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 .
Continued Examination Under 37 CFR 1.114
A request for continued examination under 37 CFR 1.114, including the fee set forth in 37 CFR 1.17(e), was filed in this application after final rejection. Since this application is eligible for continued examination under 37 CFR 1.114, and the fee set forth in 37 CFR 1.17(e) has been timely paid, the finality of the previous Office action has been withdrawn pursuant to 37 CFR 1.114. Applicant's submission filed on 04/14/2026 has been entered.
Election/Restrictions
Applicant's election without traverse of Invention group I (claims 1, 6, 8, 9, 23
and 25-27) and Species Q154S (claim 26) and Species Y147T + Q154S (claim 27) in
the reply filed on 04/23/2025 was previously acknowledged.
Claims 37, 67, 77, 81-82, 109-110, 113-114, 130, 132, 134, 136, 146, 184, 188,
190-192, 194 and 202-203 are withdrawn from further consideration pursuant to 37 CFR
1.142(b) as being drawn to a nonelected Inventions, there being no allowable generic or
linking claim. Election was made without traverse in the reply filed on 04/23/2025.
The restriction requirements are deemed proper and are maintained for the purpose of this continued examination.
Application Status
This Application is a National Stage entry under U.S.C. § 371 of PCT/US2020/018124 filed 02/13/2020.
Amendments to claims filed 04/14/2026 are hereby acknowledged. Claims 1, 23, 37, 77, 109, 130, 132, 136, 184, 190, 192, 194 and 202 are currently amended.
Claims 2-5, 7, 10-22, 24, 28-36, 38-66, 68-76, 78-80, 83-108, 111-112, 115-129, 131, 133-135, 137-145, 147-183, 185-187, 189, 193, 195-201 and 204-205 are cancelled.
Claims 37, 67, 77, 81-82, 109-110, 113-114, 132, 136, 146, 184, 188, 190-192, 194 and 202-203 are withdrawn from consideration pursuant to 37 CFR 1.142(b) as being drawn to a nonelected Inventions; Applicant elected without traverse of Invention group I (claims 1, 6, 8, 9, 23, 25-27 and 130) and Species Q154S (claim 26) and Species Y147T + Q154S (claim 27) in the reply filed on 04/23/2025.
Therefore, claims 1, 6, 8, 9, 23, 25-27, 37, 67, 77, 81-82, 109-110, 113-114, 130, 132, 136, 146, 184, 188, 190-192, 194 and 202-203 are pending. But, only claims 1, 6, 8, 9, 23, 25-27 and 130 are under consideration in this Office action.
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’s claim for benefit from US Provisional Application No.62/876,354 filed July 19, 2019 is hereby acknowledged.
Drawings
The Replacement sheets for Drawings and Figures 3B, 19, 20 and 24 filed 10/14/2025 have been acknowledged and are acceptable.
Specification
Clean and amended copy of Specification filed 10/14/2025 has been acknowledged and is acceptable.
The following rejections are new:
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 non-obviousness.
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, 8-9, 23, 25-27 and 130 are rejected under 35 U.S.C. §103 as being unpatentable over Cowan (Cowan, C.A. et al. WO 2017/077386 A1, published May 11, 2017; previously cited) in view of Joung (Joung, J.K. et al. US Patent 11,946,040 B2, published April 2, 2024, benefiting from priority of US Application No. 16/781,979 filed February 4, 2020 and Provisional Application Nos. 62/844,717 filed May 7, 2019 and 62/800,974 filed February 4, 2019; previously cited), Liu (Lui, D. et al. WO2018/027078 A1, published February 08, 2018; cited on IDS filed 06/10/2022; previously cited), and Chou (Chou, J.Y. et al. “Mutations in the Glucose-6-Phosphatase-α (G6PC) gene that cause type Ia Glycogen Storage Disease”. Human Mutation, Vol. 29, No. 7 (2008), pp: 921-930; previously cited).
Regarding claims 1 and 130, Cowan teaches a method and materials for treatment of Glycogen Storage Disease 1a (see title). Cowan teaches modulating the expression, function and/or activity of the glucose-6-phosphatase, catalytic unit (G6PC) and /or glucose -6-phosphatase (G6Pase) protein in a cell by genome editing (see abstract). Cowan teaches using CRISPR-Cas system endonucleases for gene editing (see [0036]). Cowan teaches using sgRNAs directed to one or more pathological variants in G6PC gene responsible for the disease and a donor template to correct and restore G6Pase protein activity (see [0046]-[0047], [0052]-[0059]).
