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 .
Applicants’ reply to the October 6, 2025 Office Action, filed January 6, 2026, is acknowledged. Applicants previously canceled claims 2, 4, 14-15, and 17, and now cancel claims 3 and 5. Claims 10-13 and 18-19 remain withdrawn from consideration as being drawn to a non-elected invention and/or species. Applicants amend claims 1, 6-8, 21-23, and 25-26. Claims 1, 6-9, 16, and 20-26 are under examination.
Any objection or rejection of record in the previous Office Action, mailed October 6, 2025, which is not addressed in this action has been withdrawn in light of Applicants’ amendments and/or arguments. This action is FINAL.
Priority
Receipt is acknowledged of certified copies of papers required by 37 CFR 1.55. However, it is noted that a certified translation of Chinese Patent Application No. CN 201710611651.8 has not yet been filed.
Claim Rejections - 35 USC § 112
The following is a quotation of the first paragraph of 35 U.S.C. 112(a):
(a) IN GENERAL.—The specification shall contain a written description of the invention, and of the manner and process of making and using it, in such full, clear, concise, and exact terms as to enable any person skilled in the art to which it pertains, or with which it is most nearly connected, to make and use the same, and shall set forth the best mode contemplated by the inventor or joint inventor of carrying out the invention.
The following is a quotation of the first paragraph of pre-AIA 35 U.S.C. 112:
The specification shall contain a written description of the invention, and of the manner and process of making and using it, in such full, clear, concise, and exact terms as to enable any person skilled in the art to which it pertains, or with which it is most nearly connected, to make and use the same, and shall set forth the best mode contemplated by the inventor of carrying out his invention.
Claims 8 and 23 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. This is a new matter rejection. This is a new rejection necessitated by Applicants’ amendments.
The instant specification, as well as the PCT and Chinese specifications to which the instant application claims priority, as originally filed does not provide support for the invention as now claimed: “accession number of which is Q9GZX7” at claims 8 and 23. The specification does not provide sufficient blazemarks, nor direction for the instant methods encompassing the above-mentioned limitations, as currently recited. While the Chinese priority document does list Q9GX7.1, the exact accession number is not present in the PCT or Chinese applications, as presently claimed in the instant application.
Thus, the instant claims now recite limitations which were not disclosed in the specification as-filed, and now change the scope of the instant disclosure as-filed. Such limitations recited in the present claims, which did not appear in of the instant specification, nor in the Chinese or PCT applications to which priority is claimed, introduce new concepts and violate the description requirement of the first paragraph of 35 U.S.C. § 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.
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 1, 6-9, 16, and 20-26 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. These are new or modified rejections necessitated by Applicants’ amendments.
Claim 1 recites the limitation "the complementary sequence of the polypyrimidine region" in line 36. There is insufficient antecedent basis for this limitation in the claim.
Claims 6-9, 16, and 20-26 depend from claim 1, and are therefore included in this rejection.
Claim 8 attempts to set forth a sequence for the cytosine deaminase by use of an accession number at lines 12 and 22. While inclusion of the accession qualifies as an intent to incorporate a specific sequence, this accession number fails to uniquely identify the specific sequence intended to be encompassed by the claims and is an improper incorporation by reference because sequences of accession numbers are subject to change over time. In addition, there is no information in the claim as to which depository the sequence of the accession number A9GZX7 relates.
Further, the amino acid sequence of the cytosine deaminase comprises at least 9-182, 1-182, 1-185, or 1-190, although now claimed as an accession number. However, there is still no sequence claimed to which the cytosine deaminase is compared. Thus, because there is no sequence to compare the cytosine deaminase amino acids, the metes and bounds of the claim are unclear. For the purpose of examination, the claim is interpreted to encompass any cytosine deaminase having at least 182 amino acids.
