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 .
Claims status
Applicants reply filed 4/24/2026 is acknowledged.
Claims 46 and 47 is/are newly added. Claims 26, 30-47 is/are currently pending and is/are under examination.
Claim Rejections - 35 USC § 112(b) - Withdrawn
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.
Rejection of Claim 45 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or a joint inventor (or for applications subject to pre-AIA 35 U.S.C. 112, the applicant), regards as the invention is withdrawn in light of claim amendment.
Claim Rejections - 35 USC § 102 - Withdrawn
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.
Rejection of Claim(s) 26, 35-38, 40, 42-44 under 35 U.S.C. 102(a)(1) as being anticipated by Gao et al (Nature Biotechnology, Vol. 35, No. 8, Aug 2017; IDS 11/6/2023) as evidenced by Addgene plasmid #89355 is withdrawn due to deletion of K595R and G532R double mutations that was taught by Gao.
Claim Rejections - 35 USC § 102/103 – Maintained, New for claim 46
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.
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.
Claim(s) 26, 30-45 remain and claim 46 is rejected under 35 U.S.C. 102(a)(1) as anticipated by or, in the alternative, under 35 U.S.C. 103 as obvious over Joung et al (US 2019/0010481 A1, Published Jan 10, 2019).
Regarding claim 26, Joung teaches Cas12a enzymes from various species including Lachnospiraceae bacterium with an amino acid sequence of SEQ ID No. 11 which is identical to SEQ ID NO. 1. Joung is directed to generation of modified Cas12a enzymes with altered PAM specificity [0006]. They teach that substitutions at or near PAM-proximal amino acid residues can alter the PAM preferences of both AsCpf1 and LbCpf1, generating variants of these nucleases that can recognize non-cognate PAM sequences, thereby increasing the targeting range of this platform [0079]. In Table 1, they identify the specific candidate residues in LbCas12a that are expected to alter PAM specificity; reciting each of the residues from claim 26 except K116 and E125. They teach substitution of their candidate residues with positively charged amino acids such as arginine (R), lysine (K) and histidine (H) [0148], or small amino acids such as alanine (A), glycine (G) or serine (S) [0088] are expected to alter PAM specificity. They also envision conservative substitution of residues which typically include substitutions within the following groups: glycine (G), alanine (A); valine (V), isoleucine (I), leucine (L); aspartic acid (D), glutamic acid (E), asparagine (N), glutamine (Q); serine (S), threonine (T); lysine (K), arginine (R); and phenyl alanine (F), tyrosine (Y) [0093]. Therefore, they teach LbCas12a with the following mutations K121S, K121R, D122H, D122N, D156Q, D156H, D156V, D156E, E159K, E159R, G532N, G532S, G532H, G532K, D535N, D535H, D535S, D535A, K538H, K538A, D541E, K595R, K595H, K595S.
Therefore, Joung anticipates the structures of the claimed modified LbCas12a enzymes and teaches that modifications at these candidate residues is expected to alter PAM specificity.
Although Joung does not explicitly teach if each of the candidate residues identified in their disclosure result in altered PAM specificity, recognizing at least 3 new PAMs as recited in claim 46, they teach that mutations at some of the candidate residues resulted in altered PAM specificity. For example, they show that at least substitution mutations of T167A, S170R, E174R, T539K, S542R, K54R8, N551R, N552R, M604A, and/or K607H in AsCas12a (which are orthologous to T149, T152, D156, Q529, G532, K538, D541, Y542, M592, K595 in LbCas12a) alter PAM specificity [0151-0163] (Figures 5-11). They also generate LbCas12a with T152R, D156R, G532R, K538R, D156R+G532R+K538R and show alteration in PAM specificity (Example 2, Figure 12). Therefore, they provide motivation and guidance to an ordinary artisan to generate substitution mutations at other candidate residues identified by them. In addition to anticipating the structure of several modified LbCas12a recited in the claims, Joung also renders obvious to an ordinary artisan before the effective filing date of the claimed invention to modify wild type LbCas12a enzyme at the residues identified by Joung in Table 1 with substitution mutations identified in [088, 093, 0148] to alter the PAM specificity. An ordinary artisan reasonably expects that at least some of the modifications at the residues identified by Joung would result in altered PAM specificity, including recognizing 3 new PAMs as required by claim 46, depending on the assay used because Joung provide examples showing that substitution mutations at some of the identified residues indeed altered PAM specificity.
