DETAILED CORRESPONDENCE
Claims 1-20 are currently pending and under examination in the instant application. The present application, filed on or after March 16, 2013, is being examined under the first inventor to file provisions of the AIA . An action on the merits follows.
Claim Rejections - 35 USC § 102
The following is a quotation of the appropriate paragraphs of 35 U.S.C. 102 that form the basis for the rejections under this section made in this Office action:
A person shall be entitled to a patent unless –
(a)(1) the claimed invention was patented, described in a printed publication, or in public use, on sale or otherwise available to the public before the effective filing date of the claimed invention.
(a)(2) the claimed invention was described in a patent issued under section 151, or in an application for patent published or deemed published under section 122(b), in which the patent or application, as the case may be, names another inventor and was effectively filed before the effective filing date of the claimed invention.
Claims 1-11 are rejected under 35 U.S.C. 102(a)(1) OR under 35 U.S.C. 102(a)(2) as being anticipated by WO 2015/142661, published on 9/24/15, with an effective filing date of 3/15/14, and hereafter referred to as Engels et al.
Engels et al. teaches regulatable chimeric antigen receptors (RCAR) and more specifically RCAR which are inhibitory chimeric antigen receptors (iCAR) which comprise at least one signaling domain of an inhibitory molecule (Engels et al., pages 256-258). In particular, Engels et al. teaches that the signaling domain of the inhibitory molecule is from PD-1, CTLA1, TIM3, LAG3, TIGIT, BTLA, or LAIR1 (Engels et al., page 257 and Table 12). Engels et al. further teaches that the iCAR comprises an antigen targeting domain that binds an antigen or ligand of a non-cancer cell, and more specifically that the antigen targeting domain binds to a cell surface marker associated with a particular disease, such as an autoimmune disease (Engels et al., pages 226 and 256). In addition, Engels et al. teaches that the antigen targeting domain is an scFV (Engels et al., pages 133 and 226). Engels et al. also teaches nucleic acid constructs comprising nucleic acids encoding the iCAR and immune cells, specifically T cells, comprising said nucleic acid constructs and expressing the iCAR, and kits comprising such nucleic acid or cells (Engels et al., pages 2, 224, and 258). Finally, Engels et al. teaches methods of treating a disease, such as an autoimmune disease, by administering cytotoxic cells, such as T cells or NK cells, which express an RCAR to a subject (Engels et al., pages 2, 147, and 224). Thus, by teaching all the elements of the claims as written, Engels et al. anticipates the instant invention as claimed.
Claims 1-11 are rejected under 35 U.S.C. 102(a)(2) as being anticipated by US Patent Application Publication 2015/0376296 (2015), with an effective filing date of 3/15/13, and hereafter referred to as Federov et al.
Federov et al. teaches immunoresponsive cells, such as T cells, which express an inhibitory chimeric antigen receptor, and which can be used in methods of treating disease, including autoimmune disease, nucleic acids encoding the inhibitory chimeric antigen receptors, vector comprising the nucleic acids encoding the inhibitory chimeric antigen, and kits comprising said cells and nucleic acids for treating autoimmune disease (Federov et al., paragraphs 9-17, and claims). In particular, Federov et al. teaches that the inhibitory chimeric antigen receptor comprises an scFV, and that the intracellular inhibitory signaling domain is from CTLA-4, BTLA, LAG3, or PD-1 (Federov et al., paragraphs 13, 21, 23, and 30). Thus, by teaching all the elements of the claims as written, Federov et al. anticipates the instant invention as claimed.
Claim Rejections - 35 USC § 112
The following is a quotation of the first paragraph of 35 U.S.C. 112(a):
(a) IN GENERAL.—The specification shall contain a written description of the invention, and of the manner and process of making and using it, in such full, clear, concise, and exact terms as to enable any person skilled in the art to which it pertains, or with which it is most nearly connected, to make and use the same, and shall set forth the best mode contemplated by the inventor or joint inventor of carrying out the invention.