Claim 8 recites that the mutant comprises substitution mutations at amino acid residues 10, 82, and 156, with specific substitutions being K10E, T82I, and E156G, although now claimed as an accession number. However, there is still no sequence claimed to which the cytosine deaminase is compared. Thus, because there is no sequence to compare the cytosine deaminase amino acids, the metes and bounds of the claim are unclear. For the purpose of examination, the claim is interpreted to encompass any cytosine deaminase having at least the amino acid residues K10, T82, and E156.
Claim 23 attempts to set forth a sequence for the cytosine deaminase by use of an accession number at lines 3 and 7. While inclusion of the accession qualifies as an intent to incorporate a specific sequence, this accession number fails to uniquely identify the specific sequence intended to be encompassed by the claims and is an improper incorporation by reference because sequences of accession numbers are subject to change over time. In addition, there is no information in the claim as to which depository the sequence of the accession number A9GZX7 relates.
Further, the amino acid sequence of the cytosine deaminase comprises at least 9-182, although now claimed as an accession number. However, there is still no sequence claimed to which the cytosine deaminase is compared. Thus, because there is no sequence to compare the cytosine deaminase amino acids, the metes and bounds of the claim are unclear. For the purpose of examination, the claim is interpreted to encompass any cytosine deaminase having at least 182 amino acids.
Claim 23 recites that the mutant comprises substitution mutations at amino acid residues 10, 82, and 156, with specific substitutions being K10E, T82I, and E156G, although now claimed as an accession number. However, there is still no sequence claimed to which the cytosine deaminase is compared. Thus, because there is no sequence to compare the cytosine deaminase amino acids, the metes and bounds of the claim are unclear. For the purpose of examination, the claim is interpreted to encompass any cytosine deaminase having at least the amino acid residues K10, T82, and E156.
Claim Rejections - 35 USC § 103
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 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.
Claims 1, 6-8, 16, 20-24, and 26 are rejected under 35 U.S.C. 103 as being unpatentable over Liu et al. (PCT Patent Application Publication No. WO 2017/070632, filed April 27, 2017 and cited in the Information Disclosure Statement filed May 14, 2021), as evidenced by Bannikov et al. (51(4) Molecular Biology 514-525 (2017)), in view of Gee et al. (2017 Stem Cells International 8765154, 1-11 (May 18, 2017) and Komor et al. (533 Nature 420-424, Methods (2016), and cited in the Information Disclosure Statement filed May 14, 2021). This rejection is modified as necessitated by Applicants’ amendments, and is maintained.
Regarding claim 1, Liu discloses fusion proteins of Cas9 and a deaminase (abstract). Liu discloses that the fusion protein may be used to edit splice sites in order to treat a disease (paragraph [00381]). Liu discloses delivery of the fusion protein and an sgRNA molecule to a cell in order to regulate RNA splicing of a gene (paragraphs [0005]-[0006], [00295], and paragraph [00381]). Liu discloses that the Cas9 can be active, a nickase, or inactive (i.e., having partial or no nuclease activity) (paragraphs [0005] and [0012]). Liu discloses multiple C to T conversion (paragraphs [00139]-[00140] and Figures 103-104). Liu discloses that the deaminase can be a cytosine deaminase, such as APOBEC (paragraphs [0009]-[0013]). While Liu does not explicitly disclose that the Cas9 has helicase activity, Bannikov discloses that Cas9 does have helicase activity (page 516, paragraph bridging columns 1 and 2). Liu discloses that the fusion protein can be expressed in a cell, along with the sgRNA (paragraphs [0006]-[0007] and [0032]-[0033]). Liu discloses that the sgRNA recognized by the Cas enzyme and binds to a target sequence (paragraphs [0006]-[0007] and [0032]-[0033]).
Regarding claim 6, Liu discloses that the fusion protein can include a uracil glycosylase inhibitor sequence (UGI) (paragraphs [0017]-[0018]).
Regarding claim 7, Liu discloses that the Cas9 can be active, a nickase, or inactive (i.e., having partial, or single stranded break ability, or no nuclease or DNA double-strand break ability) (paragraphs [0005] and [0012]). Liu discloses that the cytosine deaminase can be full length (paragraphs [0009]-[0010]). Liu discloses that the fusion protein can have a nuclear localization domain (paragraph [00202]).
