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 .
Claim Status
Claims 3-12, 36, 41, 68, 70 are amended. Claims 13-35, 39-40, 45-67, 71-72, 74-136, 138-149, 152-170 are cancelled.
Claims 1-12, 36-38, 41-44, 68-70, 73, 137, 150-151 are examined on the merits.
Priority
Applicant’s claim for the benefit of a Provisional Application No 63250945 filed 09/30/2021 is acknowledged
Specification
The attempt to incorporate subject matter into this application by reference to PolQ l (as described in WO2020030925), PolQ2, PolQ3, PolQ4, PolQ5 (all as described in WO2021028643), PolQ6, PolQ7 (as described in WO2020243549) (paragraph [245], page 66]), is ineffective because the essential material may only be incorporated by reference to a US PGPUB or US Patent.
The incorporation by reference will not be effective until correction is made to comply with 37 CFR 1.57(c), (d), or (e). If the incorporated material is relied upon to meet any outstanding objection, rejection, or other requirement imposed by the Office, the correction must be made within any time period set by the Office for responding to the objection, rejection, or other requirement for the incorporation to be effective. Compliance will not be held in abeyance with respect to responding to the objection, rejection, or other requirement for the incorporation to be effective. In no case may the correction be made later than the close of prosecution as defined in 37 CFR 1.114(b), or abandonment of the application, whichever occurs earlier.
Any correction inserting material by amendment that was previously incorporated by reference must be accompanied by a statement that the material being inserted is the material incorporated by reference and the amendment contains no new matter. 37 CFR 1.57(g).
Claim Objections
Claims 1, 73, 137 and 150 are objected to because of the following informalities: Each claim must start with a capital letter and end with a period, and periods may not be used elsewhere in the claims except for abbreviations See MPEP § 608.01(m).
Appropriate correction is required.
Claim Rejections - 35 USC § 112
The following is a quotation of the first paragraph of 35 U.S.C. 112(a):
(a) IN GENERAL.—The specification shall contain a written description of the invention, and of the manner and process of making and using it, in such full, clear, concise, and exact terms as to enable any person skilled in the art to which it pertains, or with which it is most nearly connected, to make and use the same, and shall set forth the best mode contemplated by the inventor or joint inventor of carrying out the invention.
The following is a quotation of the first paragraph of pre-AIA 35 U.S.C. 112:
The specification shall contain a written description of the invention, and of the manner and process of making and using it, in such full, clear, concise, and exact terms as to enable any person skilled in the art to which it pertains, or with which it is most nearly connected, to make and use the same, and shall set forth the best mode contemplated by the inventor of carrying out his invention.
Claims 1-12, 36-37, 41, 44, 68-70, 73, 137, 150-151 are rejected under 35 U.S.C. 112(a) or 35 U.S.C. 112 (pre-AIA ), first paragraph, as failing to comply with the written description requirement. The claim(s) contains subject matter which was not described in the specification in such a way as to reasonably convey to one skilled in the relevant art that the inventor or a joint inventor, or for applications subject to pre-AIA 35 U.S.C. 112, the inventor(s), at the time the application was filed, had possession of the claimed invention.
Claim 1 requires the provision of a genus of “an inhibitor” capable of inhibiting the microhomology-mediated end joining (MMEJ) pathway. Thus, the claim encompasses the provision of a genus of “inhibitors” that must function to reduce the microhomology-mediated end joining (MMEJ) pathway. The limitation “inhibitor” encompasses an exceedingly broad genus of compounds capable of inhibiting the MMEJ pathway. Under broadest reasonable interpretation, the term “inhibitor” includes but not limited to, small molecules, inhibitory RNAs, antibodies, peptides, gene-editing tools, capable of inhibiting any step or target within the MMEJ pathway, such as PARP1, PolQ/Pol θ, ligase III, etc. The specification discloses only specific MMEJ inhibitors, such as PolQ_1-7 and ART558, it fails to provide an adequate written description for the broad genus of all MMEJ inhibitors.
Claim 2 requires the provision of a genus of “an inhibitor” capable of inhibiting the non-homologous end joining (NHEJ) pathway. Thus, the claim encompasses the provision of a genus of “inhibitors” that must function to reduce the NHEJ pathway. The limitation “inhibitor” encompasses an exceedingly broad genus of compounds capable of inhibiting the NHEJ pathway. Under broadest reasonable interpretation, the term “inhibitor” includes but not limited to, small molecules, inhibitory RNAs, antibodies, peptides, gene-editing tools, capable of inhibiting any step or target within the NHEJ pathway, such as DNA-PK. The specification discloses only specific DNAPK inhibitors, such as AZD7648 and TLR1, TLR2 and M9831NX-984, it fails to provide an adequate written description for the broad genus of all NHEJ inhibitors.
Claim 36 requires the provision of a genus of “inhibitor” of PolQ. The limitation “inhibitor” encompasses an exceedingly broad genus of compounds capable of inhibiting the MMEJ pathway. Under broadest reasonable interpretation, the term “inhibitor” includes but not limited to, small molecules, inhibitory RNAs, antibodies, peptides, gene-editing tools, capable of inhibiting any step or target within the MMEJ pathway, such as PARP1, PolQ/Pol θ, ligase III, etc. The specification discloses only specific MMEJ inhibitors, such as PolQ_1-7 and ART558, it fails to provide an adequate written description for the broad genus of all MMEJ inhibitors.
