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 Election
Claims 1-2, 4-5, 8-9, 19-22, 26-28, 30, 32, 38-40 and 44-45 are pending.
Applicant’s election without traverse of Group 3, encompassing claims 26-28, 30, 32, 38-40 and 44-45 and directed to base editors, in the reply filed November 25, 2025 is acknowledged. Claims 1-2, 4-5, 8-9 and 19-22 are withdrawn from further consideration pursuant to 37 CFR 1.142(b) as being drawn to nonelected groups, there being no allowable generic or linking claim.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 26-28, 30, 32, 38-40 and 44-45 are under examination.
Drawings
The drawings are objected to because the lines, shadings, numbers and letters of FIGs 1A, 1C, 2D, 3A, 3D, 4, 6, 7A, 8D, 9A-C, 10A-B, 15A-B, 20B, 22A-F, 23B, 24, 25A-B, 26C, 27, 28, 29, 30 and 31 in the Drawings filed 5/25/2022 and the replacement sheets filed 6/23/2025 are not sufficient to provide satisfactory reproduction characteristics. 37 CFR 1.84(l) states that “all drawings must be made by a process which will give them satisfactory reproduction characteristics. Every line, number, and letter must be durable, clean, black (except for color drawings), sufficiently dense and dark, and uniformly thick and well-defined.” In the instant case, the text in the FIGs listed above is light grey, very small, of poor resolution, or otherwise not sufficiently dense and dark to permit satisfactory reproduction characteristics.
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.
Specification
The use of the terms Phusion®, Mach1TM, GlutaMAX®, MycoAlert®, ZymoPureTM, Lipofectamine®, PhusionTM, MiSeq®, CrispressoTM, Hi-Trap®, CutSmart®, Kapa®, NovaSeq®, GATK®, SuperScript®, iBlot®, TrypLE®, and Nucleofector®, which are trade names or marks used in commerce, has been noted in this application. The term should be accompanied by the generic terminology; furthermore the term should be capitalized wherever it appears or, where appropriate, include a proper symbol indicating use in commerce such as ™, SM , or ® following the term.
Although the use of trade names and marks used in commerce (i.e., trademarks, service marks, certification marks, and collective marks) are permissible in patent applications, the proprietary nature of the marks should be respected and every effort made to prevent their use in any manner which might adversely affect their validity as commercial marks.
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 26-28, 30, 32, 38-40 and 44-45 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.
Claim 26 recites “wherein the cytidine deaminase domain is selected from [10 different deaminase names] and variants thereof.” Inclusion of “and variants thereof” renders the claim indefinite because scope of variants of the recited deaminase domains is unclear. It is not clear how much a deaminase domain can be varied and still be considered “a variant thereof”. As an example, one of the deaminase domains is A3G, which is defined in the Specification as human APOBEC3G and has SEQ ID NO 242 (page 175). Another deaminase domain listed in the Specification, but not in the deaminase Markush group is APOBEC3B (SEQ ID NO 241), which has 57% identity with APOBEC3G (See OA Appendix, page 1). It is not clear if APOBEC3B is included in claim 26 based on its percent identity to A3G or not included based on its exclusion from the Markush group.
Claims 27-28, 30, 32 and 38-40 are rejected for depending from claim 26 and not remedying the indefiniteness.
Claim 27 recites “wherein the napDNAbp domain is selected from [29 different napDNAbp] and variants thereof.” Inclusion of “and variants thereof” renders the claim indefinite because scope of variants of the recited deaminase domains is unclear. It is not clear how much a napDNAbp can be varied and still be considered “a variant thereof”. As such the size and scope of the napDNAbp genus is undefined.
Claim 38 recites “wherein the two or more nuclear localization sequences (NLS) comprises…” Claim 38 depends from claim 26, which only recites “one of more NLS sequences”. As a result, “the two or more NLSs” lacks clear antecedent basis and its not clear how many NLSs are require in claim 38.
To remedy the indefiniteness, claim 38 can be amended to recite “wherein the one or more nuclear localization signals…” or “The base editor of claim 26, comprising two or more nuclear localization signals comprising the amino acid sequence….”
Claims 44-45 depend from claim 26 and recite “wherein the base editor comprises [at least 85% sequence identity to] any one of SEQ ID NOs: 257-282.” Claims 44-45 are confusing because, although they recite specific SEQ ID NOs for the base editors, some of the recited SEQ ID NOs do not comprise any of deaminase domains recited in claim 26. For instance, the Specification indicates that SEQ ID NO 265 has the APOBEC3B deaminase ([00181]), SEQ ID NO 237 has an AID deaminase domain ([00183]), SEQ ID NO 238 has a CDA deaminase domain ([00184]), and SEQ ID NO 269 has a FERNY deaminase domain ([00269]). As such it is not clear if claims 44-45 encompass, for instance, a base editor with a FERNY deaminase domain (from the SEQ ID NO) and then another deaminase from the list recited in claim 26.
