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 .
Election/Restrictions
Applicant’s election of Group I (i.e., an engineered Cas protein) in the reply filed on September 16, 2024 is acknowledged.
Claim18-21, 23-31, and 33-40 are withdrawn from further consideration pursuant to 37 CFR 1.142(b) as being drawn to a nonelected invention, there being no allowable generic or linking claim.
Amendments Received
Amendments to the claims were received and entered on 07/22/2026.
Status of Claims
Claim 16 has been cancelled.
Claims 1, 7-9, 13-15, 18-21, 23-31, and 33-44 are currently pending.
Claims 1, 7-9, 13-15, and 41-44 are under consideration, as claims 18-21, 23-31, and 33-40 are withdrawn.
Priority
The present application claims status as a 371 (National Stage) of PCT/US2020/033855 filed on May 20, 2020. Acknowledgment is made of applicant’s claim for benefit under 35 U.S.C. 119(e) of Provisional application No. 63/000,293, filed on March 26, 2020 and Provisional application No. 62/850,516, filed on May 20, 2019. The present application and all claims are being examined with an effective filing date of May 20, 2019. In future actions, the effective filing date may change due to amendments or further review of priority documents.
Withdrawn Objections
In view of Applicant’s amendments, the objection to claim 1 is hereby withdrawn.
Withdrawn Rejections
In view of Applicant’s cancellation of claim 16, all rejections of claim 16 are now moot and are hereby withdrawn.
In view of Applicant’s amendments, rejection of claim 15 under 35 USC § 112(b) is hereby withdrawn.
In view of Applicant’s amendments and remarks filed on 07/22/2026, rejections of claims 14-15 and 43 under 35 USC § 112(a) are hereby withdrawn.
Claim Interpretation
Claim 1 recites an engineered Cas protein “lacking a REC1 domain a REC2 domain”. For examination purposes, this limitation is interpreted as requiring the absence of both a REC1 domain and a REC2 domain. The specification provides guidance as to the meaning of “lacking” a Rec domain. In particular, the specification discloses that a Cas protein may “lack or substantially lack” a Rec domain, may lack “a portion” or a “substantial portion” of a Rec domain, or may lack a domain having “structural similarity” to a Rec domain (see, e.g., para 0065–0066). The specification further describes embodiments in which Rec domains are partially deleted, structurally disrupted, or no longer retain recognizable domain features. In view of these disclosures, the claim term “lacking a REC1 domain and a REC2 domain” is interpreted under the broadest reasonable interpretation as encompassing proteins in which the REC1 and REC2 domains are not structurally or functionally present as recognizable domains, including embodiments in which such domains are substantially deleted or disrupted, and does not require complete removal of every amino acid residue corresponding to those domains.
Maintained/Modified Rejections Necessitated by Amendment
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, 7-9, 13, and 41 are rejected under 35 U.S.C. 103 as being unpatentable over Tan et al. (WO 2018/074979, cited in the IDS), as evidenced by Makarova et al. (Annotation and Classification of CRISPR-Cas Systems", Methods in Molecular Biology, Vol. 1311, 2015, 27 pages, cited in the IDS) and Kapitonov, et al., ("ISC, a Novel Group of Bacterial and Archaeal DNA Transposons That Encode Cas9 Homologs", J Bacteriol., doi: 10.1128/JB.00783-15, Vol. 198, No. 5, December 28, 2015, pp. 797-807, cited in the IDS).
