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
Applicant’s election without traverse of Group I (claims 1-19), and as species the repressor fusion peptide comprising three or more repressor domains comprising ZIM3(KRAB)-MAX-MeCP2(t) corresponding to SEQ ID NO: 63 and SEQ ID NO: 64, in the reply filed on 06/01/2026 is acknowledged.
Claims 20 and 21 are withdrawn from further consideration pursuant to 37 CFR 1.142(b) as being drawn to a nonelected invention, there being no allowable generic or linking claim.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 06/01/2026.
Claims 3,10 and 16 are withdrawn from further consideration pursuant to 37 CFR 1.142(b) as being drawn to a nonelected species, there being no allowable generic or linking claim. Election was made without traverse in the reply filed on 06/01/2026.
The elected species, ZIM3(KRAB)-MAX-MeCP2(t) corresponding to SEQ ID NO: 63 and SEQ ID NO: 64, was free of the art and therefore the species have been expanded to include those taught by Ding et al., which are ZIM3, MeCP2 and KOX1.
Claims 1,2,4-9,11-15 and 17-19 are under examination.
Priority
This application claims benefit of 63/424,588, filed 11/11/2022.
Specification
The disclosure is objected to because it contains an embedded hyperlink and/or other form of browser-executable code. Applicant is required to delete the embedded hyperlink and/or other form of browser-executable code; references to websites should be limited to the top-level domain name without any prefix such as http:// or other browser-executable code. See MPEP § 608.01. See page 10, which recites “www.ncbi.nlm.nih.gov/”.
Drawings
While the drawings in the files labeled DRW.NONBW do not appear in color, it is noted that the supplemental drawings filed on 01/17/2024 include Figures with color. No petition for color drawings has been filed. If Applicant intends for the drawings to be color drawings, the guidance is being provided below.
Color photographs and color drawings are not accepted in utility applications unless a petition filed under 37 CFR 1.84(a)(2) is granted. Any such petition must be accompanied by the appropriate fee set forth in 37 CFR 1.17(h), one set of color drawings or color photographs, as appropriate, if submitted via the USPTO patent electronic filing system or three sets of color drawings or color photographs, as appropriate, if not submitted via the via USPTO patent electronic filing system, and, unless already present, an amendment to include the following language as the first paragraph of the brief description of the drawings section of the specification:
The patent or application file contains at least one drawing executed in color. Copies of this patent or patent application publication with color drawing(s) will be provided by the Office upon request and payment of the necessary fee.
Color photographs will be accepted if the conditions for accepting color drawings and black and white photographs have been satisfied. See 37 CFR 1.84(b)(2).
Claim Objections
Claims 1,2,8,9,14 and 15 are objected to because of the following informalities: Claims 1,2,8,9,14 and 15 recite acronyms. At least the first recitation of a peptide/gene name should be fully recited for clarity rather than just the abbreviation of the protein/gene name. Appropriate correction is required.
Claim Rejections - 35 USC § 101
35 U.S.C. 101 reads as follows:
Whoever invents or discovers any new and useful process, machine, manufacture, or composition of matter, or any new and useful improvement thereof, may obtain a patent therefor, subject to the conditions and requirements of this title.
Section 33(a) of the America Invents Act reads as follows:
Notwithstanding any other provision of law, no patent may issue on a claim directed to or encompassing a human organism.
Claims 14,15 and 17-19 are rejected under 35 U.S.C. 101 and section 33(a) of the America Invents Act as being directed to or encompassing a human organism. See also Animals - Patentability, 1077 Off. Gaz. Pat. Office 24 (April 21, 1987) (indicating that human organisms are excluded from the scope of patentable subject matter under 35 U.S.C. 101).
Claims 14,15 and 17-19 recite “an engineered cell comprising a CRISPR interference system”. Based on the broadest reasonable interpretation, these claims encompass that the engineered cell is within a human organism, and therefore encompasses a human organism which is therefore nonstatutory subject matter. The rejection may be overcome by reciting that the engineered cells are isolated or in vitro.
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 1,2,4-9,11-15 and 17-19 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.
