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 .
Application Status
The preliminary amendment filed March 21, 2023 is acknowledged. Claims 1-20 are pending and under examination.
Drawings
The drawings are objected to because the figures are referred to as “Figure” in the drawings. MPEP §608.02.V states that according to 37 C.F.R. 1.84(u)(1) “View numbers must be preceded by the abbreviation "FIG.".
Corrected drawing sheets in compliance with 37 CFR 1.121(d) are required in reply to the Office action to avoid abandonment of the application. Any amended replacement drawing sheet should include all of the figures appearing on the immediate prior version of the sheet, even if only one figure is being amended. The figure or figure number of an amended drawing should not be labeled as “amended.” If a drawing figure is to be canceled, the appropriate figure must be removed from the replacement sheet, and where necessary, the remaining figures must be renumbered and appropriate changes made to the brief description of the several views of the drawings for consistency. Additional replacement sheets may be necessary to show the renumbering of the remaining figures. Each drawing sheet submitted after the filing date of an application must be labeled in the top margin as either “Replacement Sheet” or “New Sheet” pursuant to 37 CFR 1.121(d). If the changes are not accepted by the examiner, the applicant will be notified and informed of any required corrective action in the next Office action. The objection to the drawings will not be held in abeyance.
Claim Objections
Claims 9 and 12 are objected to because of the following informalities:
In claim 9, line 3, “Ribonucleoprotein” is capitalized, which is grammatically incorrect. The term should not be capitalized.
Claim 12 recites “is regenerated from the cell population”. It is clear that “the cell population” must refer back to “a plurality of cells” since that is the only cell population recited. However, to maintain consistent claim language, it is suggested that “the cell population” be amended to “the plurality of cells”.
Appropriate correction is required.
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.
Claims 1-14 and 16-20 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.
Claim 1 recites “(a) introducing… - a second guide RNA that recognizes a modified targeted position in the target gene, wherein the modification consists of at least one nucleotide deletion when occurred after the cleavage by the endonuclease protein guided by the first guide RNA at the targeted position, (i) wherein the first guide RNA directs the nuclease to cleave the target gene at the targeted position, and wherein small deletions from 1-3 nucleotides are introduced by reparation at the cleavage site…” A broad range or limitation together with a narrow range or limitation that falls within the broad range or limitation (in the same claim) may be considered indefinite if the resulting claim does not clearly set forth the metes and bounds of the patent protection desired. See MPEP § 2173.05(c). In the present instance, claim 1 recites the broad recitation “at least one nucleotide deletion”, and the claim also recites “wherein small deletions from 1-3 nucleotides are introduced” which is the narrower statement of the range/limitation. The claim(s) are considered indefinite because there is a question or doubt as to whether the feature introduced by such narrower language is (a) merely exemplary of the remainder of the claim, and therefore not required, or (b) a required feature of the claims.
If Applicant intends the claim to be limited to initial deletions of only 1 to 3 nucleotides in the targeted position, the following claim language is suggested, which includes suggested enumerations for modifications and cleavage sites:
“(a) introducing… - a second guide RNA that recognizes a modified targeted position in the target gene, to generate a first cleavage site, and wherein small deletions from 1-3 nucleotides are introduced by reparation at the first cleavage site to generate a first modified targeted position in some cells, (ii) wherein the second guide RNA directs the nuclease to cleave the target gene at the first modified targeted position to generate a second cleavage site, wherein insertion of a desired nucleotide occurs by reparation of the second cleavage site, the desired nucleotide being different form the original nucleotide at this position, thereby introducing
It is also suggested to enumerate the modified targeted positions and cleavage sites in claims 2-3 for increased clarity.
Claim 2-14 and 16-20 are rejected for depending from claim 1 and not remedying the indefiniteness.
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.
Claim 15 is rejected under 35 U.S.C. 101 because the claimed invention is directed to a judicial exception (i.e., a law of nature, a natural phenomenon, or an abstract idea) without significantly more. The claim is drawn to designing guide RNAs. However, the claim does not include elements, when considered separately and in combination, that are sufficient to amount to significantly more than the judicial exceptions as outlined below.
Subject Matter Eligibility Test for Products and Processes
Step 1 - Is the Claim to a Process, Machine, Manufacture or Composition of Matter? YES
Claim 15 is directed to a method of designing guides necessary for the introduction of a specification mutation at a specific position in a target gene. Thus, the claims are directed to a statutory category (e.g., a process).