Regarding claim 8, Liu discloses that the Cas9 can include mutations at D10, including D10A, which result in a Cas9 nickase (paragraphs [0014]-[0015] and [00258]). Liu discloses that the deaminase is human APOBEC1, which has a sequence comprising 236 amino acids, which is interpreted as the APOBEC1 has at least residues 1-190 (SEQ ID NO: 282).
Regarding claim 16, Liu discloses that the Cas enzyme can be Cas9 from Streptococcus pyogenes, Staphylococcus aureus, or Streptococcus thermophilus (paragraphs [0006], [00128], and [00146]).
Regarding claim 20, Liu discloses that the method can be used to treat a disease caused by genetic mutations (paragraphs [00380]-[00381]).
Regarding claim 21, Liu discloses that the disease can be Duchenne myasthenia caused by a mutation in the DMD gene, with treatment being DMD editing of exon 51 (paragraph [00381]).
Regarding claim 22, Liu discloses fusion proteins of Cas9 and a deaminase (abstract). Liu discloses that the fusion protein may be used to edit splice sites in order to treat a disease (paragraph [00381]). Liu discloses delivery of the fusion protein and an sgRNA molecule to a cell in order to regulate RNA splicing of a gene (paragraphs [0005]-[0006], [00295], and paragraph [00381]). Liu discloses that the Cas9 can be active, a nickase, or inactive (i.e., having partial or no nuclease activity) (paragraphs [0005] and [0012]). Liu discloses that the fusion protein can include a uracil glycosylase inhibitor sequence (UGI) (paragraphs [0017]-[0018]). Liu discloses that the fusion protein can have a nuclear localization domain (paragraph [00202]). Liu discloses that the fusion protein can have a linker between the deaminase and the Cas9 (paragraph [0009]).
Regarding claim 23, Liu discloses that the Cas9 can include mutations at D10, including D10A, which result in a Cas9 nickase (paragraphs [0014]-[0015] and [00258]). Liu discloses that the deaminase is human APOBEC1, which has a sequence comprising 236 amino acids, which is interpreted as the APOBEC1 has at least residues 1-190 (SEQ ID NO: 282).
Regarding claim 24, Liu discloses that the method can employ a kit comprising the fusion protein and an sgRNA (paragraphs [0012], [0032], and [00281]-[00283]).
Liu does not explicitly disclose or suggest that the regulation of RNA splicing at intronic splice sites induces exon skipping. Liu does not explicitly disclose or suggest that alterations in splicing can result in a GT:AT mutation.
Regarding claim 1, Gee discloses targeting of dystrophin gene (DMD) using Cas9, where an sgRNA can target a splicing acceptor, which can result in exon deletion/exon skipping (Figure 1 and Table 2). Gee discloses targeting the DMD gene at exon 50 (Tables 1 and 2). Gee discloses that a fusion protein of Cas9 nickase (i.e., partial nuclease activity) and cytosine deaminase (APOBEC1 or AID homologues) can provide conversion of Cs to Ts, which correct T→C mutations (Figure 2).
Regarding claim 25, Gee discloses targeting the DMD gene at exon 50 (Tables 1 and 2).
Regarding claim 26, Gee disclose that Cas9 can be delivered to DMD patients using viral particles, such as adeno-associated viruses, adenoviruses, or herpes simplex viruses (page 8, paragraph bridging columns 1 and 2).
Regarding claim 1, Komor discloses editing of target bases using a Cas9-cytosine deaminase fusion protein (abstract). Komor discloses C→T conversions (abstract). Komor further discloses that a guide RNA can target the fusion protein to a target sequence, where the resulting G:U heteroduplex results in a permanent conversion to an A:T basepair (Figure 1). Komor discloses treatment of Duchenne muscular dystrophy with fusion proteins of Cas9 and cytosine deaminase (abstract and Figure 1).