Regarding claims 1 and 41, Tan et al. teaches that despite the potential of CRISPR-Cas for genome engineering, the system suffers from certain shortcomings, including the large size of Cas9 proteins in particular, which adversely affects delivery both in vitro and in vivo. Tan et al. further teaches that due to its large size, and the packaging limitations of commonly used delivery vectors such as adeno-associated virus (AAV), there is little capacity for incorporating Cas9 into delivery systems and that “there is little room for customization and addition of other genetic elements” as a result, thereby motivating the development of smaller, truncated variants. Tan et al. teaches engineered CRISPR-Cas proteins, wherein the polypeptide has at least 50% sequence identity to Streptococcus pyogenes Cas9 (also called SpCas9 when the source is S. pyogenes) having the amino acid sequence set forth in SEQ ID NO: 1 over its entire length, wherein said polypeptide comprises at least one deletion selected from the group consisting of ΔΗΝΗ (Δ775-909), ΔRuvCIII-b (Δ1002-1074), ΔREC1 -a (Δ510-655), ΔREC1 - b (Δ525-587), ΔREC1 -C (Δ662-710), ΔREC2 (Δ180-308), ΔREC2-a (Δ212-244), ΔREC2-b (Δ244-276), ΔREC2-C (Δ276-308), ΔREC2-d (Δ199-283), ΔREC2-e (Δ198-257), ΔREC2-f (Δ235- 286), ΔREC2-g (Δ217-266), ΔREC3 (Δ498-712) and combinations thereof, wherein the position numbering is in accordance with SEQ ID NO:1, and wherein the polypeptide has DNA-binding activity (Specification, pg. 1, lines 17-18 and pg. 2, lines 33-41). It is noted that Tan et al. explicitly demonstrates that REC domains are amenable to substantial deletion while retaining function. For example, Tan et al. discloses constructs (e.g., SEQ ID NO: 17-19) in which the REC2 domain or substantial portions of the REC1 domain are removed, while maintaining DNA-binding activity. Thus, Tan et al. demonstrates that REC domains need not remain intact and may be progressively reduced or structurally disrupted.
An invention would have been obvious to a person of ordinary skill in the art if some teaching in the prior art would have led that person to combine prior art reference teachings to arrive at the claimed invention. Before the effective filing date of the invention, Tan et al. expressly teaches that one or more domains of SpCas9 may be deleted, including deletions within REC-associated regions, and that such deletions may be combined to generate compact variants while retaining DNA-binding activity. In view of these teachings, a person of ordinary skill in the art would have been motivated to reduce Cas9 protein size through any combinations of domain deletions in order to meet delivery constraints, including generating variants having both REC1 and REC2, or substantial portions thereof, deleted, as protein size is a result-effective variable subject to routine optimization. Additionally, Tan et al. demonstrates that Cas9 tolerates multiple deletions across domains, including deletion of REC2 and substantial portions of REC1, while retaining DNA-binding activity, thereby evidencing that REC domains need not remain intact. Given Tan et al.’s teachings of combinatorial deletions and functional tolerance to truncation, such modifications would have been routine protein engineering design choices, and a person of ordinary skill in the art would have had a reasonable expectation of success in obtaining a truncated Cas protein within the claimed domain configuration. Therefore, the invention as a whole would have been prima facie obvious to a person of ordinary skill in the art before the effective filing date of the claimed invention.
Regarding claim 7, Tan et al. teaches that SpCas9 comprises a RuvC nuclease domain (see, e.g., Fig. 1), which is structurally organized into multiple subdomains, including RuvC-I, RuvC-II, and RuvC-III.
Regarding claims 8-9, Tan et al. teaches Cas9 proteins based on S. pyogenes Cas9, which “binds to a target genomic locus and catalyzes DNA cleavage”. Tan et al. further teaches that “enzymatic action by Cas9 derived from Streptococcus pyogenes or any closely related Cas9 generates double stranded breaks at target site sequences” (pg. 28., lines 21-24).
Regarding claim 13, as evidenced by Makarova et al., the SpCas9 proteins taught by Tan et al., are Class 2, Type II CRISPR-Cas proteins (pg. 2, 3rd para).
Response to Arguments for Prior Art Rejections under 35 USC § 103
In the response filed on 07/22/2026, Applicant argues that Tan’s SEQ ID NO: 26 deletes HNH and part of RuvC rather than retaining both nuclease domains while lacking REC1 and REC2. Applicant further argues that Tan’s reported losses of activity following certain deletions undermine a reasonable expectation of success. These arguments have been considered in full and are not persuasive.
The present rejection does not rely on SEQ ID NO: 26 as an example of the claimed protein. As amended, claim 1 contains no protein-size limitation and requires the presence of HNH and RuvC and the absence of REC1 and REC2. Tan expressly teaches that its identified deletions may be made individually or in different combinations. Those deletions include REC1-associated and REC2 deletions without requiring deletion of HNH or RuvC. Tan’s SEQ ID NOs: 17–19 further exemplify individual REC-associated deletions in constructs that retain the HNH and RuvC regions.
