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 under 35 U.S.C. 119(e) or under 35 U.S.C. 120, 121, 365(c), or 386(c) is acknowledged.
Status of Claims
Claims 184-204 are pending and under examination.
Claim Objection
Claim 195 should recite "the composition of 184 further comprising a donor template nucleic acid, wherein the donor template comprises a nucleic acid comprising at least a portion of a PTBP 1 gene …" to place the claim in proper form. Appropriate correction is required.
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).
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11,976,277
Claims 184, 186-190, 195 are rejected on the ground of nonstatutory double patenting as being unpatentable over claims 1-23 of U.S. Patent No. 11,976,277 (hereinafter "Fernandes") in view of Roberson (BMC Genomics 20, 528 (2019); hereinafter Roberson, See PTO-892).
Although the claims at issue are not identical, they are not patentably distinct from each other because of the reasons stated below.
Regarding claim 184, 186-188, 190, 195: Claim 1 of Fernandes is directed to a composition comprising a CRISPR nuclease and a CRISPR guide RNA. Claim 7 of Fernandes was directed to a CasX comprising a SEQ ID NO: 196, which is 100% identical to instant SEQ ID NO: 133 (See alignment below). Claim 11 of Fernandes taught that the CRISPR RNA comprises a scaffold sequence. It is noted that claims of Fernandes did not teach or suggest a gRNA comprising a targeting sequence that is complementary sequence to a PTBP1 gene target nucleic acid sequence. However, it would have been obvious for a person of ordinary skill in the art to arrive at a gRNA for CasX using routine experimentation. For example Roberson taught that CasX guide sites are relatively common in all their tested genomes (Roberson, p.4, col. 2, para 2). Roberson also taught a method to arrive at suitable guide sequences for CasX. For example Roberson “performed the annotations on the Washington University Center for High Performance Computing cluster. The motif location output included the location of the hit in the genome (contig, start, end) and the associated sequences.” Roberson “calculated the size of the reference genomes from their FASTA index files, determined the uniqueness of guide RNA sites amongst all editing sites, counted PAM usage, and annotated any overlaps with the exons of known genes. It is worth noting that uniqueness of a guide was determined only among editing sites. Presumably another site that matches the guide exactly, but does not have the PAM site would not be cleaved. A guide that overlaps an exon can likely be used to knockout the gene or knock-in coding variants at the exon.” (See Roberson, p. 2, para 2, as required by claims 186, 190). As such Roberson determined that arriving at a suitable gRNA for CasX is routine and systematic.
One of ordinary skill in the art, given the teachings of Roberson would have readily designed a gRNA complementary to PTBP1 for use with the CasX protein taught by Fernandes, as design of such RNA is routine, predictable and well documented by prior art, as shown by Roberson.
Query 1 QEIKRINKIRRRLVKDSNTKKAGKTGPMKTLLVRVMTPDLRERLENLRKKPENIPQPISN 60
QEIKRINKIRRRLVKDSNTKKAGKTGPMKTLLVRVMTPDLRERLENLRKKPENIPQPISN
Sbjct 1 QEIKRINKIRRRLVKDSNTKKAGKTGPMKTLLVRVMTPDLRERLENLRKKPENIPQPISN 60
