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 .
Claim Status
1. Claims 1-2, 4-8, and 13-17 are pending and under examination to the extent of the elected species of Cas12f.4, SEQ ID NO:1, SEQ ID NO:6, and SEQ ID NO:4.
Claims 3, 9-12, 18-24, 28, 31, 33-37, 40-42, and 44 are cancelled.
Claims 20-21, 23, 25-27, 29-30, 32, 38-39, and 43 are withdrawn from further consideration pursuant to 37 CFR 1.142(b), as being drawn to a nonelected species, there being no allowable generic or linking claim. Applicant timely traversed the restriction (election) requirement in the reply filed on March 05, 2026.
Election/Restrictions
2. The Office acknowledges receipt of Applicant’s restriction election dated March 05, 2026. Applicant elects Group I, drawn to a method of obtaining a plant cell with altered expression of at least one gene, with traverse. Applicant further elects the species of a Cas12f.4 nuclease, SEQ ID NO:1, SEQ ID NO:6, and SEQ ID NO:4.
In traversing the requirement for restriction, Applicant argues primarily that the claims no longer recite limitations regarding GC content and melting temperature, the alleged technical feature of Groups I-III is the use of a Cas12F nuclease and guide RNA to edit a promoter to alter gene expression, and that the cited prior art does not teach a soybean or corn plant cell comprising a Cas12F nuclease and guide RNA designed to target a promoter regions of at least one allele of a soybean or corn plant cell gene as recited in claim 25. Furthermore, claim 1 is not limited to any specific plant species.
Applicant’s arguments have been fully considered but are not persuasive because the claims lack unity of invention and are obvious in view of the prior art as discussed below in the rejection of the claims under 35 U.S.C. 103.
The requirement is deemed proper and is therefore made FINAL.
Priority
3. The instant Application is a 371 of PCT/US2023/062089 filed February 07, 2023. The Office acknowledges receipt of Applicant’s domestic priority document Provisional Application No. 63/267,643 filed February 07, 2022.
Information Disclosure Statement
4. The Information Disclosure Statement (IDS) submitted on March 05, 2026 is in compliance with the provisions of 37 CFR 1.97. Accordingly, the IDS has been considered only to the extent of the English translations provided. A signed copy is attached.
Specification
5. The specification is objected to because of the following:
The abstract of the disclosure does not commence on a separate sheet in accordance with 37 CFR 1.52(b)(4) and 1.72(b). A new abstract of the disclosure is required and must be presented on a separate sheet, apart from any other text.
Correction and/or clarification is required.
Claim Rejections - 35 USC § 112(b)
6. 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.
7. Claims 2 and 4-5 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.
The scope of claim 2 is indefinite. It is unclear if the recited second allele is hypomorphic, isomorphic, or wild-type prior to or as a result of the gene editing method of claim 1. The structure of the second allele with regard to the first allele and/or wild-type allele is unclear. Applicant is required to clarify the intended recitation.
The scope of claim 4 is indefinite. It is unclear if the recited second allele is an amorphic allele prior to or as a result of the gene editing method of claim 2. Is the recited second allele amorphic prior to editing with the CRISPR/Cas12F construct? Applicant is required to clarify the intended recitation.
Dependent claims are included.
Appropriate correction is required.
Claim Rejections - 35 USC § 102
8. 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.
9. Claims 1-2, 4, 7, 13-14, and 17 are rejected under 35 U.S.C. 102(a)(1) as being anticipated by Lai et al. (US-2021/0395784-A1, published 12/23/2021 (Applicant’s IDS)).
Regarding claim 1, Lai teaches a method of obtaining a plant cell with altered expression of at least one gene comprising: (i) contacting at least one promoter region of at least a first allele of the gene in the genome of the plant cell with a Cas12F nuclease and at least one guide RNA that targets the promoter region, wherein the first allele of the gene is a hypomorphic (e.g., a loss-of-function mutation), isomorphic (e.g., a silent mutation), or wild-type allele of the gene[0002-0003], [0128], [0146], [0161], [0165-0166], [0173], [0183], [0194], and (ii) selecting a plant cell, plant callus, plant part, or plant comprising at least one first deletion in the promoter region that confers the altered expression of the gene[0132], [0154-0159]. In [0173], Lai teaches that the target sequence can be any polynucleotide, including non-coding regulatory polynucleotides, which Lai defines as including promoters and other expression control elements in [0183].
Regarding claim 2, the combined teachings of Lai are as discussed above. Lai is silent as to whether the second allele is either hypomorphic, isomorphic, and/or a wild-type allele. However, the breeding and selection of offspring that are homozygous or heterozygous for a desired trait is routine and trivial for one of ordinary skill in the art. Furthermore, because the editing efficiency of CRISPR-based systems is not 100%, some alleles will inherently remain unedited (i.e., wild-type) in the first-generation offspring of plants contacted with the editing constructs.
