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 .
Priority
Applicant’s claim for the benefit of a prior-filed application No. 62182186, filed 06/19/2015 under 35 U.S.C. 119(e) or under 35 U.S.C. 120, 121, 365(c), or 386(c) is acknowledged.
Election/Restrictions
Applicant’s election of Group I, drawn to claims 1-3, 6, 9-11, 44-51 and 53 in the reply filed on 01/27/2026 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)).
Applicant’s species election of an engineered meganuclease as recited in claim 45 in the reply filed on 01/27/2026 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)).
STATUS OF CLAIMS
Claims 4-5, 7-8, 12-43, 52, and 54-68 have been cancelled.
Claims 1-3, 6, 9-11, 44-51, 53, and 69 are pending.
Claim 69 is hereby withdrawn by the examiner as being directed to non-elected invention without traverse.
Claims 1-3, 6, 9-11, 44-51, and 53 are under examination at this time.
Applicant is reminded that upon the cancelation of claims to a non-elected invention, the inventorship must be corrected in compliance with 37 CFR 1.48(a) if one or more of the currently named inventors is no longer an inventor of at least one claim remaining in the application. A request to correct inventorship under 37 CFR 1.48(a) must be accompanied by an application data sheet in accordance with 37 CFR 1.76 that identifies each inventor by his or her legal name and by the processing fee required under 37 CFR 1.17(i).
Information Disclosure Statement
The information disclosure statements (IDS) submitted on 1/22/2024 is in compliance with the provisions of 37 CFR 1.97. Accordingly, the information disclosure statement is being considered by the examiner.
Specification
Nucleotide and/or Amino Acid Sequence Disclosures
REQUIREMENTS FOR PATENT APPLICATIONS CONTAINING NUCLEOTIDE AND/OR AMINO ACID SEQUENCE DISCLOSURES
Items 1) and 2) provide general guidance related to requirements for sequence disclosures.
37 CFR 1.821(c) requires that patent applications which contain disclosures of nucleotide and/or amino acid sequences that fall within the definitions of 37 CFR 1.821(a) must contain a "Sequence Listing," as a separate part of the disclosure, which presents the nucleotide and/or amino acid sequences and associated information using the symbols and format in accordance with the requirements of 37 CFR 1.821 - 1.825. This "Sequence Listing" part of the disclosure may be submitted:
In accordance with 37 CFR 1.821(c)(1) via the USPTO patent electronic filing system (see Section I.1 of the Legal Framework for Patent Electronic System (https://www.uspto.gov/PatentLegalFramework), hereinafter "Legal Framework") as an ASCII text file, together with an incorporation-by-reference of the material in the ASCII text file in a separate paragraph of the specification as required by 37 CFR 1.823(b)(1) identifying:
the name of the ASCII text file;
ii) the date of creation; and
iii) the size of the ASCII text file in bytes;
In accordance with 37 CFR 1.821(c)(1) on read-only optical disc(s) as permitted by 37 CFR 1.52(e)(1)(ii), labeled according to 37 CFR 1.52(e)(5), with an incorporation-by-reference of the material in the ASCII text file according to 37 CFR 1.52(e)(8) and 37 CFR 1.823(b)(1) in a separate paragraph of the specification identifying:
the name of the ASCII text file;
the date of creation; and
the size of the ASCII text file in bytes;
In accordance with 37 CFR 1.821(c)(2) via the USPTO patent electronic filing system as a PDF file (not recommended); or
In accordance with 37 CFR 1.821(c)(3) on physical sheets of paper (not recommended).
When a “Sequence Listing” has been submitted as a PDF file as in 1(c) above (37 CFR 1.821(c)(2)) or on physical sheets of paper as in 1(d) above (37 CFR 1.821(c)(3)), 37 CFR 1.821(e)(1) requires a computer readable form (CRF) of the “Sequence Listing” in accordance with the requirements of 37 CFR 1.824.
If the "Sequence Listing" required by 37 CFR 1.821(c) is filed via the USPTO patent electronic filing system as a PDF, then 37 CFR 1.821(e)(1)(ii) or 1.821(e)(2)(ii) requires submission of a statement that the "Sequence Listing" content of the PDF copy and the CRF copy (the ASCII text file copy) are identical.