Query 61 TSRANLNKLLTDYTEMKKAILHVYWEEFQKDPVGLMSRVAQPASKKIDQNKLKPEMDEKG 120
TSRANLNKLLTDYTEMKKAILHVYWEEFQKDPVGLMSRVAQPASKKIDQNKLKPEMDEKG
Sbjct 61 TSRANLNKLLTDYTEMKKAILHVYWEEFQKDPVGLMSRVAQPASKKIDQNKLKPEMDEKG 120
Query 121 NLTTAGFACSQCGQPLFVYKLEQVSEKGKAYTNYFGRCNVAEHEKLILLAQLKPEKDSDE 180
NLTTAGFACSQCGQPLFVYKLEQVSEKGKAYTNYFGRCNVAEHEKLILLAQLKPEKDSDE
Sbjct 121 NLTTAGFACSQCGQPLFVYKLEQVSEKGKAYTNYFGRCNVAEHEKLILLAQLKPEKDSDE 180
Query 181 AVTYSLGKFGQRALDFYSIHVTKESTHPVKPLAQIAGNRYASGPVGKALSDACMGTIASF 240
AVTYSLGKFGQRALDFYSIHVTKESTHPVKPLAQIAGNRYASGPVGKALSDACMGTIASF
Sbjct 181 AVTYSLGKFGQRALDFYSIHVTKESTHPVKPLAQIAGNRYASGPVGKALSDACMGTIASF 240
Query 241 LSKYQDIIIEHQKVVKGNQKRLESLRELAGKENLEYPSVTLPPQPHTKEGVDAYNEVIAR 300
LSKYQDIIIEHQKVVKGNQKRLESLRELAGKENLEYPSVTLPPQPHTKEGVDAYNEVIAR
Sbjct 241 LSKYQDIIIEHQKVVKGNQKRLESLRELAGKENLEYPSVTLPPQPHTKEGVDAYNEVIAR 300
Query 301 VRMWVNLNLWQKLKLSRDDAKPLLRLKGFPSFPLVERQANEVDWWDMVCNVKKLINEKKE 360
VRMWVNLNLWQKLKLSRDDAKPLLRLKGFPSFPLVERQANEVDWWDMVCNVKKLINEKKE
Sbjct 301 VRMWVNLNLWQKLKLSRDDAKPLLRLKGFPSFPLVERQANEVDWWDMVCNVKKLINEKKE 360
Query 361 DGKVFWQNLAGYKRQEALRPYLSSEEDRKKGKKFARYQLGDLLLHLEKKHGEDWGKVYDE 420
DGKVFWQNLAGYKRQEALRPYLSSEEDRKKGKKFARYQLGDLLLHLEKKHGEDWGKVYDE
Sbjct 361 DGKVFWQNLAGYKRQEALRPYLSSEEDRKKGKKFARYQLGDLLLHLEKKHGEDWGKVYDE 420
Query 421 AWERIDKKVEGLSKHIKLEEERRSEDAQSKAALTDWLRAKASFVIEGLKEADKDEFCRCE 480
AWERIDKKVEGLSKHIKLEEERRSEDAQSKAALTDWLRAKASFVIEGLKEADKDEFCRCE
Sbjct 421 AWERIDKKVEGLSKHIKLEEERRSEDAQSKAALTDWLRAKASFVIEGLKEADKDEFCRCE 480
Query 481 LKLQKWYGDLRGKPFAIEAENSILDISGFSKQYNCAFIWQKDGVKKLNLYLIINYFKGGK 540
LKLQKWYGDLRGKPFAIEAENSILDISGFSKQYNCAFIWQKDGVKKLNLYLIINYFKGGK
Sbjct 481 LKLQKWYGDLRGKPFAIEAENSILDISGFSKQYNCAFIWQKDGVKKLNLYLIINYFKGGK 540
Query 541 LRFKKIKPEAFEANRFYTVINKKSGEIVPMEVNFNFDDPNLIILPLAFGKRQGREFIWND 600
LRFKKIKPEAFEANRFYTVINKKSGEIVPMEVNFNFDDPNLIILPLAFGKRQGREFIWND
Sbjct 541 LRFKKIKPEAFEANRFYTVINKKSGEIVPMEVNFNFDDPNLIILPLAFGKRQGREFIWND 600
Query 601 LLSLETGSLKLANGRVIEKTLYNRRTRQDEPALFVALTFERREVLDSSNIKPMNLIGVDR 660
LLSLETGSLKLANGRVIEKTLYNRRTRQDEPALFVALTFERREVLDSSNIKPMNLIGVDR
Sbjct 601 LLSLETGSLKLANGRVIEKTLYNRRTRQDEPALFVALTFERREVLDSSNIKPMNLIGVDR 660
Query 661 GENIPAVIALTDPEGCPLSRFKDSLGNPTHILRIGESYKEKQRTIQAKKEVEQRRAGGYS 720
GENIPAVIALTDPEGCPLSRFKDSLGNPTHILRIGESYKEKQRTIQAKKEVEQRRAGGYS
Sbjct 661 GENIPAVIALTDPEGCPLSRFKDSLGNPTHILRIGESYKEKQRTIQAKKEVEQRRAGGYS 720
Query 721 RKYASKAKNLADDMVRNTARDLLYYAVTQDAMLIFENLSRGFGRQGKRTFMAERQYTRME 780
RKYASKAKNLADDMVRNTARDLLYYAVTQDAMLIFENLSRGFGRQGKRTFMAERQYTRME
Sbjct 721 RKYASKAKNLADDMVRNTARDLLYYAVTQDAMLIFENLSRGFGRQGKRTFMAERQYTRME 780
Query 781 DWLTAKLAYEGLPSKTYLSKTLAQYTSKTCSNCGFTITSADYDRVLEKLKKTATGWMTTI 840
DWLTAKLAYEGLPSKTYLSKTLAQYTSKTCSNCGFTITSADYDRVLEKLKKTATGWMTTI
Sbjct 781 DWLTAKLAYEGLPSKTYLSKTLAQYTSKTCSNCGFTITSADYDRVLEKLKKTATGWMTTI 840
Query 841 NGKELKVEGQITYYNRYKRQNVVKDLSVELDRLSEESVNNDISSWTKGRSGEALSLLKKR 900
NGKELKVEGQITYYNRYKRQNVVKDLSVELDRLSEESVNNDISSWTKGRSGEALSLLKKR
Sbjct 841 NGKELKVEGQITYYNRYKRQNVVKDLSVELDRLSEESVNNDISSWTKGRSGEALSLLKKR 900
Query 901 FSHRPVQEKFVCLNCGFETHADEQAALNIARSWLFLRSQEYKKYQTNKTTGNTDKRAFVE 960
FSHRPVQEKFVCLNCGFETHADEQAALNIARSWLFLRSQEYKKYQTNKTTGNTDKRAFVE
Sbjct 901 FSHRPVQEKFVCLNCGFETHADEQAALNIARSWLFLRSQEYKKYQTNKTTGNTDKRAFVE 960
Query 961 TWQSFYRKKLKEVWKPAV 978
TWQSFYRKKLKEVWKPAV
Sbjct 961 TWQSFYRKKLKEVWKPAV 978
Regarding claim 189: Roberson taught that the CasX comprises a 4-basepair PAM: TTCN (See Roberson, p.1, col.2, para 2).
