DETAILED ACTION
The present application, filed on or after March 16, 2013, is being examined under the first inventor to file provisions of the AIA .
The claim listing filed May 17, 2024 is pending.
Claims 7, 9-19, 21, 22, 24-31, 33-35, 39-49, 51-75, 77-79, and 81-85 are canceled.
Claims 1-6, 8, 20, 23, 32, 36-38, 50, 76, 80, and 86-88 are pending.
Election/Restriction
Applicant’s election of the species of ovarian cancer, CD8+ T cell, CD28 primary intracellular signaling domain and SEQ ID NO:4, CD3
ζ
secondary intracellular signaling domain, CD28 transmembrane domain, SEQ ID NO:229, niraparib, and immune checkpoint molecule inhibitor in the reply filed on October 15, 2025 is acknowledged.
Because applicant did not distinctly and specifically point out the supposed errors in the restriction requirement, the election has been treated as an election without traverse (MPEP § 818.01(a)).
Upon further consideration, the species election requirement with respect to a specific amino acid sequence of the chimeric engulfment receptor as recited in claim 80 in the office action mailed on October 1, 2025 is withdrawn. SEQ ID NOs: 162, 71, 228, 229, 239, and 240 are rejoined.
In view of the withdrawal of the restriction requirement regarding a specific amino acid sequence of the chimeric engulfment receptor, applicant(s) are advised that if any claim presented in a divisional application is anticipated by, or includes all the limitations of, a claim that is allowable in the present application, such claim may be subject to provisional statutory and/or nonstatutory double patenting rejections over the claims of the instant application. Once the species restriction requirement of the specific amino acid sequence of the chimeric engulfment receptor is withdrawn, the provisions of 35 U.S.C. 121 are no longer applicable. See In re Ziegler, 443 F.2d 1211, 1215, 170 USPQ 129, 131-32 (CCPA 1971). See also MPEP § 804.01.
Claims 2, 4-6, and 23 have been withdrawn from further consideration pursuant to 37 CFR 1.142(b) as being drawn to nonelected inventions. It is noted that claims 2, 4-6, and 23 are drawn to non-elected species.
Claims 1, 3, 8, 20, 32, 36-38, 76, 80, and 86-88 are currently under consideration as they read on the elected invention and species.
Priority
Applicant's domestic benefit claims to the provisional applications 63/066,150, 63/087,049, and 63/226,712 is acknowledged. However, the provisional applications 63/066,150 (filed August 14, 2020) and 63/087,049 (filed October 2, 2020) upon which priorities are claimed fail to provide adequate support under 35 U.S.C. 112(a) for claims 1, 3, 8, 20, 32, 36-38, 76, 80, and 86-88 of this application.
Specifically, insufficient support was identified for the limitation of “the chimeric engulfment receptor comprising a TLR2 signaling domain” in these two provisional applications. Consequently, the claims have been accorded the priority of the filing date of the provisional application 63/226,712 on July 28, 2021.
Should Applicant disagree with the Examiner’s factual determination above, it is incumbent upon Applicant to provide a showing that specifically supports the instant claim limitations.
Claim Interpretation
Claim 76 recites “wherein the intracellular signaling domain comprises a primary intracellular signaling domain comprising a CD28 signaling domain; a secondary intracellular signaling domain comprising a CD3𝞯 signaling domain; and a tertiary intracellular signaling domain comprising a TLR2 signaling domain” in lines 5-8. The specification discloses that the designation of primary, secondary, and tertiary intracellular signaling domains includes, but is not limited to, the arrangement of the primary intracellular signaling domain at the N-terminus, secondary intracellular signaling domain in the middle, and tertiary intracellular signaling domain at the C-terminus of the intracellular portion of the chimeric Tim receptor (e.g. see page 62, lines 1-16).
Claim Objections
Claim 80 is objected to because of the following informalities: claim 80 recites the phrase “the amino acid sequence of set forth in” but it should be “the amino acid sequence set forth in” in line 2. Claim also recites SEQ ID NOs: 162 and 71 which are identical and therefore one needs to be deleted. Appropriate correction is required.
Claim Rejections - 35 USC § 112
Indefinite Language
The following is a quotation of 35 U.S.C. 112(b):
(b) CONCLUSION.—The specification shall conclude with one or more claims particularly pointing out and distinctly claiming the subject matter which the inventor or a joint inventor regards as the invention.
The following is a quotation of 35 U.S.C. 112 (pre-AIA ), second paragraph:
The specification shall conclude with one or more claims particularly pointing out and distinctly claiming the subject matter which the applicant regards as his invention.
Claims 20, 38, and 76 are rejected under 35 U.S.C. 112(b) or 35 U.S.C. 112 (pre-AIA ), second paragraph, as being indefinite for failing to particularly point out and distinctly claim the subject matter which the inventor or a joint inventor (or for applications subject to pre-AIA 35 U.S.C. 112, the applicant), regards as the invention.
Claim 20 recites the “method of any one of claim 1” in line 1, however, claim 1 only recites one method of treating cancer. Therefore, it is unclear what other methods claim 20 could be referring to. Accordingly, claim 20 is indefinite for failing to particularly point out or distinctly claim what other methods claim 20 could be dependent on other than the method of claim 1.
Claim 38 recites the limitation "the chimeric Tim receptor" in line 1, however, claim 38 depends from claim 1 which does not recite a “chimeric Tim receptor.” Accordingly, there is insufficient antecedent basis for “the chimeric Tim receptor” in the claim 38.
For the purpose of applying prior art, the limitation is being read as “the chimeric engulfment receptor.”