Claim 37 requires the provision of a genus of “inhibitor” of PolQ. The limitation “inhibitor” encompasses an exceedingly broad genus of compounds capable of inhibiting the MMEJ pathway. Under broadest reasonable interpretation, the term “inhibitor” includes but not limited to, small molecules, inhibitory RNAs, antibodies, peptides, gene-editing tools, capable of inhibiting any step or target within the MMEJ pathway, such as PARP1, PolQ/Pol θ, ligase III, etc. The specification does not disclose the identity of the inhibitors PolQ_1, PolQ_2,PolQ_3, PolQ_4, PolQ_5, PolQ_6, PolQ_7, it fails to provide an adequate written description for the broad genus of PolQ inhibitors.
Claim 38 requires the provision of a genus of “inhibitor” of PolQ. The limitation “inhibitor” encompasses an exceedingly broad genus of compounds capable of inhibiting the MMEJ pathway. The specification does not disclose the sequence of the peptide inhibitor, it fails to provide an adequate written description for the broad genus of all PolQ peptide inhibitors.
Claim 41 requires the provision of a genus of “an inhibitor” capable of inhibiting the non-homologous end joining (NHEJ) pathway. Thus, the claim encompasses the provision of a genus of “inhibitors” that must function to reduce the NHEJ pathway. The limitation “inhibitor” encompasses an exceedingly broad genus of compounds capable of inhibiting the NHEJ pathway. Under broadest reasonable interpretation, the term “inhibitor” includes but not limited to, small molecules, inhibitory RNAs, antibodies, peptides, gene-editing tools, capable of inhibiting any step or target within the NHEJ pathway, such as DNA-PK. The specification discloses only specific DNAPK inhibitors, such as AZD7648 and TLR1, TLR2 and M9831NX-984, it fails to provide an adequate written description for the broad genus of all NHEJ inhibitors.
Claim 44 requires the provision of a genus of “an inhibitor” capable of inhibiting the non-homologous end joining (NHEJ) pathway. Thus, the claim encompasses the provision of a genus of “inhibitors” that must function to reduce the NHEJ pathway. The specification does not disclose the sequence of the peptide inhibitor, it fails to provide an adequate written description for the broad genus of all DNAPK peptide inhibitors.
Claim 73 requires the provision of a genus of “an inhibitor” capable of inhibiting the microhomology-mediated end joining (MMEJ) pathway. Thus, the claim encompasses the provision of a genus of “inhibitors” that must function to reduce the microhomology-mediated end joining (MMEJ) pathway. The limitation “inhibitor” encompasses an exceedingly broad genus of compounds capable of inhibiting the MMEJ pathway. Under broadest reasonable interpretation, the term “inhibitor” includes but not limited to, small molecules, inhibitory RNAs, antibodies, peptides, gene-editing tools, capable of inhibiting any step or target within the MMEJ pathway, such as PARP1, PolQ/Pol θ, ligase III, etc. The specification discloses only specific MMEJ inhibitors, such as PolQ_1-7 and ART558, it fails to provide an adequate written description for the broad genus of all MMEJ inhibitors.
Claim 137 requires the provision of a genus of “an inhibitor” capable of inhibiting the microhomology-mediated end joining (MMEJ) pathway. Thus, the claim encompasses the provision of a genus of “inhibitors” that must function to reduce the microhomology-mediated end joining (MMEJ) pathway. The limitation “inhibitor” encompasses an exceedingly broad genus of compounds capable of inhibiting the MMEJ pathway. Under broadest reasonable interpretation, the term “inhibitor” includes but not limited to, small molecules, inhibitory RNAs, antibodies, peptides, gene-editing tools, capable of inhibiting any step or target within the MMEJ pathway, such as PARP1, PolQ/Pol θ, ligase III, etc. The specification discloses only specific MMEJ inhibitors, such as PolQ_1-7 and ART558, it fails to provide an adequate written description for the broad genus of all MMEJ inhibitors.
Claim 150 requires the provision of a genus of “an inhibitor” capable of inhibiting the microhomology-mediated end joining (MMEJ) pathway. Thus, the claim encompasses the provision of a genus of “inhibitors” that must function to reduce the microhomology-mediated end joining (MMEJ) pathway. The limitation “inhibitor” encompasses an exceedingly broad genus of compounds capable of inhibiting the MMEJ pathway. Under broadest reasonable interpretation, the term “inhibitor” includes but not limited to, small molecules, inhibitory RNAs, antibodies, peptides, gene-editing tools, capable of inhibiting any step or target within the MMEJ pathway, such as PARP1, PolQ/Pol θ, ligase III, etc. The specification discloses only specific MMEJ inhibitors, such as PolQ_1-7 and ART558, it fails to provide an adequate written description for the broad genus of all MMEJ inhibitors.
Claim 151 requires the provision of a genus of “an inhibitor” capable of inhibiting the non-homologous end joining (NHEJ) pathway. Thus, the claim encompasses the provision of a genus of “inhibitors” that must function to reduce the NHEJ pathway. The limitation “inhibitor” encompasses an exceedingly broad genus of compounds capable of inhibiting the NHEJ pathway. Under broadest reasonable interpretation, the term “inhibitor” includes but not limited to, small molecules, inhibitory RNAs, antibodies, peptides, gene-editing tools, capable of inhibiting any step or target within the NHEJ pathway, such as DNA-PK. The specification discloses only specific DNAPK inhibitors, such as AZD7648 and TLR1, TLR2 and M9831NX-984, it fails to provide an adequate written description for the broad genus of all NHEJ inhibitors.
To provide adequate written description and evidence of possession of a claimed genus, the specification must provide sufficient distinguishing identifying characteristics of the genus. The factors to be considered include disclosure of a complete or partial structure, physical and/or chemical properties, functional characteristics, structure/function correlation, and any combination thereof.
