DETAILED ACTION
Notice of Pre-AIA or AIA Status
The present application, filed on or after March 16, 2013, is being examined under the first inventor to file provisions of the AIA .
Election/Restrictions
Applicant’s election without traverse of Group I: claims 1, 4-6, 8-11, 15-17, 19-21, and 23-26 in the reply filed on 03/19/2026 is acknowledged.
Claim 27 is withdrawn from further consideration pursuant to 37 CFR 1.142(b) as being drawn to a nonelected invention, there being no allowable generic or linking claim. Election was made without traverse in the reply filed on 03/19/2026.
Applicant statement that “claims 1, 4, 6, 8-11, 15-17, 19-21, and 23-26 read on the elected species,” is not persuasive. Elected species SEQ ID NO: 25, is an S. aureus Cas9 (SaCas9) polypeptide containing three mutations at positions Y256, R314, and Q414. Claim 5 is drawn to another mutation at position R654 within the SaCas9 polypeptide and thus does not read on the elected species as the applicant identified in their statement above. Claims 15-17 are directed to Cas9 polypeptides from S. pyogenes comprising mutations at positions F518, E579, G686, and/or K929. As such, claims 15-17 do not read on the elected species, SEQ ID NO: 25.
Claims 5 and 15-17 are withdrawn from further consideration pursuant to 37 CFR 1.142(b) as being drawn to a nonelected species, there being no allowable generic or linking claim. Election was made without traverse in the reply filed on 03/19/2026.
STATUS OF CLAIMS
Claims 1, 4-6, 8-11, 15-17, 19-21, and 23-27 are pending.
Claims 5, 15-17, and 27 are withdrawn,
Claims 1, 4, 6, 8-11, 19-21, and 23-26 are under examination on the merits in this office action.
Priority
Receipt is acknowledged of certified copies of papers required by 37 CFR 1.55.
The examiner finds support for all claimed limitations within the certified copies of the foreign priority application. Therefore, the examiner is considering the filing date, 12/16/2020, of foreign application no. GB2019908.9 to be the priority date for pending claims: 1, 4-6, 8-11, 15-17, 19-21, and 23-27.
Information Disclosure Statement
The information disclosure statements (IDS) submitted on 08/15/2023 and 03/19/2026 are in compliance with the provisions of 37 CFR 1.97. Accordingly, the information disclosure statements are being considered by the examiner.
Drawings
The drawings are objected to because all figures are labelled with Figure 1, Figure 2, Figure 3, etc. and the figure labels are not correctly placed underneath the figures. The figures should be labelled FIG. 1, FIG. 2, FIG. 3, etc. and each label should be placed underneath the figure. Corrected drawing sheets in compliance with 37 CFR 1.121(d) are required in reply to the Office action to avoid abandonment of the application. Any amended replacement drawing sheet should include all of the figures appearing on the immediate prior version of the sheet, even if only one figure is being amended. The figure or figure number of an amended drawing should not be labeled as “amended.” If a drawing figure is to be canceled, the appropriate figure must be removed from the replacement sheet, and where necessary, the remaining figures must be renumbered and appropriate changes made to the brief description of the several views of the drawings for consistency. Additional replacement sheets may be necessary to show the renumbering of the remaining figures. Each drawing sheet submitted after the filing date of an application must be labeled in the top margin as either “Replacement Sheet” or “New Sheet” pursuant to 37 CFR 1.121(d). If the changes are not accepted by the examiner, the applicant will be notified and informed of any required corrective action in the next Office action. The objection to the drawings will not be held in abeyance.
Claim Objections
Claims 23-26 are objected to because of the following informalities: claim 23 recites “a CRISPR polypeptide as claimed in claim 1;” claim 24 recites “a nucleic acid molecule as claimed in claim 23;” claim 25 recites “a nucleic acid molecule as claimed in claim 23;” claim 26 recites “a CRISPR polypeptide as claimed in claim 1.” Each of the aforementioned claims do not use proper antecedent basis. “The” should be in place of “a” in each of these claims. Appropriate correction is required.