Claim 76 recites the limitation “wherein the chimeric engulfment receptor comprises: (a) an extracellular domain comprising a binding domain comprising: (i) a Tim4 IgV domain and a Tim4 mucin domain; (b) an intracellular signaling domain, wherein the intracellular signaling domain comprises a primary intracellular signaling domain comprising a CD28 signaling domain; a secondary intracellular signaling domain comprising a CD3𝞯 signaling domain; and a tertiary intracellular signaling domain comprising a TLR2 signaling domain; and(c) a CD28 transmembrane domain positioned between and connecting the extracellular domain and the intracellular signaling domain” in lines 1-10.
It is unclear whether the chimeric engulfment receptor of claim 1, which already comprises an extracellular domain comprising a binding domain comprising: (i) a Tim4 IgV domain; and(ii) a Tim4 mucin domain; an intracellular signaling domain, wherein the intracellular signaling domain comprises a CD28 signaling domain, a CD3𝞯 signaling domain, and a TLR2 signaling domain; and a transmembrane domain positioned between and connecting the extracellular domain and the intracellular signaling domain, further comprises an additional extracellular domain, intracellular signaling domain, and transmembrane domain as recited in claim 76 or if those domains correspond to those already recited in claim 1 and are in fact being further defined in claim 76.
Amending the claim to recite: “wherein the CD28 signaling domain, the CD3𝞯 signaling domain, and the TLR2 signaling domain of the chimeric engulfment receptor are primary, secondary, and tertiary intracellular signaling domains, respectively; and the transmembrane domain is a CD28 transmembrane domain” in claim of the current wherein clause would obviate this part of the rejection.
For the purpose of applying prior art, claim 76 is being read with CD28 as the primary intracellular signaling domain, CD3𝞯 as the secondary signaling domain, and TLR2 as the tertiary signaling domain (see claim interpretation above).
Written Description
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, 3, 8, 20, 32, 36-38, 50, 76, and 86-88 are rejected under 35 U.S.C. 112(a) or 35 U.S.C. 112 (pre-AIA ), first paragraph, as failing to comply with the written description requirement. The claim contains subject matter which was not described in the specification in such a way as to reasonably convey to one skilled in the relevant art that the inventor or a joint inventor, or for applications subject to pre-AIA 35 U.S.C. 112, the inventor(s), at the time the application was filed, had possession of the claimed invention.
The instant claims are drawn to a method for treating ovarian cancer, the method comprising administering to the subject an effective amount of an engineered T cell comprising: a chimeric engulfment receptor comprising a single chain chimeric protein, the single chain chimeric protein comprising:(a) an extracellular domain comprising a binding domain comprising:(i) a Tim4 IgV domain; and (ii) a Tim4 mucin domain; (b) an intracellular signaling domain, wherein the intracellular signaling domain comprises a CD28 signaling domain, a CD3𝞯 signaling domain, and a TLR2 signaling domain and (c) a transmembrane domain positioned between and connecting the extracellular domain and the intracellular signaling domain.
To support such chimeric engulfment receptors (CERs), the Applicant discloses four species pCTX1162 (SEQ ID NO: 228), pCTX1163 (SEQ ID NO: 229), pCTX1173 (SEQ ID NO: 239), and pCTX1174 (SEQ ID NO: 240) (e.g. see Table 10, spanning pages 78-80). These species comprise a TIM4 extracellular domain (SEQ ID NO: 219) which comprises the human Tim4 binding domain (SEQ ID NO:2) (e.g. see page 12, lines 13-17). A Tim4 binding domain includes a variable immunoglobulin (IgV) like domain (referred to herein as an "IgV domain") and a Mucin like domain ("referred to herein as a "mucin domain") (e.g. see page 12, lines 18-20). An exemplary human Tim4 IgV domain comprises an amino acid sequence of SEQ ID NO:34, and an exemplary human Tim4 mucin domain comprises an amino acid sequence of SEQ ID NO:35 (e.g. see page 12, lines 20-22).
The Applicant further discloses that the Tim4 binding domain may comprise or consist of an amino acid sequence having at least about 75%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, 99.5%, or 100% identity to SEQ ID NO:2 or amino acids 25-314 of SEQ ID NO:2; or that it may comprise an amino acid sequence having at least about 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, or 20 amino acid modifications (e.g., deletions, additions, substitutions) to an amino acid sequence of SEQ1D NO:2 or amino acids 25-314 of SEQ ID NO:2 (e.g. see page 28, lines 6-22).
The specification also discloses that Tim4 CERs may include an extracellular spacer domain positioned between and connecting the binding domain and transmembrane domain (e.g. see page 27). Such a spacer domain may position the binding domain away from the host cell surface to further enable proper cell/cell contact, binding, and activation (e.g. see paragraph spanning pages 28 and 29). The length of the extracellular spacer may be varied to optimize target molecule binding based on the selected target molecule, selected binding epitope, binding domain size and affinity. The extracellular spacer domain may be an immunoglobulin hinge region (e.g., IgGi,IgG2, IgG3, IgG4, igA, IgD). An immunoglobulin hinge region may be a wild type immunoglobulin hinge region or an altered wild type immunoglobulin hinge region. The extracellular spacer domain may comprise a modified IgG hinge region having an amino acid sequence of ESK'YGPPCPPCP (SEQ IDNO:3). Other examples of hinge regions that may be used in the CERs include the hinge region from the extracellular regions of type1 membrane proteins, such as CD8a, CD4, CD28 and CD7, which may be wild-type or variants thereof. The extracellular spacer domain may also comprise a CD28 hinge region having an amino acid sequence of SEQID NO:32 or all or a portion of an immunoglobulin Fe domain selected from: a CH1 domain, a CH2 domain, a CH3 domain, or combinations thereof. The extracellular spacer domain may comprise a stalk region of a type II C-lectin (the extracellular domain located between the C-type lectin domain and the transmembrane domain). Type1I C-lectins include CD23, CD69, CI72, CD94, NKG2A, and NKG2D. (e.g. see paragraph spanning pages 28 and 29).
