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 .
Application Status and Withdrawn Rejections
Applicant’s amendments filed July 10, 2026, amending claims 1, 3, 12, 45, 76-77, 105, 126-128, 135-136, 164 and 181, and canceling claims 13 and 26 are acknowledged. Claims 1, 3, 11-12, 14, 19, 45, 48, 73, 76-77, 84, 105, 125-128, 134-136, 158, 164, and 181 are pending. Claims 45, 48, 73, 76-77, 84, 125-127, 135, 158, 164 and 181 remain withdrawn from further consideration pursuant to 37 CFR 1.142(b) as being drawn to nonelected groups, there being no allowable generic or linking claim.
Claims 1, 3, 11-12, 14, 19, 105, 128, 134 and 136 are under examination.
The amendment to claims 1, 3, 105, 128 and 136 overcomes the §103 and nonstatutory double patenting (NSDP) rejections of record, as none of Yuan, Rommens, Liu and Yu teach SpCas9 domains having the specific combination of amino acid substitutions recited in the claims. It is noted that the limitation previously removed from the claims – a cytidine deaminase domain having at least 90% identity to SEQ ID NO 130 – has been added back to the independent claims.
Any other rejection or objection not reiterated herein has been overcome by amendment. Applicant' s amendments and arguments have been thoroughly reviewed, but are not persuasive to place the claims in condition for allowance for the reasons that follow.
Priority
Applicant's claim for the benefit of a prior-filed application under 35 U.S.C. 119(e) or under 35 U.S.C. 120, 121, 365(c), or 386(c) is acknowledged. Applicant has not complied with one or more conditions for receiving the benefit of an earlier filing date under 35 U.S.C. 119(e) as follows: The later-filed application must be an application for a patent for an invention which is also disclosed in the prior application (the parent or original nonprovisional application or provisional application). The disclosure of the invention in the parent application and in the later-filed application must be sufficient to comply with the requirements of 35 U.S.C. 112(a) or the first paragraph of 35 U.S.C. 112 (pre-AlA). See Transco Products, Inc. v. Performance Contracting, Inc., 38 F.3d 551, 32 USPQ2d 1077 (Fed. Cir. 1994).
The disclosure of the prior-filed application, Application No. 62/893638 fails to provide adequate support or enablement in the manner provided by 35 U.S.C. 112(a) for one or more claims of this application. The application fails to provide support for the claims under examination, since there is no disclosure therein of an SpCas9 having the combinations of amino acid substitutions recited in the independent claims. The closest disclosure is on page 270, which discloses a modified SpCas9 having amino acid substitutions D1335M, S1136Q, G1218K, E1219F, A1322R, D1332A, R1335E and T1337R. There is no disclosure of D1332K, D1335C, S1136W, G1218N, E1219W or R1335N substitutions in the ‘638 provisional application. There is also no disclosure of an H122A alteration in SEQ ID NO 130 (i.e., PpAPOBEC-1) or SEQ ID NO 127 (i.e., amAPOBEC-1 from Alligator mississippiensis). The first evidence of support for the above sequences and/or amino acid substitutions is in PCT Application PCT/US20/48510, filed August 28, 2020. As such, the effective filing date for claims 1, 3, 11-12, 14, 19, 105, 128, 134 and 136 is August 28, 2020.
Claim Rejections - 35 USC § 112(b)
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, 3, 11-12, 14, 19, 105, 128, 134 and 136 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. This a new rejection necessitated by amendment.
Claims 1, 3, 105, 128 and 136 each recite “comprising an amino acid sequence with at least 90% identity to SEQ ID NO: 69 and further comprising one of the following combinations of amino acid substitutions reference to SEQ ID NO:69: D1135M… and T1337R (225 SpCas9); D1135M… and T1337R (226 SpCas9); or D1135C…, and R1335N (244 SpCas9)…”. The parenthetical naming of the combination set renders the claim indefinite because according to the Specification “225 SpCas9”, “226 SpCas9” and “244 SpCas9” refer to specific SpCas9 proteins (pages 302-303, Description of FIG. 3A-3C). The claim recites the SpCas9 need only 90% identity to SEQ ID NO:69 and then recites the name of a specific SpCas9 protein in parentheticals. It is not clear if the claims 1) are limited to only three SpCas9 having only the recited substitutions, or 2) allow many more proteins that have the recited residues in the recited positions and can vary in 10% of the additional SpCas9 amino acids.
Claims 11-12, 14, 19, and 134 are rejected for depending from claims 3 and 128 and not remedying the indefiniteness.
To overcome this rejection, it is suggested that the claims recite either “100% identity to SEQ ID NO: 69 except for the following combinations of amino acid substitutions” or remove the parenthetical reference to the SpCas9 variant.
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, 11-12, 19, and 105 are rejected under 35 U.S.C. 103 as being unpatentable over Bryson (WO 2019217942 A1, published November 14, 2019), in view of Lee (Lee et al., Molecular Therapy (2019), 27: 1364-1371; published August 7, 2019; of record), Gaudelli (Gaudelli et al., Nature Biotechnology (2020), 38: 892-900, published April 13, 2020), Rommens (US 20060110734 A1; of record), and dbSNP1 rs113993991, https://www.ncbi.nlm.hin.gov/snp/ rs113993991 [retrieved August 14, 2025]; of record). This is a new rejection necessitated by amendment.