The specification envisions methods of increasing the efficiency of CRISPR/Cas-mediated gene insertion. In some embodiments, the method comprises inserting a polynucleotide of interest into the genome of a eukaryotic cell, the method comprising (a) adding an inhibitor of the MMEJ pathway to a composition comprising the eukaryotic cell, (b) adding a Cas effector protein to the composition, and ( c) adding the polynucleotide of interest to the composition, wherein the polynucleotide of interest is inserted into the genome of the eukaryotic cell by homology directed repair (HDR) or single-stranded template repair (SSTR) (e.g., paragraph [006]). The specification envisions the method further comprises adding an inhibitor of the non-homologous end-joining (NHEJ) pathway (e.g., paragraph [007]). The specification envisions the inhibitor of the MMEJ pathway is an inhibitor of POL Q/DNA polymerase θ (e.g., paragraph [020]). The specifications envisions the inhibitor of the NHEJ pathway is an inhibitor of DNA dependent protein kinase (DNA-PK). In some embodiments, the inhibitor of DNA-PK is M3814, M9831NX984, Nu7441, KU0060648, AZD7648, or combinations thereof. In some embodiments, the inhibitor of DNA-PK is AZD7648. In some embodiments, the inhibitor of DNA-PK is a peptide (e.g., paragraph [022]). The specification envisions inhibitor of the MMEJ pathway is any compound, molecule, or entity that inhibits, antagonizes, blocks, or decreases the activity and/or level of any component of the MMEJ pathway. The MMEJ inhibitor can be an antibody or antigen-binding fragment thereof, a peptide, soluble protein, siRNA, antisense oligonucleotide, aptamer, or small-molecule compound that inhibits, antagonizes, blocks, or decreases the activity and/or level of any component of the MMEJ pathway. In some embodiments, the MMEJ inhibitor inhibits, antagonizes, blocks, or decreases the activity and/or level of FENl (Flap endonuclease 1), DNA ligase III, MREII, NBSl (Nibrin, NBN), XRCCl (X-ray repair cross-complementing protein 1), PARPl (Poly [ADP ribose] polymerase 1), or PolQ (DNA polymerase θ). In some embodiments, the inhibitor of the MMEJ pathway is novobiocin. In some embodiments, the inhibitor of the MMEJ pathway is a PolQ inhibitor. In some embodiments, the PolQ inhibitor is ART558 (e.g., paragraph [244]). The specification envisions The NHEJ inhibitor can be an antibody or antigen-binding fragment thereof, a peptide, soluble protein, siRNA, antisense oligonucleotide, aptamer, or small-molecule compound that inhibits, antagonizes, blocks, or decreases the activity and/or level of any component of the NHEJ pathway. In some embodiments, the NHEJ pathway inhibits, antagonizes, blocks, or decreases the activity and/or level of Ku70, Ku80, DNA Ligase IV, XLF (non-homologous end joining factor 1; XRCC4-like factor), or DNA-dependent protein kinase (DNA-PK). In some
embodiments, the inhibitor of DNA-PK is M3814, M9831NX984, Nu7441, KU0060648, AZD7648, Nu5455, vanillin, wortmannin, or combinations thereof. In some embodiments, the inhibitor of DNA-PK is AZD7648 (e.g., paragraph [252]).
The examples described in the specification does disclose the inhibition of MMEJ pathway with PolQ inhibitors, such as (PolQ 1-7) and ART558 (small molecules inhibitors). The specification discloses NHEJ inhibition with DNAPK inhibitors, such as TLR1, DNAPK inhibitor TLR2, DNAPK inhibitor M9831NX-984, DNAPK inhibitor AZD7648. The specification only provides data for small molecules as an inhibitors, and is not representative of a broad inhibitors allowed by the claims. Furthermore, the examples describe in the specification does not meet the limitation of the rejected claim “an inhibitor”. There is insufficient guidance provided indicating any type of other agents capable of inhibiting MMEJ and NHEJ pathways.
The state of the art with respect to using “an inhibitor” for of MMEJ and NHEJ pathways in CRISPR-Cas mediated targeting is underdeveloped and unpredictable. Sfeir et al. (WO 2017/062754 A1) teaches agent capable of inhibiting POLQ expression comprises a polynucleotide directed to a polynucleotide in the cell that encodes POLQ (a POLQ targeting polynucleotide). The POLQ targeting polynucleotide is selected from the group consisting of an antisense oligonucleotide, an siRNA, an shRNA, a polynucleotide encoding an shRNA, or a ribozyme, and combinations thereof (e.g., paragraph [0006]). Liu et al (US 2017/0254799 A1) teaches the inhibiting effect of DNA-PKcs siRNA on NHEJ by using a CRISPR/Cas9 technology for targeting HPRT gene (e.g., paragraphs [0044]-[0045]).
Thus, the prior art does not overcome the deficiency of the specification with regard to the description of the genus of inhibitors. The teachings are consistent with the prior art demonstrating the underdeveloped and unpredictable of the nature of the invention.
The claims encompasses significantly more than what is disclosed in the specification and does not satisfy the written description requirement under 35 U.S.C 112(a).
Therefore, the skilled artisan would have reasonably concluded applicants were not in possession of the claimed invention for claims 1-12, 36-37, 41, 44, 68-70, 73, 137, 150-151.