Claim Rejections - 35 USC § 112(d)
The following is a quotation of 35 U.S.C. 112(d):
(d) REFERENCE IN DEPENDENT FORMS.—Subject to subsection (e), a claim in dependent form shall contain a reference to a claim previously set forth and then specify a further limitation of the subject matter claimed. A claim in dependent form shall be construed to incorporate by reference all the limitations of the claim to which it refers.
The following is a quotation of pre-AIA 35 U.S.C. 112, fourth paragraph:
Subject to the following paragraph [i.e., the fifth paragraph of pre-AIA 35 U.S.C. 112], a claim in dependent form shall contain a reference to a claim previously set forth and then specify a further limitation of the subject matter claimed. A claim in dependent form shall be construed to incorporate by reference all the limitations of the claim to which it refers.
Claims 32 and 44-45 are rejected under 35 U.S.C. 112(d) or pre-AIA 35 U.S.C. 112, 4th paragraph, as being of improper dependent form for failing to further limit the subject matter of the claim upon which it depends, or for failing to include all the limitations of the claim upon which it depends.
Claim 32 depends from claim 30 a recite “wherein the Cas9 nickase comprises the amino acid sequence set form in SEQ ID NO: 215.” Claim 30 recites wherein the napDNAbp domain comprises the amino acid sequence set form in SEQ ID NO: 214.” SEQ ID NO 214 has an alanine at position 840, (i.e., H840A relative to wild type Cas9), whereas SEQ ID NO 215 has histidine at position 840 (i.e., H840). Claim 32 fails to include all the limitations of claim 30 because it does not comprise a Cas9 that has a H840A substitution.
Claims 44-45 depend from claim 26 and recite “wherein the base editor comprises [at least 85% sequence identity to] any one of SEQ ID NOs: 257-282.” As indicated in paragraph 16 above, some of the SEQ ID NOs do not encode any of deaminase domains recited in claim 26. SEQ ID NO 265 has the APOBEC3B deaminase ([00181]), SEQ ID NO 237 has an AID deaminase domain ([00183]), SEQ ID NO 238 has a CDA deaminase domain ([00184]), and SEQ ID NO 269 has a FERNY deaminase domain ([00269]). This rejection is directed to the interpretation that claims 44-45 encompass base editors with a single deaminase domain, which is a APOBEC3B, AID, CDA and FERNY domain, and the APOBEC3B, AID, CDA and FERNY domains are not “variants” of the deaminase domains recited in claim 26. Under this interpretation, claims 44-45 fail to include all the limitation of the claim 26 because the recited SEQ ID NOs do not include the deaminase domains of claim 26.
Applicant may cancel the claim(s), amend the claim(s) to place the claim(s) in proper dependent form, rewrite the claim(s) in independent form, or present a sufficient showing that the dependent claim(s) complies with the statutory requirements.
Claim Rejections - 35 USC § 112(a)
The following is a quotation of the first paragraph of 35 U.S.C. 112(a):
(a) IN GENERAL.—The specification shall contain a written description of the invention, and of the manner and process of making and using it, in such full, clear, concise, and exact terms as to enable any person skilled in the art to which it pertains, or with which it is most nearly connected, to make and use the same, and shall set forth the best mode contemplated by the inventor or joint inventor of carrying out the invention.
The following is a quotation of the first paragraph of pre-AIA 35 U.S.C. 112:
The specification shall contain a written description of the invention, and of the manner and process of making and using it, in such full, clear, concise, and exact terms as to enable any person skilled in the art to which it pertains, or with which it is most nearly connected, to make and use the same, and shall set forth the best mode contemplated by the inventor of carrying out his invention.
Claim 27 is rejected under 35 U.S.C. 112(a) or 35 U.S.C. 112 (pre-AIA ), first paragraph, as failing to comply with the written description requirement. The claim(s) contains subject matter which was not described in the specification in such a way as to reasonably convey to one skilled in the relevant art that the inventor or a joint inventor, or for applications subject to pre-AIA 35 U.S.C. 112, the inventor(s), at the time the application was filed, had possession of the claimed invention.