Claims 191-192 are rejected on the ground of nonstatutory double patenting as being unpatentable over claims 1-23 of U.S. Patent No. 11,976,277 (hereinafter "Fernandes") in view of Roberson (BMC Genomics (2019); hereinafter Roberson, See PTO-892) and Ousterout et al (Nat Commun. 2015 Feb 18; See PTO-892; hereinafter “Ousterout”).
The teachings of Fernandes in view of Roberson are set forth above. Fernandes in view of Roberson did not teach a second gRNA comprising a scaffold and a targeting sequence as required by the claim. Ousterout taught that multiplex gRNA targeting to use two guide RNAs targeting the same exon or different genes are common practices in CRISPR technologies: “The versatility, efficiency and multiplexing capabilities of the CRISPR/Cas9 system enable a variety of otherwise challenging gene correction strategies. Here, we use the CRISPR/Cas9 system to restore the expression of the dystrophin gene in cells carrying dystrophin mutations that cause Duchenne muscular dystrophy (DMD). We design single or multiplexed sgRNAs to restore the dystrophin reading frame by targeting the mutational hotspot at exons 45–55 and introducing shifts within exons or deleting one or more exons.” (See Ousterout Abstract).
One of ordinary skill in the art, given the teachings of Fernandes in view of Roberson and Ousterout would have readily designed multiple gRNAs for editing same exon complementary to PTBP1 for use with the CasX protein taught by Fernandes, as design of such RNAs is routine, predictable and well documented by prior art, as shown by Roberson and Ousterout.
Claims 185, 195-196 are rejected on the ground of nonstatutory double patenting as being unpatentable over claims 1-23 of U.S. Patent No. 11,976,277 (hereinafter "Fernandes") in view of Roberson (BMC Genomics (2019); hereinafter Roberson, See PTO-892) and WO2019084148A1 (Published May 2, 2019; See PTO-892; hereinafter “Nagy”).
The teachings of Fernandes in view of Roberson are set forth above. Fernandes in view of Roberson did not teach a donor template comprising a scaffold and a targeting sequence as required by the claim. Nagy taught the use of donor template to introduce a nucleic acid into a target site. For example claim 12 of Nagy taught a method of modifying a target site using CasX, a gRNA and a donor template. As such one of ordinary skill in the art would have bene motivated to generate a composition comprising a CasX comprising the claimed sequence and a gRNA targeting PTBP1 and a template in view of the cited prior art. It is also noted that Nagy taught that the CasX nuclease further comprises a nuclear localization signal as required by claim 185.
One of ordinary skill in the art, given the teachings of Fernandes in view of Roberson and Nagy would have readily arrived at a composition comprising a gRNA targeting PTBP1 for use with the CasX protein taught by Fernandes. The person would have been motivated to further modify the composition with a donor template to insert a sequence at the target site for further modifying the target site, as design of such RNAs is routine, predictable and well documented by prior art, as shown by Roberson and Nagy.
U.S. Application No. 18/266,076
Claim 184, 186-190, 195 are provisionally rejected on the ground of nonstatutory double patenting as being unpatentable over claim 176-203 of copending Application No. 18/266,076 (reference application) in view of Roberson (BMC Genomics 20, 528 (2019); hereinafter Roberson, See PTO-892).
Although the claims at issue are not identical, they are not patentably distinct from each other because of the reasons stated below. This is a provisional nonstatutory double patenting rejection because the patentably indistinct claims have not in fact been patented.
