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 .
This action is in response to the amendment filed 07/16/2026, in which claims 1-4, 13, 16, 18 and 25 were amended, claims 26 and 28-30 were previously presented and claims 8, 31, 34, 36, 38, 39 and 41 were withdrawn due to a restriction requirement set forth in a previous office action. Claims 1-4, 13, 16, 18, 25, 26 and 28-30 are currently pending.
Applicant’s arguments have been thoroughly reviewed, but are not persuasive for the
reasons that follow. Any rejection and objections not reiterated in this action have been
withdrawn. This action is FINAL.
Priority
Acknowledgment is made of applicant’s claim for priority based on provisional applications filed as 63/317,847 on 03/08/2022 and 63/372,373 on 03/08/2022.
All claims are given the priority date of 03/08/2022.
Response to Amendments - Specification
The previous objection to the specification has been withdrawn in view of Applicant’s filing of a substitute specification on 07/16/2026.
Improper Markush Rejection
Claims 1-4, 13, 16-18, 25, 26, 28, 29 and 30 are rejected on the basis that it contains an improper Markush grouping of alternatives. See In re Harnisch, 631 F.2d 716, 721-22 (CCPA 1980) and Ex parte Hozumi, 3 USPQ2d 1059, 1060 (Bd. Pat. App. & Int. 1984). A Markush grouping is proper if the alternatives defined by the Markush group (i.e., alternatives from which a selection is to be made in the context of a combination or process, or alternative chemical compounds as a whole) share a “single structural similarity” and a common use. A Markush grouping meets these requirements in two situations. First, a Markush grouping is proper if the alternatives are all members of the same recognized physical or chemical class or the same art-recognized class, and are disclosed in the specification or known in the art to be functionally equivalent and have a common use. Second, where a Markush grouping describes alternative chemical compounds, whether by words or chemical formulas, and the alternatives do not belong to a recognized class as set forth above, the members of the Markush grouping may be considered to share a “single structural similarity” and common use where the alternatives share both a substantial structural feature and a common use that flows from the substantial structural feature. See MPEP § 2117.
The Markush grouping of claims 1 and 4 are improper because the alternatives defined by the Markush grouping do not share both a single structural similarity and a common use for the following reasons: All of the genes listed in claims 1 and 4 are very different as well as playing different roles in the process of causing leukemia.
To overcome this rejection, Applicant may set forth each alternative (or grouping of patentably indistinct alternatives) within an improper Markush grouping in a series of independent or dependent claims and/or present convincing arguments that the group members recited in the alternative within a single claim in fact share a single structural similarity as well as a common use.
Response to Arguments - Improper Markush Rejection
The previous rejection of claims 1-4, 13, 16-18, 25, 26, 28, 29 and 30 on the basis that it contains an improper Markush grouping of alternatives is maintained in view of Applicant amendments to the claims filed on 07/16/2026.
Applicant’s arguments have been fully considered and have not been found to be persuasive. Applicant argues that the claimed Markush grouping shares a single structural similarity and a common use. Applicant continues to argue that the “structural similarity” is not whether the encoded proteins of the listed genes are structurally similar, but rather, a double-stranded DNA regulatory element containing a specific nucleotide sequence recognized by a guide RNA and is targetable by a CRISPR-Cas9 complex. Applicant argues that each member of the Markush groups shares the same structural features of being a genomic regulatory DNA sequence capable of sequence-specific recognition by a gRNA-Cas9 complex, specifically, the claimed genes are all nucleic acid sequences that include protospacer sequences recognizable by a gRNA, are engageable by a Cas9 effector system, and participate in cis-regulatory chromatin architecture. Applicant continues that the Markish grouping also satisfies the requirement that alternatives belong to a “recognized class” with a common function, specifically, the class is genes whose regulatory elements were identified via functional CRISPR-based screening and perturbation modulates leukemia cell viability or growth. Applicant argues that in the application (e.g. Example 7), CRISPR-based perturbation of regulatory elements (e.g., DHS) identified a subset of genes (including LMO2, GATA1, etc.) that are functionally relevant to leukemia cell fitness. Applicant continues to argue that the genes are not an arbitrary grouping, but rather a functionally defined class of regulatory targets identified through a common screening framework. Applicant, lastly, argues that the claimed Markush grouping clearly has a common use, such that all members of the Markush group are used to target regulatory elements with a CRISPR-Cas9 system to modulate gene expression and thereby treat leukemia. Applicant argues that because each target includes a regulatory DNA sequence recognizable by a gRNA, each can be targeted by a Cas9 complex that produces the same mechanistic outcome, modulation of gene expression and treatment of leukemia.
