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 .
Detailed Action
1. Applicant’s amendments to claims 1-2 in the reply filed 5/26//2026 are acknowledged.
Claim 70 is withdrawn for being drawn to non-elected species.
As a result, claims 1-2, 5-9, 12-14, 25-27, 29-36, 41, 51, 64-68 and 70-72 are pending and claims 1-2, 5-9, 12-14, 25-27, 29-36, 41, 51, 64-68 and 71-72 are examined on the merits.
2. The rejections and objections not recited in this action are withdrawn.
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.
3. Claims 1-2, 5-9, 12-14, 25-27, 29-36, 41, 51, 64-68 and 71-72 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.
In claims 1-2, the recitation “is capable of” renders the claims indefinite. It is unclear under what condition the Cpf1 effector has such capability. The metes and bounds are not clear.
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.
4. Claims 1-2, 5-9, 12-14, 25-27, 29-36, 41, 51, 64-68 and 71 remain rejected under 35 U.S.C. 103 as being unpatentable over Begemann et al. (US Patent Application Publication No. 2017/0233756) further in view of Dickey et al. (2015, Genbank Accession AKG12737) and Zetsche et al. (2015 Cell 163:759-771).
Instant claims are drawn to an engineered CRISPR-Cas system comprising 1) a guide RNA, wherein the guide sequence hybridizes with a target sequence adjacent to PAM in a mammanlian cell and directing sequence-specific binding of a CRISPR complex to the target sequence in the mammalian cell; 2)a Cpf1 effector protein, wherein Cpf1 effector comprises a heterologous NLS and wherein the guide RNA forms a CRISPR complex with the Cpf1 effector having at least 95% identity to Moraxella bovoculi AAX11_00205 and wherein the Cpf1 effector protein is capable of inducing an indel at the target sequence in the isolated human cell; or the target sequence is within a eukaryotic cell; or wherein the CRISPR complex is capable of cleavage distally of the target sequence; or wherein the PAM comprises a 5’T-rich motif; or wherein the Cpf1 is Moraxella bovoculi AAX11_00205/Mb3Cpf1;or wherein the PAM sequence is TTN and Cpf1 effector is Mb3Cpf; or wherein the nucleic acid encoding the Cpf1 is codon optimized for expression in a eukaryotic cell; or wherein the nucleic acid encoding guide RNA and Cpf1 are on one vector; or a eukaryotic cell/particle comprising the system; or a method of modifying a target locus of interest comprising delivering the system according to claim 1 to the locus; or wherein the cell is a plant/animal cell; or wherein the target locus is a DNA molecule in vitro; or wherein the modification is a strand break; or wherein the strand break is a staggered DNA double strand break with a 4 or 5nt 5’ overhang; or wherein the polynucleotide molecule comprises one regulatory elements operably configured to express the Cpf1 effector and the guide RNA; or wherein target locus is a DNA molecule in vitro ;or wherein the polynucleotide molecule are comprised in a delivery system; or wherein the composition is delivered via a vesicle; or wherein the particle is a metal; or wherein the vesicle comprise liposomes;or wherein the viral vectors comprise adenovirus; or wherein that Cpf1 is a dead Cpf1 (dCpf1) having an inactive RuvC domain which do not cleave double-stranded DNA and that dCpf1 is fused to a transcriptional activation domain.
Begemann et al. teach that a method of modifying a nucleotide sequence at a target site in the genome of a eukaryotic cell comprising: introducing into said eukaryotic cell (i) a DNA-targeting RNA, or a DNA polynucleotide encoding a DNA-targeting RNA, wherein the DNA-targeting RNA comprises: (a) a first segment comprising a nucleotide sequence that is complementary to a sequence in the target DNA; and (b) a second segment that interacts with a Cpf1 or Csm1 polypeptide; and (ii) a Cpf1 or Csm1 polypeptide, or a polynucleotide encoding a Cpf1 or Csm1 polypeptide, wherein the Cpf1 or Csm1 polypeptide comprises: (a) an RNA-binding
portion that interacts with the DNA-targeting RNA; and (b) an activity portion that exhibits site-directed enzymatic activity, and wherein said genome of a eukaryotic
cell is a nuclear, plastid, or mitochondrial genome (claim 1); Begemann et al teach that Cpf1-crRNA complexes can cleave target DNA preceded by a short protospacer-adjacent motif (PAM) that is often T-rich and that Cpf1 can introduce a staggered DNA double-strand break with a 4-5-nt 5’overhang (paragraph [0014]. Begemann et al teach that PAM sequence is TTN (paragraph [0090]). Begemann et al teach that nuclear localization signal is linked to Cfp1 protein (paragraph [0062]). Begemann et al teach that sequence encoding Cfp1 protein is optimized for expression in a plant cell (paragraph [0140]). Begemann et al teach that the nucleic acid encoding guide RNA and Cpf1 are on one vector (paragraph [0080]). Begemann et al teach the gold particle is used for bombardment (paragraph [0247]). Begemann et al teach that the vesicle comprises liposomes (paragraph [0101]) and that the viral vectors comprise adenovirus (paragraph [0063]). Begemann et al teach that Cpf1 is from Moraxella bovoculi 237 (Table 3). Begemann et al teach that Cpf1 have an inactive RuvC domain which do not cleave double-stranded DNA and that dCpf1 is fused to a transcriptional activation domain (paragraph [0018]). Begemann et al teach that the method can be used for transformation of mammals (paragraph [0130]).
Begemann et al do not teach Cpf1 that is at least 90% identical to Cpf1 of Moraxella bovoculi AAX11_00205. Begemann et al do not teach target gene is in an isolated human cell.
Dickey et al. teach Cpf1 protein of Moraxella bovoculi AAX11_00205.