It is noted that pCTX1162 (SEQ ID NO: 228), pCTX1163 (SEQ ID NO: 229), pCTX1173 (SEQ ID NO: 239), and pCTX1174 (SEQ ID NO: 240) do not have an extracellular spacer domain.
When given the broadest reasonable interpretation in light of specification, the Tim4-based CERs of the instant invention are defined broadly to be any CER that comprises a single chain chimeric protein comprising:(a) an extracellular domain comprising a binding domain comprising:(i) any Tim4 IgV domain; and (ii) any Tim4 mucin domain; (b) an intracellular signaling domain comprising a CD28 signaling domain, a CD3𝞯 signaling domain, and a TLR2 signaling domain and (c) a transmembrane domain positioned between and connecting the extracellular domain and the intracellular signaling domain.
It is noted that the broadest claim (claim 1) does not indicate any specific structure for the Tim4 binding domain of the genus of CERs claimed.
Dependent claim 32 is drawn to a subgenus of CERs comprising a Tim4 IgV domain comprising the amino acid sequence set forth in SEQ ID NO:34 and/or the Tim4 mucin domain comprises the amino acid sequence set forth in SEQ ID NO:35. However, claim 32 still fails to recite sufficient structure of the entire Tim4 binding domain as is required for sufficient written description.
Dependent claim 38 is drawn to a subgenus of CERs which further comprise an extracellular spacer domain.
The guidelines for the Examination of Patent Applications Under the 35 U.S.C. 112, § 1 "Written Description" Requirement make clear that if a claimed genus does not show actual reduction to practice for a representative number of species, then the Requirement may be alternatively met by reduction to drawings, or by disclosure of relevant, identifying characteristics, i.e., structure or other physical and or chemical properties, by functional characteristics coupled with a known or disclosed correlation between function and structure, or by a combination of such identifying characteristics, sufficient to show the applicant was in possession of the genus (Federal Register, Vol. 66, No. 4, pages 1099-1111, January 5, 2001, see especially page 1106 column 3). In The Regents of the University of California v. Eli Lilly (43 USPQ2d 1398-1412) 19 F. 3d 1559, the court held that disclosure of a single member of a genus (rat insulin) did not provide adequate written support for the claimed genus (all mammalian insulins). In this same case, the court also noted:
“A definition by function, as we have previously indicated, does not suffice to define the genus because it is only an indication of what the gene does, rather than what it is. See Fiers, 984 F.2d at 1169-71, 25 USPQ2d at 1605-06 (discussing Amgen). It is only a definition of a useful result rather than a definition of what achieves that result. Many such genes may achieve that result. The description requirement of the patent statute requires a description of an invention, not an indication of a result that one might achieve if one made that invention. See In re Wilder, 736 F.2d 1516, 1521, 222 USPQ 369, 372-73 (Fed. Cir. 1984) (affirming rejection because the specification does “little more than outlin[e] goals appellants hope the claimed invention achieves and the problems the invention will hopefully ameliorate.”). Accordingly, naming a type of material generally known to exist, in the absence of knowledge as to what that material consists of, is not a description of that material.”
It is known that T cell immunoglobulin mucin (TIM) proteins regulate T cell activation and tolerance (e.g. see Kobayashi et al. 2007, Immunity 27, 927–940; abstract). TIM-4 is expressed on human and mouse macrophages and dendritic cells and specifically binds phosphatidylserine (PS) on the surface of apoptotic cells. TIM-4-transfected cells efficiently phagocytize apoptotic cells and mutations in the unique cavity of TIM-4 eliminates PS binding and phagocytosis (e.g. see abstract). All TIM family proteins are type I cell-surface glycoproteins and share common structural motifs including an immunoglobulin variable (IgV) domain with six cysteines, a mucin-like domain, a transmembrane domain, and a cytoplasmic domain (e.g. see page 927, paragraph spanning left and right columns). The IgV domain of TIM-4 displays a distinctive cleft formed by the CC′ and FG loops of the GFC β sheet (e.g. see page 927, right column, second paragraph). In TIM-4, the narrow cavity built by the CC′ and FG loops is a binding site for PS (e.g. see page 927, right column, second paragraph). Mutation of any of the amino acids (119–122, WFND) that line this binding cavity eliminates binding to PS and phagocytosis (e.g. see page 936, left column, fourth paragraph).
Thus, based upon the prior art, skilled artisans would reasonably understand that it is the structure of the narrow binding cavity of the IgV of Tim4 which gives rise to the functional property of engulfment. The PS ligand to which said Tim4 binds, is an inherent property which appears to necessarily be present due to conservation of critical structural elements, namely the narrow binding cavity of the IgV itself.
The art also teach that chimeric antigen receptors (CARs), which have a similar design to CERs in that they comprise an extracellular target binding domain, a transmembrane domain, and intracellular signaling components, usually comprise a spacer that provides separation of the extracellular binding domain from the cell membrane and an intracellular signaling module that mediates T-cell activation (e.g. see Hudecek et al. Cancer Immunol. Res. 2015, 3(2), 125-135; paragraph spanning pages 130 and 131). It is known that tailoring extracellular spacer length of CARs affects optimal tumor recognition for different target epitopes (e.g. see paragraph spanning pages 130 and 131). For optimal target recognition, the spacer should provide flexibility and the length and may need to vary depending on the target molecule (e.g. see page 125, right column, second paragraph).