If the "Sequence Listing" required by 37 CFR 1.821(c) is filed on paper or read-only optical disc, then 37 CFR 1.821(e)(1)(ii) or 1.821(e)(2)(ii) requires submission of a statement that the "Sequence Listing" content of the paper or read-only optical disc copy and the CRF are identical.
Specific deficiencies and the required response to this Office Action are as follows:
Specific deficiency – Nucleotide and/or amino acid sequences appearing in the specification are not identified by sequence identifiers in accordance with 37 CFR 1.821(d). Paragraphs [0024-0025] contain polypeptide sequences of greater than or equal to 4 contiguous amino acids.
Required response – Applicant must provide:
A substitute specification in compliance with 37 CFR 1.52, 1.121(b)(3) and 1.125 inserting the required sequence identifiers, consisting of:
A copy of the previously-submitted specification, with deletions shown with strikethrough or brackets and insertions shown with underlining (marked-up version);
A copy of the amended specification without markings (clean version); and
A statement that the substitute specification contains no new matter.
Drawings
The drawings are objected to because the drawings are referred to as “Figure 1”, “Figure 2”, etc. The proper reference is “FIG. 1”, “FIG. 2”, etc. 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 Interpretations
The term “sub-optimal” is being interpreted under Broadest Reasonable Interpretation (B.R.I.) to mean any recognition sequence that is recognized at any degree less than 100% of the time. Applicant provides and an example of a sub-optimal recognition sequence for meganuclease, but does not provide an example of sub-optimal recognition sequences for the other endonucleases claimed nor does applicant disclose a definition of what sub-optimal constitutes.
For customer service and compact prosecution, the use of “AAV” in dependent claims is being interpreted to mean “the AAV vector” of claim 1. For consistency of the claim language, applicants are advised to use “AAV vector” instead of “AAV” in claims 2-3, 6, 9-11, and 44-51.
Claim Objections
Claims 2-3, 6, 9-11, and 44-51 are objected to because of the following informalities:
Claims 2-3, 6, 9-11, and 44-51, 53 and 69 interchangeably use terms “the AAV” and “the AAV vector.” However, the abbreviation “AAV” is used for “adeno associated viral” in claim 1. This is confusing and the antecedent basis for these terms is not clear. This becomes confusing especially when regarding claim 53, which recites a method for producing an AAV, which implies producing an AAV particles. Thus, the applicant is using “AAV” to mean both an AAV vector and an AAV viral particle, which are not equivalent.
Claims 50 and 51 recite a recombinant DNA construct encoding said AAV vector of claim 1 or claim 47, respectively. The term encoding is used for a nucleic acid sequence that encodes an RNA molecule or polypeptide. Suggested language for claims 50 and 51 would be “a recombinant DNA construct comprising said viral vector.”
Appropriate correction is required.
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 1-3, 6, 9-11, 44-51, and 53 are rejected under 35 U.S.C. 103 as being unpatentable over Wu et. al., (US 20190275168 A1, published 09/12/2019, effective filing date 04/30/2015) in view of Wilson et. al., (US 20130023033 A1, provided in IDS), Zhang et. al., (WO 2015089351 A1, provided in IDS), Moore et. al., (NAR; 43(2): 1297-1303, 2015), Yang et. al., (Appl Environ Microbiol.; 80(13):3826-34, 2014), Riviere et. al., (Gene Therapy, Vol. 21, p. 529-532, 2014, provided in IDS), and Qiao et. al., (J Virol.;76(24):13015-2, 2002).
