DETAILED ACTION
Status of the Claims
Claims 1-28 are currently pending.
Claims 16-28 have been withdrawn as being drawn to non-elected subject matter (see below).
Claims 1-15 are examined herein.
The present application, filed on or after March 16, 2013, is being examined under the first inventor to file provisions of the AIA .
Information Disclosure Statement
The information disclosure statement (IDS) submitted on 09/12/2022 is in compliance with the provisions of 37 CFR 1.97. Accordingly, the information disclosure statement is being considered by the examiner.
Response to Restriction Requirement
Applicant’s election without traverse of Group I (claims 1-15) in the reply filed on 12/22/2025 is acknowledged.
Claims 16-28 are withdrawn from further consideration pursuant to 37 CFR 1.142(b) as being drawn to a nonelected group, there being no allowable generic or linking claim. Election was made without traverse in the reply filed on 12/22/2025.
Claim Rejections – 35 U.S.C. 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 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.
Sanson et al.
Claims 1-4, 6-8, and 13-15 are rejected under 35 U.S.C. 102(a)(1) as being anticipated by Sanson et al. ("Optimization of AsCas12a for combinatorial genetic screens in human cells", bioRxiv preprint, 28 August 2019, pp 1-29, https://doi.org/10.1101/747170, cited in the IDS of 09/12/2022).
Regarding claims 1-3, Sanson discloses a method of combinatorial genetic screening in a cancer cell, the method comprising administering to the cancer cell (e.g., cancer cell lines as per the Cell culture section on p. 22) a CRISPR-Cas12a system, wherein the CRISPR-Cas12a system comprises an enhanced Cas12a variant (e.g., an Aciduminococcus Cas12a (AsCas12a) variant that comprises a E174R and/or S542R mutation, as per Fig. 1), a modified nuclear localization signal (e.g., plural NLS sequences as per Fig. 1), and a modified dual direct repeat CRISPR RNA (“[e]ffective multiplexing with Cas12a requires delivery of multiple direct repeats (DRs) within a single array, separated by only the 20-23 nt guide sequence” as per the Development of variant direct repeat sequences section on p. 11, with some examples given in the Triple knockout with Cas12a section and Fig. 6 on pp. 16-17), whereby the CRISPR-Cas12a system mutates multiple genomic regions simultaneously and combinatorial genetic screening is achieved (e.g., “[we] conduct proof-of-principle combinatorial screens by deeply examining a set of synthetic lethal gene pairs with up to 2,400 unique constructs per pair” as per the DISCUSSION section on p. 17).
Regarding claim 4, Sanson discloses the above, wherein the enhanced Cas12a variant has increased DNA binding affinity and activity (e.g., “we introduced the amino acid point mutations to generate enCas12a, a recently-described variant of AsCas12a with increased activity” as per the Optimization of the AsCas12a protein section on p. 3, wherein the point mutations included E174R and/or S542R mutation, as per Fig. 1).
Regarding claim 8, Sanson discloses the above, wherein any one of the direct repeats is about 19 nucleotides in length (“[e]ffective multiplexing with Cas12a requires delivery of multiple direct repeats (DRs) within a single array, separated by only the 20-23 nt guide sequence” as per the Development of variant direct repeat sequences section on p. 11).
Regarding claim 13, Sanson discloses the above, further comprising a crRNA library, wherein the crRNA library comprises a plurality of crRNAs targeting a plurality of genomic regions involved in epigenetic regulation.
Regarding claims 6-7 and 14-15, Sanson discloses the above, wherein each crRNA comprises from 3' to 5' a first direct repeat sequence, a first gRNA, a second direct repeat sequence, a second gRNA, and a third direct repeat sequence (e.g., as per the Development of variant direct repeat sequences section on p. 11, with some examples given in the Triple knockout with Cas12a section and Fig. 6 on pp. 16-17).
Claim Rejections – 35 U.S.C. 103(a)
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 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.
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.
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 set forth in Graham v. John Deere Co., 383 U.S. 1, 148 USPQ 459 (1966), that are applied 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.
Sanson et al. and Zhang et al.
Claims 1-8 and 13-15 are rejected under 35 U.S.C. 103 as being unpatentable over Sanson et al. ("Optimization of AsCas12a for combinatorial genetic screens in human cells", bioRxiv preprint, 28 August 2019, pp 1-29, https://doi.org/10.1101/747170, cited in the IDS of 09/12/2022) in view of Zhang et al. (U.S. PGPub 2021/0093667 A1).
Sanson is relied on as above, however, it is noted that the reference is silent on the limitation of the modified NLS comprising six copies of an NLS, as set forth in claim 5.
Sanson identifies the number of NLSs as a parameter to be optimized, noting that when two NLSs were added that “the additional NLS site improved performance” (e.g., as per p. 4). Others such as Zhang have also identified that several NLSs may be added to improve performance (e.g., “[t]he CRISPR-Cas and/or adenosine deaminase proteins may be provided with 1 or more, such as with, 2, 3, 4, 5, 6, 7, 8, 9, 10, or more heterologous NLSs. In some embodiments, the proteins comprises about or more than about 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, or more NLSs at or near the amino-terminus, about or more than about 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, or more NLSs at or near the carboxy-terminus, or a combination of these (e.g., zero or at least one or more NLS at the amino-terminus and zero or at one or more NLS at the carboxy terminus)” as per para [0641].