Further, regarding claims 30-42, 45 which are directed to products comprising the modified LbCas12a of claim 26, Joung anticipates each of these products.
Regarding claim 30 and 45, Joung discloses several mutations in the RuvC domain of LbCas12a in Table A.
Regarding claims 31-34, Joung discloses a fusion protein in [0027] “Also provided herein are fusion proteins comprising the Cpf1 proteins described herein, fused to a heterologous functional domain, with an optional intervening linker, wherein the linker does not interfere with activity of the fusion protein.” The heterologous functional domains are polypeptides of interest that can be part of the fusion protein. They identify several adenosine deaminase (in [0033]), cytosine deaminase (in [0032]) and UGI (in [0034]).
Regarding claim 35-36, Joung discloses a nucleic acid encoding a modified LbCas12a that is linked to a promoter. Specifically, in [0039] they states “the isolated nucleic acid encodes an isolated CRISPR from Prevotella and Francisella 1 (Cpf1) protein from Lachnospiraceae bacterium ND2006 (LbCpf1), with mutations at one or more of the following positions: T152, D156, G532, and/or K538 of SEQ ID NO:11 and is operably linked to one or more regulatory domains for expressing an isolated CRISPR from Prevotella and Francisella 1 (Cpf1) protein from Lachnospiraceae bacterium ND2006 (LbCpf1), with mutations at one or more of the following positions: T152, D156, G532, and/or K538 of SEQ ID NO:11” A skilled artisan recognizes that “a regulatory domain for expressing” a nucleic acid sequence is a promoter.
Regarding claim 37, Joung discloses codon optimization of the various expression plasmids based on the cell lines used for the experiments. They state in [0133] “[0133] Protein expression plasmids were generated by cloning the human codon-optimized open reading frames of As, Fn, and MbCas12a, and the bacterial codon-optimized LbCas12a open reading frame”.
Regarding claim 38, Joung discloses a CRISPR/Cas system with a fusion protein and crRNA in example 7 (Variants of AsCas12a and LbCas12a for Base Editing Applications). They created two fusion proteins with modified LbCas12a with rAPOBEC1 and used them with 8 crRNAs [0196].
Regarding claim 39-41, Joung discloses vectors and how to produce them to include modified LbCas12a in [0118] (Expression systems).
Regarding claim 42, Joung discloses a cell with a nucleic acid encoding modified LbCas12a or fusion proteins (in [0041]).
Regarding the methods of claims 43 and 44, Joung discloses several of the modified LbCas12a enzymes of claim 26 (as discussed above) and methods of modifying/editing a target nucleic acid using a modified LbCas12a or a fusion protein comprising of LbCas12a and a crRNA (or nucleotides encoding the same). Specifically, in [0042] “In addition, provided herein are method for altering the genome of a cell, the method comprising expressing in the cell, or contacting the cell with, an isolated protein or fusion protein as described herein, and at least one guide RNA having a region complementary to a selected portion of the genome of the cell, i.e., wherein the complementary region is adjacent to a PAM sequence that corresponds to the protein or fusion protein, e.g., as shown in Table B.” and in [0043] “Also provided are methods of altering a double stranded DNA (dsDNA) molecule, the method comprising contacting the dsDNA molecule with an isolated protein or fusion protein as described herein, and a guide RNA having a region complementary to a selected portion of the dsDNA molecule, i.e., wherein the complementary region is adjacent to a PAM sequence that corresponds to the protein or fusion protein, e.g., as shown in Table B.”. Also, see example 7 as an exemplar.
Therefore, the invention as a whole was prima facie obvious to one of ordinary skill in
the art at the effective time of filing of the invention, especially in the absence of evidence to the
contrary.
Claim(s) 26, 30-32, 36-45 remain and claim 46 is rejected under 35 U.S.C. 102(a)(1) as anticipated by or, in the alternative, under 35 U.S.C. 103 as obvious over Zhang et al (US 2018/0155716 A1, Published Jun 7, 2018).
Regarding claim 26, Zhang teaches Cas12a enzymes from various species including Lachnospiraceae bacterium with an amino acid sequence of SEQ ID No. 242 which is identical to SEQ ID NO. 1. Zhang is directed to generation of modified Cas12a enzymes with altered binding properties to the target nucleic acid such as by altering binding specificity or alteration of PAM site [0252, 0325]. They teach that substitutions at conserved positively-charged residues in LbCas12a could alter enzyme binding properties and identify K116, K121, E159, K538, K591, K595, K601 as candidate residues [0241, 303, page 278-second Table]. Zhang teaches substitution of these positively-charged residues with alanine, serine, threonine, asparagine, glycine, alanine, isoleucine, leucine, tryptophan, tyrosine, valine, glutamate or aspartate [0260, 0279, 0281, 0282].