Regarding claim 1, Wu teaches “a recombinant AAV virus encoding a nucleic acid sequence comprising a CRISPR system polynucleotide sequence, wherein the polynucleotide sequence comprises: (i) one or more guide RNA sequences that hybridize to an autosomal dominant disease-related gene sequence; (ii) a second sequence encoding a codon-modified autosomal dominant disease-related gene or fragment, wherein at least one disease related mutation in the modified autosomal dominant disease-related gene or fragment has been corrected and the codon-modified autosomal dominant disease related gene or fragment cannot be recognized by one or more sg RNA sequences that hybridize to an unmodified autosomal dominant disease-related gene sequence; and (iii) a sequence encoding a Cas family enzyme” see [0091]. Wu further teaches the vector comprised a 5’ ITR (see FIG. 1A and [0022]; FIG. 9). Wu further teaches that “in addition to the sequence sufficient to direct transcription, a promoter sequence … can also include sequences of other regulatory elements that are involved in modulating transcription (e.g., enhancers, kozak sequences and introns)” see [0115]. Wu further teaches a promoter operably linked to the nuclease ([0115]: “ the use of any promoter/regulatory sequence known in the art that is capable of driving expression of the desired protein operably linked thereto;” and [0022][0031]: “FIG. 9 is a schematic representation of the self-excisional AAV/Cas9 vector. Cas9 from S. pyogenes, which is driven by a 173-bp short CMV promoter (sCMV)…” Wu further teaches “self-excisional AAV-Cas9 vectors,” comprising sgRNA-Y1 target sequences that recruit the sgRNA/CRISPR complex to induce double strand breaks in the vector encoding the Cas nuclease (see [0031]: “once the cell expresses Cas9 protein and sgRNA-Y1 simultaneously, this AAV/Cas9 vector is destroyed by Cas9 itself”). Wu further teaches the vector comprised a 3’ ITR (see FIG. 1A and [0022]; FIG. 9). Wu further teaches “wherein the CRISPR-Cas system is under the control of a promoter which controls expression of the codon-modified autosomal dominant disease-related gene product …” (see claim 12 and 29; [0015]).
Regarding claim 2, Wu teaches “a schematic representation of the self-excisional AAV/Cas9 vector,” wherein “Cas9 from S. pyogenes…is driven by a … short CMV promoter (sCMV) and terminated by a … synthetic poly-A signal (SPA) ...” See [0031].
Regarding claim 3, Wu teaches “to minimize the intensity and duration of Cas9 expression and potential off-targeting effects, self-excisional AAV-Cas9 vectors have also been generated, which have the ability to self-inactivate Cas9 expression shortly after Cas9 production. This approach comprises flanking the Cas9 gene with two sgRNA-Y1 target sites (similar to loxP sites in Cre recombinase system) to terminate Cas9 own expression (as shown in FIG. 9)” (see [0113]). Wu further teaches that “the design of self-inactivating recombinant AAV vectors (see FIG. 9) enables the inventors to control the amount and duration of Cas9 expression in target cells, and can prevent the unwanted off-target effects due to excessive expression of Cas9 protein” (see [0114]).
Regarding claim 6, Wu teaches that “the donor sequence or modified autosomal dominant disease-related gene sequence is flanked by an upstream and a downstream homology arm,” and that “the homology arms, which flank the donor sequence or modified autosomal dominant disease-related gene sequence, correspond to regions within the targeted locus of autosomal dominant disease-related gene” (see [0144]).
Regarding claim 9, Wu teaches that “single guide RNA(s) used in the methods of the present disclosure can be designed so that they direct binding of the Cas-sgRNA complexes to pre-determined cleavage sites in a genome” (see [0135]), and that “for Cas family enzyme (such as Cas9) to successfully bind to DNA, the target sequence in the genomic DNA should be complementary to the sgRNA sequence” (see [0136]). Wu further teaches “that “ChopStick” (gene deletion or gene disruption) can be used to efficiently delete and correct a gene region of interest, such as one containing a mutation” (see [0030]).
Regarding claim 10, Wu teaches “supplying the cells with wildtype autosomal dominant disease-related gene cDNA which is codon modified to evade recognition by the guide RNAs” (see abstract and claim 1). Wu further teaches “ a codon-modified autosomal dominant disease-related gene or fragment thereof, wherein at least one disease related mutation has been corrected in the codon-modified autosomal dominant disease-related gene or fragment thereof, and where the codon-modified autosomal dominant disease related gene or fragment is not recognized by the guide RNA” (see [0007] and claims 1, 13, 19 and 30).
Regarding claim 11, Wu teaches that “the codon-modified cDNA (donor-template) may be modified in such a way as to render it unrecognizable by the sgRNA(s) used to target either mutant and wt disease-related gene(s). Thus, mutations need to be introduced into a donor-template gene or fragment to avoid this donor-template gene or fragment being recognized by sgRNA(s) and consequently degraded by Cas enzyme (for example a Cas9 nuclease) which has been introduced in cells. This can be accomplished by introducing a wobble base into donor-template, thus making sure that the change in DNA results in a silent mutation, leaving the expression product of wt gene intact. The term “wobble base” as used in the present disclosure refers to a change in a one or more nucleotide bases of a reference nucleotide sequence wherein the change does not change the sequence of the amino acid coded by the nucleotide relative to the reference sequence” (see [0095]).