However, Cowan does not teach an adenosine deaminase domain, nor SEQ ID NO: 3.
However, US Patent No. 11,946,040, hereafter referred to as Joung, teaches
improving gene editing using recombinant programmable DNA binding protein comprising a mutated adenosine deaminase domain to improve the specificity of gene editing and reducing off-targets events (see title, abstract and column 1, line 34-36).
Joung states “Described herein are variants of wild type and engineered E.coli
TadA domains of the adenine DNA base editor (ABE) that have reduced unwanted off-target RNA editing activity” (column 1, lines 34-36).
Joung further states “Some promising variants (including K20A/R21A and V82G as previously published) with comparable DNA on-target and highly reduced RNA off-target are highlighted.” (see column 8, lines 17-20).
Also, a search for SEQ ID NO: 3 lead to the following result (Qy, Query = SEQ ID NO: 3; Db, Database = SEQ ID NO: 34 of US Patent No. 11,946,040 (Joung)):
RESULT 1
US-16-781-979-34
(NOTE: this sequence has 13 duplicates in the database searched.
See complete list at the end of this report)
Sequence 34, US/16781979
Patent No. 11946040
GENERAL INFORMATION
APPLICANT: THE GENERAL HOSPITAL CORPORATION
TITLE OF INVENTION: ADENINE DNA BASE EDITOR VARIANTS WITH REDUCED OFF-TARGET RNA
TITLE OF INVENTION: EDITING
FILE REFERENCE: 29539-0387001
CURRENT APPLICATION NUMBER: US/16/781,979
CURRENT FILING DATE: 2020-02-04
PRIOR APPLICATION NUMBER: 62/844,717
PRIOR FILING DATE: 2019-05-07
PRIOR APPLICATION NUMBER: 62/800,974
PRIOR FILING DATE: 2019-02-04
NUMBER OF SEQ ID NOS: 106
SEQ ID NO 34
LENGTH: 167
TYPE: PRT
ORGANISM: Artificial Sequence
FEATURE:
OTHER INFORMATION: Description of Artificial Sequence: Synthetic
polypeptide
Query Match 100.0%; Score 874; Length 167;
Best Local Similarity 100.0%;
Matches 167; Conservative 0; Mismatches 0; Indels 0; Gaps 0;
Qy 1 MSEVEFSHEYWMRHALTLAKRARDEREVPVGAVLVLNNRVIGEGWNRAIGLHDPTAHAEI 60
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 1 MSEVEFSHEYWMRHALTLAKRARDEREVPVGAVLVLNNRVIGEGWNRAIGLHDPTAHAEI 60
Qy 61 MALRQGGLVMQNYRLIDATLYVTFEPCVMCAGAMIHSRIGRVVFGVRNAKTGAAGSLMDV 120
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 61 MALRQGGLVMQNYRLIDATLYVTFEPCVMCAGAMIHSRIGRVVFGVRNAKTGAAGSLMDV 120
Qy 121 LHYPGMNHRVEITEGILADECAALLCYFFRMPRQVFNAQKKAQSSTD 167
|||||||||||||||||||||||||||||||||||||||||||||||
Db 121 LHYPGMNHRVEITEGILADECAALLCYFFRMPRQVFNAQKKAQSSTD 167
Joung teaches a sequence 100% identical to SEQ ID NO: 3 of instant application, in the form of SEQ ID NO: 34. Joung also teaches “Adenine DNA Base Editor variants with reduced Off-target RNA editing” (see title and abstract). Joung teaches modifying/mutating the Adenine DNA Base editor at different positions to obtain variants with reduced off-target editing, presenting some of them and their activities in Figure 15A-D.
Regarding claims 1 and 130, Joung teaches variants V82G in Figures 15A-B,
and 16A-B. Joung teaches that modifying residues I76, V82, D147, Q154 and substituting these residues will generate ABE variants with reduced RNA editing and therefore less Off-targets events (see Table A, columns 10-11). Joung teaches that the mutations can include substitutions with any other amino acid other than the WT amino acid (see column 11, lines 65-66).
