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 .
Status of Application/Amendments/Claims
Applicant’s response filed on 12/9/2025 has been considered. No claims have been amended. Claims 1-3 and 5-39 are pending. Claims 24-39 are currently withdrawn from further consideration pursuant to 37 CFR 1.142 (b) as being drawn to a nonelected invention, there being no allowable generic or linking claim. Claims 1-3 and 5-23 are the subject of the present Official action. The text of those sections of Title 35, U.S. Code not included in this action can be found in a prior Office action.
Priority
Applicant’s claim for the benefit of a prior-filed application PRO 62/671,969 and PCT/US2019/032541 filed on 5/15/2018 and 5/15/2019, respectively, under 35 U.S.C 119(e) or under 35 U.S.C 120, 121 or 365(c) is acknowledged.
Accordingly, the effective priority date of the instant application is granted as 5/15/2018.
Claim Interpretation
dCas9 will be given its broadest reasonable interpretation and read on any Cas9 mutant which has an inactivated HNH and Ruv C nuclease.
It is noted that without specific SEQ ID NO references, the 90% or greater sequence identity limitation described in claim 22 applies to any of the AAV serotypes at any length.
Furthermore, applicant should carefully review claims 18-20 for any instance of multiple dependent claims.
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 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.
Claims 1-3 and 5-23 are rejected under 35 U.S.C. 103 as being unpatentable over Davidon et al. WO 2017/062983, published 4/13/2017 (hereinafter Davidon, reference of record) in view of Gersbach et al. US 2019/0127713, published 5/2/2019 (hereinafter Gersbach, reference of record) as evidenced by Thakore et al. "Editing the epigenome: technologies for programmable transcription and epigenetic modulation." Nature methods 13.2 (2016): 127-137 (hereinafter Thakore, reference of record). This rejection is maintained for the same reasons as outlined in the office action mailed on 7/22/2025. A response to applicant’s traversal is found below.
Claim 1: Davidon discloses CRISPR based method for treating and preventing polyglutamine disorders including Huntington’s disease (Davidon. pg 20). Davidon describes the use of Cas9 mutants with inactivated HNH and/or RuvC nuclease (Davidon, pg 11 lines 5-15). In the case where both the HNH and RuvC are inactivated, the Cas9 mutant reads directly on the claimed catalytically inactive dCas9. Davidon describes an expression cassette comprising a first nucleic acid encoding the mutant Cas9 (dCas9) polypeptide, a second nucleic acid encoding a guide polynucleotide that targets the mutant Cas9 polypeptide to a sequence positioned 5’ of the transcriptional start site of an allele encoding a mutant HTT protein (Davidon, pg 2 lines 10-25). However, Davidon does not describe a dCas9 polypeptide fused to a transcriptional repressor as described in claim 1.
Claims 2 and 3: Davidon describes mitigating expression from mutant heterozygous HTT alleles (mHTT) by identifying single nucleotide polymorphisms (SNPs) that either cause or destroy PAM motifs critical for CRISPR editing (Davidon, pg 18 lines 15-20).
Claims 6-7: Davidon describes designing gRNAs that target the 5’ of exon 1 (within the 5’ untranslated region, within the promoter or within the first 2kb 5’ of the transcriptional start site) of an allele encoding a mutant HTT protein (Davidon, pg 2 lines 10-25).
Claims 8-10: Davidon describes mitigating expression from mutant heterozygous HTT alleles (mHTT) by identifying single nucleotide polymorphisms (SNPs) that either cause or destroy PAM motifs critical for CRISPR editing (Davidon, pg 18 lines 15-20). Davidon provides specific embodiments targeting 5’ positions within 0-100 nucleotides from a PAM sequence (Davidon, Fig 3B).
Claims 11: Davidon discloses SEQ ID NO: 133, which is a gRNA that is 46 nucleotides in length and binds to at least 10 nucleotides of SEQ ID NO: 1 (sequence alignment shown below).
PNG
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131
523
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Claims 13: Davidon discloses SEQ ID NO: 193, which is a gRNA that shares 100% sequence similarity to SEQ ID NO: 3 (sequence alignment shown below).
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133
517
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Claims 14: Davidon describes RNA guide polynucleotides (Davidon, pg 2 lines 10-25).
Claims 15-17: Davidon provides a description of polyglutamine (polyQ) disorders, which are generally caused by expanded cytosine-adenine-guanine (CAG) repeats (greater than about 36 repeats) encoding a long polyQ tract in the respective proteins (Davidon, pg 11).
Claims 18-19: Davidon describes recombinant lentiviral vectors comprising the expression cassette (Davidon, pg 13). Davidon describes recombinant AAV vectors comprising the expression cassette and the use of AAV ITR sequences (Davidon, pg 14, and Fig 9).
Claim 5: Gersbach describes the use of catalytically inactive (dCas9) nucleases fused to transcriptional repressor domains like KRAB to generate synthetic repressors capable of highly specific and potent silencing of target genes (Gersbach, para 3).
Claim 12: Gersbach describes guide polypeptides between 10-30 nucleotides in length (Gersbach, para 292).
Claims 20-23: Gersbach describes the use of recombinant AAV vectors for gene therapy applications (Gersbach, para 166-167). Gersbach describes the use of capsid and ITRs from different AAV serotypes (Gersbach, para 303, 219 and Fig 3A, 10B).