Regarding claim 44, Wu teaches that the “vectors … can comprise any of a number of promoters known to the art, wherein the promoter is constitutive, regulatable or inducible, cell type specific, tissue-specific, or species specific” see [0115].
Regarding claim 45, Wu teaches “non-limiting examples of the endonucleases include a zinc finger nuclease (ZFN), a ZFN dimer, a ZFNickase, a transcription activator-like effector nuclease (TALEN), or an RNA-guided DNA endonuclease (e.g., CRISPR/Cas9)” see [0124].
Regarding claim 46, Wu teaches that “any suitable meganuclease may be used in the present methods to create double-strand breaks in the host genome, including endonucleases in the LAGLIDADG and PI-Sce family” (see [0124].
Regarding claim 47-48, Wu teaches that “promoter/regulatory sequences useful for driving constitutive expression of a gene are available in the art and include, but are not limited to, for example… TRE (Tetracycline response element promoter),” which comprises Tet repressor biding sites, see [0115].
Regarding claim 49, Wu teaches “ tissue specific or inducible promoter/regulatory sequences which are useful for this purpose include, but are not limited to, the rhodopsin promoter, the MMTV LTR inducible promoter, the SV40 late enhancer/promoter, synapsin 1 promoter, ET hepatocyte promoter, GS glutamine synthase promoter and many others” see [0115].
Regarding claim 50, Wu teaches that “the constructs encoding the “Chop” and “Stick” components can be delivered to the subject using one or more recombinant adeno-associated viral (AAV) vectors (e.g., 1, 2, 3, 4, 5, 6, 7, 8, 9, or more AAV vectors). One or more sgRNAs can be packaged into single (one) recombinant AAV vector. The recombinant AAV vector may also include codon-modified autosomal dominant ocular disease-related gene sequence (donor template). A Cas-family nuclease can be packaged into the same, or alternatively separate recombinant AAV vectors” see [0090].
Wu does not teach: (1) wherein said vector recognition sequence is identical to a chromosomal recognition sequence present in the genome of said target cell, or wherein said vector recognition sequence is a sub-optimal recognition sequence which is recognized and cleaved by said engineered nuclease; (2) wherein said polynucleotide does not comprise more than one promoter per se; (3) wherein said polynucleotide further comprises a nucleic acid sequence encoding a ligand-inducible transcription factor; (4) wherein said recombinant DNA construct further comprises a nucleic acid sequence encoding said transcription repressor; and (5) a method for producing an AAV, said method comprising (a) transforming a packaging cell with a recombinant DNA construct; (b) transforming said packaging cell with a second recombinant DNA construct comprising a cap gene and a rep gene; and (c) transforming said packaging cell with a third recombinant DNA construct comprising adenoviral helper components.
Wilson teaches “for permanent shut down of transgene expression, the ablator… binds to the ARS of the transgene unit and ablates or excises the transgene” see [0109]. Wilson further teaches the “transgene unit refers to a DNA that comprises: (1) a DNA sequence that encodes a transgene; (2) at least one ablation recognition site (ARS) contained in a location which disrupts transgene expression, including, within or flanking the transgene or its expression control elements (e.g., upstream or downstream of the promoter and/or upstream of the polyA signal); and (3) a promoter sequence that regulates expression of the transgene” see [0096].
Wilson further teaches “a single promoter may direct expression of an RNA that contains, in a single open reading frame (ORF), two or three heterologous genes (e.g., the third and fourth transcription units, and where applicable, the first transcription unit encoding the therapeutic transgene) separated from one another by sequences encoding a self-cleavage peptide (e.g., 2A peptide, T2A) or a protease recognition site (e.g., furin). The ORF thus encodes a single polyprotein, which, either during (in the case of T2A) or after translation, is cleaved into the individual proteins. These IRES and polyprotein systems can be used to save AAV packaging space, they can only be used for expression of components that can be driven by the same promoter” see [0087].
Wilson further teaches an AAV with a PolyA sequence positioned 3’ downstream of the endonuclease sequence (see [0022], [0031], [0163]).
