DETAILED ACTION
Claims 1-4, 6-14, 18-19, 22, 26, 31, and 35-36 are currently pending.
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 1 (claims 1-4, 6-14, 18-19, 22 and 26) in the reply filed on 11/10/2025 is acknowledged.
Claims 31, and 35-36 are withdrawn from further consideration pursuant to 37 CFR 1.142(b) as being drawn to a nonelected invention, there being no allowable generic or linking claim.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 11/10/2025.
Priority
Acknowledgement is made of the instant application being a national stage entry under 35 USC 371 of international application PCT/US2021/022058, filed March 12, 2021.
Information Disclosure Statement
The information disclosure statement (IDS) submitted on 9/13/2022 is in compliance with the provisions of 37 CFR 1.97. Accordingly, the information disclosure statement is being considered by the examiner.
Specification
The use of the terms “Trima”, “Ficoll”, “SepMate”, “EasySep” and “dynabeads”, which are trade names or marks used in commerce, has been noted in this application. The terms should be accompanied by the generic terminology; furthermore the terms should be capitalized wherever they appear or, where appropriate, include a proper symbol indicating use in commerce such as ™, SM , or ® following the terms.
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 § 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.
Claim(s) 1-4, 6, 19, 22 and 26 are rejected under 35 U.S.C. 103 as being unpatentable over Roth et al., (WO 2019/226998; IDS 9/13/2022), in view of Nguyen et al., (Nature Biotechnology, Vol 38, January 2020, pages 44-49; see PTO-892) (“Nguyen”) and Nguyen et al., Supplementary Information, Nature Biotechnology, Vol 38, January 2020, 36 pages (see PTO-892) (“Nguyen Supplementary”).
Roth is directed to compositions and methods for modifying the genome of a human cell, for example, a T cell, by inserting a nucleic acid encoding a functional domain into the endogenous gene encoding cell surface proteins ([0003]).
Roth teaches the nucleic acid sequence is inserted into the T cell by introducing into the T cell a construct (i.e., donor construct) comprising:
(a) a targeted nuclease that cleaves a target region of a gene encoding the cell surface protein, in order to create an insertion site in the genome of the T cell; and
(b) the nucleic acid sequence encoding a functional domain or a functional fragment thereof, wherein the nucleic acid sequence is incorporated into the insertion site by HDR (homology directed repair) ([0099]). Upon insertion into the genome of the T cells by homologous recombination, the construct encoding the functional domain is under the control of the endogenous promoter of the cell surface protein, thus the T cells can be cultured under conditions permitting transcription of the inserted construct ([0103]).
Regarding claim 1, Roth teaches the nucleic acid sequence is introduced into the cell as a linear DNA template, e.g., single-stranded DNA template ([0133]) and the nucleic acid sequence is flanked by homologous sequences (homologous to genomic sequences) located at the 5’ and 3’ ends of the nucleic acid sequence, thus allowing recombination to occur, thereby inserting the nucleic acid sequence in the insertion site to generate a modified human T cell ([0124] and [0132]). Roth teaches the homologous sequences are about 50-1000 nucleotides in length and complementary to the genomic sequence ([0132]).
Roth further teaches the targeted nuclease includes an RNA-guided nuclease domain, i.e., a Cas9 nuclease, and the method further comprises introducing into the cell a guide RNA (gRNA) that specifically hybridizes to a target region in the genome of the T cell ([0133]). Roth teaches the targeted nuclease (i.e., Cas9), the guide RNA and the nucleic acid sequence (i.e., at least one donor template) are introduced into the cell as a ribonucleotide complex, (RNP)-DNA template complex, wherein the RNP-DNA complex comprises: (i) the RNP and (ii) the nucleic acid donor sequence. The RNP comprises the targeted nuclease and the guide RNA ([0138]).
As to the limitation regarding the donor construct comprises one or more DNA-binding protein target sequences, it is noted Roth teaches the nucleic acid donor template comprises a homology directed repair (HDR) template and one or more DNA-binding protein target sequences ([0145]), as recited in claim 1. Roth specifically teaches the nucleic acid donor template has a “shuttle sequence” i.e., one DNA-binding protein target sequence and one or more protospacer adjacent motif (PAM). Thus, the complex (RNP-DNA complex) containing the DNA-binding protein (e.g., a RNA-guided nuclease, Cas9), the donor gRNA, and the donor template can “shuttle” the donor template, without cleavage of the DNA-binding protein target sequence, to the desired intracellular location (e.g., the nucleus) such that the HDR template can integrate into the cleaved target nucleic acid. Roth discloses shuttle sequences at paragraph [0193], and further notes that these ‘shuttle’ sequences are truncated Cas9 Target Sequences (tCTS) that were added to the 5’ and 3’ ends of the HDR template ([0196]). Thus, Roth discloses an embodiment of the donor template sequence comprising two DNA-binding protein target sequences, tCTS, located at the 5’ and 3’ ends of the HDR template.