Therefore, they teach LbCas12a with the following modifications:K116R, K166N, K121S, K538Q, K538W, K538Y, K538L, K538G, K538A, K595Q, K595W, K595S.
Therefore, Zhang anticipates the structures of the claimed modified LbCas12a enzymes and teaches that modifications at these candidate residues is expected to alter PAM specificity.
Although Zhang does not explicitly teach if each of the candidate residues identified in their disclosure result in altered PAM specificity, recognizing at least 3 new PAMs as recited in claim 46, they motivate an ordinary artisan to generate substitution mutations at candidate residues identified by them. They teach methods to identify PAM sites recognized by Cas12a enzymes using both in situ analysis and in vitro analysis in E.coli and HEK cells ([1620]-[1693], Example 2 and 6, [1715], [1716], [1720]-[1723]). Therefore, in addition to anticipating several modified LbCas12a recited in the claims, Zhang also renders obvious to an ordinary artisan before the effective filing date of the claimed invention to modify wild type LbCas12a enzyme at the residues identified by Zhang (page 278-second Table) with substitution mutations identified in [0260, 0279, 0281, 0282] to alter the PAM specificity. An ordinary artisan reasonably expects to generate the modified LbCas12a and identify their PAM specificity using methods taught by Zhang and expects the modifications to alter PAM specificity, including recognizing 3 new PAMs as required by claim 46, depending on the assay used, based on Zhang’s teachings.
Further, regarding claims 30-32, 36-42 which are directed to products comprising the modified LbCas12a of claim 16, Zhang anticipates each of these products.
Regarding claim 30 and 45, Zhang discloses several mutation in the RuvC domain of LbCas12a in first Table of page 278.
Regarding claims 31-32, Zhang discloses use of their Cas12a enzymes to deliver transcriptional functional effectors by generating a fusion protein between the Cas12a enzyme and transcriptional activator/repressor, chromatin modifier [0649-0652].
Regarding claim 36, Zhang discloses use of promoters to express the LbCas12a enzyme encoded by a vector [0665-0692].
Regarding claim 37, Zhang discloses codon optimization nucleic acids coding the various Cas12a enzymes based on the host species [0218].
Regarding claim 38, Zhang discloses a CRISPR/Cas systems with LbCas12a enzymes and crRNA in example 6.
Regarding claim 35, 39-41, Zhang discloses nucleic acid vectors to deliver their LbCas12a enzyme and how to produce them in [0653--0658], Example 6.
Regarding claim 42, Zhang discloses a cell with a nucleic acid encoding modified LbCas12a in example 6.
Regarding the methods of claims 43 and 44, Zhang discloses several of the modified LbCas12a enzymes of claim 26 (as discussed above) and methods of modifying/editing a target nucleic acid comprising of LbCas12a and a crRNA (or nucleotides encoding the same) in example 6.
Therefore, the invention as a whole was prima facie obvious to one of ordinary skill in
the art at the effective time of filing of the invention, especially in the absence of evidence to the
contrary.
Claim Rejections - 35 USC § 103 - Withdrawn
The text of those sections of Title 35, U.S. Code not included in this section can be found above.
Rejection of Claim(s) 39, 41 under 35 U.S.C. 103 as being unpatentable over Gao as applied to claim 26, 38 above, and further in view of Gao is withdrawn due to the withdrawal of the rejection it relied upon.
Rejection of Claim(s) 30-34, 45 under 35 U.S.C. 103 as being unpatentable over Gao as applied to claim 26 above, and further in view of Joung is withdrawn due to the withdrawal of the rejection it relied upon.
Allowable Subject Matter
Claim 47 is objected to as being dependent upon a rejected base claim, but would be allowable if rewritten in independent form including all of the limitations of the base claim and any intervening claims.
Response to Arguments
Applicant's arguments filed 4/24/2026 with respect to the U.S.C 102/103 rejection of the claims 26, 30-45 as being unpatentable over Joung have been fully considered but they are not persuasive.