Wilson further teaches “expression of the ablator must be controlled by an inducible promoter that provides tight control over the transcription of the ablator gene e.g., a pharmacological agent, or transcription factors activated by a pharmacological agent or in alternative embodiments, physiological cues. Promoter systems that are non-leaky and that can be tightly controlled are preferred. Inducible promoters suitable for controlling expression of the ablator are e.g., response elements including but not limited to a tetracycline (tet) response element” see [0111].
Wilson further teaches “the ablator that is encoded by the second transcription unit of the recombinant DNA construct composition is an endonuclease, a recombinase, a meganuclease, or an artificial zinc finger endonuclease that binds to the ablation recognition site in the first transcription unit and excises or ablates DNA” (see [0193]). Wilson further teaches “I-SceI: a member of intron endonuclease or homing endonuclease which is a large class of meganuclease” (see [0399]).
Wilson further teaches “Inducible promoters suitable for controlling expression of the ablator are e.g., response elements including but not limited to a tetracycline (tet) response element… an ecdysone-inducible response element… a metal-ion response element … a heat shock response element… or a hormone response element,” which for example, a tetracycline (tet) response element contains Tet repressor binding sites, see [0111]; FIG. 23.
Wilson further teaches a Pharmacologically Induced Transgene Ablation DNA construct containing an ablation unit and a dimerizable TF domain unit (See [0006] and [0075] and FIG. 23). Wilson teaches that the “Dimerizable transcription factor (TF) domain unit” refers to (1) a DNA sequence that encodes the DNA binding domain of a TF fused to the dimerizer binding domain (DNA binding domain fusion protein) controlled by a promoter; and (2) a DNA sequence that encodes the activation domain of a TF fused to the dimerizer binding domain (activation domain fusion protein) controlled by a promoter. In one embodiment, each unit of the dimerizable domain is controlled by a constitutive promoter and the unit is utilized for control of the promoter for the ablator. Alternatively, one or more of the promoters may be an inducible promoter” see [0046]. Wilson teaches an AAV vector that comprises an inducible promoter and further comprises a nucleic acid sequence encoding a ligand -inducible transcription factor. This vector also comprises an internal T2A cleavage site and a PolyA sequence ([0128-1030] and FIG. 10 A-b and FIG. 23). Wilson teaches “transcription of the ablator is controlled by a tet-on/off system, a tetR-KRAB system, a mifepristone (RU486) regulatable system, a tamoxifen-dep regulatable system, or an ecdysone-dep regulatable system,” see [1093].
Wilson further teaches a recombinant DNA construct encoding an AAV vector, see claim 28.
Wilson further teaches “a packaging cell line that stably supplies rep and cap is transiently transfected with a construct encoding the transgene flanked by ITRs” (see [0148]).
Qiao teaches a “dual splicing switch, where an intron and three polyadenylation [poly(A)] sequences were inserted into the protein coding region of a gene to disrupt its transcription” in packaging cells to prevent the gene’s cytostatic and cytotoxic effects on the packaging cell. Qiao further teaches that “because of the tight control of all Rep proteins by the dual splicing switch, they…readily obtained 293 cell-based AAV packaging cell lines with both high-stability and high vector yields,” see introduction last paragraph.
Yang teaches “ I-SceI cleavage of the chromosome and the donor plasmid allows λ-Red recombination between chromosomal breaks and linear double-stranded DNA from the donor plasmid” see abstract. Yang further teaches “genetic modifications are introduced into the chromosome, and the placement of the I-SceI sites determines the nature of the recombination and the modification. This method was successfully used for cadA knockout, gdhA knock-in, seamless deletion of pepD, site-directed mutagenesis of the essential metK gene, and replacement of metK with the Rickettsia S-adenosylmethionine transporter gene” see abstract.