The following is a quotation of the first paragraph of pre-AIA 35 U.S.C. 112:
The specification shall contain a written description of the invention, and of the manner and process of making and using it, in such full, clear, concise, and exact terms as to enable any person skilled in the art to which it pertains, or with which it is most nearly connected, to make and use the same, and shall set forth the best mode contemplated by the inventor of carrying out his invention.
Claims 1-20 are rejected under 35 U.S.C. 112(a) or 35 U.S.C. 112 (pre-AIA ), first paragraph, because the specification, while being enabling for 1) a chimeric antigen receptor (CAR) or nucleic acid encoding a CAR comprising a signaling domain from a co-inhibitory molecule, where the signaling domain comprises an ITIM domain, 2) an immune cell or T/ Treg cell comprising said CAR, and 3) a method of treating chronic inflammation or immune-mediated autoimmunity comprising administering T cell/Treg cell comprising a nucleic acid encoding a CAR comprising an antigen binding domain that binds to an antigen or ligand at a site of inflammation or autoimmunity, a CD3zeta signaling domain, and a co-inhibitory ITIM containing signaling domain, does not reasonably provide enablement for making or using a CAR where the signaling domain of the co-inhibitory molecule does not contain as ITIM domain. The specification does not enable any person skilled in the art to which it pertains, or with which it is most nearly connected, to make or use the invention commensurate in scope with these claims.
The broadest set of claims, claims 1-11, recite a genus of CAR comprising a signaling domain of a co-inhibitory molecule. Claim 4 limits the signaling domain of a co-inhibitory molecule to signaling domain of Cytotoxic T-Lymphocyte Antigen 4 (CTLA-4), Lymphocyte- Activation Gene 3 (LAG-3), Programmed cell death protein 1(PD-1), T cell Immunoglobulin Mucin-3 (TIM-3), T-cell immunoreceptor with immunoglobulin (TIGIT), B-and T-lymphocyte Attenuator (BTLA), leukocyte immunoglobulin-like receptor subfamily B member 4 (LILRB4), LILRB3, CD160, 2B4, Leukocyte-Associated Immunoglobulin-like Receptor 1 (LAIR-1), CD66a, CD44, or neuropilin-1 (NRp1). Claims 12-20 recite a narrower invention where the CAR comprises an antigen targeting domain which binds to an antigen or ligand at a site of inflammation or autoimmunity, a signaling domain of Cytotoxic T-Lymphocyte Antigen 4 (CTLA-4), and a signaling domain of neuropilin-1 (NRp1).
The specification broadly discloses the CAR polypeptides, nucleic acids, and modified T cells, including Foxp3+ T or Treg cells, and further generically discloses the treatment of numerous chronic inflammatory or autoimmune diseases including diabetes, multiple sclerosis, vasculitis, arthritis, Lyme disease, Huntington’s Diseases, cystic fibrosis, and muscular dystrophy. The specification further provides a single working example which describes the preparation of a single nucleic acid encoding a CAR comprising an NKp30 antigen-specific targeting domain fused to the transmembrane and cytoplasmic domains of CTLA-4 and the cytoplasmic domain of CD3zeta. The working example states that this CAR was expressing in a packaging cell line, and states their expectation that it would be expressed in a transduced CD4+CD25+CD127- Foxp3+ Treg cell. The working examples do not provide any description of the functional activity of this CAR when expressed from any cell, including a Treg cell. The working examples further does not demonstrate any therapeutic activity for the CAR when expressed from a Foxp3+ T cell or Treg cell, or demonstrate any therapeutic activity for any T cells expressing this CAR in any subject suffering from any inflammatory or autoimmune disease.