Hudecek et al. describe the influence of length and composition of IgG-derived extracellular spacer domains on the function of CARs (e.g. see Abstract). Their studies demonstrate that CD19-CARs with a long spacer from IgG4 hinge-CH2-CH3 are functional in vitro but lack antitumor activity in vivo due to interaction between the Fc domain within the spacer and the Fc receptor–bearing myeloid cells, leading to activation-induced T-cell death. They also demonstrate that in vivo persistence and antitumor effects of CAR-T cells with a long spacer can be restored by modifying distinct regions in the CH2 domain that are essential for Fc receptor binding. Ultimately, their studies demonstrate that modifications that abrogate binding to Fc receptors are crucial for CARs in which a long spacer is obligatory for tumor recognition (e.g. see Abstract).
Thus, the prior art teaches that the length and composition of the extracellular spacer domain that lacks intrinsic signaling function can be decisive in the design of CARs for optimal in vivo activity. This logic is applicable to the instant invention because the CERs of the instant invention, similarly to CARs, comprise an extracellular binding domain and a transmembrane domain which may be separated by an extracellular spacer domain to optimize target binding and, in turn, intracellular signal transduction.
It must be noted that Bobbin et al. (“TIM-4-Chimeric Engulfment Receptor (CER) T Cells Elicit Phosphatidylserine-Dependent Cytotoxic and Innate-Like Function and Synergize with Approved PARP Inhibitors in an Ovarian Cancer Model.” Poster M195 presented at the American Society of Gene and Cell Therapy 25th Annual Meeting, May 16-20, 2021) teach CER T cells containing a wildtype TIM-4 extracellular domain and CD28, CD3ζ, and TLR2 intracellular signaling domains that synergize with subtherapeutic doses of PARPi to kill ovarian cancer cells in vitro (e.g. see conclusions). However, Bobbin et al. do not teach that their Tim4 CER T cells comprise an extracellular spacer domain.
Thus, there is no art that teaches using Tim4 CER T cells that comprise a mutant Tim4 binding domain and an extracellular spacer domain in combination with a PARPi for treating ovarian cancer.
As noted above, the specification discloses four species of CERs that comprise a Tim4 binding domain, which include an IgV domain and a mucin domain, that may comprise or consist of an amino acid sequence having at least about 75%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, 99.5%, or 100% identity to SEQ ID NO:2 or amino acids 25-314 of SEQ ID NO:2; or that it may comprise an amino acid sequence having at least about 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, or 20 amino acid modifications (e.g., deletions, additions, substitutions) to an amino acid sequence of SEQ1D NO: 2 or amino acids 25-314 of SEQ ID NO:2. However, the specification has not shown the specific amino acid residues in SEQ ID NO: 2 that can be mutated and would maintain the property of engulfment. These four CERs do not comprise an extracellular spacer domain.
Such a disclosure does not serve to provide sufficient written description of the claimed genus of CERs comprising a wildtype or variant Tim4 binding domain or subgenus further comprising an extracellular spacer domain. As it is currently claimed, the CER of the instant invention comprises the wildtype or any mutant sequence of the Tim4 binding domain that falls within the parameters set forth in the specification. This includes mutants that comprise modifications of the amino acids that line the binding cavity. However, it is known that mutations of any of the amino acids of this binding cavity eliminates binding to PS and phagocytosis (i.e. engulfment). Furthermore, the extracellular spacer domains as claimed comprise a genus that includes long spacers derived from IgG4 hinge-CH2-CH3 which can interact with Fc receptor–bearing myeloid cells, leading to activation-induced CER T-cell death.
Thus, it does not appear, based upon the limited disclosure of the four Tim4-based CERs alone, which do not comprise extracellular spacer domains, that the applicant was in possession of the necessary common attributes or features of the elements possessed by the members of the entire genus of Tim4-based CERs or subgenus further comprising an extracellular spacer domain in view of the extensive variation permitted within the Tim4 binding domain and extracellular spacer domain of the CERs as set forth in the specification.
Therefore, in view of the breadth of the claims and the limited disclosure, artisans would reasonably conclude that applicant was not in possession of the full breadth of Tim4-based CERs encompassed by the claims at the time the instant application was filed.
Enablement
Claims 1, 3, 8, 20, 32, 36-38, 50, 76, and 86-88 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 method of treating ovarian cancer by administering a PARP inhibitor and a chimeric engulfment receptor (CER) T cell that comprises a wildtype Tim4 binding domain and does not comprise extracellular spacer domain, does not reasonably provide enablement for a method of treating ovarian cancer by administering a PARP inhibitor and a CER T cell that comprises any Tim4 binding domain and an extracellular spacer 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 use the invention commensurate in scope with these claims.
The factors considered in determining whether a disclosure would require undue experimentation include:
(A) The breadth of the claims;
(B) The nature of the invention;
(C) The state of the prior art;
(D) The level of one of ordinary skill;
(E) The level of predictability in the art;
(F) The amount of direction provided by the inventor;
(G) The existence of working examples; and
(H) The quantity of experimentation needed to make or use the invention based on the content of the disclosure.
In re Wands, 8 USPQ2d, 1400 (CAFC 1988) and MPEP § 2164.01.
