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 .
Applicant’s response of 10/10/2025, including a substitute specification and replacement drawings, has been received and entered into the application file.
Claims 1, 5, 10, 14, 16, and 79 were amended in the claim set filed 10/10/2025.
Claims 153-157 were added in the claim set filed 10/10/2025.
Claims 6, 8, 62, 109, and 131 were cancelled in the claim set filed 10/10/2025.
Claims 1, 3-5, 10-12, 14, 16, 18, 19, 36, 59, 60, 75, 79, 123, and 153-157 are pending, of which claim 79 was previously withdrawn.
Accordingly, claims 1, 3-5, 10-12, 14, 16, 18, 19, 36, 59, 60, 75, 123, and 153-157 are pending and under consideration.
Election/Restrictions
Applicant previously elected Group I (claims 1, 3-6, 8, 10-12, 14, 16, 18, 19, 36, 59, 60, 75, and 123) without traverse in the reply filed on 05/21/2025. Claims 6 and 8 were subsequently cancelled in the claim set filed 10/10/2025.
Claims 62, 79, 109, and 131 were previously withdrawn from further consideration pursuant to 37 CFR 1.142(b) as being drawn to a nonelected invention, there being no allowable generic or linking claim. Election was made without traverse in the reply filed on 05/21/2025. Claims 62, 109, and 131 were subsequently cancelled in the claim set filed 10/10/2025.
In light of the search of the prior art, the species election of circular permutation at position 1028 of S. pyogenes Cas9 (SEQ ID NO: 1) was previously withdrawn.
Accordingly, claims 1, 3-5, 10-12, 14, 16, 18, 19, 36, 59, 60, 75, 123, and 153-157 are pending and under consideration.
Information Disclosure Statement
Receipt of information disclosure statements on 05/06/2022 and 10/10/2025 is acknowledged. The signed and initialed PTO-1449‘s have been mailed with this action. The Examiner thanks Applicant for drawing attention to the failure of the previously-filed IDS to appear in Patent Center. The IDS filed 05/06/2022 is now available in the file wrapper and has been considered, as reflected in the attached PTO-1449.
Status of Prior Objections/Rejections
RE: Specification
The specification was previously objected to for incorporating essential material to the claimed invention without referencing a U.S. patent, U.S. patent application publication, or SEQ ID number. The amendments to the specification reflected in the substitute specification filed 10/10/2025 have obviated the basis of the prior objections. The objections of record are hereby withdrawn. However, further review of the specification has uncovered new grounds of objection, which are set forth in detail below.
RE: Drawings
The drawings were previously objected to for being of insufficient quality to be clearly legible. The replacement drawing sheets filed 10/10/2025 have obviated the basis of the prior objections. The objections of record are hereby withdrawn.
RE: Nucleotide and/or Amino Acid Sequence Disclosures
The Examiner previously indicated that the Incorporation by Reference paragraph required by 37 CFR 1.821(c)(1) was missing or incomplete in the instant specification, and that nucleotide and/or amino acid sequences appearing in the specification were not identified by sequence identifiers in accordance with 37 CFR 1.821(d) at least at paragraph [00455]. The amendments to the specification reflected in the substitute specification filed 10/10/2025 have obviated the basis of the prior objections. The objections of record are hereby withdrawn.
RE: Claim Objections
Claim 14 was previously objected to for minor grammatical informalities. The amendments to claim14 have obviated the basis of the prior objection. The objection of record is hereby withdrawn.
RE: Claim Rejections - 35 USC § 112
Claim 14 was previously rejected under 35 U.S.C. 112, first paragraph, as based on a disclosure which is not enabling. The amendments to claim 14 have obviated the basis of the prior rejection. The rejection of record is hereby withdrawn.
RE: Claim Rejections - 35 USC § 102
►Claims 1, 3, 4, 5, 6, 8, 11, 14, 16, 18, 19, 36, 59, 60, and 75 were previously rejected under 35 U.S.C. 102(a)(1) and 102(a)(2) as being anticipated by US 2019/0233847 A1 (hereinafter Savage).
The cancellation of claims 6 and 8 renders the rejections thereof moot.
Applicant has traversed the rejection of record, asserting that the cited art does not anticipate the amended limitations of instant claim 1 in the claim set filed 10/10/2025. Given that the remaining claims depend directly or indirectly from claim 1, the remaining claims are therefore also not novel over Savage.
In response, the Examiner notes that the amendment to instant claim 1 to recite “any one of the corresponding amino acid residues in another napDNA/RNAbp” was not previously considered. Accordingly, while Applicant’s arguments have been fully considered and are found persuasive and the rejection of record is hereby withdrawn, new grounds of rejection necessitated by amendment are set forth below.
RE: Claim Rejections - 35 USC § 103
►Claim 10 was previously rejected under 35 U.S.C. 103 as being unpatentable over US 2019/0233847 A1 (hereinafter Savage) as applied to claim 1 above, and further in view of Oakes et al., 2019.
Applicant has traversed the rejection of record, asserting that the cited art does not anticipate the amended limitations of instant claim 1 in the claim set filed 10/10/2025, as set forth above. Given that the remaining claims depend directly or indirectly from claim 1, the remaining claims are therefore also not novel over Savage.
In response, the Examiner notes that the amendment to instant claim 1 to recite “any one of the corresponding amino acid residues in another napDNA/RNAbp” was not previously considered. Accordingly, while Applicant’s arguments have been fully considered and are found persuasive and the rejection of record is hereby withdrawn, new grounds of rejection necessitated by amendment are set forth below.
