DETAILED ACTION
Notice of Pre-AIA or AIA Status
The present application, filed on or after March 16, 2013, is being examined under the first inventor to file provisions of the AIA .
Priority
Applicant’s claim for the benefit of a prior-filed application under 35 U.S.C. 119(e) or under 35 U.S.C. 120, 121, 365(c), or 386(c) is acknowledged. This application is a 371 of PCT/US2021/042091 filed July 16, 2021, which claims the benefit of US Provisional Application No. 63/053,529 filed July 17, 2020. All claims have been given an effective filing date of July 17, 2020.
Claim Status
Claim listing filed on August 28, 2023 is pending. Claims 4-14, 18-20, 23, 31, 33-36, 40-52, 54-57, 59-70, 74, 76-83, 85-86, 88-89, 91, and 94-114 are canceled. Claims 3, 17, 21-22, 24-30, 32, 37, 39, 53, 58, 71, 75, 84, 87, 90, and 92 are amended. Claims 1-3, 15-17, 21-22, 24-30, 32, 37-39, 53, 58, 71-73, 75, 84, 87, 90, and 92-93 are examined upon their merits.
Information Disclosure Statement
The information disclosure statement filed on 08/28/2023 is in compliance with the provisions of 37 CFR 1.97. Accordingly, the information disclosure statement is being considered by the examiner.
Claim Rejections - 35 USC § 112
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.
Claims 1-3, 15-17, 21-22, 24-30, 32, 37-39, 53, 58, 71-73, 75, 84, 87, 90, and 92-93 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.
Claims 1 and 3 recite “a portion thereof that binds to TGFβ.” Claims 2, 21-22, 24-29, 37-39, 53, 58, 71-73, 75, 84, 87, 90, and 92-93 are dependent on Claim 1 and do not further define the claimed extracellular domain portion. This phrase is considered functional language because the feature (the portion) is defined by what it does (binds TGFβ) rather than by what it is (MPEP § 2173.05(g)). To determine if functional language is ambiguous, the following factors are considered: (1) whether there is a clear cut indication of the scope of the subject matter covered by the claim; (2) whether the language sets forth well-defined boundaries of the invention or only states a problem solved or a result obtained; and (3) whether one of ordinary skill in the art would know from the claim terms what structure or steps are encompassed by the claim. These factors are examples of points to be considered when determining whether language is ambiguous and are not intended to be all inclusive or limiting (MPEP § 2173.05(g)). Experimentation would be required to determine what portions of the TGFβR extracellular domain are capable of binding TGFβ, because it is unclear what amino acids are structurally required to accomplish the claimed function. Therefore, one of ordinary skill would not know from the claim terms what structures are encompassed by the claims. The metes and bounds of the portions that bind TGFβ cannot be readily determined, and Claims 1-3, 21-22, 24-29, 37-39, 53, 58, 71-73, 75, 84, 87, 90, and 92-93 are rejected as being indefinite.
Claims 1 and 15 recite “lacks the full-length TIR domain of full-length MyD88.” However, the specification defines the TIR domain as “e.g. amino acids 159-296” of SEQ ID NO: 128 (paragraph [0063]). The specification further teaches that the description of domains are theoretically derived based on homology analysis and alignments with similar molecules, and a specific domain, such as a specific TIR domain of MyD88 can be several amino acids (such as one, two, three, or four) longer or shorter (paragraph [0063]). Therefore, the structural definition of the TIR domain is indefinite, and one of ordinary would not clearly understand the boundaries of what is encompassed by the claim. It is unclear what MyD88 polypeptides lack the full-length TIR domain when the TIR domain is not clearly defined. For example, would a TIR domain comprising amino acids 159-195 of SEQ ID NO: 128 be considered as lacking the full-length TIR domain or be considered as a full-length TIR domain with one amino acid short? Claims 2-3, 16-17, 21, 26-29, 37-39, 53, 58, 71-73, 75, 84, 87, 90, and 92-93 are dependent on Claims 1 and 15 and do not further define the full-length TIR domain.