Applicant’s discussion of abolished reporter-gene activation following removal of RuvC addresses a deletion not proposed in the rejection. Tan’s reported changes in cleavage or reporter-gene activity following other deletions likewise do not establish that the claimed domain configuration could not reasonably be obtained. Claim 1 does not recite a minimum cleavage activity or reporter-gene activation. Accordingly, Applicant’s arguments do not overcome the rejection.
New Rejections
Applicant amended claim 1 to remove the limitation on the Cas protein’s amino acid length. Claims 14 and 15 depend from claim 1 and therefore no longer include that size limitation. This amendment necessitated consideration of the FokI–Cas9 fusion taught by Guilinger et al. and the new ground of rejection set forth below. See MPEP § 706.07(a).
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 14-15 are rejected under 35 U.S.C. 103 as being unpatentable over Tan et al. as applied to claim 1 above, and further in view of Guilinger et al. (Fusion of catalytically inactive Cas9 to FokI nuclease improves the specificity of genome modification, (2014) Nat Biotechnol 32, 577–582, cited in a previous office action).
The teachings of Tan et al. as applied to claim 1 have been discussed above. Briefly, Tan et al. teaches engineered Cas9 proteins for the purpose of, inter alia, customization and addition of other genetic elements. Specifically, Tan et al. teaches having deletions in REC-associated regions while retaining HNH and RuvC nuclease domains. However, Tan et al. does not expressly teach adding a third nuclease domain to such a protein.
Regarding claim 14, Guilinger et al. teaches a fusion protein comprising a FokI nuclease domain joined to catalytically inactive Cas9. The Cas9 portion directs the fusion protein to a target DNA sequence, while FokI supplies DNA cleavage activity. Guilinger et al. explains that cleavage requires two FokI–Cas9 fusion proteins to bind appropriately spaced target sites, thereby improving the specificity of genome modification by reducing cleavage at sites bound by only one fusion protein (p. 577, abstract and bottom of right column; p. 578, and Fig. 1a). The fused FokI domain is an additional nuclease domain relative to the HNH and RuvC domains retained in Cas9.
Regarding claim 15, Guilinger et al. further teaches that the Cas9 portion of the FokI–Cas9 fusion contains the inactivating mutations D10A and H840A (pg. 578). Tan et al. teaches that to disable cleavage function “the common practice is to mutate a catalytic residue in each of the two nuclease domains (D10A and H840A in SpCas9)” (pg. 2, lines 10-13). Therefore, the D10A and H840A mutations of Guilinger et al. inactivate the RuvC and HNH domains.
An invention would have been obvious to a person of ordinary skill in the art if some teaching in the prior art would have led that person to combine prior art reference teachings to arrive at the claimed invention. In view of Tan et al. teachings that the size of spCas9 limits the room available for adding genetic elements, it would have been obvious to a person of ordinary skill in the art before the effective filing date to engineer smaller Cas9 variants according to Tan et al.’s REC-associated deletions, and further modifying them with the FokI–Cas9 fusion taught by Guilinger et al. because Guilinger et al. teaches adding a FokI nuclease domain to catalytically inactive Cas9 results in DNA cleavage requiring two guided fusion proteins to bind appropriately spaced target sites, thereby improving cleavage specificity. A person of ordinary skill would therefore have been motivated to reduce the size of the Cas9 portion using Tan et al.’s disclosed deletions while adding Guilinger et al.’s FokI domain to provide that more specific cleavage mechanism. There is a reasonable expectation of success given Tan et al.’s successful demonstration of engineering smaller Cas9 variants for the incorporation of additional elements by deleting various domains, including REC domains, and Guilinger et al.’s successful demonstration of fusing FokI to catalytically inactive Cas9. Therefore, the invention as a whole would have been prima facie obvious to a person of ordinary skill in the art before the effective filing date of the claimed invention.
Allowable Subject Matter
Claims 42-44 are 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.
Conclusion
No claim is in condition for allowance.
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 NAGHMEH NINA MOAZZAMI whose telephone number is (703)756-4770. The examiner can normally be reached Monday-Friday, 9:00-5:00.
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If attempts to reach the examiner by telephone are unsuccessful, the examiner’s supervisor, Robert Mondesi can be reached at 408-918-7584. The fax phone number for the organization where this application or proceeding is assigned is 571-273-8300.
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/NAGHMEH NINA MOAZZAMI/ Examiner, Art Unit 1652
/ROBERT B MONDESI/ Supervisory Patent Examiner, Art Unit 1652
