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
Claims 38, 39, 41-43, and 45-47 are withdrawn from further consideration pursuant to 37 CFR 1.142(b) as being drawn to a nonelected invention, there being no allowable generic or linking claim.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 January 8. 2026.
Applicant’s election without traverse of Group A, Claims 1-4, 6-11, 18, 21, 23, 25, 32 and 37, in the reply filed on January 8. 2026. is acknowledged.
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.
Claim 37 is 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 37 recites the limitation "the target gene" in line 2. There is insufficient antecedent basis for this limitation in the claim. Claim 37 is dependent on Claim 1. Claim 1 does not recite a target gene nor require a target of any kind. It unclear what target gene Claim 37 is referencing. Claim 32 recites a target gene. Applicant may overcome this rejection by amending Claim 37 to be dependent on Claim 32.
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.
Claims 1-4, 18 and 21 are rejected under 35 U.S.C. 102(a)(1) as being anticipated by Gilbert, L., et. al., Cell, Vol. 154, p. 442-451, July 18, 2013.
Regarding Claim 1, Gilbert teaches a fusion protein comprising of at least two heterologous polypeptide domains, wherein the first polypeptide domain comprises a DNA binding protein, Cas9, and the second comprises a modulator of chromatin structure: “We further fused this modified dCas9 gene with different repressive chromatin modifier domains” (p. 443, col. 1). Therefore, Claim 1 is anticipated by Gilbert.
Regarding Claim 2, Gilbert teaches a fusion protein comprising a third domain, a blue fluorescent protein (p. 443, col. 1). Therefore, Claim 2 is anticipated by Gilbert.
Regarding Claim 3, Gilbert teaches the fusion protein wherein the first polypeptide domain comprises Cas9. Therefore, Claim 3 is anticipated by Gilbert.
Regarding Claim 4, Gilbert teaches dCas9, which comprises at least one amino acid mutation that eliminates nuclease activity of the Cas protein: “catalytically inactive Cas9 protein (dCas9)”.
Regarding Claim 18, Gilbert teaches the C-terminus of dCas9 fused to a second domain: “We further fused this modified dCas9 gene with different repressive chromatin modifier domains” (p. 443, col. 1; p. 444, Figure 1). Therefore, Claim 18 is anticipated by Gilbert.
Regarding Claim 21, Gilbert teaches the C-terminus of dCas9 fused to a third domain, a blue fluorescent protein: “We created a gene encoding a human codon-optimized dCas9 from S. pyogenes fused to two copies of a nuclear localization sequence (NLS), an HA tag, and blue fluorescent protein (BFP)” (p. 443, col. 1). Therefore, Claim 21 is anticipated by Gilbert.
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.
Claim 6 is rejected under 35 U.S.C. 103 as being unpatentable over Gilbert, L., et. al., Cell, Vol. 154, p. 442-451, July 18, 2013. as applied to Claim 4 above, and further in view of Lu, J., Nucleic Acids Research, Vol. 46, No. 5, p.1-15, published online December 9, 2017.
Regarding Claim 6, the instant specification teaches SEQ ID NO: 21 as “S. pyogenes Cas9 protein with D10A and H849A mutations” (p. 26, [00081]).
Gilbert anticipates Claim 4. Gilbert teaches “dCas9 from S. pyogenes” (p. 443, col. 1).
Gilbert does not teach SEQ ID NO: 20 or 21.
Lu teaches a fusion protein comprising dCas9 (Supplemental, p. 25, HIT direct fusion). An alignment between SEQ ID NO: 21 and Lu is attached as OA Appendix 1; the alignment shows a 99.9% match with the D10A and H849A mutations.
Regarding Claim 6, it would have been obvious to one skilled in the art before the effective filing date to have performed a simple substitution of one known element for another because Gilbert to construct the fusion protein of Claim 6 because Gilbert teaches the use of dCas9 and Lu teaches a sequence for dCas9 comprising of D10A and H849A mutations. Both Gilbert and Lu teach the use of dCas9 in fusion proteins. One of ordinary skill in the art could have substituted one known element for another, and the results of the substitution would have been predictable because both proteins are dCas9 and serve the same function. Therefore, Claim 6 is obvious over Gilbert in further view of Lu.
Claims 7-9 are rejected under 35 U.S.C. 103 as being unpatentable over Gilbert, L., et. al., Cell, Vol. 154, p. 442-451, July 18, 2013. as applied to Claim 1 above, and further in view of Crabtree, G. and Braun, S. WO 2017/074943 A1, May 4, 2017 and Uniprot, ID Q4VAX0_HUMAN, entry version 113, January 16, 2019.
Regarding Claim 7, Claim 1 is anticipated by Gilbert.
Gilbert does not recite a modulator of chromatin structure comprises a nucleosome rearranging protein.
Crabtree teaches a fusion protein comprising of a tether domain and a chromatin effector domain (p. 15, lines 34-37). Crabtree teaches the chromatin effector domain may be SS18 subunit of the BAF chromatin remodeling complex, a nucleosome rearranging protein (p. 16, lines 14-18). Crabtree describes a purpose of their invention is to modulate expression of a coding sequence from genomic locus (p. 1-2, lines 35-2).
