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 .
The examiner for this case has changed.
This Office Action is in response to communication filed, 10/14/2025, in response to non-final Office Action mailed, 07/14/2025.
Priority
This application is a 371 of PCT/US2020/058166 10/30/2020 which claims benefit of 62/929,006 10/31/2019.
Claim Status
Claims 3, 6, 8-11, 17, 22-25, 27, 31-32, 34-42, and 44-93 were previously canceled.
Claims 33 and 43 are now canceled in response to the previous Office Action.
Claims 21 and 26 are amended in response to the previous Office Action. Applicant’s statements that “[s]upport of these amendments can be found in paragraphs [0138], [0139], and [160] of the specification as filed” and that “[n]o new matter is introduced by these amendments” are acknowledged.
Claims 1-2, 4-5, 7, 12-16, 18-21, 26,2 8-30 and 33 are pending and under consideration.
Information Disclosure Statement
The information disclosure statement (IDS) submitted on 01/02/2024 is in compliance with the provisions of 37 CFR 1.97. Accordingly, the information disclosure statement is being considered by the examiner.
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.
Section 33(a) of the America Invents Act reads as follows:
Notwithstanding any other provision of law, no patent may issue on a claim directed to or encompassing a human organism.
Claims 21 is rejected under 35 U.S.C. 101 and section 33(a) of the America Invents Act as being directed to or encompassing a human organism. See also Animals - Patentability, 1077 Off. Gaz. Pat. Office 24 (April 21, 1987) (indicating that human organisms are excluded from the scope of patentable subject matter under 35 U.S.C. 101). Claims 21 is interpreted to read on a human organism because the claimed cell is comprised within a human subject. Applicant may remedy by amending to recite “an isolated cell” or “an isolated genetically modified cell.”
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 text of those sections of Title 35, U.S. Code not included in this action can be found in a prior Office action.
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 1-2, 4-5, 12-16, 18-21, 26, 29-30, and 33 are rejected under 35 U.S.C. 103 as being unpatentable over Kotin et. al. (US20180230489A1; Published: august, 16, 2018; EFD: October, 28, 2016) in view of Zhan H, et al., (Multiplexed promoterless gene expression with CRISPReader. Genome Biol. 2019 Jun 3;20(1):113).
Regarding claim 1, Kotin discloses regulatable-AAV particles composition comprising at least one regulatable element to regulate the expression of a transgene or gene (see par. [0010]). The AAV particle of Kotin is considered a nucleic acid composition because it comprises the viral genome that comprises the regulatory elements. Kotin teaches that such regulation can be the inhibition or activation of transgene or gene expression or gene replacement (see par. [0010]). Kotin teaches that such outcomes are achieved by utilizing regulatable elements encoded in the AAV particles (e.g., the payload) in such a manner as to tune or control the level or degree of expression of the payload encoded by the viral genome (see par. [0010]). Kotin further discloses that the AAV-particles may encode at least one payload wherein the payload construct may comprise one or more therapeutic protein payload sequence operably linked to a constitutive promoter such a Pol II promoter (see par. [0011], [0095], [0098], [0487], and table 2). Kotin further discloses an AAV vector that may also comprise a viral genome encoding at least one regulatable element comprising a dCAS9 fusion protein further comprising a trans activation domain wherein the promoter driving the expression of any of the regulatable elements may be a constitutive Pol II promoter such as the CMV promoter (see par. [0011], [0385], [0103], and [0098]). Kotin further discloses that the regulatable element may also comprise a single guide RNA (sgRNA) and a Pol III promoter such as the U6 promoter for expression of the sgRNA (see par. [0011], [0365], [0390]). Kotin also discloses that the therapeutic protein payload comprises one or more CRISPR recognition sequences that may be recognized by the guide RNA, these regions in which the CRISPR recognition sequence may be located include, but are not limited to the promoter region (see par. [0381]).
Regarding claim 2, Kotin discloses that AAV particles designed for expression of multiple functional RNAs or proteins in a single vector may utilize multiple promoters, including “bi-directional promoters (Pol II-based), dual promoters, combined Pol II and Pol III promoters, or dual Pol II promoters (see par. [0080]), evidencing that the pol II promoters driving separate expression cassettes within the same construct may be same promoter or different promoters. Kotin further discloses that where two or more different recognition sites are present within or flanking the regions of the payload construct (including the promoter region, see par. [0381]), these sites may be recognized by two or more different single guide RNAs (sgRNAs) (see par. [0295]). Kotin further discloses that the CRISPR regulatable elements and the payload may be located on the same viral genome or on separate viral genomes packaged in separate AAVF particles (see par. [0383]).