Riviere teaches “variable correction of Artemis deficiency by I-Sce1-meganuclease-assisted homologous recombination in murine hematopoietic stem cells” (e.g. Title). In Art-/- mouse, exon 12 of the Artemis gene had been replaced by an I-Sce1 recognition site. The I-Sce1 enzyme and the Artemis correction template were each delivered by a self-inactivating (SIN)-integrase-defective lentiviral vector, and transduction of Art-/- mHSCs with the two vectors successfully reverted the Art-/- phenotype in 2 out of 10 experiments (e.g. Abstract). Figure 1a shows vector SIN-IDLV-CMV-ISce1 (I-Sce1 vector) and Figure 1b shows vector SIN-IDLV-Art (Artemis matric vector). Figure 2a demonstrates the Art-/- mice genome contains an ISce1 recognition site, which is flanked by left and right homology arms. The Artemis matrix vector contains Ex12 flanked by right and left homology arms. The I-Sce1 enzyme cleaves at the I-Sce1 recognition site and the homologous recombination between the genome and Artemis matrix vector via the right and left homology regions results in the correction of Ex12 (exon 12) in the mouse genome (e.g. Figure 1 and 2, p. 530).
Moore teaches “sub-optimal” target recognition sequences to decrease the affinity of the nuclease complex for its target DNA (results 5th paragraph: “we performed simulations gradually decreasing the affinity of the Cas9–gRNA complex for its target DNA (Figure 3c),” and reports that less affinity for the target DNA results in an increase in residence time. Moore further teaches that a target recognition sequence within the vector located in a non-coding regions between the polynucleotide encoding the nuclease and the polynucleotide encoding the transgene, see Figure 4c and results paragraphs 7-8. Moore further teaches that “future applications” that implement their vector systems can be “used in synthetic architectures and for therapeutic gene delivery” see discussion last paragraph. Moore further teaches that they “were also interested in probing their system using an inducible promoter driving the production of the Cas9 and mKate2 transcript,” and “to accomplish this, they replaced their CMV promoter with the TRE3G system and tested various levels of doxycycline (Dox) in Tet-on cells (HEK293 cells that stably produce the transcription factor rtTA)” see results pg. 1301 right column.
Zhang teaches that “to accomplish CRISPR~Cas9 inactivation, while also achieving editing of the targeted genomic site, the CRISPR-Cas9 guide RNAs that target a desired genomic locus and the "self-inactivating" guide RNA(s) are co-delivered/co-expressed in the same cell/target tissue...” Zhang teaches “the basic concept is presented in diagram form (Figure 7a),” and that “this approach results in editing of the intended genomic site followed by the inactivation of the Cas9 nuclease gene within 48 hours (Figure 7b).” Zhang teaches that “if necessary, the addition of non-targeting nucleotides to the 5" end of the "sell- inactivating" guide RNA can be used to delay its processing and or modify its efficiency as a means of ensuring editing at the targeted genomic locus prior to CRISPR-Cas9 shutdown,” see [0327]. Zhang further teaches “ repairing said cleaved target polynucleotide by homologous recombination with an exogenous template polynucleotide, wherein said repair results in a mutation comprising an insertion, deletion, or substitution of one or more nucleotides of said target polynucleotide” see [0069].
Zhang further teaches “a method of preparing the vector, e.g., AAV or lentivirus, … comprising transfecting one or more plasmid(s) containing or consisting essentially of nucleic acid molecule(s) coding for the AAV into AAV-infectable cells, and supplying AAV rep and/or cap obligatory for replication and packaging of the AAV, In some embodiments the AAV rep and/or cap obligator for replication and packaging of the AAV are supplied by transfecting the cells with helper plasmid(s) or helper virus(es)” see [0049].
Regarding claims 1, it would have been obvious to one of ordinary skill in the art before the effective filing date to modify Wu to employ a vector recognition sequence that is identical to a chromosomal recognition sequence present in the genome of the target cell, or a sub-optimal recognition sequence recognized and cleaved by the engineered nuclease. One would have been motivated to include identical recognition sequences in both the vector and the chromosomal locus because Yang teaches that I-SceI cleavage of both the chromosome and donor plasmid allows recombination between chromosomal breaks and donor DNA, and Riviere similarly teaches correction of a genomic locus by cleavage at a genomic I-SceI recognition site followed by homologous recombination with a donor template. Alternatively, one would have been motivated to employ a sub-optimal recognition sequence because Moore teaches decreasing affinity of the Cas9-gRNA complex for a target recognition sequence in order to modulate nuclease activity and residence time, and further teaches positioning such target recognition sequences within vector architectures. Thus, one would have had a reasonable expectation of success to either employ a vector recognition sequence that is identical to a chromosomal recognition sequence or a sub-optimal recognition sequence because both Yang and Riviere demonstrate that nuclease-mediated cleavage at matching recognition sequences in the donor and genome promotes homologous recombination and targeted editing, and because Moore demonstrates that altering recognition sequence affinity predictably modulates nuclease cleavage behavior while maintaining recognition and cleavage activity.