Uniprot teaches the sequence of SS18 under ID Q4VAX0_HUMAN , which has 100% alignment with SEQ ID NO: 37.
It would have been obvious to one skilled in the art before the effective filing date to have performed a simple substitution of one known element for another because Gilbert teaches the fusion protein of Claim 1 with a modulator of chromatin structure and Crabtree teaches a specific modulator of chromatin structure, SS18, which is a nucleosome rearranging protein. Both domains of modulator of chromatin structure and SS18 are known in the art as described by Gilbert and Crabtree, and Uniprot provides the sequence of SS18. One of ordinary skill in the art could have substituted one known element for another and the results of the substation would have been predictable because Gilbert and Crabtree teach the construction of fusion proteins, and Crabtree teaches SS18 in fusion proteins. Therefore, Claim 7 is obvious over Gilbert in further view of Crabtree and Uniprot.
Regarding Claim 8, Crabtree teaches the SS18 subunit of the BAF chromatin remodeling complex. Therefore, Claim 8 is obvious over Gilbert in further view of Crabtree and Uniprot.
Regarding Claim 9, Uniprot teaches the sequence of SS18, SEQ ID NO: 37. which has 100% alignment with ID Q4VAX0_HUMAN. Therefore, Claim 8 is obvious over Gilbert in further view of Crabtree and Uniprot.
Claims 10, 11, 32, and 37 are rejected under 35 U.S.C. 103 as being unpatentable over Gilbert, L., et. al., Cell, Vol. 154, p. 442-451, July 18, 2013. as applied to Claims 1 and 2 above, and further in view of Polstein, L., et. al., Genome Research, Vol. 25, No. 8, p. 1158-1169, August 2015.
Regarding Claim 10, Claim 2 is obvious over Gilbert.
Gilbert does not teach a third polypeptide domain comprising a transcriptional activator domain.
Polstein teaches a fusion protein comprising of dCas9 and VP64: “we chose to study transcriptional activators (TALE-VP64 and dCas9-VP64)” (p. 1159, col. 2). Polstein teaches motivation for using this fusion protein for analysis of chromatin remodeling: “this permitted the analysis of chromatin remodeling concomitant with the targeted activation of silent genes” (p. 1159, col. 1). Polstein provides motivation for an additional domain for a modulator of chromatin structure for more robust changes: “the development of strategies for more robust changes to chromatin structure, including the targeted recruitment of histone modifying enzymes is an important area of future investigation” (p. 1165, col. 2).
Regarding Claim 10, It would have been obvious to one skilled in the art before the effective filing date to have performed a simple substitution of one known element for another to obtain predictable results because Gilbert teaches the fusion protein of Claim 1 comprising a third domain of blue fluorescent protein and Polstein teaches a fusion protein comprising VP64, a transcriptional activator. Both blue fluorescent protein and VP64 are known in the art as described by Gilbert and Polstein. One of ordinary skill in the art could have substituted one known element for another, and the results of the substitution would have been predictable because Gilbert and Polstein both teach fusion proteins comprising of dCas9 and both teach methods of constructing fusion proteins. Polstein provides motivation for such a construct as transcriptional activators with dCas9 allow for analysis of chromatin remodeling along with activation of silent genes, and targeted recruitment of modulator of chromatin structure are an area of further research interest. Therefore, Claim 10 is obvious over Gilbert in further view of Polstein.
Regarding Claim 11, Polstein teaches a transcriptional activator domain comprising VP64. Therefore, Claim 11 is obvious over Gilbert in further view of Polstein.
Regarding Claim 32, Gilbert anticipates Claim 1.
Gilbert does not teach wherein the protein activates transcription of a target gene or where the target gene is HBG 1/2.
Polstein teaches transcriptional activators in a fusion protein with dCas9, which activates a target gene (p. 1159, col. 2). Polstein teaches targeting HBG 1/2 loci because the products of the genes have medical relevance: “we chose the … HBG1/2 loci because the products of these …genes … gamma globin … activation of gamma globin expression is a focus of therapies for sickle cell disease” (p. 1159, col. 2). Polstein teaches successful use of their fusion protein in Figure 1C (p. 1160).
Regarding Claim 32, it would have been obvious to one skilled in the art before the effective filing date to have performed a simple substitution of one known element for another because Gilbert teaches the fusion protein of Claim 1 comprising dCas9 to target a gene with a third domain of blue fluorescent protein and Polstein teaches a fusion protein comprising VP64, a transcriptional activator, and the use of a dCas9-VP64 protein to increase the levels of mRNA expression of a target gene in a cell containing the fusion protein relative to a control. Both blue fluorescent protein and VP64 are known in the art as described by Gilbert and Polstein. One of ordinary skill in the art could have substituted one known element for another, and the results of the substitution would have been predictable because Polstein teaches successful use of a fusion protein to increase mRNA levels relative to a control. Therefore, Claim 32 is obvious over Gilbert in further view of Polstein.