Claims 1,8 and 14 recite “wherein the repressor fusion peptide comprises two or more repressor domains comprising KOX1, KRBOX1, ZIM3 or a fragment thereof, fused to MAX, MeCP2, MeCP2(t), TRIM28, RYBP, CBX1, SCMH1, CTCF, REST, MGA, KLF10, IRF2BP1, IKZF5, RCOR1, ZNF554, ZNF264, or a fragment thereof”. This recitation of two or more repressor domains comprising KOX, KRBOX1, ZIM3 or a fragment thereof, indicates that the two or more is modifying this list reciting what the two or more or fragment thereof is fused to. Similarly, claims 2,9 and 15 recite “wherein the repressor fusion peptide comprises three of more repressor domains comprising any combination of KOX1, KRBOX1, ZIM3, MAX, MeCP2t, MeCP2, or a fragment thereof, fused to TRIM28, RYBP, CBX1, SCHM1, CTCF, REST, MGA, KLF10, IRF2BP1, IKZF5, RCOR1, ZNF554, ZNF264, or a fragment thereof.
However, based on the species election, ZIM3(KRAB)-MAX-MeCP2(t), as well as other specifically disclosed combinations, the “two or more repressor domains” seems to require one from the first group (KOX1, KRBOX1, ZIM3) and two or more from the second listing. Therefore, the scope of the claims are unclear, as it is not clear what the two or more, or three or more is modifying. The claims should be reworded to more accurately recite the required combination. See pages 17-18 of as-filed specification shown below showing specific disclosed combinations).
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Claims 4-7,11-13 and 17-19 are included in the rejection because they depend from claims 1,8 and 14 and do not correct the issue.
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 2,9 and 15 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.
Claims 2,9 and 15 do not further limit the claims upon which they depend and are broader because there are additional repressor domains recited for the three or more repressor domains comprising any combination of KOX1, KRBOX1, ZIM3, MAX, MeCP2t, MeCP2 or a fragment thereof in claims 2,9 and 15, than what is allowed in claims 1,8,14 respectively (two or more repressor domains comprising KOX1, KRBOX1, ZIM3 or a fragment thereof). While “three or more repressor domains” does further limit, it is the additional domain options recited in claim 2 (MAX, MeCP2t, MeCP2) which are not recited as the choices in the “two or more repressor domains” of claim 1 that cause claim 2 to actually be broader, as well as claims 9 and 15.
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.
Claims 1,5,8 and 14 are rejected under 35 U.S.C. 102(a)(1) as being anticipated by Ding et al. (Life Science Alliance, Vol. 5, No. 6, Published 14 March 2022, pages 1-11).
Regarding claims 1,5 and 8, Ding et al. teach CRISPRi (CRISPR interference), wherein dCas9 is fused to transcriptional repressors, in combination with a specific sgRNA and the fusion proteins are recruited to promoters/enhancers of genes to modulate their transcription (page 1, right column). Ding et al. teach fusion of several transcriptional regulators to dCas9 in tandem can synergize to increase their repressive activities (page 1, right column). Ding et al. teach a bipartite expression cassette by fusing the KOX1 KRAB domain with the transcription repression domain of MeCp2 and that the dCas9-KRAB-MeCP2 fusion protein outperformed both KRAB and MeCP2 as single fusions to dCas9 (page 2, left column), and teach a dCas9-KRAB-MeCP2 vector (page 2, left column, results; Fig. 1A). Fig. 1A and 3A show the sgRNA and the dCas9-KRAB-MeCP2 fusion and cassette. Ding et al. also teach a dCas9-ZIM3-MeCP2 construct with increased silencing compared to dCas9KRAB-MeCP2 construct (page 5, left column). Ding et al. teach the dCas9-ZIM3-MeCP2 were co-transfected with sgGFP into mES cells, and results were that ZIM3 synergizes with MeCP2 as dCas-ZIM3-MeCP2 outperformed dCas-ZIM3 and dCas9-KRAB-MeCP2 to repress gene expression (page 5, right column, Fig. 3A).