Regarding claim 184, 186-188, 190, 195: Claim 1 of reference application is directed to a composition comprising a CRISPR nuclease and a CRISPR guide RNA. Claim 185 of reference application was directed to a CasX comprising a SEQ ID NO: 145, which is 100% identical to instant SEQ ID NO: 133 (See alignment below). Claim 194 of reference application taught that the CRISPR RNA comprises a scaffold sequence. It is noted that claims of reference application did not teach or suggest a gRNA comprising a targeting sequence that is complementary sequence to a PTBP1 gene target nucleic acid sequence. However, it would have been obvious for a person of ordinary skill in the art to arrive at a gRNA for CasX using routine experimentation. For example Roberson taught that CasX guide sites are relatively common in all their tested genomes (Roberson, p.4, col. 2, para 2). Roberson also taught a method to arrive at suitable guide sequences for CasX. For example Roberson “performed the annotations on the Washington University Center for High Performance Computing cluster. The motif location output included the location of the hit in the genome (contig, start, end) and the associated sequences.” Roberson “calculated the size of the reference genomes from their FASTA index files, determined the uniqueness of guide RNA sites amongst all editing sites, counted PAM usage, and annotated any overlaps with the exons of known genes. It is worth noting that uniqueness of a guide was determined only among editing sites. Presumably another site that matches the guide exactly, but does not have the PAM site would not be cleaved. A guide that overlaps an exon can likely be used to knockout the gene or knock-in coding variants at the exon.” (See Roberson, p. 2, para 2, as required by claims 186, 190). As such Roberson determined that arriving at a suitable gRNA for CasX is routine and systematic.
One of ordinary skill in the art, given the teachings of Roberson would have readily designed a gRNA complementary to PTBP1 for use with the CasX protein taught by reference application, as design of such RNA is routine, predictable and well documented by prior art, as shown by Roberson.
Query 1 QEIKRINKIRRRLVKDSNTKKAGKTGPMKTLLVRVMTPDLRERLENLRKKPENIPQPISN 60
QEIKRINKIRRRLVKDSNTKKAGKTGPMKTLLVRVMTPDLRERLENLRKKPENIPQPISN
Sbjct 1 QEIKRINKIRRRLVKDSNTKKAGKTGPMKTLLVRVMTPDLRERLENLRKKPENIPQPISN 60
Query 61 TSRANLNKLLTDYTEMKKAILHVYWEEFQKDPVGLMSRVAQPASKKIDQNKLKPEMDEKG 120
TSRANLNKLLTDYTEMKKAILHVYWEEFQKDPVGLMSRVAQPASKKIDQNKLKPEMDEKG
Sbjct 61 TSRANLNKLLTDYTEMKKAILHVYWEEFQKDPVGLMSRVAQPASKKIDQNKLKPEMDEKG 120
Query 121 NLTTAGFACSQCGQPLFVYKLEQVSEKGKAYTNYFGRCNVAEHEKLILLAQLKPEKDSDE 180
NLTTAGFACSQCGQPLFVYKLEQVSEKGKAYTNYFGRCNVAEHEKLILLAQLKPEKDSDE
Sbjct 121 NLTTAGFACSQCGQPLFVYKLEQVSEKGKAYTNYFGRCNVAEHEKLILLAQLKPEKDSDE 180
Query 181 AVTYSLGKFGQRALDFYSIHVTKESTHPVKPLAQIAGNRYASGPVGKALSDACMGTIASF 240
AVTYSLGKFGQRALDFYSIHVTKESTHPVKPLAQIAGNRYASGPVGKALSDACMGTIASF
Sbjct 181 AVTYSLGKFGQRALDFYSIHVTKESTHPVKPLAQIAGNRYASGPVGKALSDACMGTIASF 240