Similarly, Claim 21 recites wherein each MyD88 polypeptide comprises the death domain (DD) and the intermediate domain (ID) which the specification defines as “e.g. amino acids 19-109” of SEQ ID NO: 128 and “e.g. amino acids 110-155” of SEQ ID NO: 128, respectively (paragraph [0063]). The structural definitions of “the death domain” and “the intermediate domain” are indefinite for the same reasons outlined in the paragraph above pertaining to the full-length TIR domain. One of ordinary skill would not understand what amino acid structures are encompassed by “the death domain” and “the intermediate domain.”
Claims 3, 17, 30, and 32 recite sequence identity percentages with the term “about.” The specification defines that the term “about” refers to “the usual error range for the respective value readily known to the skilled person in this technical field” (paragraph [00325]). This definition is indefinite because the metes and bounds surrounding “about” as it pertains to sequence identity are unclear (MPEP § 2173.05(b)III.A). For example, would “about 85%” sequence identity as recited in Claim 17 encompass 60%, 70%, or 80% sequence identity? Claims 3, 17, 30, and 32 are rejected for the indefinite term “about.”
Claims 3 and 17 recite “a sequence of amino acids that exhibits at least or about 85%, at least or about 90%, at least or about 92%, at least or about 95%, at least or about 97% sequence identity.” There is no alternative conjunction in the list of options. For the purpose of compact prosecution, Claims 3 and 17 are interpreted as “a sequence of amino acids that exhibits at least or about 85%, at least or about 90%, at least or about 92%, at least or about 95%, or at least or about 97% sequence identity.”
Claim 15 recites a portion of TGFβR comprising the extracellular domain and the transmembrane domain, wherein the portion is less than the full-length TGFβR and lacks a functional inhibitory signaling domain of the full-length TGFβR. This phrase is considered functional language because the feature (the portion of TGFβR) is defined by what it does (lacks functional inhibitory signaling) rather than by what it is (MPEP § 2173.05(g)). The extracellular domains of TGFβR1 and TGFβR2 are defined in the specification (SEQ ID NOs: 4 and 20 respectively; sequence listing pages 120-147), and the transmembrane domains of TGFβR1 and TGFβR2 are defined in the specification (SEQ ID NOs: 6 and 22 respectively; sequence listing pages 120-147). However, it is unclear what structures are encompassed by “lacks a functional inhibitory signaling domain of the full-length TGFβR.” The specification defines that “the partial sequence of the intracellular signaling domain of the native cytokine receptor is not a functional inhibitory signaling domain capable of mediating inhibitory signaling, such that it is not capable of being phosphorylated (activated) and/or of recruiting an inhibitory adaptor molecule such as a SMAD (e.g. SMAD2 or SMAD3) in response to ligand binding to the chimeric signaling receptor. In some embodiments, the partial sequence includes between 2 and 50, such as between 2 and 25, of the N-terminal amino acids of the cytoplasmic domain of the cytokine receptor” (paragraph [00127]). This definition defines the non-functional portion of the inhibitory signaling domain by what it does not do and lists non-limiting examples of possible amino acid truncations that could accomplish this lack-of-function. From the claim language and the specification, one of ordinary skill would not understand the structural metes and bounds of what is encompassed by the non-functional portion of the TGFβR inhibitory signaling domain in Claim 15. Claims 15-16 are rejected for indefiniteness.
Claim 22 recites various amino acid ranges of the full-length MyD88 set forth in SEQ ID NO: 128. It is important to note that an amino acid sequence “set forth in” SEQ ID NO: X encompasses any fragment of two or more amino acid residues within the recited sequence. Therefore, a sequence “set forth in SEQ ID NO: 128” could comprise residues 250-290 of SEQ ID NO: 128. In this example, claiming amino acid residues 2-155 of a fragment comprising residues 250-290 is indefinite. To overcome the indefiniteness rejection, Claim 22 could recite “of the full-length MyD88 comprising SEQ ID NO: 128.”