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Figure 1A
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Figure 3A
Regarding claim 14, Ding et al. teach expression of the dCas-KRAB-MeCP2 cassette in mouse embryonic stem cells which led to long-term gene silencing in the cells (page 2, left column and right column; Fig. 1A), and also teach dCas9-KRAB-MeCP2 HEK293 cell lines and sgGFP (page 5, left column, first paragraph). Ding et al. also teach dCas9-ZIM3-MeCP2 were co-transfected with sgGFP into mES cells, and results were that ZIM3 synergizes with MeCP2 as dCas-ZIM3-MeCP2 outperformed dCas-ZIM3 and dCas9-KRAB-MeCP2 to repress gene expression (page 5, right column). Ding et al. also teach dCas9-ZIM3-MeCP2 with sgRNAs in primary human T cells (page 5, right column). Therefore, Ding et al. teach an engineered cell comprising the CRISPRi system.
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.
Claims 2,4,9,11,15 and 17 are rejected under 35 U.S.C. 103 as being unpatentable over Ding et al. as applied to claims 1,5,8 and 14 above, and further in view of ZIM3 NCBI Reference Sequence NM_052882.1 (25 Oct 2001).
Claim Interpretation: Regarding “a fragment thereof” recited in the instant claims, Page 8 of the instant specification discloses “The "fragments," whether attached to other sequences or not, can include insertions, deletions, substitutions, or other selected modifications of particular regions or specific amino acids residues, provided the activity of the fragment is not significantly altered or impaired compared to the nonmodified peptide or protein. These modifications can provide for some additional property, such as to remove or add amino acids capable of disulfide bonding, to increase its bio-longevity, to alter its secretory characteristics, etc. In any case, the fragment must possess a bioactive property, such as regulating the transcription of the target gene”. Therefore, two or more amino acids or nucleotides of any part of the recited sequences reads on a fragment thereof.
In addition, page 18 of the instant specification discloses specific combinations of three repressor fusion peptides (see below), and therefore art teaching any of these combinations reads on claims 2,11 and 15. Pages 84-85 of the instant specification show SEQ ID NO: 101 as the DNA sequence ZIM3(KRAB)-MeCP2-KOX(KRAB) and SEQ ID NO: 102 as the peptide sequence of ZIM3(KRAB)-MeCP2-KOX(KRAB).
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The teachings of Ding et al. as application to claims 1,5,8 and 14 have been described above.
While Ding et al. teach a CRISPRi system comprising a fusion of dCas9, the KOX1 KRAB domain and the transcription repression domain of MeCp2 and a fusion of dCas9- ZIM3-MeCP2, Ding et al. do not teach the specific fusion of all three repressor domains of ZIM3, MeCP2 and KOX1, which is one of the specific combinations disclosed above, with dCas9. Ding et al. do not teach the three or more repressor domains of ZIM3, MeCP2 and KOX1 comprise instant SEQ ID NO: 101 or SEQ ID NO: 102 or a fragment thereof.
However, Ding et al. teach fusion of several transcriptional regulators to dCas9 in tandem can synergize to increase their repressive activities (page 1, right column), the dCas9-KRAB-MeCP2 fusion protein outperformed both KRAB and MeCP2 as single fusions to dCas9, suggesting that the combination of these two domains leads to a synergistic reinforcement of gene repression (page 2, left column), the unexpected finding that dCas-KRAB-MeCP2 can also induce long-term epigenetic gene repression (page 2, left column). Ding et al. teach a recent screen of KRAB domain proteins identified the ZIM3 KRAB domain as a potent transcriptional repressor, with dCas9 ZIM3 outperforming dCas9-KRAB fusions in gene silencing and that GFP silencing was also increased for the dCas9-ZIM3-MeCP2 version from 87.6 to 92.5% (page 5, left column).
Before the effective filing date, the mRNA sequence of Homo sapiens ZIM3 (NCBI Ref Sequence NM_052882.1) was publicly available.
Alignment of Homo sapiens ZIM3 of NCBI Ref Sequence NM_052882.1 with instant SEQ ID NO: 101 (DNA sequence of fusion of ZIM3(KRAB)-MeCP2-KOX(KRAB) is shown below, wherein Qy is instant SEQ ID NO: 101, and Db is Homo sapiens ZIM3 of NCBI Ref Sequence NM_052882.1.
