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
Restriction:
Applicant’s election of Group I (claims 1-12, 32-33, and 43) drawn to a method of introducing a genetic change in a genome of a cell, in the reply filed on 18th Jun 2026 is acknowledged.
Claims 13-31 and 34-42 withdrawn from further consideration pursuant to 37 CFR 1.142(b) as being drawn to nonelected groups, there being no allowable generic or linking claim. Election was made without traverse in the reply filed on 18th Jun 2026 .
Status of Claims
Claims 1-12, 32-33, and 43 are present for examination.
Priority
Acknowledgment is made for this Application filed on 12/20/2023 which claims priority to provisional application 63/476,337 filed on 12/20/2022.
Objection - Specification
1. Trade name
The use of the terms PureLink, StemFlex, Matrigel, and mTeSR1, which are trade names or a 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.
2. Typos
The INCORPORATION-BY-REFERENCE OF MATERIALS FILED ON COMPACT DISC states that the file is 82,918 byes. It should state: 82,918 bytes.
Please note, the specification has not been checked to the extent necessary to determine the presence of all possible errors. Applicant’s cooperation is required in correcting any errors of which applicant may be become aware in the specification. See MPEP § 608.01 for further details.
Claim Objections
Claim 1 is objected to because of the following informalities: it is noted that the claim is a method claim with active method steps. The claim recites in line 11 introducing into the cell a variant-specific sgRNA and then it recites in line 15 contacting the genome of the cell with the variant-specific sgRNA and a Cas-based genome editing system. However, the step of “contacting” is inherent. It would be clearer to recite: wherein the variant-specific DNA and a Cas-based genome editing system contacts the genome of the cell, thereby introducing…”.
Claims 10 and 43 recite similar language as claim 1. Therefore, they are similarly objected to.
Claim 2 is objected to because of the following informalities: Claim 2 recites: wherein the method of correcting a genetic error in the genome of a cell is in vivo or ex vivo. It would be clearer to recite: wherein the method of correcting a genetic error in the genome of a cell occurs in vivo or ex vivo.
Appropriate correction is required.
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 1-12, 32-33, and 43 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 1, 10, and 43 recite the parenthetical expression “(allele-specificity)”. The metes and bounds of claim 1, 10, and 43 are rendered vague and indefinite by this parenthetical recitation because it is unclear as to whether the limitation in parenthesis is part of the instantly claimed subject matter.
Claim 1 recites the limitation "the" in “the exogenous DNA template” in the last line. There is insufficient antecedent basis for this limitation in the claim since no exogenous DNA template was identified anywhere else in claim 1. The preamble of the claim does recite “an exogenous DNA template-free Cas based genome editing system …”. However, the reference to exogenous DNA template in this case refers to the Cas-based genome editing system and not to a template that is required for the variant correction. Therefore, the reference to “the exogenous DNA template” lacks antecedent basis.
Claim 32 recites the limitation "guide RNA identified by the method of claim 1". There is insufficient antecedent basis for this limitation in the claim since no guide RNA was identified in the method of claim 1.
Those claims identified in the statement of rejection but not explicitly referenced in the rejection are also rejected for depending from a rejected claim but failing to remedy the indefiniteness therein.
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 32-33 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 recites “one guide RNA identified by the method of claim 1.” Thus, claim 32 depends from claim 1. 35 CFR 1.75 states “One or more claims may be presented in dependent form, referring back to and further limiting another claim or claims in the same application.” Because claim 32 refers back to claim 1, it is a dependent claim of claim 1.
MPEP 608.01(n) states "The fact that the independent and dependent claims are in different statutory classes does not, in itself, render the latter improper. … if claim 1 recites a method of making a product, a claim for a product made by the method of claim 1 could be a proper dependent claim. On the other hand, if claim 1 recites a method of making a specified product, a claim to the product set forth in claim 1 would not be a proper dependent claim if the product can be made by a method other than that recited in the base method claim, and thus, does not include the limitations of the base claim."
In instant case none of the steps of claim 1 are needed to make and/or use the sgRNA. Therefore claims 32-33 do not include all the limitations of claim 1, from which they depend.
Dependent claim 33 is also rejected because it depends from an improperly dependent claim.
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 § 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.
Claim(s) 1, 4-7, 9-10, 12, 32-33, and 43 are rejected under 35 U.S.C. 102(a)(1) as being anticipated by Parisa (Parisa J-P., et al., Gene Therapy (2020) 27:281–296, IDS).
