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 .
Election/Restrictions
Applicant’s election of species (claim 58: 7-chloro-4 -(4-ethyl-(2-hydroxyethyl)-amino-1-methylbutylamino)quinoline (hydroxychloroquine), claim 61: hematopoietic stem cell (HSC), and claim 64: B2M) in the reply filed on April 3, 2026 is acknowledged. Because applicant did not distinctly and specifically point out the supposed errors in the restriction requirement, the election has been treated as an election without traverse (MPEP § 818.01(a)).
Claims 60, 62, 63, and 65 withdrawn from further consideration pursuant to 37 CFR 1.142(b) as being drawn to a nonelected species, there being no allowable generic or linking claim. Election was made without traverse in the reply filed on April 3, 2026.
Accordingly, claims 52-59, 61, 64, 66-71 are examined herein.
Priority
Acknowledgment is made of applicant's claim for priority based on a US Provisional Application
No. 63/119,302 filed on 11/30/2020
Specification
The disclosure is objected to because it contains an embedded hyperlink (pg. 10, line 26) and/or other form of browser-executable code. Applicant is required to delete the embedded hyperlink and/or other form of browser-executable code; references to websites should be limited to the top-level domain name without any prefix such as http:// or other browser-executable code. See MPEP § 608.01.
Drawings
The drawings are objected to because 37 CFR 1.84 (u)(1) states “View numbers must be preceded by the abbreviation "FIG."" In the current case, the view numbers for Figures 1 to 8 are preceded by the word "Figure" instead of 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 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.
Claims 52-56, 59, 61, 66-69, and 71 are rejected under 35 U.S.C. 102(a)(1) as being anticipated by Astrakhan et al (WO 2018/035423 A1; Publication Date: Feb 22, 2018) as evidenced by Chandler et al (Enhancement of Adeno-Associated Virus-Mediated Gene Therapy Using Hydroxychloroquine in Murine and Human Tissues; Molecular Therapy: Methods & Clinical Development, 2019, 14:77-89).
Regarding claims 52 and 56, Astrakhan et al teach a method for targeted integration of an exogenous nucleic acid template at a selected locus in the genome of cells, comprising the following steps (claim 63):
contacting the cells with at least one aminoquinoline compound (e.g., “contacting the population of cells with a genome editing enhancer” (pg. 7, line 30), specifically chloroquine (pg. 9, line 2));
introducing into said cells at least one sequence-specific endonuclease that specifically targets said selected locus (e.g., “introducing an engineered nuclease to generate a double-strand break at a target site” (pg. 7, lines 30-31)),
introducing into said cells an exogenous nucleic acid template to be integrated at said locus (e.g., “introducing a donor repair template into the population of cells” (pg. 7, lines 31-32), and
cultivating the cells to induce DNA repair and integration of the exogenous nucleic acid template by homologous recombination at said selected locus targeted by said sequence-specific endonuclease (e.g., “expression of the engineered nuclease in the presence of the genome editing enhancer and the donor repair template increases the frequency of incorporation of the donor repair template at the target site by homology directed repair” (pg. 7 lines 32-33; pg. 8, lines 1-2), which is also referred as homologous recombination (pg. 19, lines 6-8)), and cells are cultured for five days post electroporation (pg. 66, lines 20-28).
Astrakhan et al teach contacting a population of cells with a genome editing enhancer (pg. 7, line 30) and specifically, chloroquine (pg. 9, line 2; claim 78) as required in claim 57. As evidenced by Chandler et al chloroquine is a 4-aminoquinoline compound, which is an aminoquinoline compound, that improves transduction efficiency (pg. 78, col. 2, para. 4), as required in claims 52 and 56.
Regarding claim 53, Astrakhan et al further teach selecting the cells which have integrated the exogenous nucleic acid template at the selected locus in their genome (e.g., “cells were then stained for CD3, CD4, and CD8 surface markers, and subjected to high-throughput volumetric flow cytometric analysis” to detect loss of CD3 cell surface marker (pg. 64, lines 15-18) through homologous recombination of a transgene encoding a green fluorescent protein in T cells (pg. 66, lines 4-6, lines 20-28)).