As indicated above in paragraph 7, the effective filing date of all examined claims is August 28, 2020. The Bryson and Gaudelli references were published within one year of the effective filing date and have one and two common author/inventors, respectively. However, Bryson names six additional inventors and Gaudelli names fifteen additional authors. Thus, both Bryson and Gaudelli constitute prior art under § 102(a)(1).
Regarding claims 1, 3, 11 and 19, Bryson teaches methods of altering genes that cause genetic disorders by editing the removal of a stop codon ([0043], [0470]). Bryson teaches such methods use a base editor comprising a polynucleotide-programmable DNA binding domain, a deaminase domain, and a guide polynucleotide wherein the guide polynucleotide targets the base editor to a target nucleotide sequence of a subject and editing is done by deaminating the nucleobase thereby treating the disorder ([0004]). Regarding (A), Bryson teaches a DNA binding domain is SpCas9 having amino acid substitutions D1135M, S1136Q, G1218K, E1219F, A1322R, D1332A, R1335E and T1337R ([0025]). Bryson teaches the amino acid sequence of wildtype SpCas9 ([0174]), which is 100% identical to SEQ ID NO: 69 of the examined application. Therefore, Bryson teaches a polynucleotide programmable DNA binding domain comprising SpCas9, having at least 90% identity to SEQ ID NO 69 and comprising D1135M, S1136Q, G1218K, E1219F, A1322R, D1332A, R1335E and T1337R. Bryson teaches the MQKFRAER SpCas9 variant recognizes the PAM 5’-NGC ([0559]). Regarding (C), Bryson teaches the SpCas9-MQKFRAER variant (herein referred to as NGC-SpCas9) fused to an adenosine deaminase domain to form a base editor ([0559]). Bryson teaches the adenosine deaminase domain is derived from TadA and called TadA7.10 ([0559]). Bryson teaches the sequence of TadA7.10 ([0059]), which is 100% identical to SEQ ID NO 23. Bryson teaches using the NGC-SpCas9-TadA7.10 base editor to convert an A-T to a G-C in a disease target site SNP ([0560]).
Bryson does not teach in a single embodiment using the NGC-SpCas9-base editor to alter a stop codon. Bryson does not teach the amino acid substitutions in the adenosine deaminase domain recited in the claims. Bryson does not teach a method for editing the SBDS polynucleotide associated with SDS.
Lee teaches a method called "CRISPR-PASS" for editing premature stop codons (Abstract). Lee teaches contacting a polynucleotide encoding EGFP that contains a premature stop codon with the adenosine base editor, ABEMax (Figure 2). Lee teaches ABEMax comprises Cas9 fused to the TadA7.10 adenosine deaminase domain (page 1364, ¶2). Lee teaches delivering ABEMax and a guide RNA directed to a premature stop codon, created a missense mutation in EGFP allowing bypass of the premature stop codon and allowing the expression of EGFP (Figure 2C-G, Supp Fig 2, Supp Table 4). Lee also teaches editing a premature stop codon in the XPC gene in cells derived from patients having xeroderma pigmentosum (Figure 3). Lee teaches the premature stop codon causes xeroderma pigmentosum. Lee teaches the method was able to restore expression by of XPC (Fig 3). Lee teaches the CRISPR-Pass method is a relevant approach for rescuing the nonsense-associated diseases with higher editing efficiencies than using homology directed repair (page 1377, ¶2). Lee teaches the ABEMax base editor can edit A nucleotides at the 7th and 8th position relative to the 5' end of the sgRNA on the strand that does not hybridize to the guide RNA (Fig 1A and Fig 2E). Lee teaches that adenines at positions 4-8 of the protospacer from the end distal to the PAM sequence can be targeted using adenosine base editors known in the art (Fig 1C; page 1368, ¶5).
Regarding (C), Gaudelli teaches further engineering the TadA7.10 deaminase domain to improve base editing efficiencies (Abstract). Gaudelli teaches evolved TadA base editors called ABE8 (Abstract). Gaudelli teaches ABE8.17 and ABE8.20 have higher base editing efficiencies and a wider editing window compared to ABE7.10 (Fig 2). Gaudelli teaches the ABE8.17 and ABE8.20 comprising TadA7.10 (i.e., SEQ ID NO 23) with V82S substitution (Supp Fig 1).
Rommens teaches that mutations in the SBDS gene are associated with SDS (Abstract). Rommens teaches that a 183TA>CT mutation results in an in frame stop codon K62X ([0124]). Rommens teaches the sequence of the wild type and 183TA>CT mutations (FIG 2a, b).
dbSNP1 teaches the rs113993991 SNP is located in the SBDS gene and results in the formation of a stop codon in the SBDS coding sequence (page 1). dbSNP1 teaches the SNP is "pathogenic" and is associated with Shwachman syndrome (page 3). dbSNP1 teaches the flanking sequence of the 183-184 TA➔ CT SNP (page 8). dbSNP1 teaches the SNP was discovered at least as early as 2010 (page 5).
