DETAILED ACTION
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 species election without traverse in the reply filed on 6/01/2026 is acknowledged.
Claims 6, 7, and 17 are withdrawn from further consideration pursuant to 37 CFR 1.142(b) as being drawn to nonelected species, there being no allowable generic or linking claim. Election was made without traverse in the reply filed on 6/01/2026.
Claims 1-4, 8-10, 13-15, and 18-24 are under consideration on the merits.
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, 8-10, 13-15, and 18-24 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.
“Represented by” as recited in claim 1 and in the context of nucleic acid sequences is a vague transitional phrase and so renders the claim indefinite. See M.P.E.P. § 2111.03. It is unclear if “represented by” is an open-ended (e.g. "comprising”) or closed (e.g. “consisting of”) transitional phrase, and if “represented by” does or does not permit any degree of variability within the claimed nucleic acid sequences. The scope of “represented by” is not clarified when read in light of the specification. Correction and/or clarification is required. Applicant might overcome this rejection by either replacing “represented by” with a transitional phrase that is clearly understood as a term of art (e.g. “comprising” or “consisting of”; presuming original support to make said amendments) or clearly setting forth on the record what degree of scope is permitted and excluded by the transitional phrase “represented by”. Correction is required.
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 24 recites the broad recitation of human fibroblasts and human kidney cells and the claim also recites (HDF) and (HEK293T), which are the narrower statement of the claimed cells, respectively. 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. Correction is required.
In so much that claims 2-4, 8-10, 13-15, and 18-24 depend from claim 1 and do not resolve the point of confusion, these claims must be rejected with claim 1 as indefinite.
Claim Rejections - 35 USC § 103
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, 9, 13-15, 18, and 21-24 rejected under 35 U.S.C. 103 as being unpatentable over Papapetrou et al. (Nature Biotechnology (2011), 29(1), 73-78 and appended Online Methods; Reference U) in view of Heo et al. (Stem Cells and Development (2015), 24(3), 393-402; Reference V) and Montague et al. (Nucleic Acids Research (2014), 42(Web Server issue), W401-W407; Reference W).
Other species were found during the search. This rejection addresses the embodiment of a generic plasmid vector encoding for Cas for claims 1, 3, and 13-15, Cas9 for claims 1 and 9, and Oct4, Sox2, Klf4, and c-Myc for claim 18.
Papapetrou teaches a method of producing induced pluripotent stem cells (iPSCs) comprising inserting nucleic acids encoding for the reprogramming factors Oct4, Sox2, Klf4, and c-Myc in lentiviral vectors into cells obtained from skin biopsy of human subjects suffering from β-thalassemia major (page 1 of the Online Methods, subheadings “Lentiviral vector construction and production” and “Human iPS cell generation”), reading in-part on claim 1, claim 18, the embodiment of human fibroblasts and human dermal fibroblasts for claims 23 and 24. Papapetrou teaches inserting a nucleic acid encoding for β-globin into several genomic safe harbor sites including Chr.1:188083272 in the iPSCs derived from human subjects suffering from β-thalassemia major and wherein the chromosome 1 insertion site meets all five safe harbor criteria (Fig. 1 and 2f, and Table 1 clone 5.10-2) and which expresses 85% of the level of a normal endogenous β-globin allele (the paragraph spanning pages 75-76 and Fig. 3b), reading in-part on claims 1 and 2. Papapetrou teaches that retroviruses efficiently integrate in the human genome with a strong bias towards actively transcribed genes but that this semi-random integration can perturb the expression of neighboring genes such as cancer-related genes (the paragraph spanning both columns on page 73), reading on claims 1 and 2.