Applicant point to figures 12 in Joung as showing that “none of the mutant LbCpf1 polypeptides of Joung recognized any new PAMs when compared to the wild type LbCpf1 polypeptide.” (page 8, para 1). Thus, Applicant argue that “Joung does not teach or suggest a modified LbCas12a polypeptide exhibiting a reduced PAM stringency and that recognizes at least one new PAM” (page 8, para 2). Further, Applicant argue that “as the modified LbCas12a of Joung did not exhibit a reduced PAM stringency and recognize at least one new PAM as compared to wild type LbCas12a”, it “fails to provide a reasonable expectation of success in achieving the presently claimed invention of a LbCas12a polypeptide having a reduced PAM stringency and that recognizes at least one new PAM as claimed” (page 8, last para). Applicant point to figure 7 in Joung that shows that S542R mutation in AsCpf1, which is homologous to G532R in LbCas12a, shows substantially increased activity at non-target PAMs in comparison to wild type AsCpf1 while G532R LbCas12a shows “no such increase” in comparison to wild type LbCas12a.
In response, at first it must be noted that Joung anticipates the structure of the claimed mutant LbCas12a. The feature of recognition of new PAMs results from the structure of the mutant LbCas12a and is thus inherent to the structure anticipated by Joung.
Furthermore, Joung provides the requisite teachings, suggestion and motivation that render the instantly claimed substitution mutations obvious. Joung provides specific guidance regarding substitution mutations at the sites disclosed by them. Specifically in para 79 and 148, Joung teach selection criteria for the amino acid residues to be substituted and that substitution with positively charge residues is “expected to increase proximity (and presumably interaction) of the side chain with the phosphodiester backbone” [0148]. As is well known in the art, Joung also envisions conservative substitution of the disclosed residues or substitution with small, uncharged residues [0088]. Furthermore, Joung teaches methods to make and test the substitution mutations (Example: Methods: [0141], [0142]—[0147]). Joung also tests some of the residues disclosed by them and show that substitution mutation at some of these sites do result in altered PAM specificity in a stringent human cell based assay (Example 1, 2). Therefore, Joung provides ample guidance to an artisan to make and test the disclosed mutations.
Regarding specific mutations in LbCas12a, single or combined, that would result in reduced PAM stringency and recognize at least one or three new PAMs, an ordinary artisan recognizes that the ability of LbCas12a, with or without any mutations, to bind and then further cleave a target is assay dependent. Low stringency in situ cleavage assays, such as used in instant specification to test most of the claimed mutations, allow for testing many PAM sites, such that many new PAM targets of a LbCas12a or its mutants maybe identified. However, high stringency assays, such as human cells based indel assay, as used for 3 single mutations in the instant specification and used by Joung, allow for testing fewer PAM sites and fewer mutants. This is identified in the instant speciation and Joung. The instant specification identifies the three assays tested from lowest to highest stringency (page 60-61), identifying the human cells based indel assay as the highest stringency. This is also noted in Joung that further notes that target site (at least exogenous vs endogenous targets) also effects assay results [150-151].
As an example of PAM recognition being assay dependent, the instant specification tested T152R, K538W and K595Y single mutations in the human cells based indel assay showing that T152R and K595Y single mutations resulted in new PAM targets. However, K538 residue that was identified as hot spot in lower stringency assays, in situ assay and bacterial PAM-binding assays, did not show similar results in HEK cells with the Applicant concluding that this mutation "on its own it bound relatively few PAMs using that assay. It may be an excellent choice to use in future double mutations rather than alone to generate INDELS in HEK293T cells" (page 91, para 1; Figure 21). Thus, it can be concluded, similar to the prior art, Applicant also identifies the same set of residues that are reasonably expected to alter LbCas12a PAM specificity however ultimate test of if a specific mutation would alter LbCas12a PAM specificity is not 100% predictable until tested experimentally.
Thus, an ordinary artisan recognizes that there is no absolute predictability with regards to which of the residues disclosed by Joung or the instant specification would necessarily result in altered PAM specificity, resulting in recognition of one or more new PAMs, as this would depend on their assay type, cell type and target. Even the instant specification does not provide absolute predictability that each of the claimed mutations would necessarily result in altered PAM specificity however there is a reasonable expectation that there is some predictability (greater than 50%) that mutations taught by Joung would result in altered PAM specificity.
Additionally, absolute predictivity is not a criteria for obviousness (See MPEP 2143.02). As noted above, Joung anticipates the structure of the modified LbCas12a and provides the requisite teachings, suggestion and motivation that render the instantly claimed substitution mutations obvious.