Regarding claims 1, 3, 11 and 19, it would have been obvious to one skilled in the art before the effective filing date of the claimed invention to have used the ngc-Cas9 DNA binding domain with Gaudelli’s ABE8.14 or ABE8.20 deaminase domain in Lee's CRISPR-Pass method for editing the nonsense mutation caused by the 183-184 TA➔ CT rs113993991 SNP in the SBDS gene. It would have amounted to 1) applying a known method for bypassing a known premature stop codon by known means and 2) the simple combination of prior art elements to yield predictable results. The skilled artisan would have expected that an ngc-Cas9-ABE8 base editor could be used to edit the "A" nucleotide on the noncoding SBDS strand thus changing the "TAA'' codon to "GAA'' because such editing would follow the known parameters of adenosine base editing as follows. The SBDS rs113993991 sequence as deduced from dbSNP and Rommens is below: SNP = lowercase; premature stop codon= bolded; PAM sequence for ngc-Cas9 = bolded and underlined; protospacer sequence with A in predicted ngc-Cas9-ABE8 window= Underlined.
5'-TTCCTTTTTGGCAACCTGACCTTagGAAACATTTACAAACACTGAG
AAGGAAAAACCGTTGGACTGGAAtcCTTTGTAAATGTTTGTGACTC-5' (coding strand)
The skilled artisan would have expected that the AA on the coding strand could be edited using an NGC-Cas9-ABE8 editor, because the targeted AA is 9 and 10 nucleotides away from the NGC PAM sequence, which Bryson teaches can be edited using an NGC-SpCas9-TadA7.10 base editor, Lee teaches is near the Cas9-ABEx window, and Gaudelli teaches the TadA8 base editors have an even wider editing window. The skilled artisan would have been motivated to use a CRISPR-PASS method to the rs113993991 SNP in the SBDS gene because Lee teaches the method can be applied to gene rescuing of pathogenic premature stop codon SNPs. Furthermore, the skilled artisan would have been motivated to substitute Gaudelli’s TadA8 domains for the Tad7.10 used in Bryson and Lee due to their increased efficiency and wider editing windows.
Regarding claim 12, the claimed guide RNA with SEQ ID NO 2 is indicated in the diagram above.
Regarding claim 105, the teachings of Bryson, Lee, Rommens, Gaudelli and dbSNP1 are recited above. The obviousness of using the NGC-SpCas9 DNA binding domain of Bryson with Gaudelli’s ABE8.14 or ABE8.20 deaminase domain in Lee's CRISPR-Pass method for editing the nonsense mutation caused by the 183-184 TA➔ CT rs113993991 SNP in the SBDS gene is recited above as for claims 1, 3, 11-12 and 19. Rommens teaches subjects with SDS have hematological disfunction ([0002]). Bryson also teaches editing in induced pluripotent stem cells ([0022]). Bryson teaches edited cells can be differentiated into red blood progenitor cells ([0014]).
It would have been obvious to one skilled in the art before the effective filing date of the claimed invention to have practiced the above obvious method specifically in iPSCs that could be differentiated into hematopoietic cells. It would have amounted to using the obvious method in a known cell type amenable to base editing and cell differentiation by known methods. The skilled artisan would have predicted that iPSCs could be edited by base editing followed by differentiation because Bryson suggests that base editing is routine in stem cells. The skilled artisan would have been motivated to have done so because Rommens teaches that SDS patients have hematological dysfunction, for which edited hematopoietic cells could be therapeutic.
Claims 1, 3, 14, 19, 105, 128, 134, 136 are rejected under 35 U.S.C. 103 as being unpatentable over Bryson (WO 2019217942 A1, published November 14, 2019), in view of Yuan (Yuan et al., Molecular Cell (2018), 27: 1364-1371, of record), in view of Rommens (US 20060110734 A1; of record), Liu (US 20190225955 A1, published July 25 2019; of record), Maianti (US 20180179503 A1, published June 28, 2018; of record) and dbSNP2 rs113993993, https://www.ncbi.nlm.hin.gov/snp/ rs113993993 [retrieved August 14, 2025]; of record). This is a new rejection necessitated by amendment.
Regarding claims 1, 3, 14 and 19, Bryson teaches methods of altering genes that cause genetic disorders by removing or adding a splice acceptor or donor ([0043]). Bryson teaches such methods use a base editor comprising a polynucleotide-programmable DNA binding domain, a deaminase domain, and a guide polynucleotide wherein the guide polynucleotide targets the base editor to a target nucleotide sequence of a subject and editing is done by deaminating the nucleobase thereby treating the disorder ([0004]). Regarding (A), Bryson teaches on DNA binding domain is SpCas9 having amino acid substitutions D1135M, S1136Q, G1218K, E1219F, A1322R, D1332A, R1335E and T1337R ([0025]). Bryson teaches the amino acid sequence of wildtype SpCas9 ([0174]), which is 100% identical to SEQ ID NOL 69 or the examined application. Therefore, Bryson teaches a polynucleotide programmable DNA binding domain comprising SpCas9, having at least 90% identity to SEQ ID NO 69 and comprising D1135M, S1136Q, G1218K, E1219F, A1322R, D1332A, R1335E and T1337R. Bryson teaches the MQKFRAER SpCas9 variant recognizes the PAM 5’-NGC ([0559]). Bryson provides a working example of NGC-spCas9 fused to an adenosine deaminase domain for base editing (Example 5). Regarding (B), Bryson teaches various cytidine deaminase (CD) domains for C to T editing ([0326]-[0336]). Bryson teaches APOBEC1 and AID are exemplary deaminase domains used in based editors, including human AID and human APOBEC-1 ([0326] and [0329]). Bryson teaches the amino acid sequence of human APOBEC-1 ([0329]), which is 96% identical to SEQ ID NO 130, as shown below:
PNG
media_image1.png
318
734
media_image1.png
Greyscale
Bryson does not teach in a single embodiment using the NGC-SpCas9-CD to correct a splice site. Bryson does not teach a method for editing the SBDS polynucleotide associated with SDS.