However, the applicant has not established that the recited target genes possess a common property or technical characteristics that provides a meaningful basis for treating them as a single Markush group. Merely identifying the genes as “target genes” or as genes associated with the same general biological pathway does not demonstrate the required technical relationship amount the alternatives. Specifically, each target gene within the group listed in independent claim 1 would require individual targeting with different sgRNAs which would require screening for sgRNAs that would be capable of targeting each individual target gene. The fact that targeting each of the recited genes may produce the same general outcome does not, by itself, establish that the genes belong to a single inventive concept.
The cited genes perform different biological roles and achieve the asserted result through materially different mechanisms. The common characterization of these genes as “targets” is merely a functional description of the claimed alternatives and does not establish the requisite technical relationship among them. Accordingly, the fact that the alternatives are capable of being associated with the same general biological outcome does not establish that they form a technically coherent Markush group.
Moreover, the specification does not provide sufficient evidence demonstrating that the asserted common property applies across the full scope of the claimed alternatives. Applicant’s arguments therefore do not overcome the rejection of claims 1-4, 13, 16-18, 25, 26, 28, 29 and 30 on the basis that it contains an improper Markush grouping of alternatives.
Response to Amendments - Claim Rejections - 35 USC § 112
The previous rejection of claims 1-4, 13, 16-18, 25, 26, 28, 29 and 30 under 35 U.S.C. 112(a) or 35 U.S.C. 112 (pre-AIA ), first paragraph, has been withdrawn due to Applicant’s amendments to the claims filed on 07/16/2026.
Claim Rejections - 35 USC § 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 (i.e., changing from AIA to pre-AIA ) 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.
(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, 13, 16, 18, 26, 28, 29 and 30 are rejected under 35 U.S.C. 102(a)(1) as being anticipated by Reilly et al (Nat Genet. 2021 Aug;53(8):1166-1176; Method pgs. 1-11 and Supplementary Data pgs. 1/9-9/9) as evidenced by Fulco et al (Science. 2016 November 11; 354(6313): 769–773; Supplemental Information Pgs. 1/32-32/32).
Regarding claims 1 and 4, Reilly teaches dCas9-KRAB (CRISPRi system) to disrupt the LMO2 promoters to create LMO2 knockdown by downregulation of the LMO2 promoter activity within K562 cells (erythroleukemia cells) (Page 1167, Fig. 1 and Method Page 3, Column 2).
Regarding claim 13, Reilly teaches the dCas9-KRAB fusion sequence used was from gifted from Fulco et al (Method Page 4, Column 1); Fulco is only cited to show Addgene Plasmid no. 60954 which was translated from a nucleotide sequence to an amino acid sequence and found to be 99% identical to instant SEQ ID NO: 20 (See NEW Appendix I; Supplemental material Page 3, Last paragraph).
Regarding claims 16 and 18, Reilly teaches dCas9-KRAB (CRISPRi system) to disrupt the LMO2 promoters to create LMO2 knockdown by downregulation of the LMO2 promoter activity within K562 cells (erythroleukemia cells) (Page 1167, Fig. 1 and Method Page 3, Column 2).
Regarding claim 26, Reilly teaches the dCas9-KRAB fusion sequence used was from gifted from Fulco et al (Method Page 4, Column 1); Fulco is only cited to show Addgene Plasmid no. 60954 which was translated from a nucleotide sequence to an amino acid sequence and found to be 99% identical to instant SEQ ID NO: 20 (See NEW Appendix I; Supplemental material Page 3, Last paragraph).
Regarding claims 28-30, Reilly teaches K562 cells with a doxycycline-inducible CRISPRi (Method Page 4, Column 1).