Applicant has further asserted that the circularly permuted Cas9 proteins disclosed in Oakes and those disclosed in the instant application were developed in different contexts and for different purposes, with the claimed fusion proteins facilitating a shifted and/or expanded editing window of the base editor(s) fused thereto. Applicant asserts that the particular amino acid positions at which Cas9 could be circularly permuted to accomplish this goal in the context of a Cas9-deaminase fusion protein would not have been obvious in view of the circular permutation of a Cas9 nuclease as disclosed in Oakes. While the Examiner agrees that the disclosure of Oakes is drawn more broadly to the development of CRISR-Cas9 circular permutants, Oakes explicitly discloses that the circularly permuted Cas9 proteins taught therein are suitable for fusion to heterologous protein domains such as base editors, as a number of the circularly permuted Cas9 proteins taught therein were disclosed to contain ideal fusion points to such domains, which previously required long linkers to gain such access (page 258, column 1, paragraph 1). Therefore, while Oakes is more broadly drawn to the development of CRISR-Cas9 circular permutants, Oakes explicitly addresses the applicability of the circularly permuted Cas9 proteins taught therein to comprise a more optimal DNA binding scaffold for fusion proteins (page 257, column 1, paragraph 2). Furthermore, when claimed subject matter is found to be disclosed in the prior art, it is considered that the claimed and disclosed subject matter must be structurally identical and therefore must have necessarily have identical properties and functions. See MPEP § 2114 and § 2173.05(g).
Accordingly, Applicant’s argument that the disclosure of Oakes does not anticipate or render obvious the particular amino acid positions at which Cas9 could be circularly permuted to accomplish the goal of expanding the editing window of a Cas9-deaminase fusion protein is not found persuasive, as set forth below.
►Claim 12 was previously rejected under 35 U.S.C. 103 as being unpatentable over US 2019/0233847 A1 (hereinafter Savage) as applied to claim 11 above, and further in view of Jeong et al., 2019.
Applicant has traversed the rejection of record, asserting that the cited art does not anticipate the amended limitations of instant claim 1 in the claim set filed 10/10/2025, as set forth above. Given that the remaining claims depend directly or indirectly from claim 1, the remaining claims are therefore also not novel over Savage.
In response, the Examiner notes that the amendment to instant claim 1 to recite “any one of the corresponding amino acid residues in another napDNA/RNAbp” was not previously considered. Accordingly, while Applicant’s arguments have been fully considered and are found persuasive and the rejection of record is hereby withdrawn, new grounds of rejection necessitated by amendment are set forth below.
►Claim 123 was previously rejected under 35 U.S.C. 103 as being unpatentable over US 2019/0233847 A1 (hereinafter Savage) as applied to claim 1 above, and further in view of Oakes et al., 2019, Pickar-Oliver and Gersbach, 2019, and US 2019/0233814 A1 (hereinafter Zhang).
Applicant has traversed the rejection of record, asserting that the cited art does not anticipate the amended limitations of instant claim 1 in the claim set filed 10/10/2025, as set forth above. Given that the remaining claims depend directly or indirectly from claim 1, the remaining claims are therefore also not novel over Savage.
In response, the Examiner notes that the amendment to instant claim 1 to recite “any one of the corresponding amino acid residues in another napDNA/RNAbp” was not previously considered. Accordingly, while Applicant’s arguments have been fully considered and are found persuasive and the rejection of record is hereby withdrawn, new grounds of rejection necessitated by amendment are set forth below.
New/Maintained Grounds of Objection/Rejection
Specification
The disclosure is objected to because of the following informalities:
The paragraphs of the substitute specification filed 10/10/2025 are improperly numbered. Page 162 of the marked-up substitute specification jumps from paragraph [0137] (which is drawn to the PACE and PANCE directed evolutionary processes) to paragraph [00435] (which is drawn to the instantly disclosed fusion protein base editors comprising an adenosine deaminase domain). It would be remedial to ensure that all paragraphs of the instant specification are properly numbered.
Appropriate correction is required.
The lengthy specification has not been checked to the extent necessary to determine the presence of all possible minor errors. Applicant’s cooperation is requested in correcting any other errors of which applicant may become aware in the specification.
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, 3-5, 10, 11, 14, 16, 18, 19, 36, 59, 60, 75, 153, 154, and 156 are rejected under 35 U.S.C. 102(a)(1) and 5 U.S.C. 102(a)(2) as being anticipated by US 2019/0233847 A1 (hereinafter Savage; as cited in the IDS filed 05/06/2022; of record).
With regard to amended instant claims 1 and 10, which recite “a fusion protein comprising: (i) a circularly permuted nucleic acid programmable DNA/RNA binding protein (napDNA/RNAbp) that is circularly permuted at any one of amino acid residues 1012, 1028, 1041, 1249, or 1300 [limited to amino acid residue 1028 or 1041 at amended instant claim 10] of a Cas9 protein having the amino acid sequence SEQ ID NO: 1, or at any one of the corresponding amino acid residues in another napDNA/RNAbp; and (ii) a nucleic acid effector domain,” as previously set forth, Savage discloses both circularly permuted Cas9 proteins and fusion polypeptides thereof (abstract). Savage specifically discloses that the circularly permuted Cas9 taught therein is fused to a fusion partner which may be a deaminase (paragraphs [0009] and [0128]). Per paragraph [0082] of the instant specification, the deaminase domain disclosed in Savage reads on the instantly claimed nucleic acid effector domain.