Yuan teaches using CRISPR-guided cytidine deaminase to correct mutations associated with aberrant splicing in human diseases (Abstract). Yuan teaches contacting a polynucleotide encoding OS9 with a dCas9-AID and guide RNAs to target the dCas9-AID to edit a C>T splice site on the non-coding strand to include Exon 13 in the OS9 mRNA (Fig 5; page e3, ¶3). Yuan teaches the C> T alteration introduces a slice acceptor site (Fig 5A and E). Yuan also teaches editing a splicing donor site can be used to inhibit translation of a pathogenic form of the dystrophin protein (Fig 5). Yuan also teaches editing a splice donor nucleotide to define an intron (Fig 4A). Yuan also teaches editing a splice donor nucleotide to define an exon (Fig 1A). Yuan teaches that dCas9-AID is an efficient and versatile means of modulating splicing (page 391, ¶1). Yuan teaches the window for efficient G>A (i.e., C>T) editing is 12-20 upstream of the PAM sequence (Fig S7J; page 392, ¶4).
Rommens teaches that mutations in the SBDS gene are associated with SDS (Abstract). Rommens teaches that a 258+2T>C mutation results in an 8bp deletion and a premature truncation of the protein by a frameshift ([0124]). Rommens teaches the 258+2T>C is predicted to disrupt the donor splice site of intron 2 ([0124], FIG 2 a,b). Rommens teaches the T>C change corresponds to an invariant T of the donor splice site, which results in the use of an alternative splice site ([0033]). Rommens teaches the sequence of the wild type and 258+2T>C mutations (FIG 2a, b).
Liu teaches cytidine base editors comprising dCas9 fused to a cytidine deaminase (FIG 11). Liu teaches one such mutation that can be targeted using the base editors with Cas9 and/or Cas9 variants with expanded PAMs is the C.258 + 2T>C SNP in the SBDS gene (Table 6). Liu also teaches that an exemplary base editing domain is human APOBEC-1 with SEQ ID NO 279 (page 29), which is over 95% identical to SEQ ID NO 130 (See OA Appendix in OA mailed December 12, 2025, page 2).
Maianti teaches using cytidine base editors with guide-RNAs to modify splicing sites (Table 3). Maianti teaches the base editors with an APOBEC1 a cytidine deaminase fused to SpCas9n (Table 3, legend). Maianti teaches the sequence of the BE3 editor comprises the rat APOBEC1 domain (page 82, SEQ ID NO 297). Maianti also teaches that the human APOBEC1 domain having SEQ ID NO 286) is a suitable deaminase domain (page 78), which is 96% identical to SEQ ID NO: 130 (See OA Appendix in OA mailed December 12, 2025, page 1). Maianti teaches the editing window for APOBEC1 domains fused dCas9 is between 9 and 15 nucleotides away from the PAM in the protospacer (Figure 5).
dbSNP2 teaches the rs113993993 SNP is a splice donor variant (page 1). dbSNP2 teaches the SNP is "likely pathogenic" and is associated with Shwachman syndrome (page 5). dbSNP2 teaches the SNP is located at the 5' end of an intron the SBDS gene (page 10). dbSNP2 teaches the flanking sequence of the rs113993993 SNP (page 8).
Regarding claims 1, 3, 14 and 19, it would have been obvious to one skilled in the art before the effective filing date of the claimed invention to have used Bryson’s NGC-SpCas9 variant in Yuan's splice site introduction method for editing the splice site mutation caused by the 258+2T>C rs113993993 SNP in the SBDS gene using a NGC-dCas9-hAPOBEC1 base editor. It would have amounted to 1) the simple substitution of one mammalian cytidine deaminase domain and one dCas9 variant for another and 2) applying a known method for correcting and/or introducing a splice donor site by known means to yield predictable results. First, the skilled artisan would predict that human APOBEC1 could be used in the method because both Bryson and Liu teaches hAPOBEC1 is an exemplary cytidine deaminase domain for use in base editors. Because the prior art recognizes the equivalence of rAPOBEC1 and hAPOBEC1 for the purpose of cytidine base editing an express suggestion to substitute one equivalent component or process for another is not necessary to render such substitution obvious. MPEP 2144.06.II. Nevertheless, the skilled artisan would have been motivated to make the substitution because both Bryson and Liu classifies hAPOBEC1 as “exemplary”.
