did not provide arguments against the rejections, but rather stated “Appellant will address the rejections by filing a Terminal Disclaimer or other appropriate action once there is an indication of allowable subject matter.” Appeal Br. 25. As no terminal disclaimers have been filed, the rejections are summarily affirmed for the reasons given by the Examiner. CONCLUSION In summary: Claims Rejected 35 U.S.C. § Reference/Basis Affirmed Reverse New Ground 29, 38 103 Cooper ’402, Gregory ’89517 31, 35, 52 54 103 Cooper ’402, Gregory ’895, 17 As indicated above, we vacate this rejection. Appeal 2021-001447 Application 14/889,686 29 Arthaud, Barber, Carrasco18 29, 38 103 Gregory ’357 29, 38 29, 31, 35, 38, 52, 54 103 Cooper ’402, Gregory ’357, Arthaud, Barber, Carrasco 29, 31, 35, 38, 52, 54 29, 31, 35, 36, 38, 52–55 Nonstatutory Double Patenting ’426 application 29, 31, 35, 36, 38, 52–55 29, 31, 36, 38, 52, 53 Nonstatutory Double Patenting ’629 application, Gregory ’357, Arthaud 29, 31, 36, 38, 52, 53 35, 54, 55 Nonstatutory Double Patenting ’629 application, Gregory ’357, Arthaud, Barber, Carrasco 35, 54, 55 Overall Outcome 29, 31, 35, 36, 38, 52–55 29, 31, 35, 38, 52, 54 TIME PERIOD FOR RESPONSE This decision contains a new ground of rejection pursuant to 37 C.F.R. § 41.50(b). Section 41.50(b) provides “[a] new ground of rejection pursuant to this paragraph shall not be considered final for judicial review.” Section 41.50(b) also provides: When the Board enters such a non-final decision, the appellant, within two months from the date of the decision, must exercise one of the following two options with respect to the new ground 18 As indicated above, we vacate this rejection. Appeal 2021-001447 Application 14/889,686 30 of rejection to avoid termination of the appeal as to the rejected claims: (1) Reopen prosecution. Submit an appropriate amendment of the claims so rejected or new Evidence relating to the claims so rejected, or both, and have the matter reconsidered by the examiner, in which event the prosecution will be remanded to the examiner. The new ground of rejection is binding upon the examiner unless an amendment or new Evidence not previously of Record is made which, in the opinion of the examiner, overcomes the new ground of rejection designated in the decision. Should the examiner reject the claims, appellant may again appeal to the Board pursuant to this subpart. (2) Request rehearing. Request that the proceeding be reheard under §41.52 by the Board upon the same Record. The request for rehearing must address any new ground of rejection and state with particularity the points believed to have been misapprehended or overlooked in entering the new ground of rejection and also state all other grounds upon which rehearing is sought. Further guidance on responding to a new ground of rejection can be found in the MPEP § 1214.01. No time period for taking any subsequent action in connection with this appeal may be extended under 37 C.F.R. § 1.136(a)(1). See 37 C.F.R. §§ 41.50(f), 41.52(b). AFFIRMED; 37 C.F.R. § 41.50(b)