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Alignment of Homo sapiens ZIM3 of NCBI Ref Sequence NM_052882.1 with instant SEQ ID NO: 102 (peptide sequence of fusion of ZIM3(KRAB)-MeCP2-KOX(KRAB) is shown below, wherein Qy is instant SEQ ID NO: 102, and Db is Homo sapiens ZIM3 of NCBI Ref Sequence NM_052882.1.
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Therefore, it would have been obvious to one of ordinary skill in the art before the effective filing date, to have combined ZIM3, MeCP2, and KOX1 KRAB to form a fusion peptide with dCas9 in the CRISPRi system of Ding et al. further in view of NCBI Ref Sequence NM_052882.1 in order to enhance gene silencing, to arrive at the instant claims with a reasonable expectation of success. There would be a reasonable expectation of success, because Ding et al. teach CRISPRi comprising sgRNA and different combinations of fusion peptides with dCas9, including KOX1(KRAB)-MeCP2 and ZIM3-MeCP2 for the same purpose of increasing gene silencing. As a general principle it is prima facie obvious to combine two compositions each of which is taught by the prior art to be useful for the same purpose, in order to form a third composition to be used for the very same purpose, the idea of combining them flows logically from their having been individually taught in the prior art. See In re Kerkhoven, 626 F.2d 846, 850, 205 USPQ 1069, 1072 (CCPA 1980) MPEP 2144.06.
Regarding the specific sequences of SEQ ID NO:102 in claims 4 and 17, and SEQ ID NO:101 in claim 11, since the mRNA sequence of Homo sapiens ZIM3 of NCBI Ref Sequence NM_052882.1 was publicly available before the effective filing date, one of ordinary skill in the art would have been able to arrive at a fragment of SEQ ID NO: 101 and a fragment of SEQ ID NO: 102 based on knowing the mRNA sequence of ZIM3 of NM_052882.1, as nucleotides 1-301 of instant SEQ ID NO: 101 aligns with nucleotides 387-687 of ZIM3 NM_052882.1 with only one mismatch, and alignment of instant SEQ ID NO: 102 (peptide) is shown with ZIM3 NM_052882.1. Given the disclosure in the instant specification cited above in the claim interpretation section regarding “fragment” (can include insertions, deletions, substitutions, or other selected modifications of particular regions or specific amino acids residues), and the fact that 300 nucleotides are identical between instant SEQ ID NO: 101 and ZIM3 NM_052882.1, and that nucleotides 387-686 of ZIM3 NM_052882.1. align with amino acids 1-100 of instant SEQ ID NO: 102, an ordinary artisan would have a reasonable expectation of success of arriving at a “fragment” of SEQ ID NO: 101 or 102 as instantly claimed, without evidence to the contrary.
Accordingly, the limitations of claims 2,4,9,11,15 and 17 would have been prima facie obvious to one of ordinary skill in the art before the effective filing date.
Claims 6,7,12,13,18 and 19 are rejected under 35 U.S.C. 103 as being unpatentable over Ding et al. as applied to claims 1,5,8 and 14 above, optionally in view of ZIM3 NCBI Reference Sequence NM_052882.1 as applied to claims 2,4,9,11,15 and 17 above, and further in view of Joung et al. (US 20140377868, Published 25 Dec 2014).
The teachings of Ding et al. as applied to claims 1,5,8 and 14 have been described above. The teachings of ZIM3 NCBI Reference Sequence NM_052882.1 as applied to claims 2,4,9,11,15 and 17 have been described above.
Ding et al. and ZIM3 NCBI Reference Sequence NM_052882.1 do not teach the catalytically inactive nuclease comprises at least 90% sequence identity to SEQ ID NO: 2 or at least 90% sequence identity to SEQ ID NO: 1, and do not teach the repressor fusion peptide is fused to a nuclear localization signal or that one or more nucleic acids in the expression vector are fused to a nuclear localization signal.
Before the effective filing date, Joung et al. taught fusion proteins comprising catalytically inactive CRISPR associated 9 (Cas9) linked to a heterologous functional domain that modifies DNA, including transcriptional repressors (paragraph 0008). Joung et al. teach the sequence of the catalytically inactive Cas9 used herein is SEQ ID NO: 3 (paragraphs 0033-0034).