Regarding claims 1, It would have been obvious to one of ordinary skill in the art before the effective filing date to modify Wu such that the polynucleotide does not comprise more than one promoter. One would have been motivated to use a single promoter because Wilson teaches expression of multiple heterologous genes from a single promoter using polyprotein strategies such as 2A peptide cleavage or IRES systems to conserve AAV packaging space. One would have had a reasonable expectation of success because Wilson demonstrates successful expression of multiple components from a single promoter within AAV vectors.
Regarding claim 49, it would have been obvious to one of ordinary skill in the art before the effective filing date to modify Wu to include a nucleic acid sequence encoding a ligand-inducible transcription factor which regulates activation of the promoter. One would have been motivated to include a ligand-inducible transcription factor because Wilson teaches AAV vectors comprising pharmacologically inducible transcription systems including tetracycline-responsive systems and dimerizable transcription factor domains for controlling nuclease or ablator expression. One would have had a reasonable expectation of success because Wilson demonstrates that ligand-inducible transcription factor systems successfully regulate expression of endonucleases within AAV vectors.
Regarding claim 51, it would have been obvious to one of ordinary skill in the art before the effective filing date to modify Wu to further comprise a nucleic acid sequence encoding a transcription repressor. One would have been motivated to include a transcription repressor because Wilson teaches constructs comprising Tet repressor-based systems and KRAB-based transcription repression systems for tightly controlling nuclease/ablator expression. One would have had a reasonable expectation of success because Wilson demonstrates that transcription repressor systems effectively regulate expression of nucleases/ablators in recombinant AAV constructs.
Regarding claims 1 and 53, it would have further been obvious to one of ordinary skill in the art before the effective filing date to modify Wu to include an intron within the AAV vector or coding region of the nuclease to prevent expression of the nuclease in packaging cells. One would have been motivated to include such an intron because Qiao teaches a dual splicing switch in which an intron and polyadenylation sequences are inserted into a coding region of a transgene(s) to disrupt transcription in packaging cells and prevent cytostatic and cytotoxic effects during AAV vector production. One would have had a reasonable expectation of success because Qiao demonstrates that insertion of an intron within a coding region of Rep and Cap effectively suppresses their expression in packaging cells and demonstrated a marked increase in stability and yields.
Regarding claim 53, it would have been obvious to one of ordinary skill in the art before the effective filing date to use Wu’s recombinant DNA construct in a method for producing an AAV by transforming a packaging cell with an AAV vector construct, a rep/cap construct, and adenoviral helper components. One would have been motivated to employ such packaging methods because Wilson teaches transfecting packaging cells with a construct encoding the transgene flanked by ITRs along with rep and cap components, and Zhang teaches preparation of AAV vectors by transfecting cells with plasmids encoding the DNA construct of interest, supplying rep and cap AAV genome components, and transfecting the cells with helper plasmids or helper viruses. One would have had a reasonable expectation of success because both Wilson and Zhang demonstrate conventional AAV production using these components.
Double Patenting
The nonstatutory double patenting rejection is based on a judicially created doctrine grounded in public policy (a policy reflected in the statute) so as to prevent the unjustified or improper timewise extension of the “right to exclude” granted by a patent and to prevent possible harassment by multiple assignees. A nonstatutory double patenting rejection is appropriate where the conflicting claims are not identical, but at least one examined application claim is not patentably distinct from the reference claim(s) because the examined application claim is either anticipated by, or would have been obvious over, the reference claim(s). See, e.g., In re Berg, 140 F.3d 1428, 46 USPQ2d 1226 (Fed. Cir. 1998); In re Goodman, 11 F.3d 1046, 29 USPQ2d 2010 (Fed. Cir. 1993); In re Longi, 759 F.2d 887, 225 USPQ 645 (Fed. Cir. 1985); In re Van Ornum, 686 F.2d 937, 214 USPQ 761 (CCPA 1982); In re Vogel, 422 F.2d 438, 164 USPQ 619 (CCPA 1970); In re Thorington, 418 F.2d 528, 163 USPQ 644 (CCPA 1969).
