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 Claims
This action is written in response to applicant’s response received May 28, 2026. Claims 1-3, 6-10, 13-14, and 20-26 are currently pending and examined herein.
4. Any 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
The instant application claims foreign priority to Japanese Patent Application No.2014-
043348 (filed March 5, 2014), which was filed in the Japanese language. On June 29, 2018,
Applicants filed an English translation of Japanese Patent Application No. 2014-043 348
accompanied by a sworn declaration by Takeshi S. Komatani attesting to the accuracy of the
translation. The translation filed June 29, 2018 of Japanese Patent Application No. 2014 -043348
indicates that the priority document describes the fusion between a Cas9 nickase and a deaminase
([0054]-[0058]), wherein a plurality of sequence recognizing modules are used to simultaneously target different target nucleotide sequences in proximity ([0046]), and the different types of cells recited by claim 7 ([0024]), use of an inducible promoter ([0027]), wherein the Cas9 nickase has the D10A or H840A mutation ([0056]), wherein the nucleic acid base-converting enzyme is a cytidine deaminase such as AID (i.e., APOBEC family deaminase) [0016],[0037] or adenosine deaminase [0015], a nucleic acid-modifying enzyme complex [0048], repairing mutation of a pathogenic gene [0045]. Accordingly, the effective filing dates of instant claims 1, 2, 6, 7, 9, 11, 13-14, and 20-26, is March 5, 2014.
However, support for the recitations “wherein the different target nucleotide sequences are present in different genes” as recited in instant claim 3, "A method of modifying one or more nucleotides of a site of a double stranded DNA in any targeted alleles on homologous chromosomes in a polyploid cell" as recited by instant claim 8, "wherein the target nucleotide sequence in the double stranded DNA is present in a gene essential for survival of the cell" as recited in instant claim 10, “the method corrects a disease-associated nucleotide variation in the targeted site of the double stranded DNA” as recited in instant claim 23, “wherein the nucleic acid base-converting enzyme is directly fused to the Cas9 nickase protein” as recited in instant claims 25-26 could not be found in the English translation of Japanese Patent Application No.2014-043348. Therefore, instant claims 3, 8, and 10 are not afforded the effective filing date of March 5, 2014.
The instant application also claims foreign priority to Japanese Patent Application No.2014-201859 (filed on September 30, 2014), which was filed in the Japanese language. On June 29, 2018, Applicants filed an English translation of Japanese Patent Application No. 2014 -201859 accompanied by a sworn declaration by Takeshi S. Komatani attesting to the accuracy of the translation. The translation filed June 29, 2018 of Japanese Patent Application No. 2014-201859 describes "in one preferable embodiment of the present invention, two or more kinds of nucleic acid sequence-recognizing modules that specifically bind to different target nucleotide sequences (which may be present in one gene of interest, or two or more different genes of interest" ([0049]) and "wherein the cell is a polyploid cell, and a site in any targeted allele on a homologous chromosome is modified" ([17]), and wherein the target gene is an "essential gene" for survival of the cell [0068]. Accordingly, the effective filing date of instant claims 3, 8, and 10 is September 30, 2014.
Declaration Filed under 37 CFR 1.132
The Declaration of Keiji Nishida under 37 CFR 1.132 filed O has been considered, and it is sufficient to overcome the prior art rejection of claim 13 because the Affidavit supports complexes comprising CRISPR-Cas9 D10A mutant nickase protein and PmCDA deaminase produced unexpected results commensurate in scope with claim 13 (pg. 6). See further discussion below in response to arguments.
Claim Rejections - 35 USC § 112
The following is a quotation of 35 U.S.C. 112(b):
(b) CONCLUSION.—The specification shall conclude with one or more claims particularly pointing out and distinctly claiming the subject matter which the inventor or a joint inventor regards as the invention.
The following is a quotation of 35 U.S.C. 112 (pre-AIA ), second paragraph:
The specification shall conclude with one or more claims particularly pointing out and distinctly claiming the subject matter which the applicant regards as his invention.