Improper Markush Grouping
Claims 1, 4, 6, 8-11, 19-21, and 23-26 are rejected on the basis that it contains an improper Markush grouping of alternatives. See In re Harnisch, 631 F.2d 716, 721-22 (CCPA 1980) and Ex parte Hozumi, 3 USPQ2d 1059, 1060 (Bd. Pat. App. & Int. 1984). A Markush grouping is proper if the alternatives defined by the Markush group (i.e., alternatives from which a selection is to be made in the context of a combination or process, or alternative chemical compounds as a whole) share a “single structural similarity” and a common use. A Markush grouping meets these requirements in two situations. First, a Markush grouping is proper if the alternatives are all members of the same recognized physical or chemical class or the same art-recognized class, and are disclosed in the specification or known in the art to be functionally equivalent and have a common use. Second, where a Markush grouping describes alternative chemical compounds, whether by words or chemical formulas, and the alternatives do not belong to a recognized class as set forth above, the members of the Markush grouping may be considered to share a “single structural similarity” and common use where the alternatives share both a substantial structural feature and a common use that flows from the substantial structural feature. See MPEP § 2117.
The Markush grouping of SEQ ID NOs: 1-15 recited in independent claim is improper because the alternatives defined by the Markush grouping do not share both a single structural similarity and a common use for the following reasons: SEQ ID Nos: 1-15 are defined as Cas polypeptides (either WT or mutant versions) from different organism and thus when aligning each to one another a common core structural sequence is not present among the group. For example, alignment of SEQ ID NO: 1 to SEQ ID NO: 2 returns a 9.2% identity score with mismatches spread through the alignment demonstrating no common core structural element. By virtue of claim dependency, all dependent claims from claim 1 necessary and inherently recite the limitations of claim 1 which recites the improper Markush group, SEQ ID NOs: 1-15.
The Markush grouping of (A) SEQ ID NOs: 1-8; or (B) SEQ ID NO: 1 and SEQ ID NO: 2 is improper because the alternatives defined by the Markush grouping do not share both a single structural similarity and a common use for the following reasons: each of SEQ ID Nos: 1-8 are defined as wild-type Cas polypeptides from different organismal species and when aligning when aligning each to one another a common core structural sequence is not present among the group. For example, alignment of SEQ ID NO: 1 to SEQ ID NO: 2 returns a 9.2% identity score with mismatches spread through the alignment demonstrating no common core structural element
The Markush grouping of a Cas9, a Cas12 or a Cas13 polypeptide is improper because the alternatives defined by the Markush grouping do not share both a single structural similarity and a common use for the following reasons: each of the Cas polypeptides are of a different type, II, V, and VI, and thus do not share a common core sequence structure.
The Markush grouping of “any one of SEQ ID NOs: 24-31” is improper because the alternatives defined by the Markush grouping do not share both a single structural similarity and a common use for the following reasons: SEQ ID Nos: 24-27 correspond to SaCas9 variants and SEQ ID Nos: 28-31 correspond to SpCas9 variants as defined by the specification, and when comparing any of the SEQ ID NOs corresponding to the SaCas9 variants to the SEQ ID Nos corresponding to the SpCas9 variant, there is only a less than 10% structural similarity with no common core sequence structure present. For example, alignment of SEQ ID NO: 24 to SEQ ID NO: 31 returns a 9.1% identity score with mismatches spread through the alignment demonstrating no common core structural element. Therefore,
To overcome this rejection, Applicant may set forth each alternative (or grouping of patentably indistinct alternatives) within an improper Markush grouping in a series of independent or dependent claims and/or present convincing arguments that the group members recited in the alternative within a single claim in fact share a single structural similarity as well as a common use.
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.
Claims 1, 4, 6, 8, 10, 19-21, and 23-26 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.