Response to Arguments - Claim Rejections - 35 USC § 102
The previous rejection of claims 1, 4, 13, 16-18, 26, 28, 29 and 30 under 35 U.S.C. 102(a)(1) as being anticipated by Tarjan et al (Nat Commun 10, 4258 (2019); Pgs. 1-8; Supplemental Information pages 1/7-7/7 and Supplemental Data Table 1) as evidenced by Hnisz et al (Science. 2016 Mar 25;351(6280):1454-1458) is withdrawn in view of Applicant amendments to the claims filed on 07/16/2026.
Claim Rejections - 35 USC § 103
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 (i.e., changing from AIA to pre-AIA ) 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 pre-AIA 35 U.S.C. 103(a) which forms the basis for all obviousness rejections set forth in this Office action:
(a) A patent may not be obtained though the invention is not identically disclosed or described as set forth in section 102, if the differences between the subject matter sought to be patented and the prior art are such that the subject matter as a whole would have been obvious at the time the invention was made to a person having ordinary skill in the art to which said subject matter 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 pre-AIA 35 U.S.C. 103(a) 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.
Claims 2, 3 and 25 are rejected under pre-AIA 35 U.S.C. 103(a) as being unpatentable over Reilly et al (Nat Genet. 2021 Aug;53(8):1166-1176; Method pgs. 1-11 and Supplementary Data pgs. 1/9-9/9) as evidenced by Fulco et al (Science. 2016 November 11; 354(6313): 769–773; Supplemental Information Pgs. 1/32-32/32), as applied to claims 1, 4, 13, 16, 18, 26, 28, 29 and 30, and further in view of Allen et al (Front. Genome Ed. 2:617910; 2021, Pgs. 1-16) and GenBank Accession number NG_054065.1 (NCBI, LOC110121452 VISTA enhancer Homo Sapiens and LMO2 gene summary on Chromosome 11, Pgs. 1/5-5/5; 2021).
The teachings of Reilly are described above and applied as before.
Regarding claims 2 and 3, instant SEQ ID NO: 350 is the target sequence within the LMO2 gene, that comprises a 23-nucleotide long sequence. Instant SEQ ID NOs: 68 and 209 are the gRNAs being claimed to target the sequence of instant SEQ ID NO: 350.
Reilly teaches the gRNA sequences for targeting the LMO2 gene for Cas9 recruitment wherein the guide RNA sequences for targeting the LMO2 gene is 100% identical to two or more consecutive nucleotides to instant SEQ ID Nos: 68, 209 and 350 (Methods Page 1, Column 1).
Reilly does not teach the entire guide sequence of SEQ ID NOs: 68 and/or 209 that would target the LMO2, specifically shown in SEQ ID NO: 350.
Instant claimed SEQ ID NO: 68 is 100% identical to 20 nucleotide sequence located on chromosome 11 of the human genome within the LMO2 gene (GenBank Accession number NG_054065.1; See PREVIOUS Appendix II).
Allen teaches guide RNAs (gRNAs) are designed to target specific genes by utilizing a 20-nucleotide sequence that is complementary to the target DNA, allowing the CRISPR-Cas9 system to create precise double-strand breaks for gene editing (Page 2, Column 1). Allen teaches designing an effective gRNA involves identifying a target sequence immediately upstream of a Protospacer Adjacent Motif (PAM) site (typically NGG for SpCas9) to ensure high on-target activity while minimizing off-target mutations (Page 2, Column 1 and Page 5, Column 1).
It would have been obvious to one of ordinary skill in the art before the effective filing date of the claimed invention to modify the teachings of Reilly to include the gRNA of instant SEQ ID NO: 68 for targeting instant SEQ ID NO: 350 as taught by Allen and GenBank Accession Number NG_054065.1 because Reilly teaches it is within the ordinary skill in the art to use gRNA sequences for targeting the LMO2 gene for Cas9 recruitment for the purpose of treating leukemia, Allen teaches guide RNAs (gRNAs) are designed to target specific genes by utilizing a 20-nucleotide sequence that is complementary to the target DNA, allowing the CRISPR-Cas9 system to create precise double-strand breaks for gene editing and GenBank Accession Number NG_054065.1 teaches the sequence claimed in instant SEQ ID NOs: 68 and 350 within the LMO2 region on Chromosome 11.
One would have been motivated to make such a modification in order to receive the expected benefit of gRNAs specific for targeting the regulatory enhancer of the LMO2 gene for treating leukemia with high on-target effects and decreased off target effects as taught by Allen and GenBank Accession Number NG_054065.1.