Claim 27 recites “wherein the napDNAbp domain is selected from… a Cas13b, a Cas13c, a Cas13d…” The Specification defines “napDNAbp” as a “nucleic acid programmable DNA binding protein” and distinguishes it from an RNA binding protein (See [0086]). As such, the napDNAbp must be able to bind DNA. The Specification lists Cas13b, Cas13c, and Cas13d as an napR/DNAbp ([0086]), but does not indicate whether it binds to DNA, RNA or both. In the art, Cas13 proteins are known to specifically bind target RNA, not DNA. In a review form 2024, Yang explains that Cas13 systems are single-subunit RNA-guided Cas endonuclease for targeting and degrading RNA (Yang et al., Nature Chemical Biology (2024), 20: 673-688; Abstract). There is no indication anywhere in Yang that Cas13 systems are capable of binding DNA. Thus, in view of the Specification and the prior art, it not predictable that Cas13 proteins could bind to DNA. As such, the skilled artisan would have concluded that Applicant did not possess a Cas13b, Cas13c, of Cas13d domain that could function as a napDNAbp.
Claim Rejections - 35 USC § 102 - Koblan
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 26-28, 32, 38-40 and 44-45 are rejected under 35 U.S.C. 102(a)(2) as being anticipated by Koblan (Koblan et al., Nature Biotechnology (2018), 36: 843-846 and Supplemental Materials; published May 29, 2018).
Regarding claim 26-28, Koblan teaches optimizing cytidine base editors (Abstract). Koblan teaches the “BE4max” fusion protein comprising (a) a rat APOBEC1 cytidine deaminase, (b) Cas9n D10A nickase, (c) two NLSs, and (d) two UGI domains (Fig 1a; Supp Sequence 2). According to the Specification, the YE1 deaminase domain is rAPOBEC1 with W90Y and R126E substitutions ([00308], [00314], [00324]). Therefore, the rAPOBEC1 deaminase domain in Koblan is a variant of YE1.
Regarding claim 32, Koblan teaches the amino acid sequence of BE4max (Supp Sequence 2). Koblan teaches the Cas9(D10A) nickase comprise the amino acid sequence of SEQ ID NO 215 (Supp Sequence 2).
Regarding claim 38, Koblan teaches the amino acid sequence of BE4max (Supp Sequence 2). Koblan teaches the NLS sequence in BE4max comprises SEQ ID NO 285 at the N-terminus and SEQ ID NO 286 at the C-terminus.
Regarding claim 39, Koblan teaches the amino acid sequence of BE4max (Supp Sequence 2). Koblan teaches order of the domains in BE4Max is NH2-NLS-APOBEC1-linker-Cas9n-linker-UGI-linker-UGI-linker-NLS (Supp Sequence 2).
Regarding claim 40, Koblan teaches the amino acid sequence of BE4max (Supp Sequence 2). Koblan teaches the linker between second UGI and the second NLS is SGGS (Supp Sequence 2).
Regarding claims 44-45, Koblan teaches the amino acid sequence of BE4max and the sequence of rAPOBEC1 that is present in BE4max (Supp Sequence 2), which is 100% identical to SEQ ID NO 257.
Claim Rejections - 35 USC § 102 - Gao
Claims 26-28, 32, 38-40 and 44-45 are rejected under 35 U.S.C. 102(a)(2) as being anticipated by Gao (US 20210171929 A1, effectively filed November 25, 2019), evidenced by Addgene1 (Plasmid #113415, pCMV-hA3G-BE3, https://www.addgene.org/113415/ [retrieved 12/18/2025]) and Addgene2 (Plasmid #112093, pCMV_BE4max, https://www.addgene.org/112093/ [retrieved 12/18/2025]).
Gao claims priority to US Provisional Application 62/940017, filed November 25, 2019. The point citations recited in rejection below are provided both for the ‘929 publication and the ‘017 application. A copy of the Provisional Specification is provided in an OA Appendix.
Regarding claim 1, Gao teaches base editors comprising fusion proteins comprising Cas9 (i.e., a napDNAbp) and cytosine deaminase domains (Abstract). Gao teaches an A3G Base editor 2.1 variant that comprises a BE4max backbone and an A3G domain and has SEQ ID NO 4 (Table 1). Gao teaches the A3G base editors were constructed by extracting the hA3G fragment from Addgene plasmid #113415 and replacing the rAPOBEC1 domain in Addgene plasmid #112093 ([0200], provisional [0180]). Gao does not expressly teach all the elements in the A3G Base editor 2.1.
Addgene1 teaches plasmid #113415 was first disclosed in 2018 (page 1) and comprises the coding sequence for (a) hAPOBEC3G deaminase domain, which is also known as A3G (page 2).