Joung also teaches that “In some embodiments, the base editors include programmable DNA binding domains such as engineered C2H2 zinc-fingers, transcription activator effector-like effectors (TALEs), and Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR) Cas RNA-guided nucleases (RGNs) and their variants, including ssDNA nickases (nCas9) or their analogs and catalytically inactive dead Cas9 (dCas9) and its analogs (e.g., as shown in Table C), and any engineered protospacer-adjacent motif (PAM) or high-fidelity variants (e.g., as shown in Table D). A programmable DNA binding domain is one that can be engineered to bind to a selected target sequence.” (see column 13, lines 6-18).
Regarding claim 130, Joung teaches using a ABE variant, wherein the CRISPR-Cas nuclease is a Cas9 or Cas12a that has ssDNA nickase activity or is a catalytically inactive Cas9 or Cas12a (see claim 8, column 193).
Joung also teaches that “ABEs have been used successfully for installation of A-to-G substitutions in multiple cell types and organism and could potentially reverse a large number of mutations known to be associated with human disease” (see column 1 at lines 65-67, and column 2, lines 1-4).
Joung does not teach a method of editing a G6PC polynucleotide comprising a SNP associated with GSD1a. However, Liu does teach G6PC and GSD1a.
Liu also teaches a method of gene editing using a fusion protein comprising a Cas9 (e.g., a Cas9 nickase) domain and adenosine deaminase domain that deaminate adenosine in DNA (see “[A]bstract” section). Liu teaches that the recombinant fusion protein Cas9 / ecTadA can create an A to G mutation (see ¶ [0005]-[0009]). Liu teaches that the fusion proteins provided improve the base editing activity (e.g. efficiency, selectivity, and specificity) (¶ [00237], line 4). Figure 15 shows the development of ABE while Figure 14 shows an example of A to G editing in mammalian cells.
Liu teaches that ABE adenosine deaminase can be obtained by directed evolution experiments for codon optimization (see ¶ [00400]) ; and Liu teaches experimentations of evolution from #1 to #7 in ¶ [00400] to [00428]. Liu teaches that evolution #2 gives rise to an amino acid residue change at position 147 from aspartic acid to Tyrosine (D>Y = Y147) (see Figure 128).
Liu does teach multiple mutations that can be accumulated in a TadA protein from E.coli and can be selected in vitro to enhance base editing efficiency (see “Base editor Efficiency”, page 392, ¶ [00357]).
Liu teaches a mutated TadA protein comprising one additional, or more mutations, including D147Y and Q154H (see pages 602-603, claims 49,50, 53 and Figure 23, e.g., pNMG-173 (pCMV_Cas9n_XTEN_ecTadA_GGS_NLS; H8Y_D108N_S127S_D147Y_Q154H).
Liu teaches that “In some embodiments, the adenosine deaminase comprises one or more of H8X, R26X, M61X, L6SX, M70X, A106X, D108X, A109X, N127X, D147X, R152X, Q154X, E155X, K161X, Q163X, and/or T166X mutation in SEQ ID NO: 1”, where X indicates any other amino acid than the corresponding amino acid in the wild type adenosine deaminase (see [00248]).
Liu also teaches that targeted editing of nucleic acid sequences is a highly promising approach to provide new therapies for human genetic diseases (see [0001]).
Liu teaches that one of diseases can be a glycogen storage disease, hypoglycemia with deficiency of glycogen synthetase in the liver (see page 171-172 [00353]). Liu specifically teaches that the targeted editing system can be used for Glycogen Storage Disease type 1A with mutations in G6PC and other mutation affecting Glucose-6-phosphate transport defect (see page 268, Table 2 “Target mutations that may be corrected using nucleobase editors, including exemplary gRNA sequences, gRNA sequences in the table correspond to SEQ ID NOs: 740-5526 from top to bottom”).
Liu teaches that the SNP that can be corrected using the claimed system is c.551G>A (p.Gly184Glu) in G6PC gene.