Second, the skilled artisan would have expected that Yuan's method could be used to edit the "C" nucleotide on the noncoding SBDS strand thus restoring the splice donor site because such editing would follow the known parameters of cytidine base editing as follows: The SBDS rs113993993 sequence as deduced from dbSNP2 and Rommens is below: SNP (mutated splice donor site) = lowercase and bolded; PAM sequence for NGC-Cas9 = bolded and underlined; protospacer sequence with C13 in predicted Cas9-APOBIC1 window = underlined
5'-TTAGCTATGCTGCAGCTGTTACCCgCCTGCTTACAGATTTCAGT
AATCGATACGACGTCGACAATGGGcGGACGAATGTCTAAAGTCA-5' (coding strand)
The skilled artisan would have expected that the C on the coding strand could be edited using dCas9-hAPOBEC-1, because the targeted C is in position 14 from the PAM with CAG (i.e., 5'-NGC) as the PAM sequence, which Maianti teaches is in the editing window for cytidine base editors using APOBEC1 enzymes. The skilled artisan would have been motivated to use NGC-dCas9-hAPOBEC-1 base editor to target the C in the known splice-donor SNP mutation because Yuan teaches targeting the splice donor sites using CRISPR-cytidine deaminases to define the length of an exon and intron. The skilled artisan would have been motivated to apply Yuan's method to the 258+2T>C SNP in the SBDS gene because both Bryson and Liu teaches CRISPR-mediated cytidine deamination can be used to correct the SNP.
Regarding claim 105, the teachings of Bryson, Yuan, Rommens, Liu, Maianti and dbSNP2 and the obviousness of applying Yuan's method to correcting a splice-site mutation in SBDS is recited above as for claims 1, 3, 14 and 19. Yuan teaches splice site editing can be performed in induced pluripotent cells (iPSCs) derived from patient's cells (page 388, ¶7-8). Yuan teaches differentiating the iPSCs into cardiomyocytes (i.e., a desired cell type).
It would have been obvious to one skilled in the art before the effective filing date of the claimed invention to have editing iPSCs derived from SBDS patient cells using the method of editing the SBDS splice site mutation rendered obvious above. It would have amounted to using known cells amenable to base-editing genome modification methods. The skilled artisan would have expected that iPSCs with the 258+2T>C SNP could be edited using NGC-dCas9-hAPOBEC1 because Yuan demonstrates editing a different site in iPSCs and differentiating the edited cells. The skilled artisan would have been motivated to do so in order to replace a patient's SBDS-mutated cells with cells comprising the corrected SNP.
Regarding claims 128 and 136, the teachings of Bryson, Yuan, Rommens, Liu, Maianti and dbSNP2 and the obviousness of applying Yuan's method to correcting a splice-site mutation in SBDS using Bryson’s NGC-SpCas9, including in cells derived from an SDS patient is recited above as for claims 1, 3, 14, 19 and 105.
Regarding claim 134, the obviousness of applying Yuan's method with a NGC-dCas9-hAPOBEC1 base editor to correcting the rs113993993 SNP splice-site mutation in SBDS, recited above as for claims 1, 3, 14, 19 and 105.
Response to Arguments - §103
Applicant’s arguments with respect to the obviousness rejections have been considered but are moot because the new ground of rejection does not rely on any reference applied in the prior rejection of record for any teaching or matter specifically challenged in the argument.
Regarding Applicant’s proffered evidence that the combination of the NGC-SpCas9 DNA binding domain together with AmAPOBEC1, PpAPOBEC1 and PpAPOBEC1 with an H112A alteration resulted in surprisingly high on-target editing activity and low bystander editing activity, it is noted that the proffered evidence is not commensurate in scope with the claims. The claims also recite adenosine base editors, for which there is no working example with the NGC-SpCas9 variants. The claims also recite deaminase domains that require merely 90% identity with SEQ ID NO 130, which is hAPOBEC-1.
Double Patenting
The nonstatutory double patenting rejection is based on a judicially created doctrine grounded in public policy (a policy reflected in the statute) so as to prevent the unjustified or improper timewise extension of the “right to exclude” granted by a patent and to prevent possible harassment by multiple assignees. A nonstatutory double patenting rejection is appropriate where the conflicting claims are not identical, but at least one examined application claim is not patentably distinct from the reference claim(s) because the examined application claim is either anticipated by, or would have been obvious over, the reference claim(s). See, e.g., In re Berg, 140 F.3d 1428, 46 USPQ2d 1226 (Fed. Cir. 1998); In re Goodman, 11 F.3d 1046, 29 USPQ2d 2010 (Fed. Cir. 1993); In re Longi, 759 F.2d 887, 225 USPQ 645 (Fed. Cir. 1985); In re Van Ornum, 686 F.2d 937, 214 USPQ 761 (CCPA 1982); In re Vogel, 422 F.2d 438, 164 USPQ 619 (CCPA 1970); In re Thorington, 418 F.2d 528, 163 USPQ 644 (CCPA 1969).
A timely filed terminal disclaimer in compliance with 37 CFR 1.321(c) or 1.321(d) may be used to overcome an actual or provisional rejection based on nonstatutory double patenting provided the reference application or patent either is shown to be commonly owned with the examined application, or claims an invention made as a result of activities undertaken within the scope of a joint research agreement. See MPEP § 717.02 for applications subject to examination under the first inventor to file provisions of the AIA as explained in MPEP § 2159. See MPEP § 2146 et seq. for applications not subject to examination under the first inventor to file provisions of the AIA . A terminal disclaimer must be signed in compliance with 37 CFR 1.321(b).