Regarding claim 25, instant SEQ ID NO: 350 is the target sequence within the LMO2 gene, that comprises a 23-nucleotide long sequence. Instant SEQ ID NOs: 68 and 209 are the gRNAs being claimed to target the sequence of instant SEQ ID NO: 350.
Reilly teaches dCas9-KRAB (CRISPRi system) to disrupt the LMO2 promoters to create LMO2 knockdown by downregulation of the LMO2 promoter activity within K562 cells (erythroleukemia cells) (Page 1167, Fig. 1 and Method Page 3, Column 2). Reilly teaches the gRNA sequences for targeting the LMO2 gene for Cas9 recruitment wherein the guide RNA sequences for targeting the LMO2 gene is 100% identical to two or more consecutive nucleotides to instant SEQ ID Nos: 68, 209 and 350 (Methods Page 1, Column 1).
Reilly does not teach the entire guide sequence of SEQ ID NOs: 68 and/or 209 that would target the LMO2, specifically shown in SEQ ID NO: 350.
Instant claimed SEQ ID NO: 68 is 100% identical to 20 nucleotide sequence located on chromosome 11 of the human genome within the LMO2 gene (Genbank Accession number NG_054065.1; See PREVIOUS Appendix II).
Allen teaches guide RNAs (gRNAs) are designed to target specific genes by utilizing a 20-nucleotide sequence that is complementary to the target DNA, allowing the CRISPR-Cas9 system to create precise double-strand breaks for gene editing (Page 2, Column 1). Allen teaches designing an effective gRNA involves identifying a target sequence immediately upstream of a Protospacer Adjacent Motif (PAM) site (typically NGG for SpCas9) to ensure high on-target activity while minimizing off-target mutations (Page 2, Column 1 and Page 5, Column 1).
It would have been obvious to one of ordinary skill in the art before the effective filing date of the claimed invention to modify the teachings of Reilly to include the gRNA of instant SEQ ID NO: 68 for targeting instant SEQ ID NO: 350 as taught by Allen and GenBank Accession Number NG_054065.1 because Reilly teaches it is within the ordinary skill in the art to use gRNA sequences for targeting the LMO2 gene for Cas9 recruitment for the purpose of treating leukemia, Allen teaches guide RNAs (gRNAs) are designed to target specific genes by utilizing a 20-nucleotide sequence that is complementary to the target DNA, allowing the CRISPR-Cas9 system to create precise double-strand breaks for gene editing and GenBank Accession Number NG_054065.1 teaches the sequence claimed in instant SEQ ID NOs: 68 and 350 within the LMO2 region on Chromosome 11.
One would have been motivated to make such a modification in order to receive the expected benefit of gRNAs specific for targeting the regulatory enhancer of the LMO2 gene for treating leukemia with high on-target effects and decreased off target effects as taught by Allen and GenBank Accession Number NG_054065.1.
Response to Arguments - Claim Rejections - 35 USC § 103
The previous rejection of claims 2, 3 and 25 under pre-AIA 35 U.S.C. 103(a) as being unpatentable over Tarjan et al (Nat Commun 10, 4258 (2019); Pgs. 1-8; Supplemental Information pages 1/7-7/7 and Supplemental Data Table 1) as evidenced by Hnisz et al (Science. 2016 Mar 25;351(6280):1454-1458), as applied to claims 1, 4, 13, 16-18, 26, 28, 29 and 30, and further in view of Allen et al (Front. Genome Ed. 2:617910; 2021, Pgs. 1-16) and GenBank Accession number NG_054065.1 (NCBI, LOC110121452 VISTA enhancer Homo Sapiens and LMO2 gene summary on Chromosome 11, Pgs. 1/5-5/5; 2021) is withdrawn in view of Applicant amendments to the claims filed on 07/16/2026.
Conclusion
No claims are allowed.
THIS ACTION IS MADE FINAL. 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 ALEXANDRA ROSE LIPPOLIS whose telephone number is (703)756-5450. The examiner can normally be reached Monday-Friday, 8:00am to 5:00pm EST.
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/ALEXANDRA ROSE LIPPOLIS/Examiner, Art Unit 1637
/CELINE X QIAN/Primary Examiner, Art Unit 1637
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