Regarding claims 54-55, Astrakhan et al further teach wherein the introduction of the sequence-specific endonuclease into the cells is performed by electroporation, and wherein said exogenous nucleic acid template to be integrated at said locus is comprised into a non-integrative viral vector, specifically AAV (e.g., “T cells were washed and electroporated with in vitro transcribed mRNA encoding a TCRα targeting megaTAL, and subsequently transduced with purified recombinant AAV encoding MND-GFP transgene cassette” (pg. 66, lines 22-24; pg. 20, lines 9-15; pg. 49, lines 18-20)
Regarding claim 59, Astrakhan et al further teach wherein said cell is a eucaryotic cell, preferably a human cell (e.g., stem cells (claim 3), immune effector cells (claim 66), T cells (claim 68)).
Regarding claim 61, Astrakhan et al further teach wherein said cell is a hematopoietic stem cell (pg. 40, lines 8-12; claim 71).
Regarding claims 66-69, Astrakhan et al further teach wherein said sequence-specific endonuclease is the following:
an RNA-guided endonuclease, specifically a CRISPR-associated nuclease: “CRISPR/Cas nuclease system comprises Cas nuclease and one or more RNas that recruit the Cas nuclease to the target site” (pg. 31, lines 11-12), and “in various embodiments, the Cas nuclease is Cas9 (pg. 31, line 27).
an RNa-guided nickase, specifically a Cas9n: “a Cas9 nuclease variant (e.g., cas9 nickase) is contemplated copmprising one or more amino acids additions, deletions, mutations, or substitutions in the HNH or RuvC-like endonuclease domains that decreases or eliminated the nuclease activity of the variant domain.” (pg. 32, lines 26-28).
a TALE-nuclease, specifically a TALEN (claim 83).
Regarding claim 71, the teachings of Astrakhan et al method to integrate an exogenous nucleic acid template at a selected locus in the genome of cells are discussed above as applied to claim 52. The method taught by Astrakhan et al comprises the recited steps (1) to (3) as discussed above. Further, Astrakhan et al teach “viral vectors comprising polynucleotides contemplated in particular embodiments can be delivered…to cells ex vivo, such as cells explanted from an individual patient…or universal donor hematopoietic stem cells, followed by reimplantation of the cells into a patient” (pg. 48, lines 29-32 and pg. 49, lines 1-4).
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 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.
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.
Claims 57 and 58 are rejected under 35 U.S.C. 103 as being unpatentable over Astrakhan et al (WO 2018/035423 A1; Publication Date: Feb 22, 2018) as applied to claim 52 above, and further in view of Chandler et al (Enhancement of Adeno-Associated Virus-Mediated Gene Therapy Using Hydroxychloroquine in Murine and Human Tissues; Molecular Therapy: Methods & Clinical Development, 2019, 14:77-89).
Regarding claims 57-58, the teachings of Astrakhan et al method to integrate an exogenous nucleic acid template at a selected locus in the genome of cells are discussed above as applied to claim 52. Astrakhan et al teach contacting a population of cells with a genome editing enhancer (pg. 7, line 30) and specifically, chloroquine (pg. 9, line 2; claim 78)
However, Astrakhan et al do not teach wherein the genome editing enhancer is hydroxychloroquine (HCQ).
Chandler et al “identified HCQ as a putative inhibitor of two key sentinels in the initiation of intracellular anti-DNA viral response: cGAS, which detects the presence of cytosolic double-stranded DNA, such as inverted terminal repeats (ITRs) that form secondary structures in single-stranded AAV genomes; and TLR9, which detects unmethylated CpG sequences, also present in AAV ITRs.” (pg. 78, col. 2, para. 2). Chandler et al further disclose that “subcellular localization of AAV revealed a strong trend toward shifting from the cytosol to the nucleus upon HCQ treatment.” (pg. 84, col. 2, para. 1). Chandler et al also “demonstrate that HCQ is able to increase GFP transgene expression following AAV transduction in vitro, ex vivo, and in vivo across a range of species.” (pg. 85, col. 1, para. 2). Further, Chandler et al teach “HCQ is known to be less retinal toxic than [chloroquine] in patients on long-term therapy” (pg. 78, col. 2, para. 4).
Thus, it would have been obvious to one of ordinary skill in the art before the effective filling date of the invention to have modified Astrakhan et al method to use hydroxychloroquine as the genome editing enhancer as taught by Chandler et al because it would have merely amounted to a simple substitution of prior art elements according to known methods to yield predictable results. The substituted component (hydroxychloroquine) and its function (increase AAV transduction) were known in the art, and both substitution components chloroquine and hydroxychloroquine are known to serve the same purpose. One would have been motivated to have done so for the advantage of increasing AAV transduction ex vivo and in vivo using a less toxic and more effective compound as taught by Chandler et al. One would have had a reasonable expectation of success in doing so because Astrakhan et al and Chandler et al teach AAV transduction in vivo using structurally similar 4-aminoquinolines, specifically chloroquine and hydroxychloroquine, respectively.