Regarding claim 4, Kotin discloses that in some embodiments, the composition may include two or more regulatable elements, wherein the second regulatable element regulates the expression of the first regulatable element, and that in some embodiments, the payload (therapeutic protein expression cassette) and the regulatable elements (the dCas9 activator protein or the gRNA) may be located on one or more separate viral genomes (see par. [0014]).
Regarding claim 5, Kotin discloses that the disclosed plasmids may contain sequences permitting replication of the transgene in eukaryotes and/or prokaryotes and selection markers for these systems. Selectable markers or reporter genes may include sequences encoding geneticin, hygromicin or purimycin resistance, among others, Para. [0031]).
Regarding claim 12, Kotin teaches an AAV vector construct encoding one or more payloads for expression in a target cell that may comprise one or more payload sequences operably linked to a tissue specific promoter which expresses only in certain tissues or cell types (see par. [0094]).
Regarding claim 13, Kotin teaches an AAV vector construct that may comprise one or more payload sequences operably linked to a constitutive promoter wherein the promoter may comprise a constitutive promoter including, but are not limited to those listed in Table 2 (see par. [0095]) which discloses the CMV promoter.
Regarding claim 14, Kotin discloses an AAV vector comprising a promoter wherein the promoter may be a Pol III promoter, such as the U6 promoter (see par. [0099]).
Regarding claim 15, Kotin discloses that filler sequences such as heterologous untranslated regions (UTRs) or regulatable elements from heterologous UTRs can be incorporated into the UTRs of the payload or the regulatable element (see par. [0420]). Kotin further teaches that regulatable elements or sequences within the 5′ and 3′ UTRs will contribute to stabilizing or destabilizing the payload or regulatable element mRNA (see par. [0420]). For example, the 5′UTRs and 3′UTRs may include translational enhancer elements, which are well known in the art (see par. [0420]).
Regarding claim 16, Kotin discloses an AAV vector wherein the 3′ UTR may further comprise a polyadenylation site, including but not limited to the SV40 polyadenylation site, see par. [0311]).
Regarding claim 18, Kotin discloses a therapeutic AAV vector comprising a payload which may comprise a nucleotide sequence or encode signaling molecules such as activators of transcription receptors of the cytokine superfamily (e.g. interleukins) (see par. [0072]).
Regarding claims 19-20, Kotin discloses that in one embodiment, the disclosed expression cassette may be delivered in a viral particle derived from an AAV vector, a lentiviral vector (see par. [0005][0032][0150]).
Regarding claim 21 and 26, Kotin discloses particles comprising nucleic acids and cells (in vivo or in culture) comprising the disclosed nucleic acids and/or particles (see par. [0029], [0427-0436]). Kotin further discloses that the delivery compositions may comprise a pharmaceutically acceptable carrier (see par. [0473-0498]).
Regarding claims 29-30, Kotin discloses that in one embodiment, the invention provides AAV particles comprising a viral genome and a capsid protein (see par. [0033]). Kotin further discloses methods for producing viral particles (e.g., AAV particles and regulatable-AAV particles) that contact a target cell to deliver a payload construct, e.g. a recombinant viral construct, which comprises a nucleotide encoding a payload molecule (see par. [0427]). Kotin further teaches that the payload construct comprises one or more polynucleotide regions encoding or comprising a payload that is flanked on one or both sides by an inverted terminal repeat (ITR) sequence [0611].
Kotin does not disclose wherein the gRNA is able to hybridize to the Pol II promoter that is present in the first and second expression cassettes.
However, Zhan teaches a gRNA that is able to hybridize to a pol II promoter present in an expression cassette that comprises a nucleic acid sequence encoding a dCas9-VP64 activator fusion protein, wherein the dCas9-VP64/gRNA complex upregulates transcription (see Results, section “CRISPR-based transcriptional factors drive promoterless Rluc transcription,” and section “Rational design of a compact AAV-CRISPR-Cas9 with CRISPReader”; Fig. 1a; Fig. 2a-c). Zhan teaches a positive feedback expression loop in which a dCas9-VP64 fusion protein binds to an sgRNA-targeting region positioned immediately upstream of, and operably linked to, a TATA box, which is the core recognition element of a Pol II promoter. This positive feedback loop Results in the dCas9-VP64/gRNA complex promoting transcription of the dCas9-VP64 coding sequence itself, thereby amplifying dCas9-VP64 expression via the sgRNA hybridizing to the promoter element driving its own expression (see Results, section “Rational design of a compact AAV-CRISPR-Cas9 with CRISPReader,” first paragraph; Fig. 2a). Zhan further teaches an embodiment in which the pol II promoter is a full constitutive promoter (SV40): a sgRNA was specifically designed to target the SV40 promoter driving expression of a Rluc reporter, and this sgRNA-promoter hybridization, in complex with dCas9-VP64, activated Rluc transcription up to ~10-fold when delivered via an all-in-one AAV vector (see Results, section “Rational design of a compact AAV-CRISPR-Cas9 with CRISPReader,” third paragraph; Fig. 2d-e). Zhan additionally teaches that this dCas9-VP64/promoter-targeting-gRNA system was successfully packaged into and delivered by a single AAV vector and was capable of activating expression of endogenous genes (VEGF, MALAT1, Apoa1) both in vitro and in vivo (see Results, sections “Rational design of a compact AAV-CRISPR-Cas9 with CRISPReader” and “In vivo gene activation in hypercholesterolemic mice”; Fig. 2f-g; Fig. 3).