Claim 37 is rejected under 35 U.S.C. 112(a) or pre-AIA 35 U.S.C. 112, first paragraph, as based on a disclosure which is not enabling. The disclosure does not enable one of ordinary skill in the art to practice the invention without the specific structures/identities of the claimed PolQ inhibitors (Pol_1 to Pol_7), which is/are critical or essential to the practice of the invention but not included in the claim(s). See In re Mayhew, 527 F.2d 1229, 188 USPQ 356 (CCPA 1976).
The following is a quotation of 35 U.S.C. 112(b):
(b) CONCLUSION.—The specification shall conclude with one or more claims particularly pointing out and distinctly claiming the subject matter which the inventor or a joint inventor regards as the invention.
The following is a quotation of 35 U.S.C. 112 (pre-AIA ), second paragraph:
The specification shall conclude with one or more claims particularly pointing out and distinctly claiming the subject matter which the applicant regards as his invention.
Claims 5-6 are rejected under 35 U.S.C. 112(b) or 35 U.S.C. 112 (pre-AIA ), second paragraph, as being indefinite for failing to particularly point out and distinctly claim the subject matter which the inventor or a joint inventor (or for applications subject to pre-AIA 35 U.S.C. 112, the applicant), regards as the invention.
Claims 5-6: The claim refers to “the Cas polynucleotide”, which lacks of antecedent basis, because its specific identity has not been previously introduced in the dependent claim 3 or in the independent claim 1. Claim 1 introduces a protein rather than a nucleic acid/polynucleotide, there is no prior explicit recitation or introduction of a “Cas polynucleotide” in claim 1 or dependent claim 3 to provide an antecedent basis for “the Cas polynucleotide”. It would be remedial to amend step b) of claim 1 to recite adding “a Cas polynucleotide encoding a Cas effector protein” or amending claims 5 and 6 to recite “a polynucleotide encoding the Cas effector protein of step (b).
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 1-12, 36, 41-42, 73, 137, 150-151 are rejected under 35 U.S.C. 102(a)(1) as being anticipated by Capurso et al. (“Capurso”, WO 2017/147056 A1).
Regarding claims 1-2, Capurso teaches that the methods are performed in a cell, such as a eukaryotic cell (e.g., paragraph 0023). Capurso teaches the method comprising: (I) contacting a selected target nucleic acid comprising a region to be modified with (a) a first agent that suppresses alternative end-joining (alt-J)/ microhomology mediated end-joining (MMEJ), and a second agent that suppresses nonhomologous end-joining (NHEJ), thereby favoring homology directed repair (HDR), and (b) a DNA binding molecule that targets the selected target nucleic acid; (2) producing one or more double-strand breaks in the targeted region using a programmable endonuclease; and (3) inserting at least a portion of a donor polynucleotide into said target nucleic acid at the double-strand break by an homology directed repair (HDR) DNA repair pathway, thereby modulating the DNA repair outcome (e.g., paragraph 0019). Capurso teaches that the site-directed nuclease can be a catalytically active Cas protein that is complexed to a guide polynucleotide. In certain embodiments, the Cas protein is a Cas9 protein, such as a Cas9 protein from Streptococcus pyogenes or an orthologous Cas9 protein (e.g., paragraph 0014).
Regarding claim 3, Capurso teaches that cells from an organism may be engineered, ex vivo, by (i) introduction of vectors comprising expression cassettes expressing the various components, (ii) direct introduction of sgRNA and/or donor polynucleotides and Cas9 proteins, or (iii) introduction of combinations of these components (e.g., paragraph [00157]).
Regarding claim 4, Capurso teaches that the Cas proteins can be delivered using a construct encoding the protein, including without limitation, naked DNA, plasmid DNA, a viral vector and mRNA for Cas expression (e.g., paragraph 0068).
Regarding claim 5, Capurso teaches that cells from an organism may be engineered, ex vivo, by (i) introduction of vectors comprising expression cassettes expressing the various components, (ii) direct introduction of sgRNA and/or donor polynucleotides and Cas9 proteins, or (iii) introduction of combinations of these components. The engineered cells are provided to an organism (e.g., patient) to be treated (e.g., paragraph [00157]).
Regarding claims 6-8, Capurso teaches that cells from an organism may be engineered, ex vivo, by (i) introduction of vectors comprising expression cassettes expressing the various components, (ii) direct introduction of sgRNA and/or donor polynucleotides and Cas9 proteins, or (iii) introduction of combinations of these components. The engineered cells are provided to an organism (e.g., patient) to be treated (e.g., paragraph [00157]). Capurso teaches that the terms "nucleic acid," "nucleotide sequence," "oligonucleotide," and "polynucleotide" are interchangeable. All refer to a polymeric form of nucleotides. The nucleotides may be deoxyribonucleotides (DNA) or ribonucleotides (RNA), or analogs thereof (e.g., paragraph [0080]).
Regarding claim 9, Capurso teaches that cells from an organism may be engineered, ex vivo, by (i) introduction of vectors comprising expression cassettes expressing the various components, (ii) direct introduction of sgRNA and/or donor polynucleotides and Cas9 proteins, or (iii) introduction of combinations of these components. The engineered cells are provided to an organism (e.g., patient) to be treated (e.g., paragraph [00157]). Capurso teaches that the terms "nucleic acid," "nucleotide sequence," "oligonucleotide," and "polynucleotide" are interchangeable. All refer to a polymeric form of nucleotides. The nucleotides may be deoxyribonucleotides (DNA) or ribonucleotides (RNA), or analogs thereof (e.g., paragraph [0080]).
Regarding claims 10-12, Capurso teaches that Cas proteins can be delivered as naked DNA, plasmid DNA or mRNA (e.g., paragraph 0068).