Claim 92 recites the limitation "the engineered cells" in line 1. There is insufficient antecedent basis for this limitation in the claim, because Claim 71 defines a singular engineered cell. To overcome the insufficient antecedent basis, Claim 92 could recite “wherein the engineered cell expresses.”
Note, Claim 1 recites “a first truncated MyD88 polypeptide” and “a second truncated MyD88 domain.” Claims 21-22 and 25-27 recite “the second MyD88 polypeptide.” It is interpreted that “polypeptide” and “domain” are synonyms that can be used interchangeably. Therefore, no rejection is made for insufficient antecedent basis. Note, Claim 28 recites “wherein n is an integer between 1 to 4, inclusive” which is interpreted to mean that n = 1, 2, 3, or 4. Note, Claim 92 recites wherein the engineered cell further comprises “an antigen-binding domain that binds to a tumor antigen associated with the cancer” but this functional language is not considered indefinite because antigen-binding domains that bind to tumor antigens (such as those exemplified in specification paragraph [00223]) are well understood in the art and were publicly available prior to the effective filing date. The method recited in Claim 92 is routinely practiced in the art to target therapies to the appropriate cancer cells.
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.
Claims 1-3, 15-17, 21-22, 24-30, 32, 37-39, 53, 58, 71-73, 75, 84, 87, 90, and 92-93 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(s) 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.
Claim 1 is directed to a chimeric signaling receptor comprising a genus of possible TGFβR extracellular domains (any portion that binds TGFβ) and a genus of possible truncated MyD88 polypeptides (lack the full-length TIR domain). Similarly, Claim 15 is directed to a chimeric signaling receptor comprising a genus of possible TGFβR extracellular domains (any portion that lacks a functional inhibitory signaling domain) and a genus of possible truncated MyD88 polypeptides (lack the full-length TIR domain). The extracellular domain can comprise the amino acid sequence set forth in SEQ ID NO: 20, a sequence at least or about 85% identical to the sequence set forth in SEQ ID NO: 20, or a functional portion thereof (Claim 3). The portion of TGFβR can comprise the amino acid sequence set forth in SEQ ID NO: 3 or a sequence at least or about 85% identical to the sequence set forth in SEQ ID NO: 3 (Claim 17). The MyD88 polypeptides can comprise various amino acid ranges of the sequence set forth in SEQ ID NO: 128 (Claim 22). The first and second MyD88 polypeptides can be set forth in SEQ ID NO: 2 (Claims 24-25). The chimeric signaling receptor can be set forth in SEQ ID NOs: 93 or 94 or exhibit at least or about 85% sequence identity to the sequences set forth in SEQ ID NOs: 93 or 94 (Claims 30 and 32).
Note, “an amino acid sequence set forth in” encompasses any fragment of two or more amino acid residues within the recited sequence. Therefore, the claim language of “set forth in SEQ ID NO: 93” and “at least at or about 85% sequence identity to the sequence set forth in SEQ ID NO: 93” encompasses a genus of thousands of possible chimeric signaling receptors. Alternative claim language to encompass the recited sequence in its entirety could recite “wherein the chimeric signaling receptor comprises SEQ ID NO: 93” (MPEP § 2111.03.I). Importantly, even if Claim 30 recited “at least 85% sequence identity to the sequence comprising SEQ ID NO: 93,” any combination of 77 amino acids could be inserted, deleted, or substituted with conservative or non-conservative changes (15% of 516 amino acids) which results in a genus of chimeric signaling receptors with substantial structural variation.
In making a determination of whether the application complies with the written description requirement of 35 U.S.C. 112, first paragraph, it is necessary to understand what Applicant has possession of and what Applicant is claiming. In order to provide adequate written description and evidence of possession of a claimed genus, the specification must provide sufficient distinguishing identifying characteristics of the genus. The factors to be considered include disclosure of complete or partial structure, physical and/or chemical properties, functional characteristics, structure/function correlation, methods of making the claimed product, or any combination thereof.