Addgene2 teaches plasmid #112093 was first published in 2018 (page 1), and comprises a coding sequence for (b) Cas9(D10A) (i.e., a napDNAbp), (c) two SV40 NLS sequences, and (d) two UGI domains (page 4).
Therefore, Gao’s A3G Base editor 2.1 inherently comprised a napDNAbp, two NLSs, 2 UGIs and an A3G cytidine deaminase domain.
Regarding claims 27 and 28, Addgene2 teaches that the napDNAbp is Cas9(D10A) (i.e., a variant of Cas9 that has nickase activity) (page 4).
Regarding claim 32, Gao teaches the sequence of the A3G Base editor 2.1 has SEQ ID NO: 4 (Table 1), which comprises SEQ ID NO 215 of the examined application (See OA Appendix, pages 2-3).
Regarding claim 38, Gao teaches the sequence of the A3G Base editor 2.1 has SEQ ID NO: 4 (Table 1), which comprises the sequence of KRTADGSEFESPKKKRKV at positions 2-19 (i.e., a first NLS comprising SEQ ID NO 285) and the sequence KRTADGSEFESPKKKRKV at position 1992-2008 (i.e., a second NLS sequence with SEQ ID NO: 286) (See OA Appendix pages 4 and 6).
Regarding claim 39, Addgene2 teaches the order of the domain coding sequences in plasmid #112093 is 5’-[SV40 NLS]-[APOBEC-1 deaminase]-[Cas9(D10A) napDNAbp]-[UGI]-[UGI]-[SV40 NLS]-3’ (page 4). Based on the central dogma of molecular biology that nucleic acids are translated 5’ – 3’ to encode a protein from the N-terminus to the C-terminus, plasmid #112093 encodes the protein NH2-[SV40 NLS]-[APOBEC-1 deaminase]-[Cas9(D10A) napDNAbp]-[UGI]-[UGI]-[SV40 NLS]-COOH. As stated above for claim 26, Gao teaches replacing the APOBEC-1 domain with the A3G domain ([0200], provisional [0180]). Therefore, the A3G base editor 2.1 inherently comprised a structure of NH2-[SV40 NLS]-[A3G deaminase]-[Cas9(D10A) napDNAbp]-[UGI]-[UGI]-[SV40 NLS]-COOH.
Regarding claim 40, Gao teaches the sequence of the A3G Base editor 2.1 has SEQ ID NO: 4 (Table 1), which comprises the sequence of SGGSSGGSSGSETPGTSESATPESSGGSSGGS at positions 403-434 (i.e., a linker comprising SEQ ID NO 301 between the A3G domain and the napDNAbp) (See OA Appendix page 4).
Regarding claim 44-45, Gao teaches the sequence of the A3G Base editor 2.1 has SEQ ID NO: 4 (Table 1), which is 100% identical to SEQ ID NO 266 of the present Application (See OA Appendix pages 4-6).
Claim Rejections - 35 USC § 103 – Gao in view of Eid and Jinek
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.
Claim 30 is rejected under 35 U.S.C. 103 as being unpatentable over Gao (US 20210171929 A1, effectively filed November 25, 2019), evidenced by Addgene1 (Plasmid #113415, pCMV-hA3G-BE3, https://www.addgene.org/113415/ [retrieved 12/18/2025]) and Addgene2 (Plasmid #112093, pCMV_BE4max, https://www.addgene.org/112093/ [retrieved 12/18/2025]) as applied to claims 26-28, 32, 38-40 and 44-45 above, and further in view of Eid (Eid et al., Biochemical Journal (2018), 475: 1955-1964) and Jinek (Jinek et al., Science (2012), 337: 816-821).
Regarding claim 30, the Specification teaches that SEQ ID NO 213 is wildtype, catalytically active SpCas9 (page 83). SEQ ID NO 214 differs from SEQ ID NO 213 by including a D10A and a H840A substitution. The Specification teaches that the D10A and H840A substitutions inactivates cleavage of the non-protospacer strand and protospacer strand, respectively (page 85). Therefore, the napDNAbp that comprises SEQ ID NO 214 is catalytically inactive SpCas9, also known as dSpCas9 or dCas9.
The teachings of Gao are recited above as for claims 26-28, 32, 38-40 and 44-45 and incorporated here. Briefly, Gao teaches a base editor comprising the structure NH2-[SV40 NLS]-[APOBEC3G deaminase]-[Cas9(D10A) – SEQ ID NO 213 with D10A]-[UGI]-[UGI]-[SV40 NLS]-COOH. Gao also teaches that catalytically inactive Cas9 (i.e., dCas9) can be fused to cytosine deaminases ([0063], provisional [0054]).