Regarding claim 1, Papapetrou does not teach inserting the reprogramming factors into any species of CASH-1 utilizing a CRISPR/Cas system comprising a delivery vehicle, nucleic acids encoding for SEQ ID NO: 1 and 2 as gRNAs, and a nucleic acid encoding for a Cas protein. Regarding claim 2, Papapetrou does not teach inserting the reprogramming factors into Chr.1:188083272 (of human cells). Regarding claim 3 and 14, Papapetrou does not teach the elected species of vector as a delivery vehicle. Regarding claim 4, Papapetrou does not teach the nucleic acids in a single delivery vehicle. Regarding claim 9, Papapetrou does not teach Cas9. Regarding claims 14 and 15, Papapetrou does not teach a plasmid vector. Regarding claim 21, Papapetrou does not teach any nucleic acid ratio of gRNA:Cas9 nucleic acid. Regarding claim 22, Papapetrou does not teach linear nucleic acids.
Heo teaches methods of generating bovine induced pluripotent stem cells (iPSCs) comprising inserting nucleic acids encoding for the reprogramming factors Oct4, Sox2, Klf4, and c-Myc (the paragraph spanning both columns on page 394), reading in-part on claim 1. Heo teaches inserting a plasmid nucleic acid encoding for GFP into the endogenous Nanog gene locus of bovine iPSCs derived from fibroblasts obtained from the ear and in bovine embryos utilizing a CRISPR/Cas9 system as proof-of-principle for generative transgenic bovine(s) as Nanog is a known pluripotency
marker (the paragraphs spanning pages 396-397 and 397-398; Fig. 3 for genomic knock-in of IPSCs; Fig. 4 for genomic knock-in of bovine embryos), reading in-part on claims 1, 3, 4, 9, and 13-15. Heo teaches that the optimal ration of gRNA:Cas9 mRNA of 1:2 (page 399, the 1st paragraph in the left column under Table 2; and, the paragraph spanning pages 394-395 for linear vectors), reading on claims 21 and 22. Heo teaches identifying potential targets CRISPR gRNAs in the bovine genome and designing said gRNAs (page 395, the paragraph spanning both columns), reading in-part on the gRNAs of claim 1.
Montague teaches “CHOPCHOP”a, an online tool for designing and predicting off-target binding of gRNAs against genes, genomic regions, or user-specific (i.e. pasted) sequences (Abstract), reading on the gRNAs of claim 1.
Regarding the Chr.1:188083272 insertion site of claims 1 and 2 and the CRISPR/Cas system of claims 1, 3, 4, 9, 13-15, 21, and 22, it would have been obvious to a person of ordinary skill in the art before the invention was filed to add the CRISPR/Cas9 system of Heo and then substitute the lentivirally integrated reprogramming factors of Papapetrou into Chr.1:188083272 of Papapetrou’s human dermal fibroblasts to yield induced pluripotent stem cells. A person of ordinary skill in the art would have had a reasonable expectation of success to do so because both Papapetrou and Heo are directed towards methods of generating iPSCs from fibroblasts, and because Heo teaches detailed methods of utilizing CRISPR/Cas9 to integrate GFP at the endogenous Nanog locus as a proof-of-principle, and because Papapetrou teaches that integration at Chr.1:188083272 meets all five safe harbor criteria and which expresses 85% of the level of a normal allele. The skilled artisan
would have been motivated to do so because Papapetrou there is a need in this art to improve methods of genomic integration in safe harbor sites because retroviruses (e.g. lentiviruses and vectors based upon said viruses) efficiently integrate in the human genome with a strong bias towards actively transcribed genes but that this semi-random integration can perturb the expression of neighboring genes such as cancer-related genes, and so the addition of Heo’s CRISPR/Cas9 system and integration of reprogramming factors at the Chr.1:188083272 would likely and predictably improve upon Papapetrou’s human iPSCs by reducing semi-random genomic integration and possible perturbation of neighboring genes.