From the specification, two chimeric signaling receptors were made that meet the criteria of Claims 1 and 15 (comprising two truncated MyD88 polypeptides): CTSR-2B (SEQ ID NO: 93) and CTSR-2C (SEQ ID NO: 94) (Table E1). Both CTSR-2B and CTSR-2C comprise the same TGFβR2 extracellular domain (SEQ ID NO: 20), the same TGFβR2 transmembrane domain (SEQ ID NO: 22), and the same truncated MyD88 polypeptides (SEQ ID NO: 2) (Table E1). CTSR-2B and CTSR-2C only differ in that CTSR-2C comprises a peptide linker between the two truncated MyD88 polypeptides and CTSR-2B does not (Table E1). Both CTSR-2B and CTSR-2C constructs were generated (Example 1). CTSR-2C was further expressed in primary human T cells (Example 1) and evaluated in in vitro and in vivo functional assays in neuroblastoma, pancreatic cancer, ovarian cancer, and lymphoma models (Examples 2-11). However, two representative species that differ only by the presence of a peptide linker are not sufficient to describe the genus of possible chimeric signaling receptors comprising substantial structural variation that is encompassed by the claims.
A "representative number of species" means that the species which are adequately described are representative of the entire genus. Thus, when there is substantial variation within the genus, one must describe a sufficient variety of species to reflect the variation within the genus. See AbbVie Deutschland GmbH & Co., KG v. Janssen Biotech, Inc., 759 F.3d 1285, 1300, 111 USPQ2d 1780, 1790 (Fed. Cir. 2014) (MPEP § 2163.05.Ib). Describing two chimeric signaling receptors without distinguishing structure-to-function attributes does not provide adequate written description of the claimed genus. The specification provides no guidance on how altering the structures of the TGFβR extracellular domain and the truncated MyD88 polypeptides could affect function. Therefore, in view of the case law directed to an appropriate number of representative species, claims 1-3, 15-17, 21-22, 24-30, 32, 37-39, 53, 58, 71-73, 75, 84, 87, 90, and 92-93 are rejected for insufficient written description.
Applicant is reminded that Vas-Cath makes clear that the written description provision of 35 U.S.C. § 112 is severable from its enablement provision (see page 1115).
Claims 1-3, 15-17, 21-22, 24-30, 32, 37-39, 53, 58, 71-73, 75, 84, 87, 90, and 92-93 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 the specific species of chimeric signaling receptors comprising SEQ ID NOs: 93 or 94, does not reasonably provide enablement for the genus of chimeric signaling receptors encompassed by the claims. 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 and use the invention commensurate in scope with these claims.
MPEP § 2164.01(a) states that there are many factors to be considered when determining whether there is sufficient evidence to support a determination that a disclosure
does not satisfy the enablement requirement and whether any necessary experimentation is
“undue”. These factors include, but are not limited to:
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.
The breadth of the claims and nature of the invention:
The nature of the invention is complex. As understood with the broadest reasonable interpretation, the claims are directed to a genus of chimeric signaling receptors comprising structural variation in TGFβR extracellular domains and truncated MyD88 polypeptides (Claims 1 and 15). The extracellular domain can comprise the amino acid sequence set forth in SEQ ID NO: 20, a sequence at least or about 85% identical to the sequence set forth in SEQ ID NO: 20, or a functional portion thereof (Claim 3). The portion of TGFβR can comprise the amino acid sequence set forth in SEQ ID NO: 3 or a sequence at least or about 85% identical to the sequence set forth in SEQ ID NO: 3 (Claim 17). The MyD88 polypeptides can comprise various amino acid ranges of the sequence set forth in SEQ ID NO: 128 (Claim 22). The first and second MyD88 polypeptides can be set forth in SEQ ID NO: 2 (Claims 24-25). The chimeric signaling receptor can be set forth in SEQ ID NOs: 93 or 94 or exhibit at least or about 85% sequence identity to the sequences set forth in SEQ ID NOs: 93 or 94 (Claims 30 and 32).