Regarding claim 36, Capurso teaches that inhibiters of PolQ can be used to suppress MMEJ (e.g., paragraph 00112).
Regarding claims 41-42, Capurso teaches suppression of the NHEJ key enzymes Ku70, Ku80, or DNA Ligase IV inhibit DNA-PK and can be used in the present methods to modulate DNA repair outcomes by inhibiting NHEJ. Such inhibitors of DNAPK include NU7441 (e.g., paragraph 00111).
Claim 73, Capurso teaches that the methods are performed in a cell, such as a eukaryotic cell (e.g., paragraph 0023). Capurso teaches the method comprising: (I) contacting a selected target nucleic acid comprising a region to be modified with (a) a first agent that suppresses alternative end-joining (alt-J)/ microhomology mediated end-joining (MMEJ), and a second agent that suppresses nonhomologous end-joining (NHEJ), thereby favoring homology directed repair (HDR), and (b) a DNA binding molecule that targets the selected target nucleic acid; (2) producing one or more double-strand breaks in the targeted region using a programmable endonuclease; and (3) inserting at least a portion of a donor polynucleotide into said target nucleic acid at the double-strand break by an homology directed repair (HDR) DNA repair pathway, thereby modulating the DNA repair outcome (e.g., paragraph 0019). Capurso teaches the cell constitutively expresses a Cas endonuclease, such as Cas9, Cpfl, or the like, the Cas endonuclease will then be recruited to the target site to cleave the DNA (e.g., paragraph [00124]).
Regarding claim 137, Capurso teaches a method of modulating DNA repair outcomes comprising: (a) an agent that suppresses alternative end-joining (alt-EJ)/microhomology mediated end-joining (MMEJ), and (b) a
DNA binding molecule that targets the selected target nucleic acid; and (2) producing one or more double-strand breaks in the targeted region using a programmable endonuclease (e.g., paragraph 0017). Capurso teaches methods of introducing polynucleotides (e.g., an expression vector) into host cells are known in the art and are typically selected based on the kind of host cell. Such methods include, transfection (e.g., paragraph [00155]). Capurso teaches that cells from an organism may be engineered, ex vivo, by (i) introduction of vectors comprising expression cassettes expressing the various components, (ii) direct introduction of sgRNA and/or donor polynucleotides and Cas9 proteins, or (iii) introduction of combinations of these components (e.g., paragraph [00157]).
Regarding claim 150, Capurso teaches a composition comprising (i) DNA binding molecule that targets the selected target nucleic acid; and producing one or more double-strand breaks in the targeted region using a programmable endonuclease (Cas 9) and (ii) agent that suppresses alternative end-joining (alt-J)/ microhomology mediated end-joining (MMEJ) (e.g., paragraph [0017]).
Regarding claim 151, Capurso teaches promoting HDR activity with an agent that suppresses NHEJ (e.g., paragraph 0022).
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.
Claims 37-38 are rejected under 35 U.S.C. 103 as being unpatentable over Capurso et al. (“Capurso”, WO 2017/147056 A1) as applied to claims 1-12, 36, 41-42, 73, 137, 150-151 above, and further in view of D’Andrea et al. (“D’Andrea”, WO 2017070198 A1).
The teachings of Capurso et al. are described above and applied as before.
Capurso does not teach inhibitor of PolQ is PolQ_1, PolQ_2,PolQ_3, PolQ_4, PolQ_5, PolQ_6, PolQ_7, as required by the instant claims. Sfeir does not teach the inhibitor of PolQ is a peptide, as required by the instant claims. However, this is cured by D’Andrea.
D’Andrea teaches method for treating HR-deficient cancer by administering a polymerase Q (PolQ) inhibitor (e.g., abstract).
D’Andrea teaches POLQ inhibitors include any agent that reduces, slows, halts, and/or prevents POLQ activity, including a small molecule, antibody or antibody fragments, peptide or antisense compound, siRNA and shRNA, and DNA and RNA aptamers (e.g., line 22, page 17). D’Andrea teaches siRNA-mediated knockdown, the following target sequences were used: POLQ (POLQ_1, POLQ_6) (e.g., line 18, page 41).
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 substitute the PolQ inhibitor (small molecule) taught by Capurso with the peptide inhibitor of PolQ taught by D’Andrea. Thus, one would have substitute the PolQ inhibitor (small molecule) disclosed by Capurso with a peptide inhibitor of PolQ in order to obtain the predictable result of inhibiting PolQ to enhance the CRISPR activity for use in chromosome editing as taught by Capurso.
Claim 43 is rejected under 35 U.S.C. 103 as being unpatentable over Capurso et al. (“Capurso”, WO 2017/147056 A1) as applied to claims 1-12, 36, 41-42, 73, 137, 150-151 above, and further in view of Stavridi et al. (“Stavridi”, Essays in Biochemistry, 2020).
The teachings of Capurso et al. are described above and applied as before.
Capurso does not teach inhibitor of DNA-PK AZD7648, as required by the instant claims. However, this is cured by Stavridi.
Stavridi teaches that NHEJ could be manipulated in the area of cancer therapy in an effort to combat resistance. Inhibiting NHEJ in conjunction with radio- or chemo-therapies could reduce the tumour cells’ ability to repair therapy-induced double-strand breaks (e.g., paragraph 3rd, page 793). Stavridi teaches the DNA-PK inhibitor AZD7648 (e.g., paragraph 2nd, page 795; Table 1). Stavridi highlighted the potential of treating cells with SCR7 to increase the efficiency of CRISPR–Cas9-mediated gene editing by inhibiting NHEJ and favoring homologous recombination (e.g., paragraph 3rd, page 796).