It would have been prima facie obvious to one of ordinary skill in the art to use the dCas9 nuclease fused to a transcriptional repressor domain like KRAB for highly specific gene silencing as described by Gersbach to target the 5’ transcriptional start site of an allele encoding the mutant HTT protein described by Davidon as a therapy for Huntington’s disease. It would have been a matter of combining prior art elements according to known methods to yield predictable results for one of ordinary skill to use the CRISPR/Cas9-based gene silencing methods of Gersbach and apply it to the same SNP targets present in mutant HTT proteins as identified by Davidon. One would have been motivated to make this combination in order to epigenetically repress transcription of mutant HTT proteins using the highly effective Cas9- KRAB effector domain disclosed by Gersbach using the gRNAs identified by Davidon. Furthermore, Gersbach demonstrates that using gRNA between 10-30 nucleotides and AAV viral vector serotypes (capsid and ITRs) results in highly specific gene silencing with low off-target effects. One would have a reasonable expectation of successes given that the transcriptional repression mechanism of dCas9-KRAB is known in the art as shown by Gersbach along with the mutational HTT targets described in the present invention.
To further show that one would have been motivated to make this combination with a reasonable expectation of success, Thakore is presented as an evidentiary reference (co-authored by Gersbach). In Table 2, Thakore lists KRAB as a known transcriptional repressor associated with dCas9 nucleases which can target gene promoters (transcriptional start sites). Thakore also describes previous work wherein zinc finger nuclease repressors were engineered to silence mutant Htt in a mouse model of Huntington’s disease and calls for similar approaches to be implemented using programable epigenetic modification with designer DNA-binding domains (e.g. dCas9). Accordingly, in the absence of evidence to the contrary, one of ordinary skill in the art would have considered the claimed invention to have been prima facie obvious to at the time the invention was made.
Response to Traversal
Applicant traverses the instant rejection by arguing that Davidon does not teach the use of dCas9 for transcriptional repression, rather describes therapeutic strategies that depend on the introduction of cleavage sites into the target gene which requires a fully functional Cas9 capable of generating double-stranded breaks or nicks in DNA. This is in contrast to the present invention which requires a catalytically inactive Cas9 (dCas9) which has both nuclease domains inactive.
This argument has been fully considered, but is not found persuasive since Davidon states “a Cas9 mutant may also be used in the instant invention (e.g. a mutant with an inactive HNH AND/OR RuvC nuclease)” (Davidon, pg 11 lines 5-15). As described in Thakore, “inactivating mutations in the RuvC and HNH domains of Cas9 generate a deactive Cas9 (dCas9) that no longer cleaves DNA but retains function as a DBD (Thakore, pg 128 col 1). Thus, the the broad description of Cas9 mutants with inactivated HNH and RuvC nucleases by Davidon reads on the instant claims to a nuclease defective Cas9. However, it is acknowledged that Davidon does not describe a dCas9 polypeptide fused to a transcriptional repressor as described in claim 1.
Applicant further argues that although Gersbach teaches dCas9 fused to a repressor domain such as KRAB to mediate transcriptional silencing, this does not involve DNA cleavage and is mechanistically distinct from that of Davidon. Applicant argues that this would therefore change the principle of operation of the prior art and their combination would not have been predictable to one of ordinary skill in the art and are therefore fundamentally incompatible systems. Applicant argues that the examiner has used hindsight reasoning to link unrelated teachings that would not have been combined by one of ordinary skill in the art.
This argument has been fully considered, but is not found persuasive since it would have been a matter of combining prior art elements according to known methods to yield predictable results for one of ordinary skill to use the CRISPR/Cas9-based gene silencing methods of Gersbach and apply it to the same SNP targets present in mutant HTT proteins as identified by Davidon. One cannot show non-obviousness by attacking references individually where the rejections are based on combinations of references, see MPEP 2145. As stated previously, Davidon expressly describes the use of dCas9 mutants which contain inactivating mutations in the RuvC and HNH domains and is therefore compatible with the disclosure of Gersbach. One would have been motivated to combine the disclosures of Gersbach and Davidon in order to epigenetically repress transcription of mutant HTT proteins using the highly effective Cas9- KRAB effector domain disclosed by Gersbach using the gRNAs identified by Davidon. Furthermore, Gersbach demonstrates that using gRNA between 10-30 nucleotides and AAV viral vector serotypes (capsid and ITRs) results in highly specific gene silencing with low off-target effects. One would have a reasonable expectation of successes given that the transcriptional repression mechanism of dCas9-KRAB is known in the art as shown by Gersbach along with the mutational HTT targets described in the present invention.
Conclusion
No claims allowed.
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 extension fee 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 ALEXANDER NICOL whose telephone number is (571)272-6383. The examiner can normally be reached on M-F 8-5 EST.
Examiner interviews are available via telephone, in-person, and video conferencing using a USPTO supplied web-based collaboration tool. To schedule an interview, applicant is encouraged to use the USPTO Automated Interview Request (AIR) at http://www.uspto.gov/interviewpractice.
If attempts to reach the examiner by telephone are unsuccessful, the examiner’s supervisor, Maria Leavitt can be reached on (571)272-1085. The fax phone number for the organization where this application or proceeding is assigned is 571-273-8300.
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Alexander Nicol
Patent Examiner
Art Unit 1634
/ALEXANDER W NICOL/Examiner, Art Unit 1634