Nature of the invention/Breadth of the claims
Independent claim 1 is drawn to a method of treating ovarian cancer by administering a PARP inhibitor and a genus of engineered T cells comprising: a chimeric engulfment receptor (CER) comprising:(a) an extracellular domain comprising a binding domain comprising:(i) any Tim4 IgV domain; and (ii) any Tim4 mucin domain; (b) an intracellular signaling domain comprising a CD28 signaling domain, a CD3𝞯 signaling domain, and a TLR2 signaling domain and (c) a transmembrane domain positioned between and connecting the extracellular domain and the intracellular signaling domain.
Dependent claim 32 is drawn to a subgenus of engineered T cells comprising CERs comprising a Tim4 IgV domain comprising the amino acid sequence set forth in SEQ ID NO:34 and/or the Tim4 mucin domain comprises the amino acid sequence set forth in SEQ ID NO:35.
Dependent claim 38 is drawn to a subgenus of CERs which further comprise an extracellular spacer domain.
It is also noted that none of the claims recite any antigen specificity of the claimed Tim4-based CERs.
State of the prior art/Predictability of the art
Artisans are well aware that T cell immunoglobulin mucin (TIM) proteins regulate T cell activation and tolerance (e.g. see Kobayashi et al. 2007, Immunity 27, 927–940; abstract). TIM-4 is expressed on human and mouse macrophages and dendritic cells and specifically binds phosphatidylserine (PS) on the surface of apoptotic cells. TIM-4-transfected cells efficiently phagocytosed apoptotic cells and mutations in the unique cavity of TIM-4 eliminated PS binding and phagocytosis (e.g. see abstract). All TIM family proteins are type I cell-surface glycoproteins and share common structural motifs including an immunoglobulin variable (IgV) domain with six cysteines, a mucin-like domain, a transmembrane domain, and a cytoplasmic domain (e.g. see page 927, paragraph spanning left and right columns). The IgV domain of TIM-4 displays a distinctive cleft formed by the CC′ and FG loops of the GFC β sheet (e.g. see page 927, right column, second paragraph). In TIM-4, the narrow cavity built by the CC′ and FG loops is a binding site for PS (e.g. see page 927, right column, second paragraph). Mutation of any of the amino acids (119–122, WFND) that line this binding cavity eliminates binding to PS and phagocytosis (e.g. see page 936, left column, fourth paragraph).
Thus, based upon the prior art, skilled artisans would reasonably understand that it is the structure of the narrow binding cavity within the Tim4 IgV domain which gives rise to the functional property of engulfment.
It is also noted that chimeric antigen receptors (CARs), which have a similar design to CERs in that they comprise an extracellular target binding domain, a transmembrane domain, and intracellular signaling components, usually comprise a spacer that provides separation of the extracellular binding domain from the cell membrane and an intracellular signaling module that mediates T-cell activation (e.g. see Hudecek et al. Cancer Immunol. Res. 2015, 3(2), 125-135; paragraph spanning pages 130 and 131). It is known that tailoring extracellular spacer length of CARs affects optimal tumor recognition for different target epitopes (e.g. see paragraph spanning pages 130 and 131). For optimal target recognition, the spacer should provide flexibility and the length and may need to vary depending on the target molecule (e.g. see page 125, right column, second paragraph).
Hudecek et al. describe the influence of length and composition of IgG-derived extracellular spacer domains on the function of CARs (e.g. see Abstract). Their studies demonstrate that CD19-CARs with a long spacer from IgG4 hinge-CH2-CH3 are functional in vitro but lack antitumor activity in vivo due to interaction between the Fc domain within the spacer and the Fc receptor–bearing myeloid cells, leading to activation-induced T-cell death. They also demonstrate that in vivo persistence and antitumor effects of CAR-T cells with a long spacer can be restored by modifying distinct regions in the CH2 domain that are essential for Fc receptor binding. Ultimately, their studies demonstrate that modifications that abrogate binding to Fc receptors are crucial for CARs in which a long spacer is obligatory for tumor recognition (e.g. see Abstract).
Thus, the prior art teaches that the length and composition of the extracellular spacer domain that lacks intrinsic signaling function can be decisive in the design of CARs for optimal in vivo activity. This logic is applicable to the instant invention because the CERs of the instant invention, similarly to CARs, comprise an extracellular binding domain and a transmembrane domain which may be separated by an extracellular spacer domain to optimize target binding and, in turn, intracellular signal transduction.
It must be noted that Bobbin et al. (“TIM-4-Chimeric Engulfment Receptor (CER) T Cells Elicit Phosphatidylserine-Dependent Cytotoxic and Innate-Like Function and Synergize with Approved PARP Inhibitors in an Ovarian Cancer Model.” Poster M195 presented at the American Society of Gene and Cell Therapy 25th Annual Meeting, May 16-20, 2021) teach CER T cells containing a wildtype TIM-4 extracellular domain and CD28, CD3ζ, and TLR2 intracellular signaling domains that synergize with subtherapeutic doses of PARPi to kill ovarian cancer cells in vitro (e.g. see conclusions). However, Bobbin et al. do not teach that their Tim4 CER T cells comprise an extracellular spacer domain.
Thus, there is no art that teaches using Tim4 CER T cells that comprise a mutant Tim4 binding domain and an extracellular spacer domain in combination with a PARPi for treating ovarian cancer.
It also must be noted that Tim4 specifically binds PS on the surface of apoptotic cells (e.g. see above). Thus, it is unpredictable to use a CER that comprises a Tim4 binding domain with no particular ligand specificity.