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 substitute the DNA-PK NU7441 inhibitor with AZD7648- inhibitor of DNA-PK, such as the NHEJ pathway is inhibited, because 1) Capurso discloses the NU7441 DNA-PK inhibitor, 2) Stavridi discloses that AZD7648 is a DNA-PK inhibitor and to increase the efficiency of CRISPR–Cas9-mediated gene editing by inhibiting NHEJ and favoring homologous recombination. Thus, one would have substitute the DNA-PK NU7441 inhibitor disclosed by Capurso with the AZD7648 inhibitor of DNA-PK in order to obtain the predictable result of increasing the efficiency of CRISPR–Cas9-mediated gene editing by inhibiting NHEJ and favoring homologous recombination.
Claim 44 is rejected under 35 U.S.C. 103 as being unpatentable over Capurso et al. (“Capurso”, WO 2017/147056 A1) as applied to claims 1-12, 36, 41-42, 73, 137, 150-151 above, and further in view of D’Souza et al. (“D’Souza”, WO 2022/133246 A1, priority date 17 December 2020).
The teachings of Capurso et al. are described above and applied as before.
Capurso does not teach DNA-PK inhibitor is a peptide, as required by the instant claims. However, this is cured by D’Souza.
D’Souza teaches methods of increasing repair of a DNA double stranded break (DSB) in an HEB gene by the homology-directed repair (HDR) pathway (e.g., abstract). D’Souza teaches a system for correcting an E6V mutation in human betaglobin (HBB) in a cell or population of cells, the system comprising: (a) a Cas9 endonuclease, an mRNA encoding the Cas9 endonuclease, or a recombinant expression vector comprising a nucleotide sequence encoding the Cas9 endonuclease; (b) a single guide RNA (sgRNA) comprising a spacer sequence corresponding to a target
sequence adjacent a PAM, the target sequence comprising a target site within intron l of HBB; and (c) a recombinant vector comprising a nucleic acid for correcting the E6V mutation (e.g., paragraph 3rd, page 4). D’Souza teaches a DNA-PK inhibitor of the disclosure is a polypeptide (e.g., paragraph 3rd, page 106).
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 substitute the DNA-PK NU7441 inhibitor with a polypeptide inhibitor of DNA-PK, such as the NHEJ pathway is inhibited, because 1) Capurso discloses the NU7441 DNA-PK inhibitor, 2) D’Souza discloses DNA-PK inhibitor of the disclosure is a polypeptide. Thus, one would have substitute the DNA-PK NU7441 inhibitor disclosed by Capurso with a peptide inhibitor of DNA-PK in order to obtain the predictable result of increasing the efficiency of CRISPR–Cas9-mediated gene editing by inhibiting NHEJ and favoring homologous recombination.
Claims 68-70 are rejected under 35 U.S.C. 103 as being unpatentable over Capurso et al. (“Capurso”, WO 2017/147056 A1) as applied to claims 1-12, 36, 41-42, 73, 150-151 above, and further in view of Ran et al. (“Ran”, WO 2015/089473 A1).
The teachings of Capurso et al. are described above and applied as before.
Capurso does not teach the lymphocyte comprising a chimeric antigen receptor, as required by the instant claim. Capurso does not teach the eukaryotic cell is a pluripotent stem cell, as required by the instant claim. However, this is cured by Ran.
Ran teaches methods of directing CRISPR complex formation in eukaryotic cells and methods for utilizing the CRISPR-Cas system. In particular the present invention comprehends optimized functional CRISPR-Cas enzyme systems (e.g., abstract). Ran teaches that enhancing NHEJ or HR efficiency is also helpful for delivery. It is preferred that HR efficiency is increased by transiently inhibiting NHEJ machineries such as Ku70 and Ku86 (e.g., paragraph 0278). Ran teaches methods may preferably be ex vivo, for example, creating a modified cell line. Another example is Chimeric Antigen Receptor (CAR) T cells which can be modified ex vivo and re-infused into a patient to target cancers (e.g., paragraph 00199). Ran teaches eukaryotic cell, for instance a mammalian cell and preferably a mouse or human cell, including stem cell lines (e.g., paragraph 00197).
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 generate Chimeric Antigen Receptor T cells, because 1) Capurso discloses increasing homozygous targeting of donor template mediated by CRISPR in presence of PolQ or DNA-PK inhibitors, 2) Ran discloses methods for utilizing the CRISPR-Cas system and that it is preferred that homologous recombination efficiency is increased by transiently inhibiting NHEJ machineries such as Ku70 and Ku86, and Chimeric Antigen Receptor (CAR) T cells which can be modified ex vivo and re-infused into a patient to target cancers. Thus, one would have generated Chimeric Antigen Receptor T cells disclosed by Ran using the CRISPR-Cas9 system in presence of PolQ inhibitor or DNA-PK inhibitor, in order to obtain the predictable result of a chimeric antigen receptor T cell ex-vivo to be re-infused to a cancer patient.
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.
The USPTO Internet website contains terminal disclaimer forms which may be used. Please visit www.uspto.gov/patent/patents-forms. The actual filing date of the application in which the form is filed determines what form (e.g., PTO/SB/25, PTO/SB/26, PTO/AIA /25, or PTO/AIA /26) should be used. A web-based eTerminal Disclaimer may be filled out completely online using web-screens. An eTerminal Disclaimer that meets all requirements is auto-processed and approved immediately upon submission. For more information about eTerminal Disclaimers, refer to www.uspto.gov/patents/apply/applying-online/eterminal-disclaimer.