A broad range or limitation together with a narrow range or limitation that falls within the broad range or limitation (in the same claim) may be considered indefinite if the resulting claim does not clearly set forth the metes and bounds of the patent protection desired. See MPEP § 2173.05(c). In the present instance, claim 1 recites the broad recitation (a) at least 90% amino acid sequence identity with one or more of the reference sequences given in SEQ ID NOs: 1-15, and the claim also recites (b) wherein, for each reference sequence to which the CRISPR polypeptide has at least 90% sequence identity, (i) the amino acid in the CRISPR polypeptide at the position which corresponds to position Y256 in SEQ ID NO: 1 is an aliphatic amino acid; and (ii) the amino acid in the CRISPR polypeptide at the position which corresponds to position R314 in SEQ ID NO: 1 is an aliphatic amino acid which is the narrower statement of the range/limitation. Limitation (a) does not require any specific required mutations; whereas, (b) requires specific positions are mutated pertaining to the 90% identity level. Therefore, (b) falls within the broad range of limitation (a) and thus (b) is a narrower limitation. It is not clear whether (b) is required or merely exemplary; however, for compact prosecution, the examiner is going to consider (b) as required limitation. The claim(s) are considered indefinite because there is a question or doubt as to whether the feature introduced by such narrower language is (a) merely exemplary of the remainder of the claim, and therefore not required, or (b) a required feature of the claims.
By virtue of claim dependency, all dependent claims, 4, 6, 8, 10, 19-21, and 23-26,necessary and inherently recite the limitations of claim 1 which recites a narrower range within a broad range and are therefore rejected along with claim 1.
A broad range or limitation together with a narrow range or limitation that falls within the broad range or limitation (in the same claim) may be considered indefinite if the resulting claim does not clearly set forth the metes and bounds of the patent protection desired. See MPEP § 2173.05(c). In the present instance, claim 6 recites the broad recitation (A) SEQ ID NOs: 1-8, and the claim also recites (B) SEQ ID NO: 1 and SEQ ID NO: 2 which is the narrower statement of the range/limitation. The claim(s) are considered indefinite because there is a question or doubt as to whether the feature introduced by such narrower language is (a) merely exemplary of the remainder of the claim, and therefore not required, or (b) a required feature of the claims.
Claim Rejections - 35 USC § 101
35 U.S.C. 101 reads as follows:
Whoever invents or discovers any new and useful process, machine, manufacture, or composition of matter, or any new and useful improvement thereof, may obtain a patent therefor, subject to the conditions and requirements of this title.
Section 33(a) of the America Invents Act reads as follows:
Notwithstanding any other provision of law, no patent may issue on a claim directed to or encompassing a human organism.
Claim 25 is rejected under 35 U.S.C. 101 and section 33(a) of the America Invents Act as being directed to or encompassing a human organism. See also Animals - Patentability, 1077 Off. Gaz. Pat. Office 24 (April 21, 1987) (indicating that human organisms are excluded from the scope of patentable subject matter under 35 U.S.C. 101).
Claim 25 recites “A host cell comprising: a nucleic acid molecule as claimed in claim 23.” The specification discloses that “the target DNA molecule is present in the genome of a cell, preferably a mammalian cell, more preferably a human cell,” page 22. Therefore, when the cell of claim 25 is present in vivo, it reads on a human organism, which is excluded from the scope of patentable subject matter under 35 U.S.C. 101 and section 33(a) of the America Invents Act. Applicant is advised to amend such that the claim recites “an isolated cell.”
Claim Rejections - 35 USC § 102
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 the appropriate paragraphs of 35 U.S.C. 102 that form the basis for the rejections under this section made in this Office action:
A person shall be entitled to a patent unless –
(a)(1) the claimed invention was patented, described in a printed publication, or in public use, on sale, or otherwise available to the public before the effective filing date of the claimed invention.