Further review of Savage has established that Table 2 of Savage discloses circular permutation of napDNA/RNAbp protein S. pyogenes Cas9 protein (corresponding to SEQ ID NO: 111, which is 100% identical to instant SEQ ID NO: 1 as shown in the alignment in Appendix I) at amino acid positions 1012 (as in amended claim 1) and 1028 (as in amended claims 1 and 10), as instantly claimed. Thus, Savage anticipates each and every limitation of instant claims 1 and 10.
With regard to claim 3, which recites “the circularly permuted napDNS/RNAbp [of the fusion protein of claim 1] is a circularly permuted Cas9 or a variant thereof, that is capable of binding DNA or RNA when complexed with a guide RNA (gRNA),” Savage discloses that the circularly permuted Cas9 proteins taught therein bind to gRNAs that direct the gRNA/circular Cas9 complex to bind to a specific nucleotide sequence within the target nucleic acid for editing to occur (paragraphs [0110], [0141], [0153], and [0160]). Thus, Savage anticipates each and every limitation of instant claim 3.
With regard to claim 4, which recites “the circularly permuted napDNA/RNAbp [of the fusion protein of claim 1] is a circularly permuted nuclease active Cas9, a circularly permuted Cas9 nickase (Cas9n), a circularly permuted inactive Cas9 (Cas9d), or a variant thereof, that is capable of binding DNA or RNA when complexed with a guide RNA (gRNA),” Savage discloses that the circularly permuted Cas9 proteins taught therein can lack a catalytically active RuvC domain and/or can lack a catalytically active HNH domain, meaning the circularly permuted Cas9 may be a nickase or may be catalytically inactive (paragraph [0073]). As set forth above regarding instant claim 3, Savage discloses a circularly permuted Cas9 that is capable of binding DNA or RNA when complexed with a guide RNA (paragraphs [0110], [0141], [0153], and [0160]). Thus, Savage anticipates each and every limitation of instant claim 4.
With regard to amended claim 5, which recites “the nucleic acid effector domain [of the fusion protein of claim 1], wherein the nucleic acid effector domain is close in proximity to a single stranded DNA (ssDNA) loop that is formed in a double stranded DNA molecule when the gRNA complexed with the fusion protein binds to a strand of the double stranded DNA molecule, as compared to a fusion protein that has a corresponding non-circularly permuted Cas9,” given that Savage anticipates the fusion protein of claim 1, as set forth above, the disclosed and claimed fusion proteins must be structurally identical and therefore must necessarily function the same. See MPEP § 2114 and § 2173.05(g). Thus, Savage anticipates each and every limitation of instant claim 5.
With regard to claim 11, which recites “the circularly permuted napDNA/RNAbp [of the fusion protein of claim 1] is a circularly permuted Cas9 derived from a S. pyogenes Cas9 (SpCas9), a S. aureus Cas9 (SaCas9), or a variant thereof, that is capable of binding DNA when complexed with a guide RNA (gRNA),” as set forth above, Savage discloses circularly permuted SpCas9 species (taught in table 2) fused to partners such as deaminases (paragraphs [0009] and [0128]). As set forth above regarding instant claim 3, Savage discloses a circularly permuted Cas9 that is capable of binding DNA or RNA when complexed with a guide RNA (paragraphs [0110], [0141], [0153], and [0160]). Thus, Savage anticipates each and every limitation of instant claim 11.
With regard to claim 14, which recites “the circularly permuted napDNA/RNAbp is derived from a Cas9 comprising an amino acid sequence that is at least 80%, 85%, 90%, 95%, 98%...or 99% identical to SEQ ID NO: 1…,” Savage discloses that SEQ ID NO: 17 taught therein is a dCas9 from which the circularly permuted Cas9 species taught therein were derived. As shown in the alignment in Appendix II, SEQ ID NO: 17 of Savage is 99.7% identical to SEQ ID NO: 1 of the instant application. Thus, Savage anticipates each and every limitation of instant claim 14.
With regard to claims 16, 153, and 154, which respectively recite “the circularly permuted napDNA/RNAbp [of the fusion protein of claim 1] comprises an amino acid sequence that is at least 80% identical”, “at least 90% identical”, or “at least 95% identical to any one of SEQ ID NOs: 295-299,” Savage discloses that the circularly permuted Cas9 proteins taught therein correspond to SEQ ID NOs: 1-16. In view of this disclosure, SEQ ID NO: 6 of Savage (which falls within the range of SEQ ID NOs: 1-16, corresponding to the circularly permuted Cas9 species taught therein) is 98.0% identical to SEQ ID NO: 295 of the instant application (as shown in the alignment in Appendix III). Thus, Savage anticipates each and every limitation of instant claims 16, 153, and 154.
With regard to claim 18, which recites “the nucleic acid effector domain [of the fusion protein of claim 1] is a deaminase domain,” as set forth above regarding instant claim 1, Savage discloses both circularly permuted Cas9 proteins and fusion polypeptides thereof (abstract). Savage specifically discloses that the circularly permuted Cas9 taught therein is fused to a fusion partner which may be a deaminase (paragraphs [0009] and [0128]). Thus, Savage anticipates each and every limitation of instant claim 18.
With regard to claim 19, which recites “the deaminase domain [of the fusion protein of claim 18] is a cytidine deaminase domain,” Savage discloses that the fusion partner of the circularly permuted Cas9 proteins and fusion polypeptides thereof taught therein may be a cytidine deaminase (abstract; paragraphs [0009] and [0123]). Thus, Savage anticipates each and every limitation of instant claim 19.