Query 241 LSKYQDIIIEHQKVVKGNQKRLESLRELAGKENLEYPSVTLPPQPHTKEGVDAYNEVIAR 300
LSKYQDIIIEHQKVVKGNQKRLESLRELAGKENLEYPSVTLPPQPHTKEGVDAYNEVIAR
Sbjct 241 LSKYQDIIIEHQKVVKGNQKRLESLRELAGKENLEYPSVTLPPQPHTKEGVDAYNEVIAR 300
Query 301 VRMWVNLNLWQKLKLSRDDAKPLLRLKGFPSFPLVERQANEVDWWDMVCNVKKLINEKKE 360
VRMWVNLNLWQKLKLSRDDAKPLLRLKGFPSFPLVERQANEVDWWDMVCNVKKLINEKKE
Sbjct 301 VRMWVNLNLWQKLKLSRDDAKPLLRLKGFPSFPLVERQANEVDWWDMVCNVKKLINEKKE 360
Query 361 DGKVFWQNLAGYKRQEALRPYLSSEEDRKKGKKFARYQLGDLLLHLEKKHGEDWGKVYDE 420
DGKVFWQNLAGYKRQEALRPYLSSEEDRKKGKKFARYQLGDLLLHLEKKHGEDWGKVYDE
Sbjct 361 DGKVFWQNLAGYKRQEALRPYLSSEEDRKKGKKFARYQLGDLLLHLEKKHGEDWGKVYDE 420
Query 421 AWERIDKKVEGLSKHIKLEEERRSEDAQSKAALTDWLRAKASFVIEGLKEADKDEFCRCE 480
AWERIDKKVEGLSKHIKLEEERRSEDAQSKAALTDWLRAKASFVIEGLKEADKDEFCRCE
Sbjct 421 AWERIDKKVEGLSKHIKLEEERRSEDAQSKAALTDWLRAKASFVIEGLKEADKDEFCRCE 480
Query 481 LKLQKWYGDLRGKPFAIEAENSILDISGFSKQYNCAFIWQKDGVKKLNLYLIINYFKGGK 540
LKLQKWYGDLRGKPFAIEAENSILDISGFSKQYNCAFIWQKDGVKKLNLYLIINYFKGGK
Sbjct 481 LKLQKWYGDLRGKPFAIEAENSILDISGFSKQYNCAFIWQKDGVKKLNLYLIINYFKGGK 540
Query 541 LRFKKIKPEAFEANRFYTVINKKSGEIVPMEVNFNFDDPNLIILPLAFGKRQGREFIWND 600
LRFKKIKPEAFEANRFYTVINKKSGEIVPMEVNFNFDDPNLIILPLAFGKRQGREFIWND
Sbjct 541 LRFKKIKPEAFEANRFYTVINKKSGEIVPMEVNFNFDDPNLIILPLAFGKRQGREFIWND 600
Query 601 LLSLETGSLKLANGRVIEKTLYNRRTRQDEPALFVALTFERREVLDSSNIKPMNLIGVDR 660
LLSLETGSLKLANGRVIEKTLYNRRTRQDEPALFVALTFERREVLDSSNIKPMNLIGVDR
Sbjct 601 LLSLETGSLKLANGRVIEKTLYNRRTRQDEPALFVALTFERREVLDSSNIKPMNLIGVDR 660
Query 661 GENIPAVIALTDPEGCPLSRFKDSLGNPTHILRIGESYKEKQRTIQAKKEVEQRRAGGYS 720
GENIPAVIALTDPEGCPLSRFKDSLGNPTHILRIGESYKEKQRTIQAKKEVEQRRAGGYS
Sbjct 661 GENIPAVIALTDPEGCPLSRFKDSLGNPTHILRIGESYKEKQRTIQAKKEVEQRRAGGYS 720
Query 721 RKYASKAKNLADDMVRNTARDLLYYAVTQDAMLIFENLSRGFGRQGKRTFMAERQYTRME 780
RKYASKAKNLADDMVRNTARDLLYYAVTQDAMLIFENLSRGFGRQGKRTFMAERQYTRME
Sbjct 721 RKYASKAKNLADDMVRNTARDLLYYAVTQDAMLIFENLSRGFGRQGKRTFMAERQYTRME 780
Query 781 DWLTAKLAYEGLPSKTYLSKTLAQYTSKTCSNCGFTITSADYDRVLEKLKKTATGWMTTI 840
DWLTAKLAYEGLPSKTYLSKTLAQYTSKTCSNCGFTITSADYDRVLEKLKKTATGWMTTI
Sbjct 781 DWLTAKLAYEGLPSKTYLSKTLAQYTSKTCSNCGFTITSADYDRVLEKLKKTATGWMTTI 840
Query 841 NGKELKVEGQITYYNRYKRQNVVKDLSVELDRLSEESVNNDISSWTKGRSGEALSLLKKR 900
NGKELKVEGQITYYNRYKRQNVVKDLSVELDRLSEESVNNDISSWTKGRSGEALSLLKKR
Sbjct 841 NGKELKVEGQITYYNRYKRQNVVKDLSVELDRLSEESVNNDISSWTKGRSGEALSLLKKR 900
Query 901 FSHRPVQEKFVCLNCGFETHADEQAALNIARSWLFLRSQEYKKYQTNKTTGNTDKRAFVE 960
FSHRPVQEKFVCLNCGFETHADEQAALNIARSWLFLRSQEYKKYQTNKTTGNTDKRAFVE
Sbjct 901 FSHRPVQEKFVCLNCGFETHADEQAALNIARSWLFLRSQEYKKYQTNKTTGNTDKRAFVE 960
Query 961 TWQSFYRKKLKEVWKPAV 978
TWQSFYRKKLKEVWKPAV
Sbjct 961 TWQSFYRKKLKEVWKPAV 978
Regarding claim 189: Roberson taught that the CasX comprises a 4-basepair PAM: TTCN (See Roberson, p.1, col.2, para 2).
Claims 184-204 are provisionally rejected on the ground of nonstatutory double patenting as being unpatentable over claim 176-203 of copending Application No. 18/266,076 (reference application) in view of Roberson (BMC Genomics (2019); hereinafter Roberson, See PTO-892) and Ousterout et al (Nat Commun. 2015 Feb 18; See PTO-892; hereinafter “Ousterout”).