As stated in the written description rejection above, “an amino acid sequence set forth in” encompasses any fragment of two or more amino acid residues within the recited sequence. Further, “at least 85% sequence identity” means that any combination of 15% of the amino acids could be inserted, deleted, or substituted with conservative or non-conservative changes. Thus, the claim language encompasses a genus of thousands of possible chimeric signaling receptors.
When analyzing the scope of enablement, the claims are analyzed with respect to the teachings of the specification and are to be "given their broadest reasonable interpretation consistent with the specification." See MPEP 2111 [R-5]; Phillips v. AWH Corp., 415 F.3d 1303, 75 USPQ2d 1321 (Fed. Cir. 2005); and In re Hyatt, 211 F.3d 1367, 1372, 54 USPQ2d 1664, 1667 (Fed. Cir. 2000). Applicant always has the opportunity to amend the claims during prosecution, and broad interpretation by the examiner reduces the possibility that the claim, once issued, will be interpreted more broadly than is justified. In re Prater, 415 F.2d 1393, 1404-05, 162 USPQ 541, 550- 51 (CCPA 1969).
The state of the prior art and level of predictability in the art:
The level of predictability in the art depends, most importantly, on whether the claimed invention can be practiced by one of ordinary skill in the art. In AMGEN INC. ET AL. v. SANOFI ET AL. (No. 21-757, decided May 18, 2023), the Supreme Court held that Amgen was not enabled for “the entire genus” of antibodies that (1) “bind to specific amino acid residues on PCSK9,” and (2) “block PCSK9 from binding to [LDL receptors]” (872 F. 3d 1367, 1372) even though Amgen identified the amino acid sequences of 26 antibodies that perform these two functions. The case law applies to the instant claims which encompass a genus of chimeric signaling receptors with required binding activity, yet the inventors have only disclosed two variants in the specification: CTSR-2B (SEQ ID NO: 93) and CTSR-2C (SEQ ID NO: 94) (Table E1).
In Amgen, the Supreme Court has stated: “An antibody' s structure does much to dictate its function—its ability to bind to an antigen and, in some instances, to block other molecules in the body from doing the same. Different antibodies have different binding and blocking capacities based on the amino acids that compose them and their three-dimensional shapes.” See id., at 11–12. Despite recent advances, aspects of antibody science remain unpredictable. For example, scientists understand that changing even one amino acid in the sequence can alter an antibody' s structure and function. See id., at 14. But scientists cannot always accurately predict exactly how trading one amino acid for another will affect an antibody' s structure and function. Ibid. The unpredictability of amino acid mutations extends to polypeptide structure and function such as the TGFβR extracellular domain required to bind TGFβ in the instant application.
The case law shows a continued lack of predictability even after the effective filing date of the instant invention, and there is no support in the Applicant’s disclosure leading one of ordinary skill to overcome the lack of predictability in the genus of amino acid variations claimed. The specification provides no guidance or direction for which 15% of the amino acid residues may be inserted, deleted, or substituted such that the functional properties of the invention are preserved (binding TGFβ and MyD88 intracellular signaling).
Level of skill in the art:
The level of skill would be high encompassing fusion protein science, binding assays, signaling assays, immunotherapy, etc.