Claim 23 is 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.
Claim 23 recites “a disease-associated nucleotide variation”, which renders the determination of the scope of the claim difficult. The specification does not define what is considered to be a disease-associated nucleotide variation. It is unclear whether the nucleotide variation comprises an insertion, mutation, and/or deletion. It is unclear how this the nucleotide variation associates with a disease. It is unclear whether the nucleotide variation causes the disease or the nucleotide variation is result of the disease. Thus, the metes and bound of the claim cannot be determined with reasonable certainty.
Claim Rejections - 35 USC § 103
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 CPR 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.
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, 6-7, 9-14, and 17-19 are rejected under 35 U.S.C. 103 as being unpatentable over Zhang (US 8697359 B1; Filling Date: Oct 15, 2013) in view of Liu (US 2015/0166980; PRO: 61/915,386 filed on Dec 12, 2013).
Regarding claim 1, Zhang teaches a method of modifying expression of a polynucleotide in a eukaryotic cell comprising a CRISPR enzyme complex with a guide sequence hybridized to a target sequence within said polynucleotide (i.e. nucleic acid-sequence recognizing molecule that specifically binds to a target nucleotide sequence in a targeted site of the double stranded DNA) (column 26, lines 45-49). Zhang teaches wherein the CRISPR enzyme directs cleavage of one strand of the double stranded DNA at the location of a target sequence (i.e. a Cas9 nickase) (Fig 21A-D; column 18, lines 33-35), and “the availability of a nickase can significantly reduce the likelihood of off-target modifications” (column 49, lines 56-58).
Zhang does not teach a Cas9 complex coupled with a nucleic acid-base converting enzyme that converts a target nucleotide to another nucleotide by introducing one or more mutations consisting of a substitution, a deletion, and an insertion.
Liu teaches a fusion protein comprising a nuclease-inactive Cas9 domain and a deaminase domain (i.e. nucleic acid-base converting enzyme) to convert one or more nucleotides in the targeted site to a different nucleotide without introducing a double strand break ([009]). Liu teaches the mutation consists of a substitution mutation, specifically a T>C or A>G point mutation to correct a point mutation in the targeted sequence associated with a disease.
It would have been obvious to one of ordinary skill in the art before the effective filling date of the invention to modify Zhang’s Cas9 nickase by incorporating the deaminase domain of Liu, specifically by substituting the nuclease-inactive Cas9 domain of Liu with the nickase Cas9 of Zhang because it would have merely amounted to a simple substitution of prior art elements according to known methods to yield predictable results. One would have been motivated to have done so for the advantage of reducing off-target modifications with the nickase variant while maintaining the nucleotide-converting functionality of the deaminase. One of ordinary skill in the art would have had a reasonable expectation of success because both Zhang and Liu teaches methods for targeted DNA editing using CRISPR Cas9 complexes.
Regarding claim 2, Zhang teaches CRISPR system can mediate multiplexed editing, wherein two or more CRISPR complexes that each comprise a nucleic sequence-recognizing module that specifically binds to a different target nucleotide sequence (column 49, lines 60-67).
Regarding claim 3, Zhang teaches wherein the different target nucleotide sequences are present in different genes, EMX1 and PVALB, (column 49, lines 60-67).
Regarding claim 6, Zhang teaches introducing “DNA molecules encoding one more gene product” comprising components of CRISPR complex (column 2, lines 30-62).
Regarding claim 7, Zhang teaches wherein the cell is a eukaryotic cell (column 3, line 38), microbial cell, yeast cell, insect yell or mammalian cell (column 14, lines 25-28).
Regarding claim 9, Zhang teaches wherein the expression one or more elements of the CRISPR system is driven by a regulatory element (Column 15, lines 55-57), and expression of CRISPR system elements were under bicistronic expression vectors in eukaryotic cells (Fig. 8A-B).