Gao does not teach the A3G base editor comprising a catalytically inactive dSpCas9.
Eid review the state of the art CRISPR base editors (Abstract). Eid teaches that catalytically inactive Cas9 variants have been fused to deaminases to tether the deaminases for gene editing purposes (page 1956, ¶1). Eid teaches dCas9 was fused to APOBEC deaminases, which successfully converted C[Wingdings font/0xE0]T in a catalytic window (page 1956, ¶5).
Jinek teaches making D10A and H840A substitutions to render SpCas9 catalytically inactive (Fig 2A).
It would have been obvious to one skilled in the art before the effective filing date of the claimed invention to have substituted dCas9 for the Cas9 nickase in the A3G base editor of Gao. It would have amounted to the simple substitution of one known Cas9-based DNA-binding domain for another by known means to yield predictable results. The skilled artisan would have predicted that the dSpCas9 with the D10A and H840A substitutions taught Jinek could be used in the A3G base editor because Eid teaches that dCas9 has been fused to APOBEC-based base editors previously for successful base editing in cells. One would have been motivated to do so to reduce nicking damage to off-targets sites of genomic DNA.
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 26-28, 32 and 38-40 rejected on the ground of nonstatutory double patenting as being unpatentable over claims 1-21 of U.S. Patent No. 11319532 in view of Koblan (Koblan et al., Nature Biotechnology (2018), 36: 843-846 and Supplemental Materials).
Patented claim 1 recites “A fusion protein comprising: (i) a nucleic acid programmable DNA binding protein (napDNAbp) domain; (ii) a cytidine deaminase domain. Patented claims 2 and 6 recite further comprising (iv) a first and a second uracil glycosylase inhibitor (UGI) domain. Patented claims 2-3 recite wherein the napDNAbp domain is a Cas9 domain, including a nuclease active Cas9 domain, a Cas9 nickase (nCas9) domain, or a nuclease inactive Cas9 (dCas9) domain. Patented claim 8 recites wherein the deaminase domain is from the APOBEC family. Patented claim 21, recites wherein the cytidine deaminase domain comprises an amino acid sequence that is at least 90% identical to the amino acid sequence of SEQ ID NO: 349, which according to the patented Specification is derived from rAPOBEC1 (i.e., is a variant of YE1). Patented claim 11 recites wherein the fusion protein comprises the structure: NH2-[Gam protein domain]-[cytidine deaminase domain]-[napDNAbp domain]-[first UGI domain]-[second UGI domain]-COOH, and wherein each instance of “]-[” comprises an optional linker.
The patented claims do not recite the fusion protein comprises one or two NLSs at the N and C terminus.
Koblan teaches optimizing cytidine base editors (Abstract). Koblan teaches the “BE4max” fusion protein comprising (a) a rat APOBEC1 cytidine deaminase, (b) Cas9n D10A nickase, (c) two NLSs, and (d) two UGI domains (Fig 1a; Supp Sequence 2). Koblan teaches the Cas9(D10A) nickase comprise the amino acid sequence of SEQ ID NO 215 (Supp Sequence 2). Koblan teaches the NLS sequence in BE4max comprises SEQ ID NO 285 at the N-terminus and SEQ ID NO 286 at the C-terminus. Koblan teaches order of the domains in BE4Max is NH2-NLS-APOBEC1-linker-Cas9n-linker-UGI-linker-UGI-linker-NLS (Supp Sequence 2). Koblan teaches the linker between second UGI and the second NLS is SGGS (Supp Sequence 2). Koblan teaches using the specific BP NLS sequences provide superior editing efficiencies in mammalian cells (Figure 1d). Koblan also teaches that an rAPOBEC1-based base editor with two UGI domains provide nearly 80% editing efficiency (Fig 1).
Regarding claims 26-28, 32 and 38-40, it would have been obvious to one skilled in the art before the effective filing date of the claimed invention to have included the two NLSs taught in Koblan at the N- and C-termini of the patented fusion protein. It would have amounted to the simple combination of known protein domains used in base editors by known means to yield predictable results. The skilled artisan would have predicted that the NLSs could be added to the patented fusion protein because both fusion proteins are based on the BE4 architecture using variants of the rAPOBEC1 deaminase domain. One would have been motivated to do so because Koblan teaches the specific NLS sequences provide superior editing efficiencies in mammalian cells.
Claims 26-28, 32 and 38-40 rejected on the ground of nonstatutory double patenting as being unpatentable over claims 1-21 of U.S. Patent No. 11913044 in view of Koblan (Koblan et al., Nature Biotechnology (2018), 36: 843-846 and Supplemental Materials).