Claim 1 is interpreted as a method of gene editing without an exogenously provided donor template comprising:
step a) identifying a target genomic sequence of the genome comprising 88% or higher homology with one or more paralogs or pseudogenes; wherein the target genomic sequence has at least one mutation and step b) introducing into the cell a mutation-specific sgRNA and a Cas-based genome editing system to cause a double stranded break in the target genomic sequence; such that gene conversion and nonallelic homologous recombination (NAHR) comprising unidirectional transfer of genomic DNA from the homologous DNA sequences (of the paralogs or pseudogenes) to the target genomic sequence occurs, without an exogenous DNA template.
For claims 10 and 43, the steps of introducing into the cell … and contacting the genome of the cell …are being interpreted as interpreted for claim 1 step b as discussed above.
Regarding claims 1, 10, and 43, Parisa is drawn to gene conversion as a means of correcting HBB sickle-cell mutation in a test HEK293T cell line (title, abstract). The HEK293T cells utilized in the study is an EGFP reporter cell that has an integrated EGFP expression cassette containing the HBB SCD mutant sequence that disrupts the EGFP reading frame , pg. 285, R col, 2nd para). Parisa teach that the paralog must have at least 88% identity to the target sequence (The GFP-reporter cells were integrated with at least one copy of GFP-expression cassette, which contains a stretch of 54-bp sequence from the HBB gene, with 88% identity to the corresponding HBD sequence (Fig. 3d); pg. 289, R col, 2nd para). Parisa teaches this is consistent with previous observations that gene conversion requires sequence homology above 88% (citing Chen, 2007, pg. 289, R col, 1st para). Parisa teaches using an RNA-guided CRISPR/Cas nuclease and a mutation-specific sgRNA. Parisa teaches HBB sgRNA1 that perfectly matches the SCD mutant sequence in the GFP reporter cassette, but has one nucleotide mismatch with the endogenous HBB sequence, and thus has reduced activity on the endogenous HBB sequence (an “off-target” for HBB sgRNA1), pg. 288 R col, 2nd para). Parisa teaches introducing HBB sgRNA1 and Cas9 into a cell (The DNA was from EGFP reporter cells transfected with plasmid DNA expressing SaCas9 and HBB sgRNA1, pg. 288 legend for Fig. 2). Parisa teaches that the gene conversion occurs in HBB from HBD sequences (the rates of HBD footprints in HBB decreased with the increase of distance from the putative DSB site, pg. 294, L col, last para; Fig. 4). Parisa teaches that observation of endogenous homologous DNA serving as template for HDR is consistent with previous observation of correcting a dominant mutation by HDR in rat using the recessive wild-type allele as the template [citing Wu, 2013]. Parisa compare their results with an exogenous donor but find that an exogenous donor is not required to be introduced alongside the nuclease, Fig. 1). Parisa conclude that CRISPR/Cas9 causes gene conversion with sequences transferring from the paralog without DSB to the one with DSBs , pg. 295, last para).
Regarding claim 4, Parisa teach a correction of the disease-causing mutation (graph shows % GFP-positive cells, Fig.2C).
Regarding claim 5, Parisa teach the pathogenic variant is HBB (abstract).
Regarding claim 6, Parisa does not teach that the target is a region with microhomology or microduplication.
Regarding claim 7, Parisa teach Cas9 (title).
Regarding claims 9 and 12, Parisa teach SaCas9 (Materials and Methods, pg. 282, R col, 1st para).
Regarding claims 32 and 33, the claims are anticipated by teachings of Parisa discussed for claims 1, 10, and 43, above. Parisa further teach plasmids were used to express the components of the Cas-based genome editing system (pSaCas9-HBB-sgRNA1 and pSaCas9-HBB-sgRNA2 were used to coexpress Cas9 and HBB-sgRNA1, Materials and Methods, pg. 282, R col, 1st para).
Thus, Parisa anticipates instant claims 1, 4-7, 9-10, 12, 32-33, and 43.
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) 2-3 are rejected under 35 U.S.C. 103 as being unpatentable over Parisa (Parisa J-P., et al., Gene Therapy (2020) 27:281–296, IDS) as applied to claims 1, 4-7, 9-10, 12, 32-33, and 43 above, and further in view of Wu (Wu et al., Cell Stem Cell, Volume 13, Issue 6,2013,Pages 659-662,ISSN 1934-5909).
Regarding claims 2 and 3, the method of claim 1 is discussed above. Parisa further teach that their observation of endogenous homologous DNA serving as template for HDR is consistent with previous observation of correcting a dominant mutation by HDR in rat using the recessive wild-type allele as the template [citing Wu].
Parisa do not demonstrate any in vivo or ex-vivo editing.
Wu teaches correcting the genetic defect (a dominant mutation in Crygc gene, cataract) in vivo and restoring gene function (by injection of CRISPR-Cas9 into zygotes; we identified 10 mice carrying genetic modifications of the mutant allele (Figure 1F); all four mice that carried the corrected allele induced by HDR were free of cataracts; pg. 661, L col, 2nd para.).