(a)(2) the claimed invention was described in a patent issued under section 151, or in an application for patent published or deemed published under section 122(b), in which the patent or application, as the case may be, names another inventor and was effectively filed before the effective filing date of the claimed invention.
Claims 1, 4, 6, 8-10, 19-21, and 24-25 are rejected under 35 U.S.C. 102(a)(1) as being anticipated by Joung et. Al., (WO 2017040348 A1, in IDS).
Regarding claims 1, 4, and 6, Joung teaches SEQ ID NO: 2, which is defined as the wild-type (WT) amino acid sequence of SaCas9, see pg. 24-25. Alignment of SEQ ID NO: 1 of the instant case, which is also defined as the wild-type amino acid sequence of SaCas9, to SEQ ID NO: 2 of Joung results in a 100% identity score. Joung further teaches mutating the WT SaCas9 sequence at positions Y256 and R314, see pg. 25 lns 39-46. Joung further teaches the mutations at positions Y256 and R314 are alanine substitutions, which alanine is an aliphatic amino acid (see pg. 7 lns. 25-26; pg. 17 lns. 15-16, 24-26, and 31-33; pg. 25 lns 39-46; and FIGs. 21A-B, 22A-B and 23). Joung further teaches that “the variant SaCas9 proteins also comprise one or more of the following mutations: Y211A; V229A; Y230A; R245A; T392A; N419A; L446A; Y651A; R654A; D786A; T787A; Y789A; T882A; K886A; N888A; A889A; L909A; N985A; N986A; R991A; R1015A; N44A; R45A; R51A; R55A; R59A; R60A; R116A; R165A; N169A; R208A; R209A; Y211A; T238A; Y239A; K248A; Y256A; R314A; N394A; Q414A; K57A; R61A; H111A; K114A; V164A; R165A; L788A; S790A; R792A; N804A; Y868A; K870A; K878A; K879A; K881A; Y897A; R901A; K906A,” see pg. 25 lns. 39-46. Juong further teaches that mutations/substitutions at these locations results in increased specificity, thereby reducing deleterious off-target effects of the CRISPR/Cas complex, and that the R654 residue contacts the DNA of the functional spacer region and that Y256, R314, and Q414 residues contact the RNA of the functional spacer region, see page 8. Therefore, Joung teaches the claimed SEQ ID NO: 1 with substitutions at positions Y256 and R314 because even if one were to substitute each and every of the 57 positions above, one would arrive at a sequence comprising substitutions at positions Y256 and R314 and with a 94.6% identity to the claimed SEQ ID NO: 1, thereby meeting the at least 90% identity limitation claimed.
Joung further teaches a SEQ ID NO: 1, which is defined as the wild-type amino acid sequence of SpCas9. Alignment of the claimed SEQ ID NO: 2 of the instant case, which is also disclosed as the wild-type amino acid sequence of SpCas9, to SEQ ID NO: 1 of Joung results in a 100% identity score, see pgs. 21-22; pg. 22 lns. 34-44.
Regarding claim 8, Joung teaches the positions Y256 and R314 may be substituted with conservative mutations such as alanine, leucine, isoleucine and valine, see pg. 23 lns. 30-33.
Regarding claim 9, Joung teaches that one or more or all of the substitutions are alanine, see pg. 17 lns. 15-16, 24-26, and 31-33; pg. 56 lns. 23-24; pg. 57 lns. 13-14; and pg. 58 ln. 31.
Regarding claim 10, Joung teaches the CRISPR polypeptide is a Cas9, see title, abstract and ret of document.
Regarding claim 19, Joung teaches the CRISPR polypeptide is a dCas9, see pg. 24 lns. 10-25.
Regarding claim 20, Joung teaches the Cas9 polypeptide is a CRISPR activator (CRISPRa) polypeptide or a CRISPR inhibitor (CRISPRi) polypeptide, see pg. 9 lns. 4-27 (“the heterologous functional domain is a transcriptional activation domain” and the heterologous functional domain is a transcriptional silencer or transcriptional repression domain”).