The teachings of Fernandes in view of Roberson are set forth above. Fernandes in view of Roberson did not teach a second gRNA comprising a scaffold and a targeting sequence as required by the claim. Ousterout taught that multiplex gRNA targeting to use two guide RNAs targeting the same exon or different genes are common practices in CRISPR technologies: “The versatility, efficiency and multiplexing capabilities of the CRISPR/Cas9 system enable a variety of otherwise challenging gene correction strategies. Here, we use the CRISPR/Cas9 system to restore the expression of the dystrophin gene in cells carrying dystrophin mutations that cause Duchenne muscular dystrophy (DMD). We design single or multiplexed sgRNAs to restore the dystrophin reading frame by targeting the mutational hotspot at exons 45–55 and introducing shifts within exons or deleting one or more exons.” (See Ousterout Abstract).
One of ordinary skill in the art, given the teachings of Fernandes in view of Roberson and Ousterout would have readily designed multiple gRNAs for editing same exon complementary to PTBP1 for use with the CasX protein taught by Fernandes, as design of such RNAs is routine, predictable and well documented by prior art, as shown by Roberson and Ousterout.
Claims 185, 195-196 are provisionally rejected on the ground of nonstatutory double patenting as being unpatentable over claim 176-203 of copending Application No. 18/266,076 (reference application) in view of in view of Roberson (BMC Genomics (2019); hereinafter Roberson, See PTO-892) and WO2019084148A1 (Published May 2, 2019; See PTO-892; hereinafter “Nagy”).
The teachings of Fernandes in view of Roberson are set forth above. Fernandes in view of Roberson did not teach a donor template comprising a scaffold and a targeting sequence as required by the claim. Nagy taught the use of donor template to introduce a nucleic acid into a target site. For example claim 12 of Nagy taught a method of modifying a target site using CasX, a gRNA and a donor template. As such one of ordinary skill in the art would have bene motivated to generate a composition comprising a CasX comprising the claimed sequence and a gRNA targeting PTBP1 and a template in view of the cited prior art. It is also noted that Nagy taught that the CasX nuclease further comprises a nuclear localization signal as required by claim 185.
One of ordinary skill in the art, given the teachings of Fernandes in view of Roberson and Nagy would have readily arrived at a composition comprising a gRNA targeting PTBP1 for use with the CasX protein taught by Fernandes. The person would have been motivated to further modify the composition with a donor template to insert a sequence at the target site for further modifying the target site, as design of such RNAs is routine, predictable and well documented by prior art, as shown by Roberson and Nagy.
U.S. Application No. 18/255,172
Claim 184, 186-190, 195 are provisionally rejected on the ground of nonstatutory double patenting as being unpatentable over claim 209-246 of copending Application No. 18/255,172 (reference application) in view of Roberson (BMC Genomics 20, 528 (2019); hereinafter Roberson, See PTO-892).
Although the claims at issue are not identical, they are not patentably distinct from each other because of the reasons stated below. This is a provisional nonstatutory double patenting rejection because the patentably indistinct claims have not in fact been patented.
Regarding claim 184, 186-188, 190, 195: Claim 1 of reference application is directed to a composition comprising a CRISPR nuclease and a CRISPR guide RNA. Claim 222 of reference application was directed to a CasX comprising a SEQ ID NO: 133, which is 100% identical to instant SEQ ID NO: 133 (See alignment below). Claim 219 of reference application taught that the CRISPR RNA comprises a scaffold sequence. It is noted that claims of reference application did not teach or suggest a gRNA comprising a targeting sequence that is complementary sequence to a PTBP1 gene target nucleic acid sequence. However, it would have been obvious for a person of ordinary skill in the art to arrive at a gRNA for CasX using routine experimentation. For example Roberson taught that CasX guide sites are relatively common in all their tested genomes (Roberson, p.4, col. 2, para 2). Roberson also taught a method to arrive at suitable guide sequences for CasX. For example Roberson “performed the annotations on the Washington University Center for High Performance Computing cluster. The motif location output included the location of the hit in the genome (contig, start, end) and the associated sequences.” Roberson “calculated the size of the reference genomes from their FASTA index files, determined the uniqueness of guide RNA sites amongst all editing sites, counted PAM usage, and annotated any overlaps with the exons of known genes. It is worth noting that uniqueness of a guide was determined only among editing sites. Presumably another site that matches the guide exactly, but does not have the PAM site would not be cleaved. A guide that overlaps an exon can likely be used to knockout the gene or knock-in coding variants at the exon.” (See Roberson, p. 2, para 2, as required by claims 186, 190). As such Roberson determined that arriving at a suitable gRNA for CasX is routine and systematic.
One of ordinary skill in the art, given the teachings of Roberson would have readily designed a gRNA complementary to PTBP1 for use with the CasX protein taught by reference application, as design of such RNA is routine, predictable and well documented by prior art, as shown by Roberson.