The filing of a terminal disclaimer by itself is not a complete reply to a nonstatutory double patenting (NSDP) rejection. A complete reply requires that the terminal disclaimer be accompanied by a reply requesting reconsideration of the prior Office action. Even where the NSDP rejection is provisional the reply must be complete. See MPEP § 804, subsection I.B.1. For a reply to a non-final Office action, see 37 CFR 1.111(a). For a reply to final Office action, see 37 CFR 1.113(c). A request for reconsideration while not provided for in 37 CFR 1.113(c) may be filed after final for consideration. See MPEP §§ 706.07(e) and 714.13.
The USPTO Internet website contains terminal disclaimer forms which may be used. Please visit www.uspto.gov/patent/patents-forms. The actual filing date of the application in which the form is filed determines what form (e.g., PTO/SB/25, PTO/SB/26, PTO/AIA /25, or PTO/AIA /26) should be used. A web-based eTerminal Disclaimer may be filled out completely online using web-screens. An eTerminal Disclaimer that meets all requirements is auto-processed and approved immediately upon submission. For more information about eTerminal Disclaimers, refer to www.uspto.gov/patents/apply/applying-online/eterminal-disclaimer.
Claim 1, 3, 11-12, 19 and 26 are provisionally rejected on the ground of nonstatutory double patenting as being unpatentable over claims 1-2, 6-11, 14, 24, 39, 60, 64-65, 67, 69 and 111 of copending Application No. 17430672 in view of Bryson (WO 2019217942 A1, published November 14, 2019). Claims 3, 11-12 and 19 are rejected in view of Lee (Lee et al., Molecular Therapy (2019), 27: 1364-1371; published August 7, 2019; of record), Rommens (US 20060110734 A1; of record) and dbSNP1 (rs113993991, https://www.ncbi.nlm.hin.gov/snp/ rs113993991 [retrieved August 14, 2025]; of record). This is a new rejection necessitated by amendment.
Copending claim 1 recites A method of treating a neurological disorder ... the method comprising: administering to the subject (i) an adenosine base editor or a nucleic acid sequence encoding the adenosine base editor and (ii) a guide polynucleotide or a nucleic acid sequence encoding the guide polynucleotide, wherein the adenosine base editor comprises a programmable DNA binding domain and an adenosine deaminase domain and an adenosine deaminase domain, wherein the adenosine deaminase domain comprises a V82S alteration at amino acid position 82 as numbered in SEQ ID NO: 2 or a corresponding position thereof, and wherein the guide polynucleotide directs the adenosine base editor to effect an A-to-G nucleobase alteration in a target gene or a regulatory element thereof associated with the neurological disorder in the subject, thereby treating the neurological disorder in the subject. Copending claim 8 recites where the SNP encodes an IDUA polypeptide with W402X (i.e., a premature stop codon). Copending claim 60 recites a method of editing a target gene or regulatory element thereof associated with a neurological disorder ... the method comprising contacting the target gene or regulatory element thereof with (i) an adenosine base editor and (ii) a guide polynucleotide, wherein the adenosine base editor comprises a programmable DNA binding domain and an adenosine deaminase domain ... wherein the guide polynucleotide directs the adenosine base editor to effect an A to-G nucleobase alteration in a target gene or a regulatory element thereof associated with the neurological disorder. Copending claim 65 recites wherein the A-to-G nucleobase alteration changes the SNP associated with the neurological disorder to a wild type nucleobase. SEQ ID NO 2 of the copending application is 92% identical to the SEQ ID NO 23 of the examined application (See OA Appendix, page 3). Therefore, the copending claims recite a method of editing a polynucleotide to alter a stop codon using a base editor comprising a guide RNA, programmable DNA domain and an adenosine deaminase domain having at least 90% identity to SEQ ID NO 23 and comprising a V82S alteration.
The copending claims do not recite an SpCas9 DNA binding domain having the instantly claimed amino acid substitutions. The copending claims do not recite the disorder is SDS and the gene is SBDS. The copending claims do not recite altering a stop codon such that it creates a missense mutation. The copending claims do not recite the guide RNA sequences targeting SBDS. The copending claims do not recite the base editor has 5’-NGC or 5NGG-3’ PAM specificity
Bryson teaches methods of altering genes that cause genetic disorders by editing the removal of a stop codon ([0043], [0470]). Bryson teaches such methods use a base editor comprising a polynucleotide-programmable DNA binding domain, a deaminase domain, and a guide polynucleotide wherein the guide polynucleotide targets the base editor to a target nucleotide sequence of a subject and editing is done by deaminating the nucleobase thereby treating the disorder ([0004]). Bryson teaches on DNA binding domain is SpCas9 having amino acid substitutions D1135M, S1136Q, G1218K, E1219F, A1322R, D1332A, R1335E and T1337R ([0025]). Bryson teaches the amino acid sequence of wildtype SpCas9 ([0174]), which is 100% identical to SEQ ID NO: 69 or the examined application. Therefore, Bryson teaches a polynucleotide programmable DNA binding domain comprising SpCas9, having at least 90% identity to SEQ ID NO 69 and comprising D1135M, S1136Q, G1218K, E1219F, A1322R, D1332A, R1335E and T1337R. Bryson teaches the MQKFRAER SpCas9 variant recognizes the PAM 5’-NGC ([0559]). Bryson teaches the SpCas9-MQKFRAER variant fused to an adenosine deaminase domain to form a base editor ([0559]). Bryson teaches the adenosine deaminase domain is derived from TadA and called TadA7.10 ([0559]). Bryson teaches the sequence of TadA7.10 ([0059]), which is 100% identical to SEQ ID NO 23. Bryson teaches using the ngc-SpCas9-TadA7.10 base editor to convert an A-T to a G-C in a disease target site SNP ([0560]).