Working examples/ Guidance in the specification
The Applicant has not disclosed any working examples that apply a Tim4-based CER that comprises a CD28 signaling domain, a CD3𝞯 signaling domain, and a TLR2 signaling domain.
Example 3 demonstrates the synergistic killing of Kuramochi cells, a human ovarian cancer cell line, with niraparib and a Tim4-based CER that does not comprise a TLR2 signaling domain (construct 13A, SEQ ID NO: 162) (e.g. see page 131, lines 11-22). Example 3 also shows the killing of Kuramochi cells by other Tim4-based CERs that do not comprise a TLR2 signaling domain (CTX140, SEQ ID NO: 195; and CTX137, SEQ ID NO: 197) (e.g. see page 131, line 23 – page 132, line 13). Indeed, example 3 does recite the application of a TLR2-comprising Tim4-based CER (CTX133) for treating a BRCA-2-mutated Kuramochi cell line, but CTX133 does not comprise a CD28 signaling domain (e.g. see page 132, lines 14-21).
Example 4 demonstrates the in vitro anti-tumor activity of two Tim4-based CER that do not comprise a TLR2 signaling domain (pCTX247, SEQ ID NO: 257; and pCTX797, SEQ ID NO: 258) in two ovarian cancer cell lines (Kuramochi and A2780) (e.g. see page 134, lines 1-7).
The Applicant has disclosed four species of Tim4-based CERs that comprise a CD28 signaling domain, a CD3𝞯 signaling domain, and a TLR2 signaling domain: pCTX1162 (SEQ ID NO: 228), pCTX1163 (SEQ ID NO: 229), pCTX1173 (SEQ ID NO: 239), and pCTX1174 (SEQ ID NO: 240) (e.g. see Table 10, spanning pages 78-80). These species comprise a TIM4 extracellular domain (SEQ ID NO: 219) which comprises the human Tim4 binding domain (SEQ ID NO:2) (e.g. see page 12, lines 13-17). A Tim4 binding domain includes a variable immunoglobulin (IgV) like domain (referred to herein as an "IgV domain") and a Mucin like domain ("referred to herein as a "mucin domain") (e.g. see page 12, lines 18-20). An exemplary human Tim4 IgV domain comprises an amino acid sequence of SEQ ID NO:34, and an exemplary human Tim4 mucin domain comprises an amino acid sequence of SEQ ID NO:35 (e.g. see page 12, lines 20-22).
The Applicant further discloses that the Tim4 binding domain may comprise or consist of an amino acid sequence having at least about 75%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, 99.5%, or 100% identity to SEQ ID NO:2 or amino acids 25-314 of SEQ ID NO:2; or that it may comprise an amino acid sequence having at least about 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, or 20 amino acid modifications (e.g., deletions, additions, substitutions) to an amino acid sequence of SEQ1D NO:2 or amino acids 25-314 of SEQ ID NO:2 (e.g. see page 28, lines 6-22).
The specification also discloses that Tim4 CERs may include an extracellular spacer domain positioned between and connecting the binding domain and transmembrane domain (e.g. see page 27). Such a spacer domain may position the binding domain away from the host cell surface to further enable proper cell/cell contact, binding, and activation (e.g. see paragraph spanning pages 28 and 29). The length of the extracellular spacer may be varied to optimize target molecule binding based on the selected target molecule, selected binding epitope, binding domain size and affinity. The extracellular spacer domain may be an immunoglobulin hinge region (e.g., IgGi,IgG2, IgG3, IgG4, igA, IgD). An immunoglobulin hinge region may be a wild type immunoglobulin hinge region or an altered wild type immunoglobulin hinge region. The extracellular spacer domain may comprise a modified IgG hinge region having an amino acid sequence of ESK'YGPPCPPCP (SEQ IDNO:3). Other examples of hinge regions that may be used in the CERs include the hinge region from the extracellular regions of type1 membrane proteins, such as CD8a, CD4, CD28 and CD7, which may be wild-type or variants thereof. The extracellular spacer domain may also comprise a CD28 hinge region having an amino acid sequence of SEQID NO:32 or all or a portion of an immunoglobulin Fe domain selected from: a CH1 domain, a CH2 domain, a CH3 domain, or combinations thereof. The extracellular spacer domain may comprise a stalk region of a type II C-lectin (the extracellular domain located between the C-type lectin domain and the transmembrane domain). Type1I C-lectins include CD23, CD69, CI72, CD94, NKG2A, and NKG2D. (e.g. see paragraph spanning pages 28 and 29).
It is noted that pCTX1162 (SEQ ID NO: 228), pCTX1163 (SEQ ID NO: 229), pCTX1173 (SEQ ID NO: 239), and pCTX1174 (SEQ ID NO: 240) do not have an extracellular spacer domain.
Amount of experimentation necessary
The instant specification discloses four species of CERs that comprise a Tim4 binding domain, a CD28 signaling domain, a CD3𝞯 signaling domain, and a TLR2 signaling domain, yet, the claims are not limited to the use of these particular Tim4-based CERs. The claimed genus encompasses CERs comprising a Tim4 binding domain may comprise or consist of an amino acid sequence having at least about 75%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, 99.5%, or 100% identity to SEQ ID NO:2 or amino acids 25-314 of SEQ ID NO:2; or that it may comprise an amino acid sequence having at least about 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, or 20 amino acid modifications (e.g., deletions, additions, substitutions) to an amino acid sequence of SEQ1D NO:2 or amino acids 25-314 of SEQ ID NO:2. These four CERs do not comprise an extracellular spacer domain.