The specification does teach that the purpose of the invention is to provide a CAR which when expressed in a T cell provides a co-inhibitory signal that activates/drives a regulatory immune pathway to activate the T cell towards an immune suppressive phenotype. The specification teaches a number of signaling domains which are identified as having co-inhibitory signaling domains as they are derived from co-inhibitory receptors and comprise an ITIM or other inhibitory motif, see specification Table 3. CTLA-4, for example, is identified as a co-inhibitory receptor which comprises an Try-Xaa-Xaa-Met (YXXM) inhibitory motif. The specification also provides a specific sequence for a intracellular signaling sequence derived from CTLA-4 (SEQ ID NO:5). However, the specification, while identifying 2B4, CD160, CD44, and Npr1 as co-inhibitory receptors, fails to provide an enabling disclosure for signaling domains derived from any of 2B4, CD160, CD44, or Npr1 which when incorporated into a CAR molecule are capable of transducing an inhibitory/co-inhibitory signal into a T cell, Treg cell, or any other immune cell. For example, the specification discloses that neuropilin (Nrp1) is not characterized as a co-inhibitory receptor (specification, page 23). The specification states that Nrp1 expression can suppress autoreactive T cells in an experimental autoimmune encephalomyelitis model, citing Solomon et al. (2001) PNAS, Vol. 108, 2040-2045, and further states that gene-expression analysis shows that Nrp-1 induced transcriptional profile is consistent with the promotion of T regulatory cell survival, citing Delgoffe et al. (2013) Nature, Vol. 501, 252-256. The specification also discloses alleged Nrp1 signaling domains provided as GENBANK accession numbers (specification, paragraph 37); however, it is noted that these accession numbers are to full length Nrp1 genes derived from a number of mammals. The specification does not disclose any specific signaling domain from Nrp-1, or any specific functional activity for any domain within the Nrp-1 protein and specifically the cytoplasmic domain of Nrp-1. Turning to the references cited by the specification, it is noted that Solomon et al. looked at Npr-1 deficient Treg cells, and while they concluded that Nrp-1 expression is important for suppressing CD4+ autoreactive immune cells, Solomon et al. does not teach that Npr-1 participates in any particular signal transduction pathway or identify any portions or domains or Npr-1 which are necessary or responsible for signaling within a T cell. Delgoffe et al. mentions the potential importance of a three amino acid SEA motif at the C-terminus of Npr-1 in recruiting PTEN for potentiating Treg function and survival, but again does not teach any specific “signaling domain” within Npr-1 or teach which sequences in the Npr-1 protein, or intracellular region in particular, which are necessary and sufficient to transduce any signal in a T cell when present within a native Npr-1 protein or any type of chimeric protein.
At the time of filing, the art teaches that Nrp-1 (neuropilin 1) is a pleiotropic glycoprotein which was first identified as an axonal adhesion protein, was later found to associate with both VEGF-A (VEGF165) and SEMA3A, and has a role in angiogenesis, arteriogenesis, cell migration, and cell adhesion (Plein et al. (2014) Microcirculation, Vol. 21, 315-323, page 316). Plein et al. teaches that Nrp-1 is a glycoprotein with a large extracellular domain responsible for binding VEGF165 and SEMA3A, a transmembrane domain, and a short cytoplasmic domain with no known catalytic activity (Plein et al., pages 316 and 318, and Figure 1). Plein et al. does teach that the cytoplasmic domain comprises a C-terminal SEA motif which can recruit synectin/GIPC1/NIP, a modulator of endocytic trafficking (Plein et al., page 316). Plein et al. postulates that since Nrp-1 lack any known catalytic activity that it transduces signals through coreceptors, such as VEGFR2 which associate with Nrp-1 through VEGF165 binding, and which activate intracellular signal transduction pathways involving ERK/MAPK, AKT1, SRC etc. (Plein et al., page 318). The Nrp-1 cytoplasmic domain SEA domain in this scenario binds to synectin/NIP and mediates endocytosis of the NRP-1 coreceptor complex (Plein et al., page 318). Takamatsu et al. further teaches that Nrp-1 bound to SEMA3A forms a complex with Plexin-A as a coreceptor in T