Lee teaches a method called "CRISPR-PASS" for editing premature stop codons (Abstract). Lee teaches contacting a polynucleotide encoding EGFP that contains a premature stop codon with the adenosine base editor, ABEMax (Figure 2). Lee teaches ABEMax comprises xCas9 (i.e., a polynucleotide programmable DNA binding domain) fused to an adenosine deaminase domain called ABE7.10 (page 1364, ¶2). Lee teaches the xCas9 has been engineered to expand the PAM specificity of Cas9 (page 1364, ¶2). Lee teaches delivering ABEMax and a guide RNA directed to a premature stop codon, created a missense mutation in EGFP allowing bypass of the premature stop codon and allowing the expression of EGFP (Figure 2C-G, Supp Fig 2, Supp Table 4). Lee also teaches editing a premature stop codon in the XPC gene in cells derived from patients having xeroderma pigmentosum (Figure 3). Lee teaches the premature stop codon (i.e., nonsense mutation) causes xeroderma pigmentosum. Lee teaches the method was able to restore expression by of XPC (Fig 3). Lee teaches the CRISPR-Pass method is a relevant approach for rescuing the nonsense-associated diseases with higher editing efficiencies than using homology directed repair (page 1377, ¶2). Lee teaches the ABEMax base editor can edit A nucleotides at the 7th and 8th position relative to the 5' end of the sgRNA on the strand that does not hybridize to the guide RNA (Fig 1A and Fig 2E). Lee teaches that adenines at positions 4-8 of the protospacer from the end distal to the PAM sequences of NGG, NRG, NG, or NAR can be targeted using adenosine base editors known in the art (Fig 1C; page 1368, ¶5). Lee also teaches that Cas9 variants that can recognize sequences with a 5' - NG PAM sequences can also be used in adenosine base editors (page 1365, ¶1). Lee teaches that adenines outside of the targeted window are also edited to guanines, albeit at low frequencies, including at positions 10 and 15 (Fig 3B).
Rommens teaches that mutations in the SBDS gene are associated with SDS (Abstract). Rommens teaches that the 183-184 TA➔ CT mutation causes a premature stop codon (i.e., introduces a stop codon) at residue K62, resulting in a K62X nonsense mutation, which is associated with SDS (Table 1).
dbSNP1 teaches the rs113993991 SNP is located in the SBDS gene and results in the formation of a stop codon in the SBDS coding sequence (page 1). dbSNP1 teaches the SNP is "pathogenic" and is associated with Shwachman syndrome (page 3). dbSNP1 teaches the flanking sequence of the 183-184 TA➔ CT SNP (page 8). dbSNP1 teaches the SNP was discovered at least as early as 2010 (page 5).
Regarding claims 1, 3 and 11-12, it would have been obvious to one skilled in the art before the effective filing date of the claimed invention to have modified the copending method to treating SDS by editing a premature stop codon in the SBDS gene using Lee's CRISPR-Pass method with Bryson’s NGC-SpCas9 and the copending adenosine deaminase domain comprising the V82S substitution with a guide RNA having SEQ ID NO 2. It would have amounted to applying the copending method to editing a known premature stop codon by known means to yield predictable results. The skilled artisan would have expected that using the copending method could be used to edit the "A" nucleotide on the noncoding SBDS strand thus changing the "TAA'' codon to "GAA'' because such editing follows Lee's parameters of adenosine base editing as follows: The SBDS rs113993991 sequence as deduced from dbSNP and Rommens is below: SNP = lowercase; premature stop codon= bolded; PAM sequence for xCas9 = bolded and underlined; protospacer sequence with A8 in predicted Cas9-ABE window = Underlined.
5'-TTCCTTTTTGGCAACCTGACCTTagGAAACATTTACAAACACTGAG
AAGGAAAAACCGTTGGACTGGAAtcCTTTGTAAATGTTTGTGACTC-5' (coding strand)
The skilled artisan would have expected that the AA on the coding strand could be edited using the copending adenosine base editor because the targeted As are in positions 10 and 11, which Lee teaches will be edited at low, but detectable frequencies. The skilled artisan would have been motivated to use the copending base editor to target the AA in the SNP because Lee teaches targeting an A on the non-coding strand for deaminase base editing such that the TAA stop codon will become a TGG codon on the coding strand (i.e., a missense mutation). The skilled artisan would have been motivated to apply the copending method to the rs113993991 SNP in the SBDS gene because Lee teaches the method can be applied to gene rescuing of pathogenic premature stop codon SNPs.
This is a provisional nonstatutory double patenting rejection.
Claims 1, 3, 14, 19, 26, 105, 128, 134 and 136 are provisionally rejected on the ground of nonstatutory double patenting as being unpatentable over claims 1-2, 6-11, 14, 24, 39, 60, 64-65, 67 and 69 of copending Application No. 18744175 in view of Bryson (WO 2019217942 A1, published November 14, 2019), Yuan (Yuan et al., Molecular Cell (2018), 27: 1364-1371), Rommens (US 20060110734 A1), Liu (US 20190225955 A1, published July 25 2019), Maianti (US 20180179503 A1, published June 28, 2018) and dbSNP2 rs113993993, https://www.ncbi.nlm.hin.gov/snp/ rs113993993 [retrieved August 14, 2025]; of record). This is a new rejection necessitated by amendment.