Regarding Claim 37, Polstein teaches targeting HBG1/2 and provides motivation as the expression product is of concern for sickle cell anemia (p. 1159, col. 2). Therefore, Claim 37 is obvious over Gilbert and Polstein.
Claims 23 and 25 are rejected under 35 U.S.C. 103 as being unpatentable over Gilbert, L., et. al., Cell, Vol. 154, p. 442-451, July 18, 2013. as applied to Claim 2 above, and further in view of Crabtree, G. and Braun, S. WO 2017/074943 A1, May 4, 2017, Uniprot, ID Q4VAX0_HUMAN, entry version 113, January 16, 2019, Polstein, L., et. al., Genome Research, Vol. 25, No. 8, p. 1158-1169, August 2015 and Lu, J., Nucleic Acids Research, Vol. 46, No. 5, p.1-15, published online December 9, 2017.
Regarding Claim 23, Claim 2 is obvious over Gilbert.
Gilbert does not teach a second polypeptide comprising SS18 or a third polypeptide comprising VPR or VP64.
Crabtree teaches a fusion protein comprising of a tether domain and a chromatin effector domain (p. 15, lines 34-37). Crabtree teaches the chromatin effector domain may be SS18 subunit of the BAF chromatin remodeling complex, a nucleosome rearranging protein (p. 16, lines 14-18). Crabtree describes a purpose of their invention is to modulate expression of a coding sequence from genomic locus (p. 1-2, lines 35-2).
Uniprot teaches the sequence of SS18 under ID Q4VAX0_HUMAN , which has 100% alignment with SEQ ID NO: 37.
Polstein teaches a fusion protein comprising of dCas9 and VP64: “[W]e chose to study transcriptional activators (TALE-VP64 and dCas9-VP64)” (p. 1159, col. 2).
Lu teaches a fusion protein comprising of dCas9 with VPR or VPH: “Tandem fusion of multiple ADs, including VP64 (V), P65 (P), and Rta (R), to dCas9 (dCas9-VPR) … further improvement of activation potency with undetectable background activity was observed when VPR was replaced with VPH (VP64, p65 and HSF1) in the same architecture (dCas9-2E-VPH)” (p. 4, col. 1).
Regarding Claim 23, It would have been obvious to one skilled in the art before the effective filing date to have performed a simple substitution of one known element for another to obtain predictable results because Gilbert teaches the fusion protein of Claim 1 comprising a second domain comprising a modulator of chromatin structure and a third domain of blue fluorescent protein, Crabtree teaches a specific modulator of chromatin structure, SS18, and Polstein and Lu teach a fusion protein comprising VP64, VPR, and VPH, transcriptional activators.
Regarding the second domain, both domains of modulator of chromatin structure and SS18 are known in the art as described by Gilbert and Crabtree, and Uniprot provides the sequence of SS18. One of ordinary skill in the art could have substituted one known element for another and the results of the substation would have been predictable because Gilbert and Crabtree teach the construction of fusion proteins, and Crabtree teaches SS18 in fusion proteins.
Regarding the third domain, blue fluorescent protein, VP64, VPR and VPH are known in the art as described by Gilbert, Polstein, and Lu. One of ordinary skill in the art could have substituted one known element for another, and the results of the substitution would have been predictable because Gilbert and Polstein both teach fusion proteins comprising of dCas9 and both teach methods of constructing fusion proteins. Polstein provides motivation for such a construct as transcriptional activators with dCas9 allow for analysis of chromatin remodeling along with activation of silent genes, and targeted recruitment of modulator of chromatin structure are an area of further research interest. Lu provides motivation for the use of VPH as “improvement of activation potency” (p. 4, col. 1). Therefore, Claim 23 is obvious over Gilbert in further view of Crabtree, Uniprot, Polstein, and Lu.
Regarding Claim 25, the instant specification teaches SEQ ID NO: 64 or 66 as a fusion protein comprising VPH, dCas9 and SS18 (p. 2, [0005]), which is an embodiment of Claim 23. Claim 23 is obvious over Gilbert in further view of Crabtree, Uniprot, Polstein, and Lu as described above. An alignment with the sequence of VPH and dCas9, taught by Lu (Supplement, p. 25-26, HIT direction fusion) followed by the sequence of SS18 taught by Uniprot is attached as OA Appendix 2; the assembled sequence is VPH (VP64, p64, HSF1) followed by dCas9 and SS18, which has an alignment of 89.7%, which is greater than the 75% of Claim 25. Therefore, Claim 25 is obvious over Gilbert in further view of Crabtree, Uniprot, Polstein, and Lu.
Conclusion
No claims are allowed.
Any inquiry concerning this communication or earlier communications from the examiner should be directed to Krishna Nuggehalli Ravindra whose telephone number is (571)272-2758. The examiner can normally be reached M-Th, alternate F, 8a-5p est.
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/K.N.R./ Examiner, Art Unit 1636
/NEIL P HAMMELL/ Supervisory Patent Examiner, Art Unit 1636