Claims 1-12, 36-38, 41-44, 68-70, 73, 137, 150-151 are provisionally rejected on the ground of nonstatutory double patenting as being unpatentable over claims 1-12, 36, 41-44, 68-70, 73, 137, 150-151, of copending Application No. 19469699 (hereinafter ‘699 application) in view of D’Andrea et al. (“D’Andrea”, WO 2017070198 A1).
Although the claims at issue are not identical, they are not patentably distinct from each other. Claim 1 of ‘699 is drawn to “A method of inserting a polynucleotide of interest into a genome of a eukaryotic cell, the method comprising: a. adding an inhibitor of the microhomology-mediated end joining (MMEJ) pathway to a composition comprising the eukaryotic cell, b. adding a Cas effector protein to the composition, c. adding the polynucleotide of interest to the composition, wherein the polynucleotide of interest is inserted into the genome by homology directed repair (HDR) or single-stranded template repair (SSTR), wherein the inhibitor of the MMEJ pathway is an inhibitor of PolQ, selected from a compound of formula (I). Accordingly claim 1of the ‘699 anticipates instant claim 1.
Claim 2 of ‘699 is drawn to “The method of claim 1, wherein (a) further comprises adding an inhibitor of the non- homologous end joining (NHEJ) pathway. Accordingly claim 2 of the ‘699 anticipates instant claim 2.
Claim 3 of ‘699 is drawn to “The method of claims 1 or 2, further comprising: (d) adding a polynucleotide comprising: an RNA guide sequence; a Cas-binding region; a DNA template sequence, or combinations thereof to the composition. Accordingly claim 3 of the ‘699 anticipates instant claim 3.
Claim 4 of ‘699 is drawn to “The method of any of claims 1-3, wherein the Cas effector protein is added in (b) by adding a Cas polynucleotide encoding the Cas effector protein. Accordingly claim 4 of the ‘699 anticipates instant claim 4.
Claim 5 of ‘699 is drawn to “The method of any of claims 1-4, wherein one or more of (i) the polynucleotide of interest, (ii) the polynucleotide of (d), or (iii) the Cas polynucleotide are encoded on a vector. Accordingly claim 5 of the ‘699 anticipates instant claim 5.
Claim 6 of ‘699 is drawn to “The method of any of claims 1-4, wherein (i) the polynucleotide of interest, (ii) the polynucleotide of step (d), and (iii) the Cas polynucleotide are encoded on a single vector. Accordingly claim 6 of the ‘699 anticipates instant claim 6.
Claim 7 of ‘699 is drawn to “The method of any of claims 1-6, wherein the polynucleotide of interest is added as DNA. Accordingly claim 7 of the ‘699 anticipates instant claim 7.
Claim 8 of ‘699 is drawn to “The method of any of claims 1-6, wherein the polynucleotide of step (d) is added as DNA. Accordingly claim 8 of the ‘699 anticipates instant claim 8.
Claim 9 of ‘699 is drawn to “The method any of claims 1-6, wherein the polynucleotide of step (d) is added as RNA. Accordingly claim 9 of the ‘699 anticipates instant claim 9.
Claim 10 of ‘699 is drawn to “The method of any of claims 1-6, wherein the Cas effector polynucleotide is added as DNA. Accordingly claim 10 of the ‘699 anticipates instant claim 10.
Claim 11 of ‘699 is drawn to “The method any of claims 1-6, wherein the Cas polynucleotide is added as RNA. Accordingly claim 11 of the ‘699 anticipates instant claim 11.
Claim 12 of ‘699 is drawn to “The method of any of claims 1-6, wherein the Cas polynucleotide is added as mRNA. Accordingly claim 12 of the ‘699 anticipates instant claim 12.
Claim 36 of ‘699 is drawn to “The method of any of claims 1-35, wherein the inhibitor of PolQ is a compound of formula (I). Accordingly claim 36 of the ‘699 anticipates instant claim 36.
Claim 41 of ‘699 is drawn to “The method of any of claims 2-38, wherein the inhibitor of the NHEJ pathway is an inhibitor of DNA-dependent protein kinase (DNA-PK). Accordingly claim 41 of the ‘699 anticipates instant claim 41.
Claim 42 of ‘699 is drawn to “The method of claim 41, wherein the inhibitor of DNA-PK is M3814, M9831/VX984, Nu7441, Nu7026, KU0060648, AZD7648, or combinations thereof. Accordingly claim 42 of the ‘699 anticipates instant claim 42.
Claim 43 of ‘699 is drawn to “The method of claim 42, wherein the inhibitor of DNA-PK is AZD7648. Accordingly claim 43 of the ‘699 anticipates instant claim 43.
Claim 44 of ‘699 is drawn to “The method of claim 41, wherein the inhibitor of DNA-PK is a peptide. Accordingly claim 44 of the ‘699 anticipates instant claim 44.
Claim 68 of ‘699 is drawn to “The method of any of claims 1-67, wherein the eukaryotic cell is a lymphocyte. Accordingly claim 68 of the ‘699 anticipates instant claim 68.
Claim 69 of ‘699 is drawn to “The method of claim 68, wherein the lymphocyte comprises a chimeric antigen receptor (CAR) or a T cell receptor (TCR). Accordingly claim 69 of the ‘699 anticipates instant claim 69.
Claim 70 of ‘699 is drawn to “The method of any of claims 1-67, wherein the eukaryotic cell is a pluripotent stem cell. Accordingly claim 70 of the ‘699 anticipates instant claim 70.