Zetsche et al. teach using Cpf1 to modify target gene in human cell (Figure 7).
Given the knowledge that Cpf1 can be used for genome editing in various organisms including mammalian cells, it would have been obvious for skilled in the art to perform it in human cell as taught in Zetsche et al. It would also have been obvious to try the Cpf1 of Dickey et al. given the teaching of Zetsche et al. that Cpf1 is from Moraxella bovoculi 237 do not work well in human cell and that orthologs from different strains of the same species may work better in human cells(LbCpf1 vs Lb2Cpf1 in Figure 7).
Although the combined teachings do not teach target gene is in an isolated human cell, such limitation is merely considered as an obvious design choice given that a human cell is an obvious option for mammals as taught by Begemann et al (paragraph [0130]).
Although the combined teaching do not teach explicitly that the Cpf1 effector protein is capable of inducing an indel at the target sequence in the isolated human cell such feature would have been obviously exhibited by the Moraxella bovoculi AAX11_00205 of Dickey et al.
Although the combined teachings do not teach target locus is a DNA molecule in vitro, such limitation is merely considered as an obvious design choice.
Applicants traverse in the paper filed 5/26/2026. Applicants’ arguments have been fully considered but were not found persuasive.
Applicants argue that the teaching of Sun et al. support Applicants’ position in that the unpredictability eliminates any inference of likely success based on sequence homology alone (response, page 9).
The Office first note that Applicants claims a genus of Cpf1 that is 95% identical to instant SEQ IDNO: 792, any such claims are based on sequence homology only.
Still further, the “unpredictability” taught by Sun et al. is indeed to support the Office’s position in that it provides a reason to try the Cpf1 of Dickey et al. given that Zetsche et al. teach that Cpf1 from Moraxella bovoculi 237 do not work well in human cell and that orthologs from different strains of the same species may work better in human cells(LbCpf1 vs Lb2Cpf1 in Figure 7).
Applicants again argue that Zetsche et al. that Cpf1 from Moraxella bovoculi 237 of Zetsche et al. has at least 95% sequence identity to instant Cpf1 of SEQ ID NO:792 or 794 whereas LbCpf1 and Lb2Cpf1 only share 41.7% sequence similarity (response, pages 8-9). Therefore, there is no motivation to try instant Cpf1 of SEQ ID NO:792 or 794 given that Cpf1 from Moraxella bovoculi 237 of Zetsche et al does not work well in human cell (response, page 9).
The Office contends that it is well established in the art that two homologous Cas9 genes from two different strains of the same species with high homology could still exhibit distinct features given the minor difference in a conserved domain (2019 Sun et al. Molecular Cell 76:938-952). Therefore, 83% sequence homology does not suggest these two proteins would for sure function similarly according the teaching of Sun.
Applicant further argue that Zetsche teaches away from using other MbCpf1 orthologs in human cell (response, page 10).
The Office contends that Zetsche may teach away from using Cpf1 from Mb 237 strain. However, Zetsche teaches that orthologs from different strains of the same species may work better in human cells (LbCpf1 vs Lb2Cpf1 in Figure 7). Therefore, in stead of teaching away, Zetsche suggest Cpf1 from other strain of Mb may also work better in human cells.
Applicants finally argue that the office failed to identify a finite number of predictable solutions with a reasonable expectation of success (response, pages 10-11).
The Office contends that the there are not many MbCpf1 orthologs from various strains from M. bovoculi available at the time of filing, therefore, it is considered as from a finite number of choices.
5. Claims 1-2, 5-9, 12-14, 25-27, 29-36, 41, 51, 64-68 and 72 remain rejected under 35 U.S.C. 103 as being unpatentable over Begemann et al. (US Patent Application Publication No. 2017/0233756) further in view of Dickey et al. (2015, Genbank Accession AKG12737) and Zetsche et al. (2015 Cell 163:759-771) as for claims 1-2, 5-9, 12-14, 25-27, 29-36, 41, 51, 64-68 and 71, further in view of Crabtree et al. (US 6,171,781).
Claims 1-2, 5-9, 12-14, 25-27, 29-36, 41, 51, 64-68 and 71 are discussed above. Claim 72 further contains the limitation that the Cpf1 effector protein is fused to at least two heterologous NLSs.
The teachings of Begemann et al further in view of Dickey et al. and Zetsche et al. are discussed above.
The teachings of Begemann et al further in view of Dickey et al. and Zetsche et al. fail to teach that the Cpf1 effector protein is fused to at least two heterologous NLSs.
Crabtree et al. teachan NF-AT polypeptide that is covalently linked to one or two copies of a heterologous NLS results in constitutive nuclear localization (column 33, line 35).
It would have been obvious for skilled in the art to fuse the Cpf1 with two copies of a heterologous NLS according to the teaching of Crabtree et al.. One would have been motivated to do so given the teaching of Crabtree et al. that such modification would results in constitutive nuclear localization.
Conclusion
No claim is allowed.
Applicant's amendment necessitated the new ground(s) of rejection presented in this Office action. Accordingly, THIS ACTION IS MADE FINAL. See MPEP § 706.07(a). Applicant is reminded of the extension of time policy as set forth in 37 CFR 1.136(a).
A shortened statutory period for reply to this final action is set to expire THREE MONTHS from the mailing date of this action. In the event a first reply is filed within TWO MONTHS of the mailing date of this final action and the advisory action is not mailed until after the end of the THREE-MONTH shortened statutory period, then the shortened statutory period will expire on the date the advisory action is mailed, and any extension fee pursuant to 37 CFR 1.136(a) will be calculated from the mailing date of the advisory action. In no event, however, will the statutory period for reply expire later than SIX MONTHS from the date of this final action.
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/LI ZHENG/Primary Examiner, Art Unit 1662
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