Regarding claim 21, Joung teaches the CRISPR polypeptide is fused to a DNA-modifying domain or a heterologous functional domain or an effector domain, see claims 15-28 (“fused to a heterologous functional domain,” and “the heterologous functional domain is an enzyme that modifies the methylation state of DNA” or “the heterologous functional domain is an enzyme that modifies a histone subunit”).
Regarding claim 24, Joung teaches a vector encoding the CRISPR polypeptide, see claim 34.
Regarding claim 25, Joung teaches a host cell comprising a vector encoding the CRISPR polypeptide, see claim 35.
Claim Rejections - 35 USC § 103
In the event the determination of the status of the application as subject to AIA 35 U.S.C. 102 and 103 (or as subject to pre-AIA 35 U.S.C. 102 and 103) is incorrect, any correction of the statutory basis (i.e., changing from AIA to pre-AIA ) for the rejection will not be considered a new ground of rejection if the prior art relied upon, and the rationale supporting the rejection, would be the same under either status.
The following is a quotation of 35 U.S.C. 103 which forms the basis for all obviousness rejections set forth in this Office action:
A patent for a claimed invention may not be obtained, notwithstanding that the claimed invention is not identically disclosed as set forth in section 102, if the differences between the claimed invention and the prior art are such that the claimed invention as a whole would have been obvious before the effective filing date of the claimed invention to a person having ordinary skill in the art to which the claimed invention pertains. Patentability shall not be negated by the manner in which the invention was made.
The factual inquiries for establishing a background for determining obviousness under 35 U.S.C. 103 are summarized as follows:
1. Determining the scope and contents of the prior art.
2. Ascertaining the differences between the prior art and the claims at issue.
3. Resolving the level of ordinary skill in the pertinent art.
4. Considering objective evidence present in the application indicating obviousness or nonobviousness.
This application currently names joint inventors. In considering patentability of the claims the examiner presumes that the subject matter of the various claims was commonly owned as of the effective filing date of the claimed invention(s) absent any evidence to the contrary. Applicant is advised of the obligation under 37 CFR 1.56 to point out the inventor and effective filing dates of each claim that was not commonly owned as of the effective filing date of the later invention in order for the examiner to consider the applicability of 35 U.S.C. 102(b)(2)(C) for any potential 35 U.S.C. 102(a)(2) prior art against the later invention.
Claims 1, 4, 6, 8-11, 19-21, and 23-26 are rejected under 35 U.S.C. 103 as being unpatentable over Joung et. Al., (WO 2017040348 A1, in IDS) in view of Xie et. al., (PLOS Biology 18(7), e3000747, published 2020, in IDS) and Zhang et. al., (WO 2016205759 A1, in IDS).
The teaching of Joung are incorporated herein by reference to the 102 rejection above.
While Joung teaches mutating SaCas9 CRISPR polypeptides at positions Y256, R314, Q414, and R654, among other suggested positions, and that a mutant SaCas9 CRISPR polypeptide may comprise 1, 2, 3, 4, or more mutations, Joung does not explicitly teach or provide examples of the specific mutational configurations as in any one of the claimed SEQ ID Nos: 24 -31 of the instant case, nor does Joung teach the corresponding nucleotide sequences (SEQ ID NOs: 32-39) corresponding to the mutational configurations of SEQ ID Nos: 24 -31. Joung further does not teach a kit with the CRISPR polypeptides.