Step 2A, Prong One - Does the Claim Recite an Abstract Idea, Law of Nature, or Natural Phenomenon? YES
Judicial exceptions that are abstract ideas have been identified by the courts by way of example, including mental processes. Claim 15 recites 5 judicial exceptions 1) identifying nucleotides/bases that need to be replaced to modify the specified position, 2) identifying a PAM near the specific position, 3) designing a first guide to cleave the dsDNA at the specified position, 4) designing a second guide that is specific for the deletion of the nucleotide(s), 5) designing a third guide if two nucleotides are to be deleted, and 6) designing a fourth guide if three nucleotides are to be deleted. Each of these six steps is a mental process that can be performed in the human mind with merely the aid of pencil and paper. The skilled artisan need only apply the known parameters of CRISPR guide RNA design, which are exemplified in Cigan (US 20180273960 A1; FIG. 6). Identifying a target site is as simple as looking at a sequence of nucleotides in a known gene. Cigan teaches to find an SpCas9 PAM, one only need to scan the target region with their eyes to find a 5’-NGG motif. Then to design a first guide RNA, one only need to record with pencil and paper the 20 nucleotides upstream of the PAM sequence. Cigan also teaches the repair of a SpCas9 cleavage site occurring 3 nucleotides upstream of the PAM sequence often results in a deletion of 1-3 nucleotides (FIG 1). To design the 2nd, 3rd and 4th guide RNA, one only need to remove 1 nucleotide from the 1st, 2nd and 3rd guide RNA sequence, respectively. Thus, each of the designing steps is a process that can be performed in the human mind. MPEP 2106.04(a)(2).III. Although a pencil and paper would aid the skilled artisan in keeping track of the guide sequences and possible deletions, MPEP 2106.04(a)(2).III. states “[t]he courts do not distinguish between mental processes that are performed entirely in the human mind and mental processes that require a human to use a physical aid (e.g., pen and paper or a slide rule) to perform the claim limitation. See, e.g., Benson, 409 U.S. at 67, 65, 175 USPQ at 674-75, 674”. Thus, each of the 6 steps in the claimed method constitutes a judicial exception.
Step 2A, Prong Two - Does the Claim Recite an Additional Elements that Integrate the Judicial Exception into a Practical Application? NO
The Supreme Court has long distinguished between principles themselves, which are not patent eligible, and the integration of those principles into practical applications, which are patent eligible. The phrase "integration into a practical application" requires an additional element or a combination of additional elements in the claim to apply, rely on, or use the judicial exception in a manner that imposes a meaningful limit on the judicial exception, such that it is more than a drafting effort designed to monopolize the exception. In this case, there are no additional elements recited other than the six mental processes that are judicial exceptions.
Step 2B - Does the Claim Recite Additional Elements that Amount to Significantly More than the Judicial Exception? NO
The Supreme Court has identified a number of considerations for determining whether a claim with additional elements amounts to "significantly more" than the judicial exception(s) itself. The claim as a whole is evaluated as to whether it amounts to significantly more than the recited exception, i.e., whether any additional element, or combination of additional elements, adds an inventive concept to the claim (MPEP 2106.05). However, in this case, there are no additional elements recited other than the six mental processes that are judicial exceptions and therefore the method does not amount to "significantly more" than the judicial exceptions.
Claim Rejections - 35 USC § 102
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.
(a)(2) the claimed invention was described in a patent issued under section 151, or in an application for patent published or deemed published under section 122(b), in which the patent or application, as the case may be, names another inventor and was effectively filed before the effective filing date of the claimed invention.
Claims 1, 4, 6-14, 18 and 20 are rejected under 35 U.S.C. 102(a)(1) as being anticipated by Cigan (US 20180273960 A1; published September 27, 2018).
Regarding claim 1, Cigan teaches generating an edited gene of interest (i.e., a method for introducing a specific mutation at a specified position of a target gene) using nonhomologous end joining (NHEJ) (Example 5, [0019], [0269]-[0272]; FIG 6). Cigan teaches identifying an endogenous target site selected for modification (i.e., a specific site within a cell of an organism) ([0019], [0271], FIG 6A). Cigan teaches designing and providing a first guide RNA that targets the targeted position ([0019], [0271], FIG 6A). Cigan teaches an endonuclease cleaves the targeted position, which is repaired through NHEJ resulting in 1 nucleotide deletion ([0019], [0271], FIG 6B). Cigan teaches designing and providing a second guide RNA that targets the modified site with the 1-nucleotide deletion ([0019], [0271], FIG 6B). Cigan teaches cleavage of the modified site by the endonuclease, which is repaired through NHEJ by insertion of a single nucleotide that is different than the original nucleotide ([0019], [0271], FIG 6C). Cigan teaches Cas9 and guide RNAs are delivered into maize embryos by particle bombardment (i.e., introducing the guide RNAs and endonuclease into cells of a plurality of cells) ([0251]). Cigan teaches the NHEJ-mediated nucleotide replacement method as an alternative to using homology-directed repair of Example 2, which is interpreted as a teaching to use the NHEJ-mediated nucleotide replacement method in the maize cells of Example 2 ([0269]-[0270]).
Regarding claim 4, Cigan teaches the insertion of a single nucleotide after cleavage with the second guide RNA results in the change of a proline residue to a serine residue (i.e., the position is in a codon of a gene encoding a protein and the insertion results in the change of amino acid) (FIG 6C).
Regarding claim 6, Cigan teaches Cas9 and guide RNAs are delivered into maize embryos by particle bombardment (i.e., wherein the plurality of cells is a tissue of an organism) ([0251]). Cigan teaches the NHEJ-mediated nucleotide replacement method as an alternative to using homology-directed repair of Example 2, which is interpreted as a teaching to use the NHEJ-mediated nucleotide replacement method in the maize cells of Example 2 ([0269]-[0270]).