Although Roth does not explicitly disclose the DNA-binding protein target sequence (i.e., tCTS) forming a double-stranded duplex with a complementary polynucleotide sequence, it is noted that Roth teaches the presence of the “shuttle sequence” permits the complex comprising Cas9, the donor gRNA and the donor template to “shuttle” the HDR donor template to the desired intracellular location and subsequent integration of the HDR template into the T cell genome.
Nguyen is directed to modified repair templates for increasing genome editing efficiency, particularly comprising truncated Cas9 target sequences (tCTSs) added at the ends of the homology-directed repair (HDR) template for interacting with Cas9 ribonucleoproteins (RNPs) for shuttling of the template to the cell nucleus, thus enhancing HDR efficiency by approximately two- to fourfold (Abstract and Fig. 1a).
Nguyen’s Fig. 1a is illustrated directly below for convenience:
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Nguyen’s Fig. 1a illustrates the tCTS sequences binding with Cas9 comprising nuclear localization sequences (NLS). Nguyen teaches attempting to recruit Cas9 RNPs with nuclear localization sequences (NLSs) to the HDR template by enhancing Watson-Crick interactions (i.e., complementary nucleotide interactions), thus testing HDR enhancement by targeting a dCas9–NLS ‘shuttle’ to the ends of an HDR template by coding 20 bp Cas9 target sequences (CTSs) at the ends of the homology arms (Supplementary Fig. 1) (page 44, left col, last paragraph to right col, second paragraph).
Nguyen teaches use of a single catalytically active Cas9–NLS RNP would suffice for both on-target genomic cutting and ‘shuttling’ if the HDR template were designed with 16 bp truncated CTSs (tCTSs) that enable Cas9 binding (i.e., DNA-binding target sequences) but do not enable cutting (Fig. 1a and Supplementary Fig. 2). Nguyen teaches that, with the proper sequence orientation, the addition of tCTSs markedly improved knock-in efficiency of a 1.5 kb DNA sequence inserting a reprogrammed TCRα and TCRβ specificity at the endogenous TRAC (T cell receptor α constant) locus (Fig. 1b and Supplementary Fig. 2). This tCTS shuttle system also improved genome targeting efficiencies across a variety of loci in different primary human T cell subsets (Fig. 1c, d and Supplementary Fig. 3) (right col, second paragraph).
Nguyen’s Supplementary Fig. 2a is copied below for convenience:
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Nguyen notes the experimental data demonstrates that coupling (duplex) an HDR template comprising tCTSs to a Cas9–NLS RNP can enhance genome targeting efficiency without requiring modification of the protein or gRNA (page 45, left col).
Further, as illustrated in Nguyen’s Fig 1a and Supplementary Fig. 2a, it is considered that the tCTSs (truncated gRNA sites) comprise DNA-binding protein target sequences that form a double-stranded duplex with the complementary Cas9-NLS RNPs via the disclosed gRNA, which reads on a complementary polynucleotide sequence.
Thus, Nguyen evidences the truncated Cas9 target sequences of Roth, that permit “shuttling” of the HDR donor template to the desired intracellular location and subsequent integration of the HDR template into the T cell genome, comprise at least one DNA-binding protein target sequences that forms a double-stranded duplex with a complementary polynucleotide sequence (gRNA).
Thus, although Roth does not explicitly disclose the DNA-binding protein target sequence (i.e., tCTS) forming a double-stranded duplex with a complementary polynucleotide sequence, Nguyen has evidenced that Roth’s disclosed truncated Cas9 target sequences render obvious a donor template comprising a single-stranded homology directed repair template (HDRT) and one or more DNA-binding protein target sequences, wherein at least one DNA-binding protein target sequence forms a double stranded duplex with a complementary polynucleotide sequence, that is, Roth teaches the limitations required by the current claims and as all limitations are found in one reference it is held that a composition comprising a single-stranded homology directed repair template (HDRT) and one or more DNA-binding protein target sequences, wherein at least one DNA-binding protein target sequence forms a double stranded duplex with a complementary polynucleotide sequence is within the scope of the teachings of Roth, and thus renders the invention of claim 1 prima facie obvious. The rationale to support this conclusion of obviousness is that the single reference provides the teachings and suggestion to prepare homology directed repair templates having DNA-binding protein target sequences that form double-stranded duplexes with complementary polynucleotide sequences. Furthermore, there is no evidence on the record that shows that the claimed limitation has any greater or unexpected results than that exemplified by Roth.
Regarding claim 2, as set forth above, Roth teaches the donor construct comprises a single-stranded donor template (i.e., a first polynucleotide comprising a single donor template) and Nguyen evidences that Roth’s disclosed tCTSs comprises at least one second polynucleotide comprising complementary polynucleotide sequence that duplexes with the Cas9-NLS RNPs via the disclosed gRNA, thus meeting the limitations of claim 2.