With regard to claim 36, which recites “the nucleic acid effector domain [of the fusion protein of claim 18] comprises an adenosine deaminase,” Savage discloses that the fusion partner of the circularly permuted Cas9 proteins and fusion polypeptides thereof taught therein may be an adenosine deaminase (abstract; paragraphs [0009] and [0128]). Thus, Savage anticipates each and every limitation of instant claim 36.
With regard to claim 59, which recites “a nucleic acid that encodes the fusion protein of claim 1,” Savage discloses that the fusion proteins taught therein (which anticipate the fusion protein of claim 1, as set forth above) may be encoded in nucleic acid sequences (paragraphs [0166-0169]). Thus, Savage anticipates each and every limitation of instant claim 59.
With regard to claim 60, which recites “a vector comprising the nucleic acid of claim 59,” Savage discloses that the nucleotide sequence encoding the fusion proteins taught therein (as set forth above) may be packaged into an expression vector such as an rAAV vector (paragraphs [0170-0171]). Thus, Savage anticipates each and every limitation of instant claim 60.
With regard to claim 75, which recites “a cell comprising the fusion protein of claim 1,” Savage discloses host cells comprising the fusion proteins taught therein (which anticipate the fusion protein of claim 1, as set forth above) (paragraph [0209]). Thus, Savage anticipates each and every limitation of instant claim 75.
With regard to claim 156, which recites “the fusion protein [of claim 1] comprises an amino acid sequence that is at least 80% identical to any one of SEQ ID NOs: 72-81,” Savage discloses that SEQ ID NO: 26 taught therein is a circularly permuted Cas9 protein (paragraph [0057]). As shown in the alignment in Appendix IV, SEQ ID NO: 26 of Savage is 81.0% identical to instant SEQ ID NO: 72. Thus, Savage anticipates each and every limitation of instant claim 156.
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.
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.
Claims 1, 3-5, 10, 11, 14, 16, 18, 19, 36, 59, 60, 75, 153, 154, and 156 are rejected under 35 U.S.C. 103 as being unpatentable over US 2019/0233847 A1 (hereinafter Savage; as cited in the IDS filed 05/06/2022; of record) in view of Oakes et al., 2019 (as cited in the IDS filed 05/06/2022; of record).
With regard to amended instant claims 1 and 10, which recite “a fusion protein comprising: (i) a circularly permuted nucleic acid programmable DNA/RNA binding protein (napDNA/RNAbp) that is circularly permuted at any one of amino acid residues 1012, 1028, 1041, 1249, or 1300 [limited to amino acid residue 1028 or 1041 at amended instant claim 10] of a Cas9 protein having the amino acid sequence SEQ ID NO: 1, or at any one of the corresponding amino acid residues in another napDNA/RNAbp; and (ii) a nucleic acid effector domain,” as previously set forth, Savage discloses both circularly permuted Cas9 proteins and fusion polypeptides thereof (abstract). Savage specifically discloses that the circularly permuted Cas9 taught therein is fused to a fusion partner which may be a deaminase (paragraphs [0009] and [0128]). Per paragraph [0082] of the instant specification, the deaminase domain disclosed in Savage reads on the instantly claimed nucleic acid effector domain.
Further review of Savage has established that Table 2 of Savage discloses circular permutation of S. pyogenes Cas9 protein (corresponding to SEQ ID NO: 111, which is 100% identical to instant SEQ ID NO: 1 as shown in the alignment in Appendix I) at amino acid positions 1012 (as in amended claim 1) and 1028 (as in amended claims 1 and 10), as instantly claimed.
While Savage does not disclose circular permutation at amino acid residue numbers 1041 (as in amended claims 1 and 10) or 1249 (as in amended claim 1) of a Cas9 protein having the amino acid sequence SEQ ID NO: 1 (which corresponds to canonical S. pyogenes Cas9 per paragraph [0010] of the instant specification), this deficiency is cured by Oakes et al., 2019.
Oakes et al., 2019 also discloses CRISPR-Cas9 circular permutants (abstract). Table 1 of Oakes et al., 2019 discloses key SpCas9 circular permutants, including circular permutants involving amino acid residues 1041 and 1249, as instantly claimed (see also Figure S1). Oakes et al., 2019 additionally discloses that the circularly permuted SpCas9 produced with amino acid residue 1249 exhibits at least 80% of the activity of a wild-type SpCas9 (page 257, column 1, paragraph 2). As set forth above, Oakes explicitly discloses that the circularly permuted Cas9 proteins taught therein are suitable for fusion to heterologous protein domains such as base editors, as a number of the circularly permuted Cas9 proteins taught therein were disclosed to contain ideal fusion points to such domains, which previously required long linkers to gain such access (page 258, column 1, paragraph 1). Thus, Oakes et al., 2019 discloses SpCas9 circular permutants produced with amino acid residues 1041 and 1249, as in amended instant claim 1, as well as SpCas9 circular permutants produced with amino acid residue 1041, as in amended instant claims 1 and 10.
With regard to claim 3, which recites “the circularly permuted napDNS/RNAbp [of the fusion protein of claim 1] is a circularly permuted Cas9 or a variant thereof, that is capable of binding DNA or RNA when complexed with a guide RNA (gRNA),” Savage discloses that the circularly permuted Cas9 proteins taught therein bind to gRNAs that direct the gRNA/circular Cas9 complex to bind to a specific nucleotide sequence within the target nucleic acid for editing to occur (paragraphs [0110], [0141], [0153], and [0160]). Thus, Savage discloses a circularly permuted Cas9 that is capable of binding DNA or RNA when complexed with a guide RNA, as instantly claimed.