Regarding claim 7, the teachings of Cigan regarding the replacement of a single nucleotide using the claimed method is recited above for claim 1.
Regarding claims 8, 18 and 20, Cigan teaches the endonuclease is Cas9 from Streptococuss pyogenes (i.e., SpCas9), which requires a 5’-NGG PAM sequence ([0043], [0236]; FIG 6).
Regarding claim 9, Cigan teaches the Cas9 and the guide RNAs are delivered to maize embryos as expression cassettes (i.e., by a DNA vector) (0236], [0251]). Cigan teaches the NHEJ-mediated nucleotide replacement method as an alternative to using homology-directed repair of Example 2, which is interpreted as a teaching to use the NHEJ-mediated nucleotide replacement method in the maize cells of Example 2 ([0269]-[0270]).
Regarding claims 10-14, Cigan teaches screening for maize cells (i.e., plant cells) with the modified sites and allowing the cells to develop into callus tissue (i.e., cells in which the target gene has been mutated are recovered) ([0251]). Cigan teaches plants regenerated from the callus comprising the edited genes ([0252]). Cigan teaches the NHEJ-mediated nucleotide replacement method as an alternative to using homology-directed repair of Example 2, which is interpreted as a teaching to use the NHEJ-mediated nucleotide replacement method in the maize cells of Example 2 ([0269]-[0270]).
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.
Claims 2-3, 5, 15-17 and 19 are rejected under 35 U.S.C. 103 as being unpatentable over Cigan (US 20180273960 A1; published September 27, 2018), as applied to claims 1, 4, 6-14, 18 and 20 above, and further in view of Gasior (US 20210087573 A1, priority to at least May 7, 2019).
The teachings of Cigan are recited above in paragraphs 24-30 and incorporated here. Cigan also teaches that SpCas9 cleavage can generate deletions of two nucleotides (FIG 1).
Cigan does not teach a third and a fourth guide RNA to replace a second and third nucleotide in a targeted position.
Gasior teaches 2-nucleotide and 3-nucleotide deletions are generated ~10-15% of the time upon NHEJ-mediated repair after SpCas9 cleavage in maize, while a single nucleotide insertion occurs 15-70% (FIG. 7A-D; [0021]). Gasior teaches designing guide RNAs that target NHEJ-generated mutations for the purpose of cleaving (Fig 2B; [0417]). Gasior teaches using the guide RNA targeted to the NHEJ-repaired target to induce another Cas9-cleavage, which may be repaired again by NHEJ (Fig 2B; [0417]). Gasior teaches the cycle of designing guide RNAs to NHEJ-mediated repair products can be continually repeated (Fig 2B; [0417]).
Regarding claims 2, 3 and 5, it would have been obvious to one skilled in the art before the effective filing date of the claimed invention to have repeated the steps of Cas9-mediated cleavage to insert a single nucleotide into a targeted position in the method of Cigan to replace two or three nucleotides that were deleted in the first round NHEJ mediated repair. It would have amounted to a duplication of Cigan’s second step according to the teachings of Gasior that guide RNAs can be designed to NHEJ-generated products in a recursive and repetitive manner. The skilled artisan would have predicted that additional guide RNAs could be designed to secondary and tertiary NHEJ-generate products upon Cigan’s single nucleotide insertion because Gasior teaches that guide RNA targeting sequences can continually be designed using the known NHEJ-mutation patterns at targeted positions. Additionally, Gasior teaches that three nucleotide deletions are generated at several loci in maize at percentages amenable to recovering cells with the desired mutations. MPEP 2144.04 states that duplication of parts/steps is prima facie obvious. Nevertheless, the skilled artisan would have been motivated to repeat Cigan’s guide RNA design and NHEJ-mediated 1-nucleotide insertion steps to replace 2-3 nucleotides in the targeted gene to increase the range of codon-changes possible with Cigan’s method, including changing two adjacent codons.
Regarding claim 15, Cigan teaches the design of the initial guide RNA targeted to the target position by identifying the bases that need to be replaced and identifying the SpCas9 PAM sequence near the desired modification site ([0019]; Fig 6). The obviousness of designing a third and fourth guide RNA to target a 2- and 3- nucleotide deletion and recursive introduction of a 2nd and 3rd nucleotide is recited above as for claims 2 and 3.
Regarding claims 16-17 and 19, Cigan teaches the endonuclease is Cas9 from Streptococuss pyogenes (i.e., SpCas9), which requires a 5’-NGG PAM sequence ([0043], [0236]; FIG 6). Gasior teaches using SpyCas9 guide RNAs for recursive targeting of NHEJ-generated sequences ([0409]).
Conclusion
No claims are allowable.
Any inquiry concerning this communication or earlier communications from the examiner should be directed to CATHERINE KONOPKA whose telephone number is (571)272-0330. The examiner can normally be reached Mon - Fri 7- 4.
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/CATHERINE KONOPKA/Primary Examiner, Art Unit 1635