Amount of direction provided by inventor and the existence of working examples:
The specification teaches two chimeric signaling receptors that meet the criteria of Claims 1 and 15 (comprising two truncated MyD88 polypeptides): CTSR-2B (SEQ ID NO: 93) and CTSR-2C (SEQ ID NO: 94) (Table E1). Both CTSR-2B and CTSR-2C comprise the same TGFβR2 extracellular domain (SEQ ID NO: 20), the same TGFβR2 transmembrane domain (SEQ ID NO: 22), and the same truncated MyD88 polypeptides (SEQ ID NO: 2) (Table E1). CTSR-2B and CTSR-2C only differ in that CTSR-2C comprises a peptide linker between the two truncated MyD88 polypeptides and CTSR-2B does not (Table E1). Both CTSR-2B and CTSR-2C constructs were generated (Example 1). CTSR-2C was further expressed in primary human T cells (Example 1) and evaluated in in vitro and in vivo functional assays in neuroblastoma, pancreatic cancer, ovarian cancer, and lymphoma models (Examples 2-11). However, two species that only differ by a peptide linker are not sufficient to describe the genus of possible chimeric signaling receptors encompassed by the claims. No guidance is provided on preferable mutations in the TGFβR extracellular domain or truncated MyD88 polypeptides such that the functional properties are maintained. A person having ordinary skill in the art would have to make a substantial inventive contribution in order to make and characterize a representative number of chimeric signaling receptor species to encompass the claimed genus.
The quantity of experimentation needed to make or use the invention based on the content of the disclosure:
In light of the unpredictability surrounding the claimed subject matter, the undue breadth of the claimed invention’s intended use, and the lack of adequate guidance, one wishing to make and practice the presently claimed invention would be unable to do so without engaging in undue experimentation. Given that structure is essential to function, a person having ordinary skill in the art would have to perform further experimentation to systematically make the structural variants encompassed by the claims and screen their individual characteristics in order to practice the invention commensurate with the scope of the claims. Functional characteristics are especially important in Claim 90 which is directed to a method of treating cancer by administering an engineered cell comprising the chimeric signaling receptor.
The instant specification does not enable the invention to make and use the entire genus of chimeric signaling receptors claimed; therefore, Claims 1-3, 15-17, 21-22, 24-30, 32, 37-39, 53, 58, 71-73, 75, 84, 87, 90, and 92-93 are rejected.
Allowable Subject Matter
No claim is allowed. However, a chimeric signaling receptor comprising a TGFβR2 extracellular domain comprising SEQ ID NO: 20, a transmembrane domain, and two truncated MyD88 polypeptides each comprising SEQ ID NO: 2 is enabled and free of the prior art.
The closest relevant art is Boyerinas US 2019/0350974 (of record in IDS) which teaches that chimeric signaling receptors with TGFβR extracellular domains can be fused to intracellular signaling domains that promote immune function in order to redirect immunosuppressive signaling in the tumor microenvironment to immunostimulatory signaling (paragraphs [0010]-[0015]). Boyerinas teaches that the TGFβ signal convertor can convert an immunosuppressive TGFβ signal to an IL-18-mediated immunostimulatory signal by comprising an IL-18R1 intracellular signaling domain (paragraph [0291]). Boyerinas teaches that IL-18 signaling through IL-18R1 results in activation through the MyD88 adaptor protein and IRAK4 phosphorylation (paragraph [0289]) but does not teach wherein the intracellular signaling domain specifically comprises two truncated MyD88 polypeptides. Spencer US 2016/0058857 (of record in IDS) teaches chimeric antigen receptors comprising intracellular signaling domains comprising MyD88 and CD40 (abstract and Fig. 2) wherein the MyD88 polypeptide can be a truncated MyD88 polypeptide lacking the TIR domain (paragraph [0012]). However, Spencer teaches that MyD88 and CD40 (MC) synergize as activation signaling molecules in human T cells, and that a CAR molecule should benefit from inclusion of the composite MC signaling domain (paragraph [0543], emphasis added). Therefore, it would not be obvious to make an intracellular signaling domain comprising MyD88 without CD40, much less an intracellular signaling domain comprising two MyD88 polypeptides as repeating the same protein in an intracellular signaling domain is not routine in the art (as evidenced by Smirnov et al. Front Immunol. 2024 Fig. 1).
Conclusion
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/SARAH COOPER PATTERSON/Examiner, Art Unit 1675
/JEFFREY STUCKER/Supervisory Patent Examiner, Art Unit 1675
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