It would have been obvious to one with ordinary skills in the art before the effective filing date of the claimed invention to have adapted the gene editing method of Cowan, using a recombinant fusion protein Cas9 with a modified TadA taught by Joung and Liu, and modified/corrected a SNP responsible for GSD1 in a G6PC enzyme as taught by Cowan and suggested by Liu. It would have been a substitution of one cas9/gRNA system taught by Cowan, for another Cas9/gRNA system, wherein the Cas9 is a fusion protein taught by Joung and Liu, with the capability of operating with less off-target RNA editing, allowing for a higher accuracy for base editing due to the mutated adenine deaminase base editor domain of TadA comprising alterations, including Y147 and Q154. It would have been obvious to have tried and tested multiple types of amino acid substitutions as suggested by Joung at the position suggested by Joung, to obtain an effective recombinant protein with high efficiency. One with reasonable skills in the art motivated in higher accuracy, and motivated in treating GSD1a and editing the G6PC enzyme, could have performed these substitutions with a reasonable expectation of success and would arrived at the claimed invention.
Regarding claim 23, Joung teaches that in one embodiment, the adenosine deaminase includes a wild type or engineered E. coli TadA monomer (see column 2, lines 34-35). Liu teaches that the adenosine deaminase domain is a monomer comprising an adenosine deaminase variant or a heterodimer comprising a wild-type adenosine deaminase domain and an adenosine deaminase variant (see ¶ [0003]-[0004] and figure 140).
Regarding claim 25, Joung teaches adenosine deaminase domain comprising amino acid alteration I76, V82, F149 and Q154 (see table A). As seen in the alignment above, Joung teaches these alterations in reference to SEQ ID NO: 3, in the form of SEQ ID NO: 34. Joung also teaches that the amino acid substitutions can be any other amino acid but the wild type amino acid (see column 11).
Regarding claim 26, Joung teaches H123 amino acid position, as a
position that would decrease off-target editing once substituted (see Table A). Liu teaches a substitution H123Y in multiple engineered ABEs. For example, in Table 4, page 410, pNMG-336 (L84F_A160V_D108N_H123Y_D147Y_E155V_I156Y). Liu also teaches that “In some embodiments, the adenosine deaminase comprises one or more of H8Y, R26W, M611, L6SQ, M70V, A106T, D108N, Al09T, N127S, D147Y, R152C, Q154H or Q154R, E155G or E155V or E155D, K161Q, Q163H, and/or T166P mutation (see [00248]).
Regarding claim 27, Liu teaches ABEs modified with multiple amino acids substitutions, for example in Table 4, pNMG-162(H8Y_D108N_S127S_D147Y_Q154H).
Liu also teaches “In some embodiments, the adenosine deaminase comprises
one, two, three, four, five, six, seven, or eight mutations selected from the group consisting of H8Y, M611, M70V, D128N, N127S, Q154R, E155G and Q163H (see [00250]).
Regarding claims 23, 25-27, the obviousness of combining the references Cowan, Joung and Liu has been described above.
Regarding claims 6, 8 and 9, Cowan teaches examples of SNPs to target in G6PC genes: R83C (rs1801175) and Q347X (rs80356487) (see Examples 98, page 166, [00804]).
Cowan refers to Chou in their disclosure (see [0006]). Chou teaches different types of GSD1, and that GSD1a and GSD1b have been characterized at the molecular level (see “[I]ntroduction”, left column, lines 1-12). Chou teaches a list of mutations described in prior art in Table 1, in which a non-glutamine amino acid substitution at position 347 and a non-arginine amino acid substitution at position 83 are taught (see page 924, Table 1).
Chou teaches a list of G6PC mutations associated with GSD1a (see Table 1). Chou teaches a G6PC having a non-glutamine (X) amino acid at position 347 or a non-arginine (X) amino acid at position 83 (see Table 1, Table 2 and figure 3). Chou teaches that p.Q347X is truncated by 11 amino acids at the carboxyl terminus, therefore is truncated, i.e. prematurely terminated (see page 926, left column, second ¶). Chou teaches in Table 2, that 33% of Caucasians with GSD1a carry a p.R83C mutation, 98% of Jewish with GSD1a carry a p.R83C mutation and 18% of Caucasians with GSD1a carry a p.Q347X mutation. Chou teaches that the prevalent mutations identified in the 676 alleles from Caucasian GSD1a patients are p.R83C (33%) and p.Q347X (18%) (see page 926, right column, lines 22-23).
Chou teaches an updated list of mutations in G6PC responsible for GSD1a and teaches about the genetic heterogeneity (see Table 1, pages 924-925).