Claim 73 of ‘699 is drawn to “A method of inserting a polynucleotide of interest into a genome of a eukaryotic cell, the method comprising: a. adding an inhibitor of the microhomology-mediated end joining (MMEJ) pathway to a composition comprising the eukaryotic cell, b. adding the polynucleotide of interest to the composition, wherein the genome comprises a genomically integrated Cas polynucleotide, and wherein the polynucleotide of interest is inserted into the genome by homology directed repair (HDR) or single-stranded template repair (SSTR), wherein the inhibitor of the MMEJ pathway is an inhibitor of PolQ, selected from a compound of formula (I). Accordingly claim 73 of the ‘699 anticipates instant claim 73.
Claim 137 of ‘699 is drawn to “A method of inserting a polynucleotide into a genome of a eukaryotic cell, the method comprising: a. adding an inhibitor of the microhomology-mediated end joining (MMEJ) pathway to a composition comprising the eukaryotic cell, b. transfecting the eukaryotic cell with: i. a vector encoding a Cas effector protein, ii. a vector comprising a polynucleotide of interest, iii. a vector comprising a polynucleotide comprising: an RNA guide sequence; a Cas-binding region; a DNA template sequence, or combinations thereof, wherein the vector of (i), (ii) and (iii) can be on the same vector or different vectors, and wherein the polynucleotide of interest is inserted into the genome by homology directed repair (HDR) or single-stranded template repair (SSTR), wherein the inhibitor of the MMEJ pathway is an inhibitor of PolQ, selected from a compound of formula (I). Accordingly claim 137 of the ‘699 anticipates instant claim 137.
Claim 150 of ‘699 is drawn to “A composition comprising: a. a Cas effector protein or a vector encoding a Cas effector protein; and b. an inhibitor of the microhomology-mediated end joining (MMEJ) pathway, wherein the inhibitor of the MMEJ pathway is an inhibitor of PolQ, selected from a compound of formula (I), any stereoisomer thereof, pharmaceutically acceptable salt thereof, or combination thereof. Accordingly claim 150 of the ‘699 anticipates instant claim 150.
Claim 151 of ‘699 is drawn to “The composition of claim 150, further comprising an inhibitor of the non- homologous end joining (NHEJ) pathway. Accordingly claim 151 of the ‘699 anticipates instant claim 151.
‘699 does not teach wherein the inhibitor of PolQ is PolQ_1, PolQ_2,PolQ_3, PolQ_4, PolQ_5, PolQ_6, PolQ_7, as required by the instant claim. ‘699 does not teach the inhibitor of PolQ is a peptide, as required by the instant claim. However, this is cured by D’Andrea.
D’Andrea teaches method for treating HR-deficient cancer by administering a polymerase Q (PolQ) inhibitor (e.g., abstract).
D’Andrea teaches POLQ inhibitors include any agent that reduces, slows, halts, and/or prevents POLQ activity, including a small molecule, antibody or antibody fragments, peptide or antisense compound, siRNA and shRNA, and DNA and RNA aptamers (e.g., line 22, page 17). D’Andrea teaches siRNA-mediated knockdown, the following target sequences were used: POLQ (POLQ_1, POLQ_6) (e.g., line 18, page 41).
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 substitute the PolQ inhibitor with a peptide inhibitor of PolQ, because 1) ‘699 discloses a method of inserting a polynucleotide of interest into a genome of a eukaryotic cell, the method comprising: a. adding an inhibitor of the microhomology-mediated end joining (MMEJ) pathway to a composition comprising the eukaryotic cell, b. adding a Cas effector protein to the composition, c. adding the polynucleotide of interest to the composition, wherein the polynucleotide of interest is inserted into the genome by homology directed repair (HDR) or single-stranded template repair (SSTR), wherein the inhibitor of the MMEJ, 2) D’Andrea discloses POLQ inhibitors include peptide. Thus, one would have substitute the PolQ inhibitor disclosed by ‘699 with a peptide inhibitor of PolQ in order to obtain the predictable result of inhibiting PolQ to enhance the CRISPR activity for homologous recombination use in genome editing.
This is a provisional nonstatutory double patenting rejection.
Conclusion
Any inquiry concerning this communication or earlier communications from the examiner should be directed to JULIO GOMEZ RODRIGUEZ whose telephone number is (571)270-0991. The examiner can normally be reached Monday - Friday 8:00 am - 5:00 pm.
Examiner interviews are available via telephone, in-person, and video conferencing using a USPTO supplied web-based collaboration tool. To schedule an interview, applicant is encouraged to use the USPTO Automated Interview Request (AIR) at http://www.uspto.gov/interviewpractice.
If attempts to reach the examiner by telephone are unsuccessful, the examiner’s supervisor, Jennifer Dunston can be reached at 5712722916. The fax phone number for the organization where this application or proceeding is assigned is 571-273-8300.
Information regarding the status of published or unpublished applications may be obtained from Patent Center. Unpublished application information in Patent Center is available to registered users. To file and manage patent submissions in Patent Center, visit: https://patentcenter.uspto.gov. Visit https://www.uspto.gov/patents/apply/patent-center for more information about Patent Center and https://www.uspto.gov/patents/docx for information about filing in DOCX format. For additional questions, contact the Electronic Business Center (EBC) at 866-217-9197 (toll-free). If you would like assistance from a USPTO Customer Service Representative, call 800-786-9199 (IN USA OR CANADA) or 571-272-1000.
/JULIO WASHINGTON GOMEZ RODRIGUEZ/Examiner, Art Unit 1637
/NEIL P HAMMELL/Supervisory Patent Examiner, Art Unit 1636
Prosecution Insights