Regarding Applicants allegations regarding Joung’s result in Figure 12a as showing “no such increase” in activity at non-target PAMs in comparison to wild type LbCas12a, Joung states regarding this figure that the single substitution mutations results in “modest increase” with non-canonical PAMs and that the triple substitution mutations resulted in “substantial increase” ([0177], Table B). Thus, considering that Joung showed that at least some of the substitution mutations resulted in altered PAM specificity to some extent, an artisan has a reasonable expectation that the residues and substitution mutations disclosed by Joung would result in a modified LbCas12a with altered PAM specificity. According to MPEP 2145, when “There had been ample suggestion in the prior art that the claimed method would have worked. Absolute predictability is not a necessary prerequisite to a case of obviousness. Rather, a degree of predictability that one of ordinary skill would have found to be reasonable is sufficient”.
Applicant's arguments filed 4/1/2026 with respect to the U.S.C 102/103 rejection of the claims 26, 30-32, 36-45 as being unpatentable over Zhang have been fully considered but they are not persuasive.
Applicant allege that, “Zhang provides a table that lists over 90 different locations in Cpf1 nucleases that could be used to generate mutants with enhanced specificity. Zhang does not teach or suggest that mutation of any one of the candidate positions results in a modified LbCas12a polypeptide exhibiting a reduced PAM stringency and that recognizes at least one new PAM as compared to wild type LbCas12a” (page 10, para 1). Applicant also allege that “Zhang fails to generate any actual mutated LbCas12a polypeptides. Nor does Zhang direct the ordinarily skilled artisan to a modified LbCas12a polypeptide having a mutation as claimed.” (page 10, para 2). Applicant also note that residues, such as K591, identified by Zhang as potential for increasing PAM specificity were not identified in Applicant’s in vitro assay (page 15, para 2).Thus, Applicant conclude that “Zhang not only fails to disclose each and every element of the presently claimed invention, but further fails to provide the ordinarily skilled artisan with a
reasonable expectation of success in arriving at the claimed invention” (page 10, para 2).
In response, at first it must be noted that Zhang anticipates the structure of the claimed mutant LbCas12a. The feature of recognition of new PAMs results from the structure of the mutant LbCas12a and is thus inherent to the structure anticipated by Zhang.
Furthermore, Zhang provides specific guidance regarding substitution mutations at the sites disclosed by them. Specifically in Examples 16 and 17, Zhang teach selection criteria for the amino acid residues to be substituted. Zhang note previously taught strategies used for modifying Cas9 enzymes are applicable to LbCas12a. They suggest altering the positively charged residues in the binding groove with residues that change the charge or introduce stearic hindrance to produce altered PAMs [0260]. Zhang teaches methods to make and test the substitution mutations (Example 7: Methods). Although, Zhang does not test the residues disclosed by them, they provide ample guidance to an artisan to generate and test the disclosed mutations. As noted by Zhang, considering that substitution mutations in the residues of the binding grove have previously resulted in altered PAM specificity, an artisan has a reasonable expectation that the residues and substitution mutations disclosed by Zhang would result in a modified LbCas12a with altered PAM specificity. According to MPEP 2145, when “There had been ample suggestion in the prior art that the claimed method would have worked. Absolute predictability is not a necessary prerequisite to a case of obviousness. Rather, a degree of predictability that one of ordinary skill would have found to be reasonable is sufficient”.
Regarding the argument that some residues identified by Zhang as potential for increasing PAM specificity were not identified in Applicant’s in vitro assay, this does not support an argument pertaining to lack of reasonable expectation of success. As noted above, an ordinary artisan recognizes that the ability of LbCas12a, with or without any mutations, to bind and then further cleave a target is assay dependent. To this end, even the instant specification shows that there is no guarantee that each of the single mutations claimed would result in altered PAM specificity in each assay. Nevertheless, teachings from the prior art such as Zhang provide a reasonable expectation to an artisan that the residues and substitution mutations disclosed by Zhang could result in a modified LbCas12a with altered PAM specificity in some assays.
Conclusion
No claim is allowed however Claim 47 is identified as allowable.
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 nonprovisional extension fee (37 CFR 1.17(a)) 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 mailing date of this final action.
Any inquiry concerning this communication or earlier communications from the examiner should be directed to MATASHA DHAR whose telephone number is (571)272-1680. The examiner can normally be reached M-F 8am-4pm (EST).
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/MATASHA DHAR/Examiner, Art Unit 1632
/EMILY A CORDAS/Primary Examiner, Art Unit 1632
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