Regarding claim 4, in addition to the teachings discussed above, Lai teaches amorphic alleles (i.e., knocking out genes)[0146].
Regarding claim 13, in addition to the teachings discussed above, Lai teaches wherein the target sequence (i.e., promoter targeting region) is located at the 3’ end of a protospacer adjacent motif (PAM) comprising the sequence 5’-TTN, wherein N is A, G, T, or C[0003], [0089], [0107] (see Figure 3b).
Regarding claim 14, in addition to the teachings discussed above, Lai teaches wherein the at least one guide RNA comprises SEQ ID NO:6 (see Lai’s SEQ ID NO:16; see pp. 05-06 of the attached STIC search results).
Regarding claim 17, in addition to the teachings discussed above, Lai teaches knocking out genes[0146]. Knocking out a gene results in a complete loss of function, which is a greater than 2-fold decrease in expression of the gene in comparison to a control lacking the deletion.
Accordingly, the claimed invention is anticipated by the prior art.
Claim Rejections - 35 USC § 103
10. 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.
11. Claims 1-2, 4-8, and 13-17 are rejected under 35 U.S.C. 103 as being unpatentable over Lai et al. (US-2021/0395784-A1, published 12/23/2021 (Applicant’s IDS)) in view of Ricroch et al., (Emerging Topics in Life Sciences. 2017; 1:169–182 (U)) as evidenced by Xu et al., (Journal of Genetics and Genomics. 2016; 43(8):529-532 (V)).
Regarding claim 1, Lai teaches a method of obtaining a plant cell with altered expression of at least one gene comprising: (i) contacting at least one promoter region of at least a first allele of the gene in the genome of the plant cell with a Cas12F nuclease and at least one guide RNA that targets the promoter region, wherein the first allele of the gene is a hypomorphic (e.g., a loss-of-function mutation), isomorphic (e.g., a silent mutation), or wild-type allele of the gene[0002-0003], [0128], [0146], [0161], [0165-0166], [0173], [0183], [0194], and (ii) selecting a plant cell, plant callus, plant part, or plant comprising at least one first deletion in the promoter region that confers the altered expression of the gene[0132], [0154-0159].
Ricroch also teaches the use of CRISPR-based gene editing systems to edit wild-type coding and/or promoter sequences to introduce loss-of-function mutations that reduce the expression of target genes in various crop species (Abstract; pp. 171-176, Table 1).
The combination of Lai and Ricroch teaches, suggests, and provides motivation for methods of obtaining a plant cell with altered expression of at least one gene comprising: (i) contacting at least one promoter region of at least a first allele of the gene in the genome of the plant cell with a Cas12F nuclease and at least one guide RNA that targets the promoter region, wherein the first allele of the gene is a wild-type allele of the gene, and (ii) selecting a plant cell, plant callus, plant part, or plant comprising at least one first deletion in the promoter region that confers the altered expression of the gene.
The level of ordinary skill in the plant biotechnology art is high as evidenced by both Lai and Ricroch. It would have been prima facie obvious for one of ordinary skill in the art at time of filing to modify the method of Lai with the teachings of Ricroch to design a CRISPR/Cas12F gene editing system for targeting the promoter and/or coding regions of a gene to introduce deletions into and alter the expression of said gene. One of ordinary skill would have been motivated to do so for several reasons. First, the use and design of CRISPR-Cas constructs and guide RNAs is routine in the art. Second, as demonstrated by Ricroch, it is well-established in the biological arts that the expression level of a gene can be altered by mutating either the coding region or regulatory regions (e.g., a promoter region) of a gene. Third, Lai teaches that Cas12F-based editing systems have advantages over Cas9-based editing systems due to their suitability for multiple gene editing and need for only a single guide RNA, which reduces off-target gene editing. Finally, both Lai and Ricroch teach and suggest that the disclosed CRISPR/Cas editing systems are suitable for editing a variety of crop species with global economic importance. Accordingly, one of ordinary skill in the art would have been motivated to produce the claimed invention with a reasonable expectation of success and without any surprising or unexpected results.
Regarding claim 2, the combined teachings of Lai and Ricroch are as discussed above. Lai is silent as to whether the second allele is either hypomorphic, isomorphic, and/or a wild-type allele. However, the breeding and selection of offspring that are homozygous or heterozygous for a desired trait is routine and trivial for one of ordinary skill in the art. Furthermore, because the editing efficiency of CRISPR-based systems is not 100%, some alleles will inherently remain unedited (i.e., wild-type) in the first-generation offspring of plants contacted with the editing constructs. Accordingly, one of ordinary skill in the art would have been motivated to produce the claimed invention with a reasonable expectation of success and without any surprising or unexpected results.