With regard to claim 4, which recites “the circularly permuted napDNA/RNAbp [of the fusion protein of claim 1] is a circularly permuted nuclease active Cas9, a circularly permuted Cas9 nickase (Cas9n), a circularly permuted inactive Cas9 (Cas9d), or a variant thereof, that is capable of binding DNA or RNA when complexed with a guide RNA (gRNA),” Savage discloses that the circularly permuted Cas9 proteins taught therein can lack a catalytically active RuvC domain and/or can lack a catalytically active HNH domain, meaning the circularly permuted Cas9 may be a nickase or may be catalytically inactive (paragraph [0073]). As set forth above regarding instant claim 3, Savage discloses a circularly permuted Cas9 that is capable of binding DNA or RNA when complexed with a guide RNA (paragraphs [0110], [0141], [0153], and [0160]). Thus, Savage discloses a circularly permuted Cas9 nickase and a circularly permuted inactive Cas9, as instantly claimed.
With regard to amended claim 5, which recites “the nucleic acid effector domain [of the fusion protein of claim 1], wherein the nucleic acid effector domain is close in proximity to a single stranded DNA (ssDNA) loop that is formed in a double stranded DNA molecule when the gRNA complexed with the fusion protein binds to a strand of the double stranded DNA molecule, as compared to a fusion protein that has a corresponding non-circularly permuted Cas9,” given that Savage and Oakes et al., 2019 collectively disclose the fusion protein of claim 1, as set forth above, the disclosed and claimed fusion proteins must be structurally identical and therefore must necessarily function the same. See MPEP § 2114 and § 2173.05(g).
With regard to claim 11, which recites “the circularly permuted napDNA/RNAbp [of the fusion protein of claim 1] is a circularly permuted Cas9 derived from a S. pyogenes Cas9 (SpCas9), a S. aureus Cas9 (SaCas9), or a variant thereof, that is capable of binding DNA when complexed with a guide RNA (gRNA),” as set forth above, Savage discloses circularly permuted SpCas9 species (taught in table 2) fused to partners such as deaminases (paragraphs [0009] and [0128]). As set forth above regarding instant claim 3, Savage discloses a circularly permuted Cas9 that is capable of binding DNA or RNA when complexed with a guide RNA (paragraphs [0110], [0141], [0153], and [0160]). Thus, Savage discloses a circularly permuted Cas9 derived from a S. pyogenes Cas9, as instantly claimed.
With regard to claim 14, which recites “the circularly permuted napDNA/RNAbp is derived from a Cas9 comprising an amino acid sequence that is at least 80%, 85%, 90%, 95%, 98%...or 99% identical to SEQ ID NO: 1…,” Savage discloses that SEQ ID NO: 17 taught therein is a dCas9 from which the circularly permuted Cas9 species taught therein were derived. As shown in the alignment in Appendix II, SEQ ID NO: 17 of Savage is 99.7% identical to SEQ ID NO: 1 of the instant application. Thus, Savage discloses derivation of a circularly permuted napDNA/RNAbp from a Cas9 comprising an amino acid sequence that is at least 99% identical to SEQ ID NO: 1, as instantly claimed.
With regard to claims 16, 153, and 154, which respectively recite “the circularly permuted napDNA/RNAbp [of the fusion protein of claim 1] comprises an amino acid sequence that is at least 80% identical”, “at least 90% identical”, or “at least 95% identical to any one of SEQ ID NOs: 295-299,” Savage discloses that the circularly permuted Cas9 proteins taught therein correspond to SEQ ID NOs: 1-16. In view of this disclosure, SEQ ID NO: 6 of Savage (which falls within the range of SEQ ID NOs: 1-16, corresponding to the circularly permuted Cas9 species taught therein) is 98.0% identical to SEQ ID NO: 295 of the instant application (as shown in the alignment in Appendix III). Thus, Savage discloses a circularly permuted Cas9 comprising an amino acid sequence that is at least 95% identical to SEQ ID NO: 295, as instantly claimed.
With regard to claim 18, which recites “the nucleic acid effector domain [of the fusion protein of claim 1] is a deaminase domain,” as set forth above regarding instant claim 1, Savage discloses both circularly permuted Cas9 proteins and fusion polypeptides thereof (abstract). Savage specifically discloses that the circularly permuted Cas9 taught therein is fused to a fusion partner which may be a deaminase (paragraphs [0009] and [0128]). Thus, Savage discloses a fusion protein comprising a circularly permuted napDNA/RNAbp and a deaminase domain, as instantly claimed.
With regard to claim 19, which recites “the deaminase domain [of the fusion protein of claim 18] is a cytidine deaminase domain,” Savage discloses that the fusion partner of the circularly permuted Cas9 proteins and fusion polypeptides thereof taught therein may be a cytidine deaminase (abstract; paragraphs [0009] and [0123]). Thus, Savage discloses a fusion protein comprising a circularly permuted napDNA/RNAbp and a cytidine deaminase domain, as instantly claimed.
With regard to claim 36, which recites “the nucleic acid effector domain [of the fusion protein of claim 18] comprises an adenosine deaminase,” Savage discloses that the fusion partner of the circularly permuted Cas9 proteins and fusion polypeptides thereof taught therein may be an adenosine deaminase (abstract; paragraphs [0009] and [0128]). Thus, Savage discloses a fusion protein comprising a circularly permuted napDNA/RNAbp and an adenosine deaminase, as instantly claimed.