It would have been obvious to one of ordinary skill, in the art at the time, to practice the claimed method in vivo or ex-vivo because Wu teaches an in vivo application of Parisa’s method which also utilizes an endogenous DNA template to correct a genetic defect.
See PharmaStem Therapeutics, Inc. v. Viacell, Inc., 491 F.3d 1342, 83 USPQ2d 1289 (Fed. Cir. 2007), in which, the Federal Circuit pointed out that the patentee, PharmaStem, had not invented an entirely new procedure or new composition with a showing of experimental proof that umbilical cord and placental blood could be used to effect hematopoietic reconstitution in mice, because the prior art had already shown that umbilical cord and placental blood-based compositions contained hematopoietic stem cells, and that hematopoietic stem cells were useful for the purpose of hematopoietic reconstitution. The Fed. Circuit stated that by extrapolation, one of ordinary skill in the art would have expected this reconstitution method to work in humans as well.
Thus, one of ordinary skill in the art would have reasonable expectation of success in practicing a method that does not require any additional effort or skill needed to practice other than that already suggested by the references cited.
Thus, Parisa in view of Wu make obvious instant claims 2 and 3.
Claim(s) 8 and 11 are rejected under 35 U.S.C. 103 as being unpatentable over Parisa (Parisa J-P., et al., Gene Therapy (2020) 27:281–296, IDS) as applied to claims 1, 4-7, 9-10, 12, 32-33, and 43 above, and further in view of Hsu (Hsu, P., et al., Nat Biotechnol 31, 827–832, 2013, IDS).
Regarding claims 8 and 11, the method of claim 1 is discussed above. Parisa further teach the gRNA that performed better at correcting the genetic defect was gRNA1, that was immediately adjacent to the PAM (ACTCCT). See the position of this gRNA from Fig. 2A reproduced below:
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The genetic defect that is to be corrected is the 2nd nucleotide after the PAM.
Parisa do not teach the pathogenic variant is immediately adjacent to the PAM.
Hsu teaches SpCas9 tolerates mismatches between guide RNA and target DNA at different positions in a sequence-dependent manner, sensitive to the number, position and distribution of mismatches (abstract). Hsu teaches single-base specificity generally ranges from 8 to 14 bp, immediately upstream of the PAM, indicating a sequence-dependent, mismatch-sensitive boundary that varies in length (Fig. 2b, Supplementary Fig. 7 and Supplementary Table 5). Therefore, a gRNA.
It would have been prima facie obvious to a person of ordinary skill in the art at the time the effective filing date to design a gRNA comprising a variant within 1-7 bp immediately upstream of the PAM, because such a gRNA would be specific for the variant, and not WT, as one would conclude. This range of 1-7bp includes a variant immediately adjacent to the PAM as required by instant claims. Thus, one of skill in the art would consider the sequence of the gene to be corrected, as gene sequence is one of the elements of gRNA design taught by Hsu, and if the sequence allows, design a gRNA including the pathogenic variant immediately adjacent to the PAM, namely to arrive at the claimed invention. One of ordinary skill in the art would have been motivated to do so because Hsu had already demonstrated that single base specificity generally ranges from 8 to 14 bp, immediately upstream of the PAM. See MPEP 2144.05 II and In re Williams, 36 F.2d 436, 438, 4 USPQ 237 (CCPA 1929) ("It is a settled principle of law that a mere carrying forward of an original patented conception involving only change of form, proportions, or degree, or the substitution of equivalents doing the same thing as the original invention, by substantially the same means, is not such an invention as will sustain a patent, even though the changes of the kind may produce better results than prior inventions."). One of ordinary skill in the art would have reasonable expectation of success in making such a gRNA because Hsu had provided a detailed study on gRNA design and Parisa had demonstrated efficiency of a similar gRNA.
Thus, Parisa in view of Hsu make obvious instant claims 8 and 11.
Therefore the invention as a whole would have been prima facie obvious to one ordinary skill in the art before the effective filing date of the claimed invention to a person having ordinary skill in the art to which the claimed invention pertains.
Conclusion
No claims are allowed.
Correspondence
Any inquiry concerning this communication or earlier communications from the examiner should be directed to SHABANA MEYERING, Ph.D. whose telephone number is (703)756-4603. The examiner can normally be reached M - F: 9am to 5pm EST.
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SHABANA S. MEYERING, Ph.D.
Examiner
Art Unit 1635
/SHABANA S MEYERING/Examiner, Art Unit 1635
/CATHERINE KONOPKA/Primary Examiner, Art Unit 1635
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