Regarding claim 4, in addition to the teachings discussed above, Lai teaches amorphic alleles (i.e., knocking out genes)[0146].
Regarding claim 5, the combined teachings of Lai and Ricroch are as discussed above. Though Lai is silent to deletions in promoter regions, Ricroch teaches such deletions as discussed above. It would be both routine and trivial for one of ordinary skill in the art to select a transformed plant, plant cell, or callus comprising deletions within the promoter regions of both alleles of a target gene; one of ordinary skill in the art is readily capable of breeding a plant and selecting homozygous offspring harboring a trait of interest without any surprising or unexpected results.
Regarding claim 6, in addition to the teachings discussed above, Lai teaches targeting multiple genes[0003], [0174]. Lai is silent to the introduction of multiple guide RNAs.
Ricroch teaches the introduction of several distinct guide RNAs targeting distinct sequences are introduced into the plant cell containing the gene of interest to produce a population of plant cells, plant calli, plant parts, or plants comprising distinct deletions in the target site and wherein the plant cell, plant callus, plant part, or plant comprising the gene allele with the deletion in the promoter region of the first and/or second allele of the gene and/or altered transcription level is selected from the population of plant cells (p. 174, Table 1; see Xu et al., p. 530, Figure 1).
The combination of Lai and Ricroch renders obvious distinct guide RNAs targeting distinct promoter regions of the gene of the plant cell containing the gene to produce a population of plant cells, plant calli, plant parts, or plants comprising distinct deletions in the promoter of the gene and wherein the plant cell, plant callus, plant part, or plant comprising the gene allele with the deletion in the promoter region of the first and/or second allele of the gene and/or altered transcription level is selected from the population of plant cells. Though neither Lai or Ricroch suggest introducing multiple guide RNAs independently, the separate and independent introduction of said guide RNAs would provide no unique or surprising results in comparison to the method taught by Ricroch, wherein distinct guide RNAs are introduced on the same expression vector. Additionally, though Ricroch teaches targeting multiple genes with the distinct guide RNAs, one of ordinary skill in the art immediately understand that said guide RNAs could be designed to target the same target sequence to increase the efficiency of mutating that target sequence.
Regarding claim 7, in addition to the teachings discussed above, Lai teaches Cas12f.4 nuclease[0196-0200].
Regarding claim 8, in addition to the teachings discussed above, Lai teaches a Cas12F nuclease comprising SEQ ID NO:1 (see Lai SEQ ID NO:1; see pp. 01-04 of attached STIC search results).
Regarding claim 13, in addition to the teachings discussed above, Lai teaches wherein the target sequence (i.e., promoter targeting region) is located at the 3’ end of a protospacer adjacent motif (PAM) comprising the sequence 5’-TTN, wherein N is A, G, T, or C[0003], [0089], [0107] (see Figure 3b).
Regarding claim 14, in addition to the teachings discussed above, Lai teaches wherein the at least one guide RNA comprises SEQ ID NO:6 (see Lai’s SEQ ID NO:16; see pp. 05-06 of the attached STIC search results).
Regarding claim 15, in addition to the teachings discussed above, Lai does not teach SEQ ID NO:4. However, a Cas12F nuclease encoded by SEQ ID NO:4 would provide no surprising or unexpected results in comparison to the Cas12F nucleases taught by Lai and is, therefore, prima facie equivalent to the Cas12F nucleases taught by Lai. See MPEP 2183.
Regarding claim 16, in addition to the teachings discussed above, Lai teaches wherein the deletions comprise about 10 to 20 base pairs of DNA in the target region (Figure 3).
Regarding claim 17, in addition to the teachings discussed above, Lai teaches knocking out genes[0146]. Knocking out a gene results in a complete loss of function, which is a greater than 2-fold decrease in expression of the gene in comparison to a control lacking the deletion.
Accordingly, one of ordinary skill in the art would have been motivated to produce the claimed invention with a reasonable expectation of success and without any surprising or unexpected results.
Conclusion
12. No claim is allowed.
Examiner’s Contact Information
13. Any inquiry concerning this communication or earlier communications from the examiner should be directed to DEQUANTARIUS JAVON SPEED whose telephone number is (703)756-4779. The examiner can normally be reached M-F; 9AM-5PM ET.
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If attempts to reach the examiner by telephone are unsuccessful, the examiner’s supervisor, Amjad Abraham can be reached on (571)-270-7058. The fax phone number for the organization where this application or proceeding is assigned is 571-273-8300.
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/DEQUANTARIUS JAVON SPEED/Junior Examiner, Art Unit 1663
/Amjad Abraham/SPE, Art Unit 1663