With regard to claim 59, which recites “a nucleic acid that encodes the fusion protein of claim 1,” Savage discloses that the fusion proteins taught therein (which anticipate the fusion protein of claim 1, as set forth above) may be encoded in nucleic acid sequences (paragraphs [0166-0169]). Thus, Savage discloses a nucleic acid that encodes the fusion protein of claim 1 (collectively disclosed by Savage and Oakes et al., 2019), as instantly claimed.
With regard to claim 60, which recites “a vector comprising the nucleic acid of claim 59,” Savage discloses that the nucleotide sequence encoding the fusion proteins taught therein (as set forth above) may be packaged into an expression vector such as an rAAV vector (paragraphs [0170-0171]). Thus, Savage discloses a vector comprising a nucleic acid that encodes the fusion protein of claim 1 (collectively disclosed by Savage and Oakes et al., 2019), as instantly claimed.
With regard to claim 75, which recites “a cell comprising the fusion protein of claim 1,” Savage discloses host cells comprising the fusion proteins taught therein (which anticipate the fusion protein of claim 1, as set forth above) (paragraph [0209]). Thus, Savage discloses a cell comprising the fusion protein of claim 1 (collectively disclosed by Savage and Oakes et al., 2019), as instantly claimed.
With regard to claim 156, which recites “the fusion protein [of claim 1] comprises an amino acid sequence that is at least 80% identical to any one of SEQ ID NOs: 72-81,” Savage discloses that SEQ ID NO: 26 taught therein is a circularly permuted Cas9 protein (paragraph [0057]). As shown in the alignment in Appendix IV, SEQ ID NO: 26 of Savage is 81.0% identical to instant SEQ ID NO: 72. Thus, Savage discloses a fusion protein comprising an amino acid sequence that is at least 80% identical to instant SEQ ID NO: 72, as instantly claimed.
Given that Savage discloses fusion proteins comprising circularly permuted Cas9 (circularly permuted at amino acid positions 1012 and 1028) and a nucleic acid effector domain such as deaminases, as well as nucleic acids encoding the same, vectors comprising the same, and cells comprising the same, and that Oakes et al., 2019 discloses functional, circularly permuted SpCas9 species produced with amino acid residues 1041 and 1249, it would have been obvious to someone of ordinary skill in the art before the effective filing date of the claimed invention to substitute the circularly permuted Cas9 disclosed in Savage (at residues 1012 and 1028) with the circularly permuted SpCas9 disclosed in Oakes et al., 2019 (at residues 1041 and 1249) to predictably produce a fusion protein comprising a functional circularly permuted SpCas9 that provides an ideal point for fusing heterologous functional domains such as base editors or deaminases. One would have been motivated to make such a modification in order to receive the expected benefit of producing a fusion protein comprising a functional circularly permuted SpCas9 that provides an ideal point for fusing heterologous functional domains such as base editors or deaminases.
Claim 12 is rejected under 35 U.S.C. 103 as being unpatentable over US 2019/0233847 A1 (hereinafter Savage; as cited in the IDS filed 05/06/2022; of record), as applied to claim 11 above (see section Claim Rejections - 35 USC § 102), and further in view of US 2020/0172931A1 (hereinafter Liu; as cited in the IDS filed 05/06/2022).
Claim 12 is rejected under 35 U.S.C. 103 as being unpatentable over US 2019/0233847 A1 (hereinafter Savage; as cited in the IDS filed 05/06/2022; of record) in view of Oakes et al., 2019 (as cited in the IDS filed 05/06/2022; of record), as applied to claim 11 above, and further in view of Jeong et al., 2019 (of record).
The disclosure of Savage, as well as the combined disclosures of Savage and Oakes et al., 2019 are described above and applied as before. However, these disclosures do not teach the SpCas9 or SaCas9 variants SpCas9-VQR, SpCas9-VRER, or SaCas9-KKH of instant claim 12.
With regard to claim 12, which recites “the variant of the SpCas9 or SaCas9 [of the fusion protein of claim 11] is selected from the group consisting of SpCas9-VQR, SpCas9-VRER, and SaCas9-KKH,” while Savage and Oakes et al., 2019 disclose circularly permuted Cas9 species derived from S. pyogenes Cas9 (Table 2 and Table 1, respectively) as in instant claim 11, they do not disclose that these circularly permuted Cas9 species are derived from SpCas9-VQR, SpCas9-VRER, or SaCas9-KKH. However, Jeong et al., 2019 discloses that engineered Cas9 variants VQR and VRER successfully target genomic sites containing non-canonical protospacer-adjacent motif sequences (PAMs), thereby expanding the targetable range of genomic editing with CRISPR-Cas9 (abstract). The VQR variant is explicitly disclosed to be an SpCas9-VQR variant (page 2, paragraph 3). Thus, Jeong et al., 2019 discloses that SpCas9 variants such as the VQR variant are capable of targeting genomic sites near non-canonical PAM sequences, thereby expanding the targetable range of genomic editing with CRISPR-Cas9.