Chou also teaches about the possibilities of genetic modifiers responsible for the phenotype, in view of the established phenotype heterogeneity and lack of a stringent genotype-phenotype association in GSD1a (See page 927, “[F]uture prospects” section, right column, lines 1-7). Chou states that even with current level of understanding of the mutations and their consequences, there are no current alternatives to the standard of care (same ¶, lines 7-10), thus the efforts towards gene therapy. Chou also teaches that gene therapy, with somatic replacement of G6PC activity does not produce equivalent recovery in the kidney and liver, and does not produce sustainable recovery (see page 927, right column, lines 9-25). The gene therapy so far does not provide sustainable recovery, while life-threatening events occur later in life of subjects with GSD1a (see same, lines 25-31), therefore there is a motivation for establishing stable genetic modifications and for specifically analyzing each mutation in search of genetic modifiers.
Cowan and Liu both teach a method of editing specific SNPs in G6PC gene causing GSD1a .
Therefore, it would have been obvious to one with ordinary skills in the art before the effective filing date of the claimed invention to have combined the teachings of Cowan, Joung, Liu and Chou and modified/corrected the SNP taught by Cowan, i.e., Q347X and R83C (or R83H (Table 1)), since these two SNPs are most prevalent as taught by Chou. A modified gene editing system as taught by Cowan modified by Joung and Liu, could have been used to modify the G6PC gene and alter a SNP associated with GSD1a. One with ordinary skills in the art, motivated in treating GSD1a and effecting a SNP responsible for GSD1a with high precision, could have performed this modification and obtain a method of editing a Q347X or R83C mutation in the genomic sequence of G6PC polynucleotide.
The level of skills in the art is high. Therefore, one motivated in improving editing and correcting a SNP responsible for GSD1a could have performed these modifications with a reasonable expectation of success and would arrived at the claimed invention.
Therefore, the combination of Cowan, Joung, Liu and Chou renders the elements of claims 6, 8-9 obvious and unpatentable.
Response to Arguments
Applicant's arguments filed 04/14/2026 have been fully considered but they are not persuasive. Applicant’s arguments with respect to claims 1, 6, 8, 9, 23, 25-27 and 130 have been considered but are moot because the new ground of rejection does not rely on the same combination of references applied in the prior rejection of record.
The rejections of claims 1 , 6, 8, 9, 23, 25-27 and 130 under 35 U.S.C. §103 as being unpatentable over Cowan (Cowan, C.A. et al. WO 2017/077386 A1, published May 11, 2017) in view of Joung (Joung, J.K. et al. US Patent 11,946,040 B2, published April 2, 2024, benefiting from priority of US Application No. 16/781,979 filed February 4, 2020 and Provisional Application Nos. 62/844,717 filed May 7, 2019 and 62/800,974 filed February 4, 2019), Liu (Lui, D. et al. WO2018/027078 A1, published February 08, 2018), and Chou (Chou, J.Y. et al. “Mutations in the Glucose-6-Phosphatase-α (G6PC) gene that cause type Ia Glycogen Storage Disease”. Human Mutation, Vol. 29, No. 7 (2008), pp: 921-930), establish a prima facie case of Obviousness.
Cowan teaches the treatment of GSDIa using a CRISPR/Cas system targeting the mutations in G6PC gene responsible for the disease. Joung teaches a better system for reducing off-target editing, using mutated TadA4 protein domains to combine with Cas9 endonuclease domains for specific and targeted modifications. Liu teaches the same system, with an overlapping list of mutant TadA domains, as relevant for editing mutations in G6PC gene, and treat GSDIa. Cowan refers to Chou, for picking mutations in G6PC gene, and Chou presents a list of mutations and their prevalence in human populations, and doing so, teaches motivation for picking the mutations.
Note: Applicant also states “Furthermore, "[o]bjective evidence relevant to the issue of obviousness must be evaluated by Office personnel. Id. at 17-18, 148 USPQ at 467. Such evidence, sometimes referred to as 'secondary considerations,' may include evidence of commercial success, long-felt but unsolved needs, failure of others, and unexpected results" (M.P.E.P. 2141(II), emphasis added)”.”
Examiner encourages Applicant to submit an Affidavit/Declaration with arguments demonstrating unexpected results for consideration.
Conclusion
No claim is allowed.
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/A.D./Examiner, Art Unit 1636
/NANCY J LEITH/Primary Examiner, Art Unit 1636
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