A timely filed terminal disclaimer in compliance with 37 CFR 1.321(c) or 1.321(d) may be used to overcome an actual or provisional rejection based on nonstatutory double patenting provided the reference application or patent either is shown to be commonly owned with the examined application, or claims an invention made as a result of activities undertaken within the scope of a joint research agreement. See MPEP § 717.02 for applications subject to examination under the first inventor to file provisions of the AIA as explained in MPEP § 2159. See MPEP § 2146 et seq. for applications not subject to examination under the first inventor to file provisions of the AIA . A terminal disclaimer must be signed in compliance with 37 CFR 1.321(b).
The filing of a terminal disclaimer by itself is not a complete reply to a nonstatutory double patenting (NSDP) rejection. A complete reply requires that the terminal disclaimer be accompanied by a reply requesting reconsideration of the prior Office action. Even where the NSDP rejection is provisional the reply must be complete. See MPEP § 804, subsection I.B.1. For a reply to a non-final Office action, see 37 CFR 1.111(a). For a reply to final Office action, see 37 CFR 1.113(c). A request for reconsideration while not provided for in 37 CFR 1.113(c) may be filed after final for consideration. See MPEP §§ 706.07(e) and 714.13.
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Claims 1-3, 6, 9-11, 44-51, and 53 are rejected on the ground of nonstatutory double patenting as being unpatentable over claims 1-21 of U.S. Patent No. 10,662,440 B2 in view of Qiao et al. (J. Virol. 76(24):13015-13025, 2002) and Wilson et al. (US 2013/0023033 A1).
The instant claims differ from the claims of U.S. Patent No. 10,662,440 B2 in that they additionally recite: (a) an intron prevents expression of the engineered nuclease in a packaging cell, and (b) a polynucleotide comprising no more than one promoter.
U.S. Patent No. 10,662,440 B2 claims a viral vector comprising a nucleic acid sequence encoding an engineered nuclease comprising a first exon, an intron, and a second exon; a promoter operably linked to the nucleic acid encoding the engineered nuclease; and a vector recognition sequence recognized and cleaved by the nuclease and positioned within the intron.
The teachings of Qiao and Wilson are incorporated herein by reference to the 103 rejection above. It would have been obvious to one of ordinary skill in the art to modify the viral vector of U.S. Patent No. 10,662,440 B2 to include an intron configured to prevent nuclease expression in packaging cells as taught by Qiao and to configure the vector to utilize a single promoter as taught by Wilson. One of ordinary skill in the art would have been motivated to do so in order to reduce toxicity during vector production and conserve viral vector packaging space. One would have had a reasonable expectation of success because Qiao teaches inserting an intron within a coding sequence to disrupt transcription and prevent expression of a gene in packaging cells successfully avoids cytotoxic effects, and Wilson teaches expression of multiple components from a single promoter using polyprotein or self-cleaving peptide systems successfully conserves viral vector packaging space.
Claims 1-3, 6, 9-11, 44-51, and 53 are provisionally rejected on the ground of nonstatutory double patenting as being unpatentable over claims 1, 6-8, 21, 23, 25, 35, 41-44, 46-47, 51, 60, and 99 of copending Application No. 17/998,419.
Although the claims at issue are not identical, they are not patentably distinct from each other because the copending claims recite a recombinant DNA construct comprising a nucleic acid sequence encoding an engineered nuclease, a promoter driving expression of the nuclease, an intron positioned upstream of the nuclease coding sequence, and two or more engineered nuclease construct recognition sequences that are cleaved by the engineered nuclease to inactivate the construct, while the instant claims recite an AAV vector comprising a nuclease coding sequence including an intron, a promoter driving expression of the nuclease, and a vector recognition sequence cleaved by the nuclease to reduce persistence of the vector. The differences between the claims, including recitation of an AAV vector, use of a single recognition sequence instead of multiple recognition sequences, functional characterization of the intron, and inclusion of additional regulatory elements, represent obvious variations of the same self-cleaving nuclease vector architecture and would have been expected to perform the same function of limiting nuclease expression and reducing vector persistence.
This is a provisional nonstatutory double patenting rejection because the patentably indistinct claims have not in fact been patented.
Conclusion
No claims are allowed.
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/COREY LANE BRETZ/Patent Examiner, 1635
/RAM R SHUKLA/ Supervisory Patent Examiner, Art Unit 1635
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