cells, and postulates that signaling through the complex is transduced through the plexin component, with Nrp-1 serving to support or strengthen SEMA3A binding in the complex (Takamatsu et al. (2012) Trends in Immunology, Vol. 33(3), 127-135, see page 128 and Figure 1). Delgoffe et al., cited by the specification as noted above, teaches that SEMA4A also binds to Nrp1 and in T cells, specifically Treg cells, can recruit PTEN and restrain TCR activated Akt phosphorylation and signal transduction thus potentiating Treg function and survival (Delgoffe et al. (2013) Nature, Vol. 501(7466), 252-256, see page 252 and Supplemental Figure 15). According to Delgoffe et al., this Treg Npr-1 activity appears to only be important for Treg suppression of anti-tumor immune responses and inflammatory colitis, not autoimmunity (Delgoffe et al., page 252). While Delgoffe et al. focuses on demonstrating the binding of SEMA4A to Nrp-1, the prior art, such as Takamatsu et al. cited above, teaches that SEMA4A binds to a number of other receptors present on T cells, such as TIM-2 and various plexin-B subfamily members (Takamatsu et al., pages 128 and 131, and Figure 1). However, based on the teachings of Takamatsu et al. and Plein et al., that Nrp-1 transduces signals as part of a complex between Nrp-1, a ligand, and a coreceptor, it is unclear whether the Nrp-1-SEMA4A binding and subsequent signal transduction occur through the Nrp-1 protein itself or as part of larger complex with a plexin co-receptor on T cells. Further, the prior art of record is clear that the intracellular portion of Nrp-1 does not have any catalytic activity itself, and while the three amino acid SEA domain at the C-terminus has been implicated in recruitment of either NIP or PTEN, there are no teachings that such recruitment by itself results in any specific signaling versus signaling through co-receptors associated in complex with Nrp-1. Thus, the prior art does not provide specific guidance for any “signaling” domain present in the intracellular region of Nrp-1 and further does not teach how any sequence derived from Nrp-1 can be used in a chimeric protein such as a chimeric antigen receptor to transduce any type of signal within a Treg cell as claimed. Thus, the teachings of the prior art of record demonstrate that the understanding of signal transduction following ligation of Nrp-1 and any of its known ligands in a T cell was in its infancy, with the identification and elucidation of Nrp-1 ligand binding, complex formation, co-receptor association, and intracellular signaling partners/signaling pathways having barely begun. The state of the prior art as discussed above highlights the undeveloped and unpredictable nature of using any putative “signaling” domain from Nrp-1 within a CAR which also comprises a CTLA-4 signaling domain, a CD3 zeta signaling domain, or both CTLA-4 and CD3 zeta signaling domains, as the effects of any Nrp-1 sequence on the functionality of such as CAR could not have been predicted a priori.
In regards to CD44, CD44 is not taught by the specification to include either an ITIM or ITSM motif. In reference to CD44, the specification provides a single paragraph disclosing that CD44 is a cell adhesion molecule which is the major hyaluronan receptor, and has been implicated in the binding, endocytosis, and metabolism of hyaluronan (HA) (specification, paragraph 36). Paragraph 36 further cites Teder et al. (2002) Science, Vol. 296, 155-158, for teaching that in bleomycin-induced acute lung injury, CD44-deficient mice show an enhanced and persistent inflammatory response due to impaired clearance of apoptotic neutrophils and HA fragments from the injury site. Paragraph 36 of the specification also cites Kawana, et al. (2008) J. Immunol. Vol.180, 4235-45, for showing that CD44 directly associates with TLR2 when stimulated by the TLR2 ligand zymosan and that the cytoplasmic domain of CD44 is crucial for its regulatory effect on TLR signaling. In addition, paragraph 36 states that CD44 negatively regulates in vivo inflammation mediated by Toll-Like Receptors (TLRs) via NF-.kappa.B activation, which leads to proinflammatory cytokine production. The specification also discloses alleged CD44 signaling domains provided as GENBANK accession numbers (specification, paragraph 36); however, it is noted that these accession numbers are to 8 full length CD44 isoforms, and do not identify any “signaling” domain(s).