Patented claim 1 recites A cytidine deaminase protein variant comprising an amino acid sequence that is at least 95% identical to the amino acid sequence of SEQ ID NO: 15 [rAPOBEC1], wherein the amino acid sequence of the cytidine deaminase protein variant includes at least three mutations at a position selected from the group consisting of R33, G45, N57, N65, Y75, T101, F113, A123, S149, A165, H166, T204, F205, and W224 of SEQ ID NO: 15 [rAPOBEC1] (i.e., a variant YE1). Patented claim 13 recites A fusion protein comprising: (i) a RNA-programmable nuclease (i.e., an napDNAbp); (ii) the cytidine deaminase protein variant of claim 1; and (iii) a uracil glycosylase inhibitor (UGI) domain. Patented claims 14-15 recite wherein the RNA-programmable nuclease is a Cas9 domain comprising an amino acid sequence that is at least 85% identical to the amino acid sequence provided in SEQ ID NO: 20 or 21 and is a Cas9 nickase domain (i.e., is SEQ ID NO 215).
The patented claims do not recite a second UGI or one or more NLSs.
The teachings of Koblan are recited above in paragraph 58 and are incorporated here.
Regarding claims 26-28, 32 and 38-40, it would have been obvious to one skilled in the art before the effective filing date of the claimed invention to have included the two NLSs taught in Koblan at the N- and C-termini and an additional UGI as taught in Koblan and fused together the components in of the patented complex. It would have amounted to the simple combination of known protein domains used in base editors by known means to yield predictable results. The skilled artisan would have predicted that the NLSs and a second UGI could be added to the patented fusion protein because both fusion proteins are based on the BE4 architecture using variants of the rAPOBEC1 deaminase domain. One would have been motivated to do so because Koblan teaches the specific NLS sequences provide superior editing efficiencies in mammalian cells and teaches that two UGIs in the base editor provide nearly 80% editing efficiency.
Claims 26-28, 32 and 38-40 rejected on the ground of nonstatutory double patenting as being unpatentable over claims 1-34 of U.S. Patent No. 12344869 in view of Koblan (Koblan et al., Nature Biotechnology (2018), 36: 843-846 and Supplemental Materials).
Patented claim 1 recites A complex comprising: (i) a Cas9 protein; (ii) a cytidine deaminase; (iii) a uracil glycosylase inhibitor (UGI) protein, wherein the complex deaminates a cytidine in a target nucleic acid sequence. Patented claim 2 recites wherein the Cas9 protein is a Cas9 nickase. Patented claim 3 recites wherein the nCas9 comprises an amino acid sequence having at least 85% sequence identity to the amino acid sequence provided in SEQ ID NO: 10, and wherein the amino acid sequence provided in SEQ ID NO: 10 further comprises a D10A mutation (i.e., the Cas9n comprises SEQ ID NO 215 of the examined application). Patneted claim 16 recites wherein the deaminase is a rat APOBEC1 (rAPOBEC1) deaminase comprising one or more mutations selected from the group consisting of W90Y, R126E, and R132E of SEQ ID NO: 284 (i.e., is a variant of at least YE1) or (vi) is a human APOBEC3G (hAPOBEC3G) (i.e., an A3G).
The patented claims do not recite a second UGI or one or more NLSs. The patented claims do not recite the elements are in a fusion protein.
The teachings of Koblan are recited above in paragraph 58 and are incorporated here.
Regarding claims 26-28, 32 and 38-40, it would have been obvious to one skilled in the art before the effective filing date of the claimed invention to have included the two NLSs taught in Koblan at the N- and C-termini and an additional UGI as taught in Koblan and fused together the components in of the patented complex. It would have amounted to the simple combination of known protein domains used in base editors by known means to yield predictable results. The skilled artisan would have predicted that the NLSs and a second UGI could be added to the patented fusion protein because both fusion proteins are based on the BE4 architecture using variants of the rAPOBEC1 deaminase domain. One would have been motivated to do so because Koblan teaches the specific NLS sequences provide superior editing efficiencies in mammalian cells and teaches that two UGIs in the base editor provide nearly 80% editing efficiency. The skilled artisan would have been motivated to fused the elements together and will a reasonable expectation of success because Koblan demonstrates such a fusion protein of the base editor complex components.
Claims 26-28, 32 and 38-40 rejected on the ground of nonstatutory double patenting as being unpatentable over claims 1-34 of U.S. Patent No. 12344869 in view of Koblan (Koblan et al., Nature Biotechnology (2018), 36: 843-846 and Supplemental Materials).