Query 1 QEIKRINKIRRRLVKDSNTKKAGKTGPMKTLLVRVMTPDLRERLENLRKKPENIPQPISN 60
QEIKRINKIRRRLVKDSNTKKAGKTGPMKTLLVRVMTPDLRERLENLRKKPENIPQPISN
Sbjct 1 QEIKRINKIRRRLVKDSNTKKAGKTGPMKTLLVRVMTPDLRERLENLRKKPENIPQPISN 60
Query 61 TSRANLNKLLTDYTEMKKAILHVYWEEFQKDPVGLMSRVAQPASKKIDQNKLKPEMDEKG 120
TSRANLNKLLTDYTEMKKAILHVYWEEFQKDPVGLMSRVAQPASKKIDQNKLKPEMDEKG
Sbjct 61 TSRANLNKLLTDYTEMKKAILHVYWEEFQKDPVGLMSRVAQPASKKIDQNKLKPEMDEKG 120
Query 121 NLTTAGFACSQCGQPLFVYKLEQVSEKGKAYTNYFGRCNVAEHEKLILLAQLKPEKDSDE 180
NLTTAGFACSQCGQPLFVYKLEQVSEKGKAYTNYFGRCNVAEHEKLILLAQLKPEKDSDE
Sbjct 121 NLTTAGFACSQCGQPLFVYKLEQVSEKGKAYTNYFGRCNVAEHEKLILLAQLKPEKDSDE 180
Query 181 AVTYSLGKFGQRALDFYSIHVTKESTHPVKPLAQIAGNRYASGPVGKALSDACMGTIASF 240
AVTYSLGKFGQRALDFYSIHVTKESTHPVKPLAQIAGNRYASGPVGKALSDACMGTIASF
Sbjct 181 AVTYSLGKFGQRALDFYSIHVTKESTHPVKPLAQIAGNRYASGPVGKALSDACMGTIASF 240
Query 241 LSKYQDIIIEHQKVVKGNQKRLESLRELAGKENLEYPSVTLPPQPHTKEGVDAYNEVIAR 300
LSKYQDIIIEHQKVVKGNQKRLESLRELAGKENLEYPSVTLPPQPHTKEGVDAYNEVIAR
Sbjct 241 LSKYQDIIIEHQKVVKGNQKRLESLRELAGKENLEYPSVTLPPQPHTKEGVDAYNEVIAR 300
Query 301 VRMWVNLNLWQKLKLSRDDAKPLLRLKGFPSFPLVERQANEVDWWDMVCNVKKLINEKKE 360
VRMWVNLNLWQKLKLSRDDAKPLLRLKGFPSFPLVERQANEVDWWDMVCNVKKLINEKKE
Sbjct 301 VRMWVNLNLWQKLKLSRDDAKPLLRLKGFPSFPLVERQANEVDWWDMVCNVKKLINEKKE 360
Query 361 DGKVFWQNLAGYKRQEALRPYLSSEEDRKKGKKFARYQLGDLLLHLEKKHGEDWGKVYDE 420
DGKVFWQNLAGYKRQEALRPYLSSEEDRKKGKKFARYQLGDLLLHLEKKHGEDWGKVYDE
Sbjct 361 DGKVFWQNLAGYKRQEALRPYLSSEEDRKKGKKFARYQLGDLLLHLEKKHGEDWGKVYDE 420
Query 421 AWERIDKKVEGLSKHIKLEEERRSEDAQSKAALTDWLRAKASFVIEGLKEADKDEFCRCE 480
AWERIDKKVEGLSKHIKLEEERRSEDAQSKAALTDWLRAKASFVIEGLKEADKDEFCRCE
Sbjct 421 AWERIDKKVEGLSKHIKLEEERRSEDAQSKAALTDWLRAKASFVIEGLKEADKDEFCRCE 480
Query 481 LKLQKWYGDLRGKPFAIEAENSILDISGFSKQYNCAFIWQKDGVKKLNLYLIINYFKGGK 540
LKLQKWYGDLRGKPFAIEAENSILDISGFSKQYNCAFIWQKDGVKKLNLYLIINYFKGGK
Sbjct 481 LKLQKWYGDLRGKPFAIEAENSILDISGFSKQYNCAFIWQKDGVKKLNLYLIINYFKGGK 540
Query 541 LRFKKIKPEAFEANRFYTVINKKSGEIVPMEVNFNFDDPNLIILPLAFGKRQGREFIWND 600
LRFKKIKPEAFEANRFYTVINKKSGEIVPMEVNFNFDDPNLIILPLAFGKRQGREFIWND
Sbjct 541 LRFKKIKPEAFEANRFYTVINKKSGEIVPMEVNFNFDDPNLIILPLAFGKRQGREFIWND 600
Query 601 LLSLETGSLKLANGRVIEKTLYNRRTRQDEPALFVALTFERREVLDSSNIKPMNLIGVDR 660
LLSLETGSLKLANGRVIEKTLYNRRTRQDEPALFVALTFERREVLDSSNIKPMNLIGVDR
Sbjct 601 LLSLETGSLKLANGRVIEKTLYNRRTRQDEPALFVALTFERREVLDSSNIKPMNLIGVDR 660
Query 661 GENIPAVIALTDPEGCPLSRFKDSLGNPTHILRIGESYKEKQRTIQAKKEVEQRRAGGYS 720
GENIPAVIALTDPEGCPLSRFKDSLGNPTHILRIGESYKEKQRTIQAKKEVEQRRAGGYS
Sbjct 661 GENIPAVIALTDPEGCPLSRFKDSLGNPTHILRIGESYKEKQRTIQAKKEVEQRRAGGYS 720
Query 721 RKYASKAKNLADDMVRNTARDLLYYAVTQDAMLIFENLSRGFGRQGKRTFMAERQYTRME 780
RKYASKAKNLADDMVRNTARDLLYYAVTQDAMLIFENLSRGFGRQGKRTFMAERQYTRME
Sbjct 721 RKYASKAKNLADDMVRNTARDLLYYAVTQDAMLIFENLSRGFGRQGKRTFMAERQYTRME 780
Query 781 DWLTAKLAYEGLPSKTYLSKTLAQYTSKTCSNCGFTITSADYDRVLEKLKKTATGWMTTI 840
DWLTAKLAYEGLPSKTYLSKTLAQYTSKTCSNCGFTITSADYDRVLEKLKKTATGWMTTI