The specification, while alluding to the use of a CD44 signaling domain, does not disclose any specific signaling domain from CD44, or any specific functional activity for any domain within the cytoplasmic domain of CD44. Turning to the references cited by the specification, Teder et al., cited in the specification, teaches that CD44 is important in clearing HA (nonsulfated glycosaminoglycan hyaluronan) which accumulated at sites of inflammation and tissue injury (Teder et al., page 155). Teder et al. demonstrates bleomycin induced lung injury and inflammation associated with increases in HA is increased in CD44 deficient mice, and that administration of bone marrow expressing wild type CD44 reduces both HA and inflammation in this mouse model (Teder et al., page 156-158). CD44 binding and clearance of HA is a function of the full length CD44 molecule. Teder et al. does not teach that the cytoplasmic domain of CD44 has any specific anti-inflammatory role in reducing inflammation in this mouse model, and further does not teach or suggest that the cytoplasmic domain of CD44 can be used as a signaling domain in a chimeric receptor to affect the effector or regulatory function of T cells or other immune cells in which is expressed, particularly for the purpose of treating any inflammatory or autoimmune disease. Kawana et al., also cited by the specification, actually teaches that a considerable number of publications have reported that CD44 expression plays a crucial role in a variety of inflammatory diseases and that CD44 expression is upregulated on a number of inflammatory cells in these diseases (Kawana et al., page 4235). Kawana et al. teaches that inhibiting CD44 can inhibit inflammation in arthritis, cutaneous inflammation, experimental autoimmune encephalomyelitis, and IL-2 induced vascular leak syndrome (Kawana et al., page 4235). Kawana et al. does acknowledge the teachings of Teder regarding the role of CD44 in reducing HA and thus inflammation in bleomycin-induced acute lung injury, and further demonstrates that CD44 can negatively regulate TLR2 signaling in zymosan induced inflammation, an effect that appears to require the a full length CD44 molecule including the cytoplasmic domain, (Kawana et al., pages 4235, and 4242-4244. However, Kawana et al. does not teach that the CD44 cytoplasmic domain, by itself or when part of fusion protein, can be used to transduce signals directly or indirectly in any type of immune cell, or teach the effects of any such putative CD44 mediated signals on the effector or regulatory functions of immune cells such as T cells, B cells, dendritic cells, macrophages, or eosinophils. In fact, Kawana et al. states that it is evident that the function of CD44 in inflammation is complex and involves multiple cells types, ligands, and signaling pathways (Kawana et al., page 4236). Other publications from the prior art support this variable role of CD44 in various cell types. Baatan et al., for example, teaches that CD44 expression on T cells has been shown to be upregulated on naïve T lymphocytes following exposure to microbes, and that the relevance of CD44 expression to T-cell responses or homeostasis has been largely unexplored (Baatan et al. (2010) Communicative & Integrative Biology, Vol. 3(6), 508-512, see page 508). Baatan et al. does teach that CD44 is involved in the regulation of CD4 T cell survival, but not other T cell subpopulations, and further teaches that in Treg cells, CD44 is associated with the expression of FoxP3 and the cytokines TGFb1 and IL-10 (Baatan et al., page 509). However, again, Baatan et al. does not teach any specific signaling domains present in the cytoplasmic region of CD44 or show that any portion of the intracellular region of CD44 can mediate any particular type of signal in any type of T cell. In fact, Baatan et al. explicitly states that CD44 lacks intrinsic signaling activity and the signaling pathways coupled to CD44 are not fully defined (Baatan et al., page 510). Thus, the prior art at the time of filing establishes that the state of the art for the role of CD44 in inflammation and autoimmunity, and the role of CD44 in immune cells, including T cells and Treg cells, was largely undefined and unpredictable, with CD44 expression linked to both inducing/increasing inflammation in some models of inflammatory and autoimmune disease, and in reducing inflammation in other models. The prior art also establishes the unpredictability at the time of filing for identifying and using a “signaling” domain from CD44 in immune cells due to both the art-recognized lack of intrinsic signaling activity by the CD44 molecule, and the fact that the intracellular pathways by which CD44 mediates its pleiotropic effects on various cells had not been fully elucidated. Further, the prior art, like the specification, does not provide specific guidance for any “signaling” domain present in the intracellular region of CD44 and further does not teach how any putative “signaling” sequence derived from CD44 can be used in a chimeric protein such as a chimeric antigen receptor to transduce any type of signal within any immune cell, including and T cell or Treg cell as claimed. The state of the prior art as discussed above highlights the undeveloped and unpredictable nature of using any putative “signaling” domain from CD44 within a CAR by itself, or with any of signaling domain form any one or more of the co-inhibitor receptor recited in the claims, as the effects of any CD44 sequence on the functionality of such as CAR could not have been predicted a priori.