It would have been obvious to one with ordinary skill in the art before the effective filing date of the claimed invention to modify Liu’s (as evidenced by Bannikov) Cas9-cytosine deaminase method of regulating splice sites with Gee and Komor because Gee and Komor provide for results of the deamination reaction, which will produce the claimed exon skipping, as well as providing for specific changes to genes, such as the DMD gene, as disclosed by each of Liu (as evidenced by Bannikov), Gee, and Komor. It addition it would have been obvious to one with ordinary skill in the art that the Cas9-cytosine deaminase/sgRNA Liu (as evidenced by Bannikov), Gee, and Komor can be delivered using the virus particles of Komor because this is a well-known method of delivering nucleic acids for expression in a cell both in vivo and in vitro. One of ordinary skill in the art would have been motivated to deliver the Cas9-cytosine deaminase/sgRNA to a cell or a patient in order to correct disease related genetic mutations.
Claim 25 is rejected under 35 U.S.C. 103 as being unpatentable over Liu (as evidenced by Bannikov) in view of Gee and Komor, as applied to claims 1, 3, 6-8, 16, 20-24, and 26 above, and further in view of Sazani et al. (U.S. Patent No. 8,871,918, issued October 28, 2014). This rejection is modified as necessitated by Applicants’ amendments, and is maintained.
Liu (as evidenced by Bannikov), Gee, and Komor disclose a method for regulating RNA splicing of a gene in a cell, as discussed above.
Liu (as evidenced by Bannikov), Gee, and Komor fail to disclose or suggest that the DMD gene is targeted by an sgRNA binds to a sequence in the DMD exon 50, such that the target binding region of the sgRNA is SEQ ID NO: 51.
Sazani discloses antisense molecules that can bind do a target site in the human dystrophin gene to induce exon skipping (abstract and column 3, lines 37-42). Sazani discloses that the molecules target a splice site of preprocessed human dystrophin and can be complementary to the messenger RNA dystrophin transcript (column 4, lines 35-41). Sazani disclose the same targeting sequence as instant SEQ ID NO: 51 (SEQ ID NO: 288) (Appendix I).
It would have been obvious to one with ordinary skill in the art before the effective filing date of the claimed invention to use Sazani’s targeting sequence in DMD exon 50 in the method of inducing exon skipping disclosed and suggested by Liu (as evidenced by Bannikov), Gee, and Komor because using Sazani’s targeting sequence to induce exon skipping in the method disclosed and suggested by Liu (as evidenced by Bannikov), Gee, and Komor because this will provide a more targeted approach to correcting the genetic disease causing Duchenne myasthenia, as required by the claims.
Response to Amendments and Arguments
Regarding the rejections of claims 8 and 23 under 35 U.S.C. § 112(b)/second paragraph, it is noted that Applicants are attempting to claim that the cytosine deaminase has the sequence based on the accession number Q9GZX7. However, not only is a depository not given in the claims or the specification (and is only recited as Q9GZX7.1 in the Chinese priority document, the metes and bounds of the claims are still unclear and indefinite because neither amino acid residues 9-182 nor mutations at amino acid residues 10, 82, and 156 can be determined because there is no SEQ ID NO: associated with either limitation.
Regarding the rejections under 35 U.S.C. § 103, Applicants’ arguments have been fully considered, but are not deemed to be persuasive. Applicants assert that the cited prior art references do not disclose or suggest the “critical, interrelated technical features” of the amended claims, and do not account for the invention’s “unexpected technical effects.” Applicants assert that there is not motivation to combine the cited prior art references. Applicants assert 1) that the Cas/Cpf1 enzyme based fusion protein is not disclosed; 2) the precise definitions of single-strand break or no DNA double-strand break ability is not disclosed; 3) that the three specific mutations (AG→AA, GT→AT, and multiple Cs→Ts) are not disclosed; and 4) that synergistic sgRNA-enzyme specific recognition for splice site targeting is not disclosed.