Applicant is directed to In re Aller, Lacey, and Hall, 105 USPQ 233 (C.C.P.A. 1955), where the court found
"More particularly, where the general conditions
of a claim are disclosed in the prior art, it is
not inventive to discover the optimum or workable
ranges by routine experimentation."
Routine optimization is not considered inventive and no evidence has been presented that the selection of six NLSs was other than routine or that the results should be considered unexpected in any way as compared to the closest prior art.
It would have been prima facie obvious to a person of ordinary skill in the art prior to the effective filing date of the application to optimize the number of NLSs as per Zhang in the system of Sanson. One of ordinary skill in the art would have been motivated to do so since Sanson was explicitly looking to optimize their Cas12a system and had already seen an increase in performance with the addition of two NLSs.
One of ordinary skill in the art would have had a reasonable expectation of success as of the application’s effective filing date in combining the teachings of the prior art references to arrive at the invention as presently claimed since it would merely require the cloning of multiple NLS sequence into the expression vector, which is well within reach of the skilled artisan.
Sanson et al. and Lu et al.
Claims 1-4 and 6-15 are rejected under 35 U.S.C. 103 as being unpatentable over Sanson et al. ("Optimization of AsCas12a for combinatorial genetic screens in human cells", bioRxiv preprint, 28 August 2019, pp 1-29, https://doi.org/10.1101/747170, cited in the IDS of 09/12/2022) in view of Lu et al. (U.S. PGPub 2019/0100769 A1, cited in the IDS of 09/12/2022).
Sanson is relied on as above, however, it is noted that while Sanson discloses a proof-of-principle combinatorial genetic screening (“Here we present the development of AsCas12a for large scale genetic screens in human cells [and] and conduct proof-of-principle combinatorial screens by deeply examining a set of synthetic lethal gene pairs with up to 2,400 unique constructs per pair” as per the DISCUSSION section on p. 17), it is noted that the reference has not explicitly yet applied their method to identify genomic regions involved in cancer pathogenesis, as set forth in claim 9, to identify epigenetic interactions that are synthetic sick/lethal interactions, as set forth in claims 10-11, and to further design a cancer treatment based on the screening results, as set forth in claim 12.
Regarding claim 9, Lu discloses a combinatorial CRISPR screening method to identify genomic regions involved in cancer pathogenesis (“[a] pooled combinatorial genetic screen with OVCAR8-ADR-Cas9 cells was initiated to identify gRNA combinations that regulate cancer cell proliferation” as per para [0128]).
Regarding claims 10-11, Lu discloses a combinatorial CRISPR screening method to identify epigenetic interactions that are synthetic sick/lethal interactions (“[w]e validate this optimized AsCas12a toolkit by targeting 12 synthetic lethal gene pairs with up to 400 guide pairs each, and demonstrate effective triple knockout via flow cytometry” as per the Abstract and that “[t]he methods described herein allow for the identification of novel epigenetic target gene pairs that inhibit cancer cell proliferation and the potential development of synergistic drug therapies” as per para [0134]).
Regarding claim 12, Lu discloses a combinatorial CRISPR screening method to design a cancer treatment based on the screening results (“[a]lso described herein compositions of inhibitors of epigenetic genes and methods for reducing cell proliferation and/or treating cancer”, as per the abstract and specifically that they disclose a “method for treating cancer in a subject, comprising administering to the subject a combination of two or more inhibitors targeting two or more epigenetic genes selected from the combinations of epigenetic genes set forth in Table 2, wherein each of the two or more inhibitors are administered in an effective amount” as per Claim 40 of Lu).
It would have been prima facie obvious to a person of ordinary skill in the art prior to the effective filing date of the application to modify the combinatorial screening method for cancer of Lu with the CRISPR-Cas12a system of Sanson. One of ordinary skill in the art would have been motivated to do so since Sanson explicitly discloses multiple reasons to use Cas12a instead of Cas9, including their development of it as “a robust system for combinatorial applications of CRISPR technology”, as per the Abstract, “the compact design of AsCas12a arrays leads to significant advantages when synthesizing and sequencing DNA compared to Cas9-based approaches” as per the Multiplexing to assay synthetic lethal interaction section on p. 13, and discloses “the simplicity of synthesizing and sequencing AsCas12a guide constructs compared to Cas9-based approaches, and suggests that the former will become the preferred tool for these studies”, as per the DISCUSSION section on pp. 17-18.
One of ordinary skill in the art would have had a reasonable expectation of success as of the application’s effective filing date in combining the teachings of the prior art references to arrive at the invention as presently claimed since Sanson has already provided the initial proof-of-concept methodology and validated its potential use (e.g., as per the Abstract and DISCUSSION section on pp. 17-18).
Conclusion
No claims are allowed.
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/JEREMY C FLINDERS/
Primary Examiner, Art Unit 1684