Likewise for 2B4 and CD160, while the specification states that both of these molecules are co-inhibitory molecules, the specification fails to provide sufficient guidance for any specific signaling domain from 2B4 or CD160 with any specific inhibitory activity in any immune cell including a T cell or Treg cell. At the time of filing, Lee et al. teaches that 2B4 is an unusual NK receptor which does not contain either an ITIM or ITAM domain, but which has stimulatory activity in cells (Lee et al. (2004) J. Exp. Med., Vol. 199(9), 1245-1254, see page 1245). Lee et al. does teach that while 2B4 has an immunoreceptor tyrosine-based switch motif (ITSM) in the cytoplasmic domain, the ITSM domains are stimulatory domains (Lee et al., page 1255). Lee et al. teaches that 2B4 interacts with intracellular SH2D1A, and that mutations in SH2D1A can result in an inhibitory signal from 2B4. However, neither Lee et al., nor the instant specification, teach a signaling domain from 2B4 which is inherently inhibitory or under which conditions a signaling domain from 2B4 may be inhibitory in any and all immune cells. Turning to CD160, the art at the time of filing teaches that the main isoform of CD160 is in fact a GPI anchored protein, which has an single IgV-like extracellular domain and a GPI anchor (del Rio et al. (2010) J. Leuk. Biol., Vol. 87, 223-235, see page 231). Thus, the GPI isoform of CD160 does not in fact have any cytoplasmic domain and neither the prior art nor the specification identify any co-inhibitory domain derived from the IgV-like extracellular domain or the GPI anchor. Giustiniani et al. further teaches that while a second isoform of CD160 with a short cytoplasmic tail has been identified, the signals transduced through this molecule are activating signals, not inhibitory signals (Giustiniani et al. (2009) J. Immunol., Vol. 182, 63-71, see page 63). Neither the prior art nor the instant specification teach a signaling domain obtained form any isoform of CD160 which is inherently inhibitory or under which conditions a signaling domain from CD160 may be inhibitory in any and all immune cells.
Therefore, in view of the underdeveloped and unpredictable state of the prior art at the time of filing for using any non-ITIM “signaling domain” as an inhibitory domain in a CAR, the underdeveloped and unpredictable state of the prior art at the time of filing for using any signaling domain derived from Nrp-1, CD44, 2B4, or CD160 as an inhibitory signaling domain in a CAR, the lack of guidance provided by the specification for specific sequences present within any non-ITIM signaling domain, and Nrp1, CD44, 2B4, and CD160 in particular which are capable of transducing inhibitory signals within a T cell or any other type of immune cell, particularly in the context of a CAR comprising additional signaling domains from other proteins, the lack of working examples demonstrating the construction or use of any CAR comprising a non-ITIM containing “signaling domain”, the lack of any working examples demonstrating a therapeutic effect from the administration of any T cell or Treg cells expressing a CAR comprising any non-ITIM containing “signaling domain”, and the breadth of the claims, it would have required undue experimentation to make and use the invention as claimed.
No claims are allowed.
Any inquiry concerning this communication from the examiner should be directed to Anne Marie S. Wehbé, Ph.D., whose telephone number is (571) 272-0737. If the examiner is not available, the examiner’s supervisor, Maria Leavitt, can be reached at (571) 272-1085. For all official communications, the technology center fax number is (571) 273-8300. Please note that all official communications and responses sent by fax must be directed to the technology center fax number. For informal, non-official communications only, the examiner’s direct fax number is (571) 273-0737. For any inquiry of a general nature, please call (571) 272-0547.
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Dr. A.M.S. Wehbé
/ANNE MARIE S WEHBE/Primary Examiner, Art Unit 1634