Regarding claim 10, Liu teaches using CRISPR dCas9 systems with deaminase to correct point mutations in disease-associated genes, including PI3KCA ([0009]) whose function is essential for survival of the cell. Thus, it would be obvious to one of ordinary skill in the art before the effective filling date of the invention to further apply this teaching of Liu, with the teachings discussed in claim 1, to edit a target nucleotide sequence in genes essential for cell viability. One of ordinary skill in the art would have had a reasonable expectation of success following the method taught by Liu.
Regarding claim 11, the obviousness to link a Cas9 nickase (i.e. nucleic acid sequence-recognizing module) to a deaminase (nucleic acid base-converting enzyme) is discussed above as applied to claim 1.
Regarding claim 14, Zhang teaches wherein “other examples of mutations that render Cas9 a nickase include, without limitation, H840A, N854A, and N863A” (column 18, lines 47-49).
Regarding claims 20-22, and 24, the obviousness to link a Cas9 nickase to a deaminase is discussed above as applied to claim 1. Liu further teaches the deaminase is an APOBEC family cytidine deaminase or an adenosine deaminase ([0008]).
Regarding claim 23, Liu further teaches “the deamination corrects a point mutation in the sequence associated with the disease or disorder” ([0009]), which positively teachings the method corrects a disease-associated nucleotide variation in the targeted site of the double stranded DNA. Liu also teaches the method is performed in cells obtained from a subject (i.e., wherein the cell is a mammalian cell) ([0037]).
Regarding claims 25-26, the obviousness to link a Cas9 nickase to a deaminase is discussed above as applied to claim 1. Liu further teaches the deaminase is fused to the N-terminus or C-terminus of the Cas9 domain (i.e., directly fused) ([0008]).
Claim 8 is rejected under 35 U.S.C. 103 as being unpatentable over Zhang (US 8697359 B1; Filling Date: Oct 15, 2013) in view of Liu (US 2015/0166980; PRO: 61/915,386 filed on Dec 12, 2013) as applied to claim 1, and further in view of Kim (WO 2014/065596 A1; Published Date: May 1, 2014; Filing Date: Oct 23, 2013)
The teachings of Zhang and Liu and the obviousness to link CRISPR Cas9 nickase to a deaminase are discussed above as applied to claim 1.
However, Zhang or Liu does not teach modifying a targeted site in a double stranded DNA in each of two or more targeted alleles on homologous chromosomes in a polyploid cell.
Kim teaches using CRISPR Cas9 systems to introduce modifications at a targeted site on alleles in a diploid cell. Fig 22 shows a conceptual diagram of a diploid cell containing different biallelic mutations (C) and identical biallelic mutations (D). It is noted that the biology definition for polyploid is cells containing more than two sets of chromosomes found in a diploid cell, which indicates that diploid cells are not polyploid cells. However, the specification defines a polyploid cell as “diploid, triploid, tetraploid and the like” ([0035]) and Example 8 (pg. 40) discloses “simultaneous editing of Ade1 and Can1 genes were performed in budding yeast YPH501 strain as a diploid strain”. Thus, the diploid cell and teachings of Kim meet the requirement of the claim. Further, the introduction of mutations (either different or identical biallelic mutations) into homologous alleles inherently satisfies the limitation of each of two or more targeted alleles on homologous chromosomes.
It would have been obvious to one of ordinary skill in the art before the effective filling date of the invention to have applied the method of claim 1 to modify targeted sites in in a polyploid cell because one would have the ability to introduce point mutation modifications on multiple alleles simultaneously. Given the substantial amount of guidance provided by Kim in targeting multiple alleles and detecting successful editing, one of ordinary skill in the art would have had performed the method of claim 8 with a reasonable expectation of success.
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.
Claims 1-3, 6-9, 10, 13-14, and 20-26 are rejected on the ground of nonstatutory double patenting as being unpatentable over claims 1-6 of U.S. Patent No. 10,655,123 B2 (referred to as Nishida 1) in view of Zhang (US 8697359 B1; Filling Date: Oct 15, 2013) and Liu (US 2015/0166980; PRO: 61/915,386 filed on Dec 12, 2013).