It would have been obvious to a person having ordinary skill in the art (PHOSITA) before the effective filing date to modify the AAV vector of Kotin, which discloses a dCas9-activator fusion protein and a gRNA as regulatable elements wherein CRISPR recognition sequences may be located in the promoter region of the payload’s pol II promoter, with the teachings of Zhan, to arrive at a gRNA specifically designed to hybridize to the pol II promoter driving expression of the dCas9-activator fusion protein itself and the payload. A PHOSITA would have been motivated to do so because Zhan expressly teaches that designing an sgRNA to hybridize to the pol II promoter of a dCas9-VP64 activator construct establishes a positive feedback loop that amplifies dCas9-activator expression and increases downstream transcriptional activation of the target gene, and further demonstrates that this same sgRNA-promoter-hybridization design (targeting a full constitutive Pol II promoter, e.g., SV40) can be packaged into a single AAV vector to achieve robust, AAV-deliverable transcriptional activation, directly addressing the AAV payload-size and expression-efficiency goals already pursued by Kotin. A PHOSITA would have had a reasonable expectation of success because Zhan had already reduced this specific gRNA-to-Pol-II-promoter-hybridization/dCas9-VP64 activation design to practice, demonstrating successful transcriptional activation of both reporter constructs and endogenous genes (VEGF, MALAT1, Apoa1) in vitro and in vivo via a single AAV vector, such that applying this known, validated design strategy to the promoter driving the dCas9-activator cassette of Kotin’s AAV-based regulatable expression system would have predictably yielded the claimed result using known techniques without undue experimentation.
Claims 7 is rejected under 35 U.S.C. 103 as being unpatentable over Kotin et. al. (US20180230489A1; Published: august, 16, 2018; EFD: October, 28, 2016), in view of Zhan H, et al., (Multiplexed promoterless gene expression with CRISPReader. Genome Biol. 2019 Jun 3;20(1):113), as applied to claim 1 above, and further in view of Cranenburgh et. al. (US20070259430A1; Published: November, 8, 2007; EFD: July, 1, 2005).
The teachings if Kotin and Zhan are incorporated herein by reference to the 103 rejection above.
Kotin and Zhan do not teach wherein the antibiotic resistance gene on one or more of the nucleic acid molecules Is flanked by a loxP site.
However, Cranenburgh discloses a process for the removal of selectable marker gene sequences, in particular antibiotic gene sequences, from nucleic acid molecules (see par. [0001] and claim set). The process comprising culturing a cell comprising a nucleic acid molecule comprising a selectable marker gene flanked by site-specific recombinase recognition sites under conditions such that an endogenous site-specific recombinase in the cell acts to excise the selectable marker gene by site-specific recombination between the site-specific recombinase recognition sites (see par. [0010]). Cranenburgh further discloses examples of site-specific recombinases/target sites used for antibiotic gene excision including Cre/loxP (see par. [0007]). Cranenburgh further discloses that the retention of selectable marker genes whether they are integrated into the chromosome or present on plasmids, is undesirable and gives rise to a number of problems, for example, they constitute a metabolic burden in recombinant protein production (see par. [0003], and [0004]).
It would have been prima facie obvious to one of ordinary skill in the art before the effective filing date of the claimed invention to have modified the AAV vector of Kotin with the loxP sites of Cranenburgh. The skilled artisan would have been motivated to do so because Cranenburgh teaches that the use of loxP sites flanking the antibiotic resistance gene can be used to excise the antibiotic resistance gene to prevent undesirable complications that can interfere with therapeutic recombinant protein production such as metabolic burden.