Regarding the gRNAs of claim 1, it would have been obvious to a person of ordinary skill in the art before the invention was filed to try and design SEQ ID NO: 1 and 2 as gRNAs specific for the human Chr.1:188083272 locus over Papapetrou, Heo, and Montague. See M.P.E.P. § 2144(E). In this case, 1) Papapetrou there is a need in this art to improve methods of genomic integration in safe harbor sites because retroviruses (e.g. lentiviruses and vectors based upon said viruses) efficiently integrate in the human genome with a strong bias towards actively transcribed genes but that this semi-random integration can perturb the expression of neighboring genes such as cancer-related genes, 2) Heo and Montague as a whole teach a finite number of identified, predictable potential solutions to design gRNAs and predict possible off-target binding of gRNAs at any particular genomic site of interest, and so 3) person of ordinary skill in the art could have pursued the known potential solutions of designing and utilizing gRNAs specific for the human Chr.1:188083272 locus with a reasonable expectation of success. The skilled artisan would have been motivated to do so because "a person of ordinary skill has good reason to pursue the known options within his or her technical grasp. If this leads to the anticipated success, it is likely that product [was] not of innovation but of ordinary skill and common sense. In that instance the fact that a combination was obvious to try might show that it was obvious under § 103."KSR, 550 U.S. at 421, 82 USPQ2d at 1397.
Therefore, the invention as a whole would have been prima facie obvious to a person of ordinary skill before the invention was filed.
Claims 8-10 are rejected under 35 U.S.C. 103 as being unpatentable over Papapetrou, Heo, and Montague as applied to claims 1 and 3 above, and further in view of Cong et al. (Science (2013), 339(6121), 819-823; Reference X) as evidenced by Addgene plasmid #42335 (Reference U2).
The teachings of Papapetrou, Heo, and Montague are relied upon as set forth above.
Regarding claim 8, Papapetrou, Heo, and Montague do not teach the elected species of non-viral vector of pX335-U6-Chimeric_BB-CBh-hSpCas9n(D10A). Regarding claim 9, Papapetrou, Heo, and Montague do not teach the elected species of Cas9 nickase. Regarding claim 10, Papapetrou, Heo, and Montague do not teach Cas protein derived from Streptococcus sp.
Cong teaches pX335-U6-Chimeric_BB-CBh-hSpCas9n(D10A) as evidenced by Addgene plasmid #42335 (see the 3rd page for citing the plasmid to Cong), which encodes for a D10A substitution in Streptococcus pyogenes Cas9 (i.e. SpCas9n) which then converts the wildtype Cas9 to a DNA nickase capable of repairing nicked genomic DNA seamlessly or through homology directed repair (HDR) and as measured by the lack of indels (i.e. insertions and/or deletions) by the D10A SpCas9 mutant (the paragraph spanning pages 821-822; Fig. 4a-b), reading on claims 8-10
Regarding claims 8-10, it would have been obvious to a person of ordinary skill in the art before the invention was filed to substitute the pX335-U6-Chimeric_BB-CBh-hSpCas9n(D10A) plasmid encoding for the D10A SpCas9 mutant of Cong as evidenced by Addgene plasmid #42335 for the CRISPR/Cas9 system of Heo in Papapetrou’s methods of generating human iPSCs. A person of ordinary skill in the art would have had a reasonable expectation of success to do so because both Heo and Cong are directed towards CRISPR/Cas9 systems and nucleic acids encoding for Cas9 therein. The skilled artisan would have been motivated to do so because Cong teaches that the D10A SpCas9 mutant is advantageous to repair nicked genomic DNA seamlessly or through homology directed repair (HDR), and so would predictably improve upon the CRISPR/Cas9 system of Heo in Papapetrou’s methods of generating human iPSCs by generating less or no indels.
Therefore, the invention as a whole would have been prima facie obvious to a person of ordinary skill before the invention was filed.
Claims 18 and 19 are rejected under 35 U.S.C. 103 as being unpatentable over Papapetrou, Heo, and Montague as applied to claims 1 and 3 above, and further in view of Buganim et al. (Cell Stem Cell (2014), 15, 295-309; Reference V2).
The teachings of Papapetrou, Heo, and Montague are relied upon as set forth above.