Regarding claims 1-2, 6, 7, 9, 13-14, 20, Nishida 1 recites a method of modifying a nucleic acid base in a particular region of a genome, without cleaving double-stranded DNA. Nishida 1 further teaches a contacting step performed using a CRISPR-Cas9 nickase protein that is linked to a cytidine deaminase and results in instantly recited limitations. Nishida 1 further recites the same current claimed cell type, same Cas9 nickase’s mutations and cleavage activity, nucleotide modifications, and same limitations in the contacting step recites in instant claims 2, 6, and 7. Nishida 1 further recites the method comprises a step of introducing an expression vector that meets limitations in instant claim 9.
Regarding claims 11-12, Nishida 1 does not explicitly teach a nucleic acid-modifying enzyme complex, a nucleic acid or a nucleic acid combination encoding fusion proteins for the nucleic acid-modifying enzyme complex. However, these products recited in claims 11-12 represent the essential components for practicing the method of Nishida 1, and do not recite any structural or functional features that patentably distinguish them from the CRISPR-Cas9 complexes inherently used in the method of Nishida 1. Any differences between the claimed products and the elements required by Nishida 1 are obvious variants.
Regarding claim 3, Nishida 1 does not recite instantly claimed limitations.
However, Zhang teaches a method of modifying expression of a polynucleotide in a eukaryotic cell comprising a CRISPR enzyme complex with a guide sequence hybridized to a target sequence within said polynucleotide (i.e. nucleic acid-sequence recognizing molecule that specifically binds to a target nucleotide sequence in a targeted site of the double stranded DNA) (column 26, lines 45-49). Zhang teaches wherein the CRISPR enzyme directs cleavage of one strand of the double stranded DNA at the location of a target sequence (i.e. a Cas9 nickase) (Fig 21A-D; column 18, lines 33-35), and “the availability of a nickase can significantly reduce the likelihood of off-target modifications” (column 49, lines 56-58). Zhang teaches CRISPR system can mediate multiplexed editing, wherein two or more CRISPR complexes that each comprise a nucleic sequence-recognizing module that specifically binds to a different target nucleotide sequence (column 49, lines 60-67), wherein the different target nucleotide sequences are present in different genes, EMX1 and PVALB, (column 49, lines 60-67).
Thus, it would have been obvious to one of ordinary skill in the art to design Nishida 1’s Cas9 nickase to target different nucleotide sequences in different genes as taught by Zhang because it would have merely amounted to applying a known technique to a known device ready for improvement to yield predictable results. Nishida 1 method already comprises two or more CRISPR-Cas systems each specifically binding to a different target nucleotide sequence, and Zhang teaches similar CRISPR-Cas systems can target different genes for multiplexed editing, which is an improvement of Nishida 1’s CRISPR-Cas system. One would have had a reasonable expectation of success in doing so because both Nishida 1 and Zhang teach a method of modifying a nucleic acid base using CRISPR-Cas systems without cleaving both strands of the DNA.
Regarding claims 10 and 23, Nishida 1 does not recite wherein the target nucleotide sequence is present in a gene essential for survival of the cell.
Liu teaches a fusion protein comprising a nuclease-inactive Cas9 domain and a deaminase domain (i.e. nucleic acid-base converting enzyme) to convert one or more nucleotides in the targeted site to a different nucleotide without introducing a double strand break ([009]). Liu teaches the mutation consists of a substitution mutation, specifically a T>C or A>G point mutation to correct a point mutation in disease-associated genes, including PI3KCA ([0009]) whose function is essential for survival of the cell.
It would have been obvious to one of ordinary skill in the art to modify Nishida 1’s target nucleotide sequence to a gene essential for survival of the cell or to correct a disease-associated nucleotide variation as taught by Liu because it would have merely amounted to a simple substitution of prior art elements according to known methods to yield predictable results. One would have been motivated to have done so for the advantage of correcting point mutations in disease-associated genes. One of ordinary skill in the art would have had a reasonable expectation of success because both Nishida 1 and Liu teach a method of introducing point mutations in a gene using CRISPR-Cas systems fused to deaminase.