Claims 28 is rejected under 35 U.S.C. 103 as being unpatentable over Kotin et. al. (US20180230489A1; Published: august, 16, 2018; EFD: October, 28, 2016) in view of Zhan H, et al., (Multiplexed promoterless gene expression with CRISPReader. Genome Biol. 2019 Jun 3;20(1):113), as applied to claims 1 and 21 above, and further in view of Vijayasankaran et. al. (US20130281355A1; Published: October 24, 2013; EFD: March 15, 2013)
The teachings if Kotin and Zhan are incorporated herein by reference to the 103 rejection above.
Further regarding claim 28, Kotin teaches “cells (in vivo or in culture) comprising the nucleic acids…” wherein, the “nucleic acids include any genetic element (vector) which may be delivered to a host cell, e.g., naked DNA, plasmid, phage, transposon, cosmid, episome, a protein in a non-viral delivery vehicle (e.g., a lipid-based carrier), virus, etc., which transfers the sequences carried thereon.” [0029]-[0030]. Kotin further teaches the “[t]he polynucleotide (e.g., transgene or payload) can be carried on any suitable vector, e.g., a plasmid, which is delivered to a host cell,” that “[t]he plasmids… may be engineered such that they are suitable for replication and, optionally, integration in prokaryotic cells, mammalian cells, or both,” and that “[t]hese plasmids may contain sequences permitting replication of the transgene in eukaryotes and/or prokaryotes,” see [0031]. Kotin further teaches that “the payload may encode a gene therapy product,” and that [a] gene therapy product may comprise a polypeptide, RNA molecule, or other gene product that, when expressed in a target cell, provides a desired therapeutic effect,” such that it may substitute for a non-functional gene that is absent or mutated,” see [0048]. Kotin further teaches that “[g]rowing conditions for insect cells in culture, and production of heterologous products in insect cells in culture are well-known in the art…” [0429].
Kotin and Zhan do not disclose a method of producing a therapeutic protein, the method comprising culturing the cells under conditions to allow for expression of the therapeutic protein and isolating the therapeutic protein from the cells.
However, Vijayasankaran discloses methods of producing a therapeutic polypeptide (e.g. IL-10 or an antibody; see par. [0053]) by growing in a cell culture medium (i.e., culturing in a cell culture medium) a cell comprising an isolated nucleic acid encoding the polypeptide (see par. [0017], and [0121]). Vijayasankaran also discloses that any composition disclosed therein can comprise the polypeptide at a concentration that provides a therapeutically effective amount of the polypeptide when administered to a subject (i.e., an amount effective in the prevention or treatment of a disorder for the treatment of which the polypeptide is effective) (see par. [0160]). Vijayasankaran further discloses “the step of isolating the polypeptide from the cell culture medium,” see [0164], exemplary embodiments.
It would have been prima facie obvious to one of ordinary skill in the art before the effective filing date of the claimed invention to combine Kotins therapeutic nucleic acids with Vijayasankarans method for producing therapeutic polypeptides. The skilled artisan would have been motivated to do so because Vijayasankaran teaches that their method can yield a therapeutically effective concentration of the therapeutic polypeptide. The skilled artisan would have had a reasonable expectation of success because the method is standard practice in the field.
Response to Applicant Remarks/Amendments/Arguments
Any rejections/objections not repeated in this Office action are hereby withdrawn.
Applicant’s amendments, see amendments to specification, filed 10/14/2025, with respect to the use of the terms which are trademark names or marks used in commerce are acknowledged and remedy the objection. The objection of the specification has been withdrawn.
Applicant has canceled claim 43, previously rejected under 35 U.S.C. 112(a). The rejection has been withdrawn.
Applicant's amendments and arguments filed 10/14/2025 have been fully considered but they are not persuasive. Applicant amended claims 21 and 26, previously rejected under 35 USC § 101 to recite “a genetically modified cell.” The amendment does not remedy. A genetically modified cell still reads on a human organism. Thus, claim 21 remains rejected under 35 USC § 101. However, the examiner in further consideration has withdrawn the rejection of claim 26 under 35 USC § 101, as claim 26 is directed to a pharmaceutical composition.
Applicant’s arguments regarding rejections under 35 USC § 103 with respect to claims 1-2, 4-5, 12-16, 18-21, 26, 28-30, and 33 have been considered but are moot because the new ground of rejection does not rely on any reference applied in the prior rejection of record for any teaching or matter specifically challenged in the argument.
Conclusion
No claims are allowed.
Any inquiry concerning this communication or earlier communications from the examiner should be directed to COREY LANE BRETZ whose telephone number is (571)272-7299. The examiner can normally be reached M-F 7:30am - 6:30pm.
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/COREY LANE BRETZ/Examiner, Art Unit 1635
/RAM R SHUKLA/Supervisory Patent Examiner, Art Unit 1635
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