Given that Savage and Oakes et al., 2019 collectively disclose the circularly permuted fusion protein of claim 11 (as set forth above), and that Jeong et al., 2019 discloses that the SpCas9-VQR variant is capable of targeting genomic sites near non-canonical PAM sequences, it would have been obvious to someone of ordinary skill in the art before the effective filing date of the claimed invention to circularly permute the SpCas9-VQR variant disclosed in Jeong et al., 2019 for use in the fusion protein collectively disclosed by Savage and Oakes et al., 2019 to predictably produce a fusion protein comprising a circularly permuted SpCas9-VQR that is capable of targeting genomic sites near non-canonical PAM sequences. One would have been motivated to make such a modification in order to receive the expected benefit of producing a fusion protein comprising a circularly permuted SpCas9-VQR that is capable of targeting genomic sites near non-canonical PAM sequences, thereby expanding the targetable range of genomic editing with a circularly permuted Cas9 fusion protein.
Claims 123 is rejected under 35 U.S.C. 103 as being unpatentable over US 2019/0233847 A1 (hereinafter Savage; as cited in the IDS filed 05/06/2022; of record), as applied to claim 1 above (see section Claim Rejections - 35 USC § 102), and further in view of US 2020/0172931A1 (hereinafter Liu; as cited in the IDS filed 05/06/2022).
Claim 123 is rejected under 35 U.S.C. 103 as being unpatentable over US 2019/0233847 A1 (hereinafter Savage; as cited in the IDS filed 05/06/2022; of record) in view of Oakes et al., 2019 (as cited in the IDS filed 05/06/2022; of record), as applied to claim 1 above, and further in view of Pickar-Oliver and Gersbach, 2019 (of record), and US 2019/0233814 A1 (hereinafter Zhang; of record).
The disclosure of Savage, as well as the combined disclosures of Savage and Oakes et al., 2019 are described above and applied as before. However, these disclosures do not teach the pharmaceutical composition of instant claim 123.
With regard to claim 123, which recites “a pharmaceutical composition comprising the fusion protein of claim 1,” while Savage and Oakes et al., 2019 disclose circularly permuted Cas9 species derived from S. pyogenes Cas9 (Table 2 and Table 1, respectively) as in instant claim 1, they do not disclose a pharmaceutical composition comprising the same. However, Oakes et al., 2019 discloses that circular permutation of Cas9 is relevant to biomedicine, as it can be used to re-engineer the molecular sequence of Cas9 to both better control its activity and create a more optimal DNA binding scaffold for fusion proteins, such as those disclosed in Savage (abstract; page 256, column 1, paragraph 2). Additionally, regarding the nucleic acid effector domain of instant claim 1 (which is disclosed to be a deaminase per Savage (paragraph [0128])), Pickar-Oliver and Gersbach, 2019 disclose that fusion of deaminases (i.e. cytidine deaminases or adenosine deaminases) to Cas9 produces base editors, capable of directing single-base editing (figures 2 and 3; page 495, column 1, paragraphs 2 and 4). Pickar-Oliver and Gersbach, 2019 further disclose that these improved CRISPR-Cas based tools have significant relevance toward clinical use in gene and cell therapies (abstract). Thus, Oakes et al., 2019 discloses that circularly permuted Cas9 facilitates better control of its activity and optimal fusion protein formation, such as fusion to deaminase domains capable of base editing when complexed with Cas9, which has therapeutic relevance as disclosed by Pickar-Oliver and Gersbach, 2019. While Savage, Oakes et al., 2019, and Pickar-Oliver and Gersbach, 2019 do not disclose a pharmaceutical composition comprising therapeutic Cas9 such as the instantly claimed fusion protein, pharmaceutical compositions to deliver Cas9 therapeutics are well-known in the art. For example, Zhang discloses that CRISPR machinery is routinely delivered in conjunction with pharmaceutically acceptable carriers or excipients to form a pharmaceutical composition, as instantly claimed (paragraphs [0411], [0412], and [0459]).
Given that Savage and Oakes et al., 2019 collectively disclose the circularly permuted fusion protein of claim 11 (as set forth above), that Oakes et al., 2019 specifically discloses that circular permutation of Cas9 facilitates better control of its activity and optimal fusion protein formation, such as fusion to deaminases (which are disclosed to have therapeutic relevance when fused to Cas9 to form a base editor per Pickar-Oliver and Gersbach, 2019), and that Zhang discloses that CRISPR machinery is routinely delivered in pharmaceutical compositions, it would have been obvious to someone of ordinary skill in the art before the effective filing date of the claimed invention to deliver the fusion protein of claim 1 (as set forth above) using a pharmaceutical composition to predictably deliver therapeutically effective circularly permuted Cas9 fusion proteins, such as base editors, to patients in need thereof. One would have been motivated to make such a modification in order to receive the expected benefit of delivering therapeutically effective circularly permuted Cas9 fusion proteins, such as base editors, to patients in need thereof.
Claims 156 and 157 are rejected under 35 U.S.C. 103 as being unpatentable over US 2019/0233847 A1 (hereinafter Savage; as cited in the IDS filed 05/06/2022; of record), as applied to claim 1 above (see section Claim Rejections - 35 USC § 102), and further in view of US 2020/0172931A1 (hereinafter Liu; as cited in the IDS filed 05/06/2022).
Claims 156 and 157 are rejected under 35 U.S.C. 103 as being unpatentable over US 2019/0233847 A1 (hereinafter Savage; as cited in the IDS filed 05/06/2022; of record) in view of Oakes et al., 2019 (as cited in the IDS filed 05/06/2022; of record), as applied to claim 1 above, and further in view of US 2020/0172931A1 (hereinafter Liu; as cited in the IDS filed 05/06/2022).