SEQ ID NO: 3 of Joung et al. (Db) is 100% identical to all 1368 amino acids of instant SEQ ID NO: 2 (Qy). See the alignment below (Note: only the beginning and end portions of the alignment are provided due to the length).
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Joung et al. recites fusion proteins of catalytically inactive CRISPR associated 9 (Cas9) linked to a heterologous functional domain that modifies DNA (claims 1-8) as well as nucleic acids encoding the fusion proteins (claims 9-12) and expression vectors comprising the nucleic acid (claims 13-16). Therefore, as the amino acid sequence taught by Joung et al. of the catalytically inactive Cas9 is the same as instant SEQ ID NO: 2, the corresponding nucleic acid sequence would also be the same as that of instant SEQ ID NO: 1.
Regarding the nuclear localization signal in claims 7,13 and 19, Joung et al. taught the fusion protein includes a nuclear localization domain which provides for the protein to be translocated to the nucleus. Several nuclear localization sequences (NLS) are known, and any suitable NLS can be used. For example, many NLSs have a plurality of basic amino acids, referred to as a bipartite basic repeats. An NLS containing bipartite basic repeats can be placed in any portion of chimeric protein and results in the chimeric protein being localized inside the nucleus (paragraph 0052).
Therefore, it would have been obvious to one of ordinary skill in the art before the effective filing date, to have substituted the dCas9 of Ding et al. with the catalytically inactive Cas9 of SEQ ID NO: 3 of Joung et al. to arrive at the instant claims with a reasonable expectation of success. There would be a reasonable expectation of success as this amounts to simple substitution of one known element for another to obtain predictable results, and because Joung et al. pertains to CRISPR and fusion proteins of catalytically inactive CRISPR associated 9 (Cas9) linked to a heterologous functional domain that modifies DNA, including transcriptional repressors (paragraph 0008). One of ordinary skill in the art would have been motivated to do so because Joung et al. taught proteins of catalytically inactive CRISPR associated 9 (Cas9) of SEQ ID NO: 3 linked to a heterologous functional domain that modifies DNA, and that although the present description exemplifies transcriptional activation domains, other heterologous functional domains (e.g., transcriptional repressors, enzymes that modify the methylation state of DNA (e.g., DNA methyltransferase (DNMT) or TET proteins), or enzymes that modify histone subunit (e.g., histone acetyltransferases (HAT), histone deacetylases (HDAC), or histone demethylases)) as are known in the art can also be used (paragraph 0034).
Accordingly, the limitations of claims 6,12 and 18 would have been prima facie obvious to one of ordinary skill in the art before the effective filing date.
It would have been obvious to one of ordinary skill in the art to have provided a nuclear localization signal fused to the repressor fusion peptide of Ding et al., one or more nucleic acids encoding the repressor fusion peptides of Ding et al. fused to a nuclear localization signal in an expression vector, as well as an engineered cell of Ding et al. comprising the repressor fusion peptide fused to a nuclear localization signal based on the teachings of Joung et al. with a reasonable expectation of success, as this would have amounted to combining prior art elements according to known methods to yield predictable results. One of ordinary skill in the art would have been motivated to do so because Joung et al. taught the fusion protein includes a nuclear localization domain which provides for the protein to be translocated to the nucleus and that several nuclear localization sequences (NLS) are known, and any suitable NLS can be used and can be placed in any portion of chimeric protein and results in the chimeric protein being localized inside the nucleus.
Accordingly, the limitations of claims 7,13 and 19 would have been prima facie obvious to one of ordinary skill in the art before the effective filing date.
Conclusion
Claims 1,2,4-9,11-15 and 17-19 are rejected.
Any inquiry concerning this communication or earlier communications from the examiner should be directed to STEPHANIE L SULLIVAN whose telephone number is (703)756-4671. The examiner can normally be reached Monday-Friday, 7:30-3:30 EST.
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/STEPHANIE L SULLIVAN/Examiner, Art Unit 1635
/ABIGAIL VANHORN/Primary Examiner, Art Unit 1636
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