Xie teaches “the off-target effects of wild-type (WT) SaCas9 at single-nucleotide (single-nt) resolution and…a directional screening system to identify novel SaCas9 variants with desired properties in human cells,” see abstract. Xie teaches “novel SaCas9 variants with reduced off-target effects in human cells… without compromising…cleavage activity,” see pg. 2 paragraph 4. Xie teaches “enhanced-fidelity SaCas9 (efSaCas9) (variant Mut268 harboring the single mutation of N260D), which could effectively distinguish and reject single base-pair mismatches,” and has “dramatically reduced off-target effects (approximately 2- to 93-fold improvements)…compared to WT,” see abstract. Xie further teaches SaCas9 CRISPR polypeptides comprising alanine substitutions at Y256 and Q414, see pg. 9 and FIG. 4E. Xie further teaches that the Y256A substitution did not substantially alter the cleavage activity of SaCas9 and that “a Q414A variant exhibited even higher fidelity than N260D while retaining most on-target activity,” see pg. 9 para 2. Xie further teaches combining these substitutions to access “whether these residues act collaboratively or independently,” see pg. 9 para. 2. Xie further teaches that “in the context of the Q414A…variant, the introduction of N260D no longer had any phenotype (Fig 4E)” and that the “N260 likely functions through Q414, which makes direct, functionally important contacts to the 5’ region of the guide RNA,” see pg. 9 para. 3.
Zhang teaches “The sugar–phosphate backbone of the PAM-distal region (A3–U6) of the sgRNA interacts with the REC lobe (Thr238, Tyr239, Lys248, Tyr256, Arg314, Asn394 and Gln414) (see Figure 3). Accordingly, it is envisaged that one or more of these residues in Sa or corresponding residues in orthologs may be mutated to increase or disrupt (reduce) stabilization of the guide’s PAM-distal region (A3–U6), as required.” See [00257].
Zhang further teaches kits comprising the CRISRP polypeptides or nucleic acids encoding them, see section titled “kits” and [00505-00506].
It would have been obvious to a person of ordinary skill in the art (PHOSITA) before the effective filing date to modify the wild-type SaCas9 sequence of Joung to include alanine substitutions at positions Y256, R314, and Q414, thereby arriving at the claimed and elected SEQ ID NO: 25, and to generate nucleic acid sequence encoding the resulting mutant CRISR polypeptide of SEQ ID NO: 25, thereby arriving at claimed SEQ ID NO: 33. It would have further been obvious to include the CRISPR polypeptide or nucleic acid encoding the polypeptide in a kit.
A PHOSITA would have been motivated because Joung teaches that residues including Y256, R314, and Q414 contact the guide RNA and that substitutions at these positions, including alanine substitutions, increase specificity and reduce off-target effects, and further teaches that SaCas9 variants may include one, two, three, four, or more mutations. In further support of Joung, Xie teaches that substitutions at Y256 and Q414 improve fidelity and further teaches combining these specific substitutions to affect guide RNA interactions to evaluate collaborative effects. Also, in further support of Joung, Zhang teaches that residues Tyr256, Arg314, and Gln414 interact with the PAM-distal region of the sgRNA and expressly suggests mutating one or more of these residues to increase or reduce stabilization of the guide RNA as required. Zhang further teaches producing a kit with the CRISPR system.
A PHOSITA would have had a reasonable expectation of success because each reference teaches that substitutions at residues contacting the guide RNA predictably modulate specificity: Xie demonstrates that combining mutations in this interaction network yields functional high-fidelity SaCas9 variants without loss of activity, and Joung teaches that multiple substitutions may be combined in a single SaCas9 variant, thereby indicating that combining substitutions at Y256, R314, and Q414 would predictably produce a functional CRISPR polypeptide with altered specificity, and that generating nucleic acid sequences encoding such variants would involve routine codon substitution starting from the known WT SaCas9 coding sequence.
Conclusion
No claims are allowed.
Any inquiry concerning this communication or earlier communications from the examiner should be directed to COREY LANE BRETZ whose telephone number is (571)272-7299. The examiner can normally be reached M-F 7:30am - 6:30pm.
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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.
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/COREY LANE BRETZ/Patent Examiner, 1635
/RAM R SHUKLA/Supervisory Patent Examiner, Art Unit 1635
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