Patented claim 1 recites A fusion protein comprising: (i) a Cas9 domain, wherein the Cas9 domain when in conjunction with a bound guide RNA (gRNA) specifically binds to a target nucleic acid sequence; (ii) a cytidine deaminase domain, wherein the cytidine deaminase domain deaminates a cytosine base in a single-stranded portion of the target nucleic acid sequence when in conjunction with the Cas9 domain and the gRNA; and (iii) an uracil glycosylase inhibitor (UGI) domain, wherein the UGI domain inhibits a uracil-DNA glycosylase. Patented claim 2 recites wherein the Cas9 domain comprises the amino acid sequence provided in SEQ ID NO: 674 (i.e., 100% identical to SEQ ID NO 215). Patented claims 9 recites wherein the cytidine deaminase domain is a rat APOBEC1 (rAPOBEC1) deaminase comprising one or more mutations selected from the group consisting of W90Y, R126E, and R132E (i.e., is a variant of YE1). Patented claim 18 recites the fusion protein further comprises an NLS sequence. Patented claim 20 recites the structure of the fusion protein is NH2-[cytidine deaminase domain]-[Cas9 domain]-[UGI domain]-[NLS]-COOH. Patented claim 21 recites the linker between the UGI domain and the NLS is SGGS.
The patented claims do not recite a second UGI or a second NLS with the recited sequence at the N-terminus.
The teachings of Koblan are recited above in paragraph 58 and are incorporated here.
Regarding claims 26-28, 32 and 38-40, it would have been obvious to one skilled in the art before the effective filing date of the claimed invention to have included a second NLS with the instantly claimed sequence that is taught in Koblan at the N-terminus and an additional UGI as taught in Koblan. It would have amounted to the simple combination of known protein domains used in base editors by known means to yield predictable results. The skilled artisan would have predicted that the NLSs and a second UGI could be added to the patented fusion protein because both fusion proteins are based on the BE4 architecture using variants of the rAPOBEC1 deaminase domain. One would have been motivated to do so because Koblan teaches the specific NLS sequences provide superior editing efficiencies in mammalian cells and teaches that two UGIs in the base editor provide nearly 80% editing efficiency.
Claims 26-28 and 38-40 rejected on the ground of nonstatutory double patenting as being unpatentable over claims 1-34 of U.S. Patent No. 12281338 in view of Koblan (Koblan et al., Nature Biotechnology (2018), 36: 843-846 and Supplemental Materials).
Patented claim 1 recites a fusion protein comprising an amino acid sequence that is at least 85% identical to SEQ ID NO: 81. The patented Specification teaches that SEQ ID NO 81 is also called “GeoBE4” whose structure is illustrated in Fig 2. Patented figure 2 indicated that SEQ ID NO 81 comprises (a) an APOBEC1 deaminase domain (i.e., a variant of at least YE1)-a linker- XTEN-GeoCas9n (a Cas9 napDNAbp)-UGI-UGI. Therefore, patented claim 1 encompasses a base editor comprising elements (a), (b) and (d). The patented SEQ ID NO 81 comprises a SGGSGGSGGS.
The patented claims do not recite the base editor comprises one of more NLS domains.
The teachings of Koblan are recited above in paragraph 58 and are incorporated here.
Regarding claims 26-28 and 38-40, it would have been obvious to one skilled in the art before the effective filing date of the claimed invention to have included two NLS with the instantly claimed sequences that are taught in Koblan at the N-terminus and C-terminus of the patented rAPOBEC1-GeoCas9 base editor. It would have amounted to the simple combination of known protein domains used in base editors by known means to yield predictable results. The skilled artisan would have predicted that two NLSs could be added to the patented fusion protein because both fusion proteins are based on the BE4-Cas9n architecture using variants of the rAPOBEC1 deaminase domain. One would have been motivated to do so because Koblan teaches the specific NLS sequences at the N- and C-terminus provide superior editing efficiencies in mammalian cells.
Claims 26-28, 30, 38-40 and 44 provisionally rejected on the ground of nonstatutory double patenting as being unpatentable over claim 1-2, 9, 21-22, 24, 35, 41, and 52-54 of copending Application No. 17593020. Claims 38-40 are rejected in view of in view of Koblan (Koblan et al., Nature Biotechnology (2018), 36: 843-846 and Supplemental Materials).