The applied reference has a common Applicant, Assignee, and Inventor with the instant application. Based upon the earlier effectively filed date of the reference (07/28/2017), it constitutes prior art under 35 U.S.C. 102(a)(2).
This rejection under 35 U.S.C. 103 might be overcome by: (1) a showing under 37 CFR 1.130(a) that the subject matter disclosed in the reference was obtained directly or indirectly from the inventor or a joint inventor of this application and is thus not prior art in accordance with 35 U.S.C.102(b)(2)(A); (2) a showing under 37 CFR 1.130(b) of a prior public disclosure under 35 U.S.C. 102(b)(2)(B); or (3) a statement pursuant to 35 U.S.C. 102(b)(2)(C) establishing that, not later than the effective filing date of the claimed invention, the subject matter disclosed and the claimed invention were either owned by the same person or subject to an obligation of assignment to the same person or subject to a joint research agreement. See generally MPEP § 717.02.
The disclosure of Savage, as well as the combined disclosures of Savage and Oakes et al., 2019 are described above and applied as before. However, these disclosures do not teach the fusion protein amino acid sequences of instant claims 156 and 157.
With regard to claims 156 and 157, which respectively recite “the fusion protein [of claim 1] comprises an amino acid sequence that is at least 80%” or “90% identical to any one of SEQ ID NOs: 72-81,” while Savage and Oakes et al., 2019 disclose circularly permuted Cas9 species derived from S. pyogenes Cas9 (Table 2 and Table 1, respectively) as in instant claim 1 (set forth above), they do not disclose amino acid sequences that are at least 90% identical to any one of SEQ ID NOs: 72-81, as instantly claimed.
However, this deficiency is cured by Liu, which discloses evolved base editors (and fusion proteins comprising the same) with increased efficiency and/or decreased requirement for specific sequence-context at an editing site (abstract; paragraph [0013]). Liu discloses that SEQ ID NO: 15 taught therein corresponds to an evolved base editor fusion protein (paragraphs [0020], [0372], and [0374]; claim 87). As shown in the alignment in Appendix V, SEQ ID NO: 15 of Liu is 92.9% identical to instant SEQ ID NO: 76. Thus, Liu discloses a fusion protein amino acid sequence that is at least 90% identical to instant SEQ ID NO: 76, as instantly claimed.
Given that Savage and Oakes et al., 2019 collectively disclose the circularly permuted fusion protein of claim 1 (as set forth above), that Liu discloses evolved base editors (and fusion proteins comprising the same) comprising SEQ ID NO: 15 taught therein with increased efficiency and/or decreased requirement for specific sequence-context at an editing site, it would have been obvious to someone of ordinary skill in the art before the effective filing date of the claimed invention to utilize the fusion protein disclosed in Liu in the circularly permuted fusion protein collectively disclosed by Savage and Oakes et al., 2019 to predictably produce a circularly permuted fusion protein with increased efficiency and/or decreased requirement for specific sequence-context at an editing site. One would have been motivated to make such a modification in order to receive the expected benefit of producing a circularly permuted fusion protein with increased efficiency and/or decreased requirement for specific sequence-context at an editing site.
Allowable Subject Matter
Claim 155 is objected to as being dependent upon a rejected base claim, but would be allowable if rewritten in independent form including all of the limitations of the base claim and any intervening claims.
The following is a statement of reasons for the indication of allowable subject matter:
While sequences up to 99.9% identical to instant SEQ ID NOs: 295-299 (i.e. SEQ ID NO: 34 of Savage is 99.9% identical to instant SEQ ID NO: 298) were publicly available prior to the effective filing date of the claimed invention, the only sequences comprising the instantly claimed sequences were neither publicly available nor effectively filed prior to the effective filing date of the claimed invention. For example, although SEQ ID NO: 15 of US 2023/0021641 A1 (as cited in the IDS filed 05/21/2025) comprises 100% identity to instant SEQ ID NO: 298, this sequence was not disclosed in the provisional application filed 08/23/2018 and thus is not entitled to an effective filing date of 08/23/2018. The next filing date (08/174/2019) post-dates the effective filing date of the instant application (08/08/2019), meaning SEQ ID NO: 15 of US 2023/0021641 A1 (as cited in the IDS filed 05/21/2025) was not effectively filed prior to the effective filing date of the instant application, as required for a rejection under 35 U.S.C. § 102(a)(2). Accordingly, SEQ ID NOs: 295-299 are considered to be free of the prior art.
Conclusion
Claims 1, 3-5, 10-12, 14, 16, 18, 19, 36, 59, 60, 75, 123, 153, 154, 156, and 157are rejected.
Claim 155 is objected to.
Applicant's amendment necessitated the new ground(s) of rejection presented in this Office action. Accordingly, THIS ACTION IS MADE FINAL. See MPEP § 706.07(a). Applicant is reminded of the extension of time policy as set forth in 37 CFR 1.136(a).
A shortened statutory period for reply to this final action is set to expire THREE MONTHS from the mailing date of this action. In the event a first reply is filed within TWO MONTHS of the mailing date of this final action and the advisory action is not mailed until after the end of the THREE-MONTH shortened statutory period, then the shortened statutory period will expire on the date the advisory action is mailed, and any nonprovisional extension fee (37 CFR 1.17(a)) pursuant to 37 CFR 1.136(a) will be calculated from the mailing date of the advisory action. In no event, however, will the statutory period for reply expire later than SIX MONTHS from the mailing date of this final action.
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/SARAH E ALLEN/ Examiner, Art Unit 1637