Regarding claims 18 and 19, Papapetrou, Heo, and Montague do not teach elected species of reprogramming factors consisting of Oct4, Sox2, and Klf4.
Buganim teaches that removing Myc from OSKM factors (i.e. OSKM = Oct4, Sox2, Klf4, and Myc) reduces 4n (chromosomal) multiploidy vs OSKM-transduced iPSCs derived from mouse embryonic fibroblasts (MEFs) (the paragraph spanning pages 296-297; subheading “Cell culture and Mice” for iPSC generation), reading on claims 18 and 19.
Regarding claims 18 and 19, it would have been obvious to a person of ordinary skill in the art before the invention was filed to further remove the Myc/c-Myc of Papapetrou in Papapetrou’s method of generating iPSCs in view of Heo and Montague. A person of ordinary skill in the art would have had a reasonable expectation of success to do so because both Papapetrou and Buganim are directed towards methods of generating iPSCs from fibroblasts. The skilled artisan would have been motivated to do so because Buganim teaches that removing Myc as a species of reprogramming factor improves the generated iPSCs by reducing 4n (chromosomal) multiploidy and would thus improve upon the iPSC generation methods of Papapetrou in view of Heo and Montague.
Therefore, the invention as a whole would have been prima facie obvious to a person of ordinary skill before the invention was filed.
Claim 20 is rejected under 35 U.S.C. 103 as being unpatentable over Papapetrou, Heo, and Montague as applied to claims 1 and 3 above, and further in view of Hockemeyer et al. (Cell Stem Cell (2008), 3, 346-353; Reference W2) and Brambrink et al. (Cell Stem Cell (2008), 2, 151-159; Reference X2).
The teachings of Papapetrou, Heo, and Montague are relied upon as set forth above.
Regarding claim 20, Papapetrou, Heo, and Montague do not teach wherein expression of the reprogramming factor is controlled with doxycycline.
Hockemeyer teaches that generating iPSCs with doxycycline-inducible lentiviral vectors encoding for Oct4, Sox2, and Klf4 (i.e. “3 factor”) improves conversion of fibroblasts to iPSCs from 0.26% to 2.04% (Fig. 3C), reading on claim 20. Hockemeyer cites Brambrink for the doxycycline-inducible lentiviral vectors (1st paragraph under Results on page 346), reading on claim 20.
Brambrink teaches that the doxycycline-inducible lentiviral vectors comprises a tetracycline operator and minimal CMV promoter in the FUW plasmid (page 158, subheading “Viral Constructs”), reading on claim 20.
Regarding claim 20, it would have been obvious to a person of ordinary skill in the art before the invention was filed to add the tetracycline operator and minimal CMV promoter from the doxycycline-inducible vectors of Hockemeyer to the vector(s) of Papapetrou in view of Heo and Montague. A person of ordinary skill in the art would have had a reasonable expectation of success to do so because Hockemeyer cites Brambrink for the doxycycline-inducible lentiviral vectors and Brambrink teaches detailed methods of generating the doxycycline-inducible vectors, and because both Papapetrou and Hockemeyer are directed towards methods of generating iPSCs from fibroblasts. The skilled artisan would have been motivated to do so because Hockemeyer teaches that doxycycline-inducible expression of the reprogramming factors predictably improves the conversion rate of fibroblasts to iPSCs and so the addition of the tetracycline operator and minimal CMV promoter would predictably improve upon the iPSC generation methods of Papapetrou in view of Heo and Montague.
Therefore, the invention as a whole would have been prima facie obvious to a person of ordinary skill before the invention was filed.
Conclusion
No claims are allowed. No claims are free of the art.
Any inquiry concerning this communication or earlier communications from the examiner should be directed to SEAN C BARRON whose telephone number is (571)270-5111. The examiner can normally be reached 7:30am-3:30pm EDT/EST (M-F).
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, Sharmila Landau can be reached at 571-272-0614. 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.
/Sean C. Barron/Primary Examiner, Art Unit 1653
Prosecution Insights