Copending claim 1 recites fusion proteins compris[ing] (i) a nuclease inactive Cas9 (dCas9) domain and (ii) a deaminase domain, and a guide RNA (gRNA) bound to the dCas9 domain, wherein each of the fusion proteins of the plurality comprises an amino acid sequence that is at least 90% identical to any one of SEQ ID NOs: 3,6-8, or 10-15. The copending Specification teaches that SEQ ID NO 11 comprises cytidine base editor 4 ([00131]). Copending SEQ ID NO 11 has 100% identity to SEQ ID NO 257 except for amino acids 1-20 and the last ~ 20 amino acids. Copending SEQ ID NO 11 comprises PKKKRK at its C-terminus (i.e., a NLS sequence). Thus, the copending fusion protein comprises (a) an rAPOBEC1 deaminase (i.e., a YE1 variant), (b) a dCas9 napDNAbp, (c) at least one NLS and (d) two UGI domains. As such copending claim 1 anticipates examined claims 26-28, 30 and 44.
Regarding claims 38-40, the teachings of Koblan are recited above in paragraph 58 and are incorporated here. It would have been obvious to one skilled in the art before the effective filing date of the claimed invention to have included two NLS with the instantly claimed sequences that are taught in Koblan at the N-terminus and C-terminus of the patented BE4 base editor. It would have amounted to the simple combination of known protein domains used in base editors by known means to yield predictable results. The skilled artisan would have predicted that two NLSs could be added to the patented fusion protein because both fusion proteins are based on the BE4-Cas9 architecture using variants of the rAPOBEC1 deaminase domain. One would have been motivated to do so because Koblan teaches the specific NLS sequences at the N- and C-terminus provide superior editing efficiencies in mammalian cells.
This is a provisional nonstatutory double patenting rejection.
Claims 26-28, 32, 38-40 and 44 provisionally rejected on the ground of nonstatutory double patenting as being unpatentable over claims 303-325 of copending Application No. 19/202976 in view of in view of Koblan (Koblan et al., Nature Biotechnology (2018), 36: 843-846 and Supplemental Materials).
Copending claim 303 A nucleotide sequence encoding recites a fusion protein comprising (b) a Cas9 domain, (a) a cytidine deaminase domain, and (d) a uracil glycosylase inhibitor (UGI) domain. Copending claim 305 recites wherein the Cas9 domain is a Cas9 nickase (nCas9) domain that cuts a nucleotide target strand of a nucleotide duplex, wherein the nucleotide target strand is the strand that binds to a gRNA. Copending claim 306 recites wherein the Cas9 domain is a Cas9 nickase (nCas9) domain that comprises a D10A mutation in the amino acid sequence provided in SEQ ID NO: 10 (i.e., comprises SEQ ID NO 215). Copending claim 309 recites wherein the APOBEC family deaminase is selected from the group consisting of APOBECI deaminase, APOBEC2 deaminase, APOBEC3A deaminase, APOBEC3B deaminase, APOBEC3C deaminase, APOBEC3D deaminase, APOBEC3F deaminase, APOBEC3G deaminase, and APOBEC3H deaminase. Copending claim 311 recites wherein the cytidine deaminase domain is a rat APOBECI (rAPOBEC1) deaminase comprising one or more mutations selected from the group consisting of W90Y, R126E, and R132E of SEQ ID NO: 284, or one or more corresponding mutations in another APOBEC deaminase (i.e., a variant of YE1). Copending claim 322 recites wherein the fusion protein comprises the structure: NH2-[cytidine deaminase domain]-[Cas9 domain]-[UGI domain]-[NLS]-COOH, and wherein each instance of "-" comprises an optional linker. Copending claim 323 recites wherein the UGI domain and the NLS are linked via a linker comprising the amino acid sequence: SGGS.
The copending claims do not recite a second UGI or a second NLS with the recited sequence at the N-terminus.
The teachings of Koblan are recited above in paragraph 58 and are incorporated here.
Regarding claims 26-28, 32 and 38-40, it would have been obvious to one skilled in the art before the effective filing date of the claimed invention to have included a second NLS with the instantly claimed sequence that is taught in Koblan at the N-terminus and an additional UGI as taught in Koblan to the copending fusion protein. It would have amounted to the simple combination of known protein domains used in base editors by known means to yield predictable results. The skilled artisan would have predicted that the NLSs and a second UGI could be added to the patented fusion protein because both fusion proteins are based on the BE4 architecture using variants of the rAPOBEC1 deaminase domain. One would have been motivated to do so because Koblan teaches the specific NLS sequences provide superior editing efficiencies in mammalian cells and teaches that two UGIs in the base editor provide nearly 80% editing efficiency.
This is a provisional nonstatutory double patenting rejection.
Conclusion
No claims are allowable.
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/CATHERINE KONOPKA/Examiner, Art Unit 1635