Regarding claim 20-22, and 24, the obviousness to modify Nishida 1’s target nucleotide sequence to genes as taught by Liu is discussed above as applied to instant claim 10. Liu further teaches the deaminase is an APOBEC family cytidine deaminase or an adenosine deaminase ([0008]).
Regarding claims 25-26, Nishida 1 does not recite wherein the nucleic acid base-conversting enzyme is directly fused to the Cas9 nickase protein.
Liu further teaches teaches the deaminase is fused to the N-terminus or C-terminus of the Cas9 domain (i.e., directly fused) ([0008]).
Thus, it would have obvious to one of ordinary skill in the art to modify Nishida 1’s fusion protein linkage to direct fusion as taught by Liu because it would have merely amounted to a simple substitution of prior art elements according to known methods to yield predictable results. One of ordinary skill in the art would have had a reasonable expectation of success because both Nishida 1 and Liu teach a complex or fusion protein comprising a CRISPR-Cas protein and a deaminase.
Claim 8 are rejected on the ground of nonstatutory double patenting as being unpatentable over claims 1-6 of U.S. Patent No. 10,655123 B2 (referred to as Nishida 1) in view of Kim (WO2014/065596 A1; Published Date: May 1, 2014).
Patented claims of Nishida 1 are discussed above.
Nishida 1 does not recite modifying a targeted site in double stranded genomic DNA in each of two or more targeted alleles on homologous chromosomes in a polyploid cell.
Kim teaches a method of using CRISPR Cas9 systems to introduce modifications at a targeted site by error-prone non-homologous end-joining repairs on alleles in a diploid cell. The specification defines a polyploid cell as “diploid, triploid, tetraploid and the like” ([0035]). Thus, it would be obvious to one of ordinary skill in the art before the effective filling date of the invention to have applied the method of Nishida 1 to modify targeted sites in two or more alleles on homologous chromosomes in a polyploid cell because one would have the ability to introduce point mutation modifications on multiple alleles simultaneously. It would be predictable to one skilled in the art to combine the teachings as Kim teaches targeting multiple alleles using CRISPR-Cas9 systems and detecting successful editing.
Claims 11, 24, and 26 are rejected on the ground of nonstatutory double patenting as being unpatentable over claims 1-4 of U.S. Patent No. US11718846B2 (referred to as Nishida 2) in view of Zhang (US 8697359 B1; Filling Date: Oct 15, 2013).
Patented claims of Nishida 2 recites a nucleic acid-modifying enzyme complex that specifically binds to a target nucleotide sequence in a double stranded DNA, wherein the complex comprises a nucleic acid base-converting enzyme fused to SH3 ligand and a nucleic acid sequence-recognizing module CRISPR-Cas9 protein fused to SH3 domain. Instant claim 11 recites the nucleic acid base-converting enzyme is linked to a nucleic acid sequence-recognizing module, which under the broadest reasonable interpretation, the instantly claimed linkage encompasses covalent and non-covalent linkages including but not limited to, direct fusion and interaction between binding domains. Thus, although Nishida 2’s complex is fused via a SH3 ligand/domain, it still meets instant claim limitation. Nishida 2 further recites wherein the complex is capable of converting one or more nucleotides in the targeted site to other one or more nucleotides. Nishida 2 further recites wherein the nucleic acid base-converting enzyme is AID (i.e., APOBEC family deaminase).
Nishida 2 further recites both DNA cleavage abilities of the Cas9 protein are inactivated while instant claim requires a Cas9 nickase.
The teachings of Zhang are discussed above as applied to patented claims of Nishida 1. Specifically, Zhang teaches “the availability of a nickase can significantly reduce the likelihood of off-target modifications” (column 49, lines 56-58).