Regarding claim 3, Roth at [0145] teaches embodiments comprising both one and two DNA-binding protein target sequences. Thus, Roth teaches the limitations required by the current claims and as all limitations are found in one reference it is held that donor template comprising only one DNA-binding protein target sequence and hybridizes to the complementary polynucleotide sequence is within the scope of the teachings of Roth, and thus renders the invention of claim 3 prima facie obvious. The rationale to support this conclusion of obviousness is that the single reference provides the teachings and suggestion to prepare homology directed repair templates having one DNA-binding protein target sequence. Furthermore, there is no evidence on the record that shows that the claimed limitation has any greater or unexpected results than that exemplified by Roth.
Regarding claim 4, it is noted that Roth teaches the DNA-binding protein target sequence is located at the 5’ terminus or the 3’ terminus of the HDR template ([0145]), thus meeting the limitation of claim 4.
Regarding claim 6, Nguyen’s Fig. 1a and Nguyen’s Supplementary Fig. 2a illustrate the donor template comprises a first tCTS (DNA-binding protein target sequence) located at the 5’ terminus of the donor template and second tCTS located at the 3’ terminus of the donor template, wherein the first tCTS duplexes with a first complementary gRNA of the 5’ Cas9-NLS complex and the second tCTS duplexes with a second complementary gRNA of the 3’ Cas9-NLS complex, thus meeting the limitations of claim 6.
Regarding claim 19, Roth teaches the HDR donor template comprises one or more protospacer adjacent motifs (PAMs), specifically that the PAMs can be located at the 5’ or 3’ terminus of the HDR template ([0145]), thus meeting the limitation of claim 19.
Regarding claim 22, Roth, in view of Nguyen, renders obvious the donor construct of claim 1. Roth further teaches the construct comprises a targetable nuclease, e.g., Cas9, and truncated Cas9 target sequences (tCTS) (i.e., DNA-binding protein) ([0133], [0145]), thus meeting the limitations of claim 22.
Regarding claim 26, it is noted that Nguyen’s Fig. 1a and Nguyen’s Supplementary Fig. 2a illustrate the donor template of Roth would comprise a target guide RNA located at the DNA insertion site, and the donor template further comprises truncated gRNA sequence, i.e., donor gRNA, thus meeting the limitation of claim 26.
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, 22 and 26 are rejected on the ground of nonstatutory double patenting as being unpatentable over claims 1 and 4 of U.S. Patent No. 12,359,179 (“U.S. ‘179”). Although the claims at issue are not identical, they are not patentably distinct from each other because claims 1 and 4 of U.S. ‘179 claim the following:
A composition for modifying a target nucleic acid, comprising: (a) a targetable nuclease; (b) a DNA-binding protein; and (c) a donor template comprising a homology directed repair (HDR) template, two or more protospacer adjacent motifs (PAMs), and two or more DNA-binding protein target sequences.
4. The composition of claim 1, wherein the composition further comprises a target guide RNA (gRNA) and a donor gRNA; wherein the target gRNA is complementary to the target nucleic acid; and wherein each of the DNA-binding protein target sequences hybridizes to the donor gRNA or a portion thereof.
Claim 4 of U.S. ‘179 anticipates claims 1, 22 and 26 given the limitation “wherein each of the DNA-binding protein target sequences hybridizes to the donor gRNA or a portion thereof” reads on a DNA-binding protein target sequence that forms a double-stranded duplex with a complementary polynucleotide sequence, as recited in instant claim 1.
Allowable Subject Matter
Claims 7-14 and 18 are 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.
Regarding Claims 7-14, it is noted none of the references cited by the Applicant nor those reviewed by the Examiner upon searching the appropriate data bases teach or fairly suggest the donor construct of claim 1, wherein the donor construct comprises (a) a first donor template comprising a first DNA-binding protein target sequence located at or proximal to the 3' terminus of the first donor template, and (b) a second donor template comprising a second DNA-binding protein target sequence located at or proximal to the 3' terminus of the second donor template, wherein the first DNA-binding protein target sequence hybridizes to the second DNA-binding protein target sequence (as recited in claim 7); or wherein the DNA-binding protein target sequence and the complementary polynucleotide sequence form a hairpin (as recited in claim 9).
Regarding claim 18, it is noted a sequence search was conducted regarding SEQ ID NOs: 30-35. No prior art was identified.
Conclusion
No claim is allowed.
Examiner Contact Information
Any inquiry concerning this communication or earlier communications from the examiner should be directed to E. YVONNE PYLA whose telephone number is (571)270-7366. The examiner can normally be reached M-F 9am - 6pm.
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E. YVONNE PYLA
Primary Examiner
Art Unit 1633
/EVELYN Y PYLA/Primary Examiner, Art Unit 1633