To begin, Applicants appear to be attacking each cited prior art reference individually. However, one cannot show nonobviousness by attacking references individually where the rejections are based on combinations of references. In re Keller,642 F.2d 413, 208 USPQ 871 (CCPA 1981); In re Merck & Co., Inc., 800 F.2d 1091, 231 USPQ 375 (Fed. Cir. 1986). Here, each of the cited prior art references discloses, and together the references suggest a method of regulating RNA splicing of a gene in a cell. For example, Liu discloses fusion proteins of Cas9 and a deaminase that may be used to edit splice sites in order to treat a disease. And Liu discloses that the Cas9 can be active, a nickase, which provides a single stand break ability, or inactive, which provides for lacking the ability to provide double stranded nucleic acid breaks. Regarding the mutational ability, Liu discloses multiple C to T conversion. Further, while Liu does not explicitly disclose that the Cas9 has helicase activity, Bannikov discloses that Cas9 does have helicase activity.
Regarding Applicants’ assertions regarding Cpf1, Applicants are correct that Liu discloses a Cas9-deaminase fusion protein. However, the claim is written in the alternative, and Liu’s and Komor’s disclosure of the Cas9-deaminase fusion protein satisfies the claim limitations. As does Liu’s disclosure of multiple C→T mutations, Gee’s targeting of DMD exon 50, and Komor’s Cas9-cytosine deaminase and C→T and G:U→A:T conversions.
Regarding Applicants’ discussion of Bannikov, this reference is cited as an evidentiary reference, showing that Cas9 has helicase activity. And the additional secondary references provide each of the additional claim limitations. Gee, for example provides for exon skipping and C→T conversions using Cas9 systems for treating DMD patients. Komor also provides for use of Cas9-cytosine deaminase fusion proteins and shows editing for treatment of DMD, as well as G:U→A:T conversion. Therefore, the cited prior art references, taken together, and as a whole, provides one of ordinary skill in the art a roadmap leading directly to the claimed invention.
Applicants assert that there are synergistic effects that are not shown by any single reference. However, contrary to Applicants’ assertion and attacking of the individual references, it is the combination of references that provide the exact results that one ordinarily skilled in the art would have expected, having Liu, as evidenced by Bannikov in view of Gee and Komor (with or without Sazani, who also discloses exon skipping the targeting sequence in DMD exon 50). Each of the cited references, taken together and as a whole, would have led one of ordinary skill in the art directly to the claimed invention.
In addition, Applicants have not shown that that synergistic sgRNA-enzyme specific recognition for splice site targeting would be unexpected. Applicants’ invention do show exon skipping, but fail to provide objective and factually supported evidence that such levels of exon skipping efficiency are unpredictable. Rather, because Liu, as evidenced by Bannikov, and in view of Gee and Komor (with or without Sazani), the combination of references, each disclosing either Cas9-cytosine deaminase fusion proteins for targeting sequences/inducing exon skipping and/or treating DMD by targeting a specific exon (exon 50). Applicants have provided only arguments of counsel, Applicants have provided only arguments of counsel, and arguments of counsel cannot take the place of factually supported objective evidence. See, e.g., In re Huang, 100 F.3d 135,139-40, 40 USPQ2d 1685, 1689 (Fed. Cir. 1996); In re De Blauwe, 736 F.2d 699, 705, 222 USPQ 191, 196 (Fed. Cir. 1984).
For all these reasons and those listed above, Liu, as evidenced by Bannikov, in view of Gee and Komor (with or without Sazani) renders the instant invention obvious.
Conclusion
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.
Any inquiry concerning this communication or earlier communications from the examiner should be directed to NANCY J LEITH whose telephone number is (313)446-4874. The examiner can normally be reached Monday - Thursday 8:00 AM - 6:30 PM.
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NANCY J. LEITH
Primary Examiner
Art Unit 1636
/NANCY J LEITH/Primary Examiner, Art Unit 1636