There is insufficient objective evidence that the specific species disclosed in the specification can be extrapolated to provide guidance and direction for how to use CERs with any mutant Tim4 binding domain or an extracellular binding domain. The specification does not show the specific amino acid residues in SEQ ID NO: 2 that can be mutated and would maintain the property of engulfment, especially in the absence of ligand specificity. The specification also does not show and CER T cells that comprise an extracellular spacer domain and are used for treating ovarian cancer.
Regarding, the absence of the recitation of ligand specificity in the claims, the specification provides insufficient direction or guidance regarding how to use a CER comprising any Tim4 binding domain, in the absence of ligand specificity for PS that would retain substantially the same property of engulfment of the Tim4-based CERs of the instant disclosure (see Detailed Description, etc.)
Tim4 specifically binds PS on the surface of apoptotic cells and TIM-4-transfected cells efficiently phagocytosed apoptotic cells in a PS-dependent manner. The IgV domain of TIM-4 displays a distinctive cleft formed by the CC′ and FG loops of the GFC β sheet which is the binding site for PS. Mutation of any of the amino acids that line this binding cavity eliminates binding to PS and phagocytosis.
It is noted that knowledge of ligand specificity is critical for the skilled artisan to employ Tim4-based CERs in various modalities (e.g. detection or diagnostic assays, bioassays, treatment), including those consistent with the instant disclosure (see specification, including the Detailed Description).
Thus, based on the content of the disclosure in view of the prior art, a skilled artisan, through extensive trial-and-error experimentation, would have to make CERs that comprise any Tim4 binding domain, an extracellular spacer domain, a CD28 signaling domain, a CD3𝞯 signaling domain, and a TLR2 signaling domain, validate their function by demonstrating engulfment (i.e. phagocytosis), and use them in a method of treating ovarian cancer with a reasonable expectation of success.
It is well-known that that Tim4-directed phagocytosis is based on Tim4 specifically binding to PS on apoptotic cells. Therefore, given that no ligand specificity is recited in the claims, the validation step noted above requires undue further experimentation in order to determine which cells express PS and are therefore the target for engulfment. Furthermore, since neither the specification or the art teach a Tim4 CER T cells that comprises an extracellular spacer domain, the treatment step, also noted above, requires undue further experimentation in order to determine what type and length of spacer that would be able to be used to treat. This quantity of experimentation goes beyond what is considered “a reasonable degree of experimentation” and constitutes undue further experimentation in order to enable the use of Tim4-based CERs for the breadth of what is claimed.
Given that the structure of narrow binding cavity of Tim4 is essential to its function and the unpredictability in the art with respect to using CERs that comprise mutant Tim4 binding domains for directing PS-dependent phagocytosis, that tailoring extracellular spacer length of CARs affects optimal tumor recognition for different target epitopes, and long spacers derived from IgG4 hinge-CH2-CH3 which can interact with Fc receptor–bearing myeloid cells, leading to activation-induced CER T-cell death; a person having ordinary skill in the art would have to perform undue experimentation in order to use the entire genera or subgenus comprising an extracellular spacer domain of Tim4-based CERs encompassed by the claims commensurate in scope with the breadth of the claims.
Thus, the specification does not enable one of ordinary skill in the art to use the entire genus or subgenus comprising an extracellular spacer domain of engineered T cells comprising a Tim4-based CER in a method of treating ovarian cancer as it is currently claimed and therefore claims 1, 3, 8, 20, 32, 36-38, 50, 76, and 86-88 are rejected under 35 U.S.C. 112(a).
Claim Rejections - 35 USC § 102
In the event the determination of the status of the application as subject to AIA 35 U.S.C. 102 and 103 (or as subject to pre-AIA 35 U.S.C. 102 and 103) is incorrect, any correction of the statutory basis (i.e., changing from AIA to pre-AIA ) for the rejection will not be considered a new ground of rejection if the prior art relied upon, and the rationale supporting the rejection, would be the same under either status.
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.
Claims 1, 3, 8, 32, 36, 37, 50, 76, and 86-88 are rejected under 35 U.S.C. 102(a)(1) as being anticipated by Bobbin et al. 2021 (“TIM-4-Chimeric Engulfment Receptor (CER) T Cells Elicit Phosphatidylserine-Dependent Cytotoxic and Innate-Like Function and Synergize with Approved PARP Inhibitors in an Ovarian Cancer Model.” Poster M195 presented at the American Society of Gene and Cell Therapy 25th Annual Meeting, May 16-20, 2021).
Given that the instant claims are recorded the priority date of the filing date of the provisional application 63/226,712 on July 28, 2021 for the reasons stated above, Bobbin et al. made public in May 2021 is deemed to be a prior art under 35 USC 102(a)(1).
Bobbin et al. teach chimeric engulfment receptor (CER) T cells containing a TIM-4 extracellular domain and CD28, CD3ζ, and TLR2 intracellular signaling domains are activated to produce cytokines and kill solid tumor cells in response to engagement with their target, phosphatidylserine (PS), in vitro (e.g. see conclusions). Cell-surface PS expression is induced by PARPi in viable A2780 cells, an advanced ovarian cancer cell line. CER T cells synergize with subtherapeutic doses of PARPi, including niraparib (e.g. see fourth column under “results continued” and “CER T Cells Demonstrate Synergistic Cytotoxic Activity With Niraparib and Olaparib Against A2780 Cells”), to kill ovarian cancer cells in vitro (e.g. see conclusions).