It would have been obvious to one of ordinary skill in the art modify Nihsida 2’s inactive Cas9 protein to a nickase as taught by Zhang because it would have merely amounted to a simple substitution of prior art elements according to known methods to yield predictable results. One would have been motivated to have done so for the advantage of reducing off-target modifications with the nickase variant while maintaining the nucleotide-converting functionality of the deaminase. One of ordinary skill in the art would have had a reasonable expectation of success because both Zhang and Nishida 2 teach nucleic acid-modifying enzyme complexes comprising CRISPR-Cas systems.
Response to Arguments
Applicant argues “the nCas9(D10A)-PmCDA1 configuration achieved approximately 100-fold greater on-target editing frequency than the corresponding dCas9-PmCDA1 configuration. This result was unforeseen from Zhang and Liu…” (pg. 8, section A, para. 1).
Applicant’s arguments have been fully considered and they are persuasive. Further, the Examiner pointed out in the previous Office Action mailed on 11/28/2025, pg. 17, response to argument v, that Figure 2 of Nishida et al (Science, 2016, 353, 6305) shows “nCas9(D10A) achieved nearly 100-fold enhancement of on-target mutation frequency as compared with dCas9-PmCDA, indicating that the key contribution to activity enhancement arises from the difference between Cas9 variants (nickase as compared to nuclease-inactive)”. The prior art, particularly Zhang (cited supra) recognizes that Cas9 nickase can significantly reduce the likelihood of off-target modifications (col. 49, lines 56-59). However, the prior art does reasonably teach or predictably suggest that substitution of a dCas9 with a Cas9 nickase would result in editing frequency observed in Nishida et al. Thus, Applicant’s evidence of unexpected properties rebuts the prima facie case of obviousness of claim 13, which scope of the claim is directed to a Cas9 D10A mutant nickase protein. Accordingly, 35 U.S.C. 103 rejection of claim 13 is withdrawn in view of the secondary consideration of unexpected results.
Applicant argues that “the directly on-point comparison – nCas9(D10A)-PmCDA1 vs dCas9-PmCDA1 is within scope of the amended independent claims” (pg. 8, section A, para. 2).
Applicant’s arguments have been fully considered but they are not persuasive. The scope of the independent claims is not limited to Cas9 D10A mutant nickase only. Rather, independent claims encompass any Cas9 protein having nickase activity, including, for example the H840A nickase protein. Per MPEP 716.02(d) “the “objective evidence of nonobviousness must be commensurate in scope with the claims which the evidence is offered to support”. In other words, the showing of unexpected results must be reviewed to see if the results occur over the entire claimed range. In re Clemens, 622 F.2d 1029, 1036, 206 USPQ 289, 296 (CCPA 1980)” Nishida et al do not establish unexpected results for the full scope of Cas9 nickases encompassed by the independent claims. As evidenced in Fig. 2A, reproduced below, the nCas9(H840A)-PmCDA configuration does not exhibit an improved on-target editing frequency than the corresponding dCas9-PmCDA configuration. Instead, the nCas9(H840A)-PmCDA exhibits approximately 100-fold lesser on-target editing frequency than dCas9-PmCDA. Thus, this evidence is insufficient to rebut the prima facie case because the unexpected results limited to nCas9(D10A)-PmCDA are not commensurate in scope with the claims. Accordingly, the 35 U.S.C. rejections for claims 1-3, 6-10, 14, and 20-26 are maintained.
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Applicant argues that SH3-related recitations from claims 1, 8, and 11 have been deleted, and such that the specific scope of the double-patenting analysis has been materially altered (pg. 9, last paragraph).
Applicant’s arguments have been fully considered but they are not persuasive. U.S. Patent No. 10,665,123 (referred as Nishida 1) recites a method of introducing a mutation into a desired nucleotide in a targeted site of a double stranded DNA, comprising a complex that meets instantly claimed limitations. Nishida 1 recites the complex comprises a nucleic acid base converting enzyme that is a deaminase linked to a nCas9(D10A) nickase protein, which anticipates instant claims. Further, Nishida 1 in view of Liu (cited supra) renders instant claims 25 and 26 obvious, wherein the nucleic acid base-converting enzyme is directly fused to the Cas9 nickase protein as discussed above. Thus, the double patenting rejections of claims 1-3, 6-9, 10, 13-14, and 20-26 are maintained.