Copending claim 1 recites A method of editing a nucleobase of a survival of motor neuron 2 (SMN2) polynucleotide, the method comprising contacting the SMN2 polynucleotide with a guide polynucleotide and a base editor comprising a fusion protein or a protein complex comprising a nucleic acid programmable DNA binding protein (napDNAbp) domain and a deaminase domain, wherein said guide polynucleotide targets said base editor to effect an alteration of the nucleobase of the SMN2 polynucleotide. Copending claim 8 recites wherein alteration of the nucleobase is associated with an increase in full-length polynucleotides encoding the SMN2 polypeptide transcribed from the SMN2 polynucleotide; and/or wherein alteration of a nucleobase in the SMN2 polynucleotide results in an increase in the number of transcripts transcribed from the SMN2 polynucleotide that include Exon 7. Copending claim 9 recites wherein the altered nucleobase in the SMN2 polynucleotide is associated with an alteration in splicing. Copending claim 11 recites wherein the napDNAbp domain comprises a variant of SpCas9 having an altered PAM specificity and the deaminase is an APOBEC deaminase domain.
The copending claims do not recite a specific SEQ ID NO or origin from the APOBEC deaminase domain. The copending claims do not recite a specific SpCas9 variant. The copending claims do not recite the disorder is SDS, the gene is SBDS, or the SNP is rs113993993 in the SBDS gene. The copending claims do not recite induced pluripotent cells.
The teachings of Bryson, Yuan, Rommens, Liu, Maianti and dbSNP2 are recited above in paragraphs 28 and 30-34 and incorporated here.
It would have been obvious to one skilled in the art before the effective filing date of the claimed invention to have modified the copending method for treatment of SDS by editing the mutated splice donor site in the SBDS gene using Yuan's method of modulating splice sites, substituting Bryson’s NGC-SpCas9 PAM variant, and substituting generic APOBEC deaminase domain for the human APOBEC-1 deaminase taught in Bryson, Liu and Maianti, which is over 90% identical to SEQ ID NO 130. It would have amounted to 1) substituting a known APOBEC domain and known SpCas9 PAM variant that can be used for base editing for a generic one, and 2) applying the copending method to editing a mutated splice site by known means to yield predictable results. The skilled artisan would predict that human APOBEC1 could be used in the method because Liu and Maianti teach hAPOBEC1 is a “suitable” and “exemplary” cytidine deaminase domain for use in base editors. The skilled artisan would have expected that the copending method could be applied to editing the "C" nucleotide in the SBDS gene thus restoring the "GT" donor site following Yuan's parameters with the NGC-SpCas9 varaint because such editing would follow the known parameters of cytidine base editing as indicated above in paragraphs 35-36. The skilled artisan would have expected that the C on the non-coding strand could be edited using the copending NGC-dSpCas9-APOBEC, because the targeted C is in the predicted window using the known NGC-dCas9 PAM (i.e., 5'-NGC). The skilled artisan would have been motivated to apply the copending method of editing the mutated splice site in SBDS using Yuan's method because Yuan teaches the method can be used to define exons and introns.
This is a provisional nonstatutory double patenting rejection.
Response to Arguments - NSDP
Applicant’s arguments with respect to the NSDP rejections have been considered but are moot because the new ground of rejection does not rely on any reference applied in the prior rejection of record for any teaching or matter specifically challenged in the argument.
Applicant also argues that the '175 co-pending application has a later US filing date than the present application and the NSDP rejection over the '175 should be withdrawn (Remarks, page 26). Examiner agrees that the '175 co-pending application has a later US filing date. However, MPEP 804.1.B.1.(b).(i) makes clear that a provisional double patenting rejection should be made and maintained by the examiner until the rejection has been overcome by amendment or the rejection is the only rejection remaining in an application having the earlier patent term filing date. Because the claims are still rejected under §112(b), §103 and another provisional NSDP rejection over an application with an earlier US filing date, the rejection for nonstatutory double patenting over the co pending '175 application is maintained.
Conclusion
No claims are allowed.
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 CATHERINE KONOPKA whose telephone number is (571)272-0330. The examiner can normally be reached Mon - Fri 7- 4.
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, Ram Shukla can be reached at (571)272-0735. The fax phone number for the organization where this application or proceeding is assigned is 571-273-8300.
Information regarding the status of published or unpublished applications may be obtained from Patent Center. Unpublished application information in Patent Center is available to registered users. To file and manage patent submissions in Patent Center, visit: https://patentcenter.uspto.gov. Visit https://www.uspto.gov/patents/apply/patent-center for more information about Patent Center and https://www.uspto.gov/patents/docx for information about filing in DOCX format. For additional questions, contact the Electronic Business Center (EBC) at 866-217-9197 (toll-free). If you would like assistance from a USPTO Customer Service Representative, call 800-786-9199 (IN USA OR CANADA) or 571-272-1000.
/CATHERINE KONOPKA/Primary Examiner, Art Unit 1635
Prosecution Insights