Claims 64 and 70 are rejected under 35 U.S.C. 103 as being unpatentable over Astrakhan et al (WO 2018/035423 A1; Publication Date: Feb 22, 2018) as applied to claim 52 above, and further in view of Bartsevich et al (WO 2017/112859 A1; Publication Date: June 29, 2017).
Regarding claim 64, the teachings of Astrakhan et al method to integrate an exogenous nucleic acid template at a selected locus in the genome of cells are discussed above as applied to claim 52. Astrakhan et al further teach targeting genes including but not limited to: BCL11A, CCR5, TRAC, PD1, and GR (pg. 33, lines 17-28).
However, Astrakhan et al do not teach wherein said selected locus in said cell is B2M.
Bartsevich et al teach “a method of producing a genetically-modified eukaryotic cell comprising an exogenous sequence of interest inserted into a chromosome” (claim 41), comprising the following steps: (a) introducing a meganuclease into the eukaryotic cell; (b) transfecting the eukaryotic cell with a nucleic acid comprising a sequence of interest by a recombinant AAV vector (claim 44); wherein the meganuclease recognizes and cleaves a second recognition sequence located in the beta-2 microglobulin gene (i.e., B2M), and “wherein said genetically-modified eukaryotic cell exhibits reduced cell-surface expression of B2M (claim 47). Bartsevich et al further teach “wherein said exogenous sequence of interest further comprises sequences homologous to sequences flanking said second cleavage site, and wherein said sequence of interest is inserted at said second cleavage site by homologous recombination” (claim 60).
Thus, it would have been obvious to one of ordinary skill in the art before the effective filling date of the invention to have modified Astrakhan et al method to target the B2M gene as taught by Bartsevich et al because it would have merely amounted to a simple substitution of prior art elements according to known methods to yield predictable results. The substituted component (B2M gene) and its function (encodes for beta-2 microglobulin that is common to all major histocompatibility complex (MHC) class I molecules) were known in the art. One would have been motivated to have done so for the advantage of suppressing expression of beta-2 microglobulin which associates with MHC class I molecules for expression at CAR T cell surfaces and consequently render the CAR T cells from being recognized and killed by host cytotoxic T cells. One would have had a reasonable expectation of success in doing so because Astrakhan et al and Bartsevich et al both teach method of integrating exogenous nucleic acids at selected locus in T cells wherein the method comprises sequence-specific endonucleases, exogenous nucleic acid donor template, integration by homologous recombination, and delivery via recombinant AAV vector into T cells, with the sole different being Bartsevich et al teach targeting the B2M gene in a CAR T cell whereas Astrakhan et al teach targeting the BCL11A gene in a CAR T cell.
Regarding claim 70, the teachings of Astrakhan et al to integrate an exogenous nucleic acid template at a selected locus in the genome of cells are discussed above as applied to claim 52. Astrakhan et al further teach wherein the nucleic acid template comprise one or more homology arms that flank the double-strand break site (pg. 34, lines 10-13) and a therapeutic gene or fragment thereof (pg. 35, lines 28-30).
However, Astrakhan et al do not teach wherein the nucleic acid template is a short single-stranded oligodeoxynucleotide.
Bartsevich et al teach a method of introducing exogenous nucleic acid at a selected locus in the genome comprising a sequence-specific endonuclease and integration by homologous recombination. The teachings of Bartsevich et al on this method are discussed above as applied to claim 64. Further, Bartsevich et al teach “the nucleic acid encoding the sequence of interest is introduced into the eukaryotic cell using a single-stranded DNA template” ([0060]).
The obviousness to modify Astrakhan et al method to target the B2M gene as taught by Bartsevich et al is discussed above as applied to claim 64. Following this rationale, it would have also been obvious have use a single-stranded DNA template for the advantage of following the method taught by Bartsevich et al and ensure reproducibility to yield predictable results. One would have had a reasonable expectation of success in doing so because Bartsevich et al taught a method of engineering genetically-modified T cells by homologous recombination of a single-stranded DNA template at the B2M gene using sequence-specific endonuclease.
Conclusion
No claims are allowable.
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QIWEN SU-TOBON
Examiner
Art Unit 1636
/NEIL P HAMMELL/Supervisory Patent Examiner, Art Unit 1636
Prosecution Insights