The CERs were designed as single-chain chimeric proteins composed of different combinations
of the following domains: (a) the TIM-4 extracellular domain that binds PS; (b) the transmembrane domain of TIM-4 or CD28; (c) the intracellular CD28 and CD3ζ signaling domain that serve as T-cell activators; and (d) the intracellular TLR-2 signaling domain to enhance APC-like function (e.g. see second column, under “Results”). CD8+ T cells were transduced with the CER (e.g. see second column, under “Results”). CER T cells, in T-cell optimizer media containing IL-2, IL-7, and IL-15, were co-cultured (or administered) to A2780 cells in the presence of niraparib (e.g. see first column, under “Methods”).
Bobbin et al. also contemplate the application of their Tim4 CER T cells in vivo thereby anticipating the instant limitation of “administering” the engineered T cell (e.g. see conclusions).
It is noted that the amino acid sequences recited in claims 32, 37, and 50 for the Tim4 IgV (SEQ ID NO: 35), Tim4 mucin (SEQ ID NO: 35), CD28 transmembrane domain (SEQ ID NO: 7), and CD28 (SEQ ID NO: 4), CD3𝞯 (SEQ ID NO: 5), and TLR2 (SEQ ID NO: 222) signaling domains are the wildtype amino acid sequences. Therefore, while Bobbin et al. do not explicitly recite the amino acid sequences of these domains, a skilled artisan would reasonably assume that the Bobbin et al.’s Tim4 extracellular domain, which comprises an IgV and a mucin domain, CD28 transmembrane domain, and CD28, CD3𝞯, and TLR2 intracellular signaling domains are the wildtype proteins and would necessarily have the same amino acids sequences as recited in instant claim 32, 37, and 50, especially without evidence to the contrary.
It is further noted that Bobbin et al. teach the arrangement of the intracellular signaling domains for CER-1236, from N- to C-terminus, as CD28, CD3𝞯, and TLR2 (e.g. see Figure 2, copied below) which is identical to that described for the primary, secondary, and tertiary signaling domains of claim 76
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579
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(see claim interpretation above).
Figure 2 of Bobbin et al. 2021
Therefore, the reference teachings anticipate the instant invention.
Claim Rejections - 35 USC § 103
The following is a quotation of 35 U.S.C. 103 which forms the basis for all obviousness rejections set forth in this Office action:
A patent for a claimed invention may not be obtained, notwithstanding that the claimed invention is not identically disclosed as set forth in section 102, if the differences between the claimed invention and the prior art are such that the claimed invention as a whole would have been obvious before the effective filing date of the claimed invention to a person having ordinary skill in the art to which the claimed invention pertains. Patentability shall not be negated by the manner in which the invention was made.
The factual inquiries for establishing a background for determining obviousness under 35 U.S.C. 103 are summarized as follows:
1. Determining the scope and contents of the prior art.
2. Ascertaining the differences between the prior art and the claims at issue.
3. Resolving the level of ordinary skill in the pertinent art.
4. Considering objective evidence present in the application indicating obviousness or nonobviousness.
This application currently names joint inventors. In considering patentability of the claims the examiner presumes that the subject matter of the various claims was commonly owned as of the effective filing date of the claimed invention(s) absent any evidence to the contrary. Applicant is advised of the obligation under 37 CFR 1.56 to point out the inventor and effective filing dates of each claim that was not commonly owned as of the effective filing date of the later invention in order for the examiner to consider the applicability of 35 U.S.C. 102(b)(2)(C) for any potential 35 U.S.C. 102(a)(2) prior art against the later invention.
Claim 20 is rejected under 35 U.S.C. 103 as being unpatentable over Bobbin et al. 2021 (“TIM-4-Chimeric Engulfment Receptor (CER) T Cells Elicit Phosphatidylserine-Dependent Cytotoxic and Innate-Like Function and Synergize with Approved PARP Inhibitors in an Ovarian Cancer Model.” Poster M195 presented at the American Society of Gene and Cell Therapy 25th Annual Meeting, May 16-20, 2021) in view of Drew et al. 2019 (Ann. Oncol. 30(5), v485-v486).
The teachings of Bobbin et al. are outlined in the 102 rejection above.
Bobbin et al. do not teach that the combination of Tim4 CER T cells and a PARPi for treating ovarian cancer further comprises an immune checkpoint molecule inhibitor.
Drew et al. teach the combination of olaparib, a PARPi, and the anti-programmed cell death ligand1 antibody, durvalumab, an immune checkpoint molecule inhibitor, for treating ovarian cancer in a phase II study (e.g. see background). The combination of olaparib and durvalumab was well tolerated and showed promising median progression-free survival (PFS) (11.1 months) and duration of response (DoR) (10.2 months) (e.g. see results and conclusions). Median PFS and DoR for patients with fewer prior lines of chemotherapy was not yet reached, suggesting that these patients may derive a greater benefit from the combination. The complete response (CR) rate of seven was higher than anticipated (e.g. see results and conclusions).
It would have been prima facie obvious to one of ordinary skill in the art before the effective filing date of the claimed invention to have modified Bobbin et al. to incorporate the teachings of Drew et al. to include that the combination of Tim4 CER T cells and a PARPi for treating ovarian cancer further comprises an immune checkpoint molecule inhibitor. Given that CER T cells synergize with subtherapeutic doses of PARPi to kill ovarian cancer cells in vitro; and the success of combining the immune checkpoint molecule inhibitor, durvalumab, with the PARPi, olaparib, in the treatment of ovarian cancer; a skilled artisan, with the goal of improving the treatment of ovarian cancer with a combination of Tim4 CER T cells and a PARPi, would further include a immune checkpoint molecule inhibitor, such as durvalumab, in the treatment regimen with a reasonable expectation of success.
Claim 38 is rejected un