Applicant argues that “the claims of Nishida 2 recite a Cas9 protein in which both DNA cleavage abilities are inactivated, and thus fail to teach or suggest a Cas9 nickase protein in which only one of two DNA cleavage abilities of the Cas9 nickase protein is inactivated recited in instant claim 11” (pg. 10, section 03, para. 2).
Applicant’s arguments have been fully considered but they are not persuasive because Nishida 2 in view of Zhang (cited supra) renders instant claims 11, 24, and 26 obvious as discussed above. Specifically, Zhang teaches the advantages of restoring one of two DNA cleavage abilities of Cas9 nickase protein to significantly reduce off-target modifications. Thus, it would have been obvious to modify Nishida 2’s dCas9 protein to a Cas9 nickase. It is noted that Applicant’s evidence of unexpected results is insufficient to rebut the prima facie case of obviousness because the results shown for nCas9(D10A)-PmCDA are not commensurate in scope with the claims as discussed above in section 16. Thus, the double patenting rejections of claims 11, 24, and 26 are maintained.
Allowable Subject Matter
Claim 13 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.
The following is a statement of reasons for the indication of allowable subject matter:
Claim 13 is drawn to a method of modifying a targeted site of a double stranded DNA with at least one complex that comprises a nucleic acid base-converting enzyme (e.g., deaminase) and a CRISPR-Cas9 D10A mutant nickase protein that cleaves one strand of the double stranded DNA. The method further comprises converting a target nucleotide to another nucleotide by the nucleic acid base-converting enzyme. The prior art, particularly Zhang (cited supra) recognizes that Cas9 nickase can significantly reduce the likelihood of off-target modifications (col. 49, lines 56-59) and Liu (cited supra) establishes a complex comprising a dCas9 and deaminase can achieve the claimed method of modifying a targeted site of a double stranded DNA. However, the prior art does reasonably teach or predictably suggest that substitution of a dCas9 with a Cas9 nickase would result in editing frequency observed in Fig 2A of Nishida et al (Science, 2016, 353, 6305), where nCas9(D10A) achieved nearly 100-fold enhancement of on-target mutation frequency as compared with dCas9-PmCDA. Thus, Applicant’s evidence of unexpected properties rebuts the prima facie case of obviousness of claim 13.
Conclusion
The prior art made of record and not relied upon is considered pertinent to applicant’s disclosure. Wang (Simultaneous editing of three homoeoalleles in hexaploid bread wheat confers heritable resistance to powdery mildew, Nat. Biotech. 2014, 32 (9), 947-951; DOI: 10.1038/nbt.2969; Published online: July 20, 2014) teaches simultaneously introduce mutations in three homoeoalleles in hexaploidy bread wheat by using zinc-finger nucleases (Abstract). Although Wang states “we have yet to cover CRISPR-Cas9 lines mutated in all three TaMLO alleles”, Wang also teaches using CRISPR-Cas9 system to mutate a single TaMLO allele and identifying four independent mutants, each carrying different mutations in the TaMLO-A1 allele (Fig. 1d, e; pg. 950, left-column, second paragraph). Thus, Wang demonstrates the state of the art for multi-allelic genome editing in polyploid cells, and teaches known strategies a person ordinary skill in the art would use to expand CRISPR-Cas9 editing to more than two alleles. One also would have had a reasonable expectation of success by following the method taught by Wang.
No claims are allowable.
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 QIWEN SU-TOBON whose telephone number is (571)272-0331. The examiner can normally be reached Monday - Friday, 8:00am-4:30pm.
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, Neil Hammel can be reached at 571-270-5919. 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.
QIWEN SU-TOBON
Examiner
Art Unit 1636
/NEIL P HAMMELL/Supervisory Patent Examiner, Art Unit 1636
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