Sbjct 781 DWLTAKLAYEGLPSKTYLSKTLAQYTSKTCSNCGFTITSADYDRVLEKLKKTATGWMTTI 840
Query 841 NGKELKVEGQITYYNRYKRQNVVKDLSVELDRLSEESVNNDISSWTKGRSGEALSLLKKR 900
NGKELKVEGQITYYNRYKRQNVVKDLSVELDRLSEESVNNDISSWTKGRSGEALSLLKKR
Sbjct 841 NGKELKVEGQITYYNRYKRQNVVKDLSVELDRLSEESVNNDISSWTKGRSGEALSLLKKR 900
Query 901 FSHRPVQEKFVCLNCGFETHADEQAALNIARSWLFLRSQEYKKYQTNKTTGNTDKRAFVE 960
FSHRPVQEKFVCLNCGFETHADEQAALNIARSWLFLRSQEYKKYQTNKTTGNTDKRAFVE
Sbjct 901 FSHRPVQEKFVCLNCGFETHADEQAALNIARSWLFLRSQEYKKYQTNKTTGNTDKRAFVE 960
Query 961 TWQSFYRKKLKEVWKPAV 978
TWQSFYRKKLKEVWKPAV
Sbjct 961 TWQSFYRKKLKEVWKPAV 978
Regarding claim 189: Roberson taught that the CasX comprises a 4-basepair PAM: TTCN (See Roberson, p.1, col.2, para 2).
Claims 184-204 are provisionally rejected on the ground of nonstatutory double patenting as being unpatentable over claim 209-246 of copending Application No. 18/255,172 (reference application) in view of Roberson (BMC Genomics (2019); hereinafter Roberson, See PTO-892) and Ousterout et al (Nat Commun. 2015 Feb 18; See PTO-892; hereinafter “Ousterout”).
The teachings of Fernandes in view of Roberson are set forth above. Fernandes in view of Roberson did not teach a second gRNA comprising a scaffold and a targeting sequence as required by the claim. Ousterout taught that multiplex gRNA targeting to use two guide RNAs targeting the same exon or different genes are common practices in CRISPR technologies: “The versatility, efficiency and multiplexing capabilities of the CRISPR/Cas9 system enable a variety of otherwise challenging gene correction strategies. Here, we use the CRISPR/Cas9 system to restore the expression of the dystrophin gene in cells carrying dystrophin mutations that cause Duchenne muscular dystrophy (DMD). We design single or multiplexed sgRNAs to restore the dystrophin reading frame by targeting the mutational hotspot at exons 45–55 and introducing shifts within exons or deleting one or more exons.” (See Ousterout Abstract).
One of ordinary skill in the art, given the teachings of Fernandes in view of Roberson and Ousterout would have readily designed multiple gRNAs for editing same exon complementary to PTBP1 for use with the CasX protein taught by Fernandes, as design of such RNAs is routine, predictable and well documented by prior art, as shown by Roberson and Ousterout.
Claims 185, 195-196 are provisionally rejected on the ground of nonstatutory double patenting as being unpatentable over claim 209-246 of copending Application No. 18/255,172 (reference application) in view of in view of Roberson (BMC Genomics (2019); hereinafter Roberson, See PTO-892) and WO2019084148A1 (Published May 2, 2019; See PTO-892; hereinafter “Nagy”).
The teachings of Fernandes in view of Roberson are set forth above. Fernandes in view of Roberson did not teach a donor template comprising a scaffold and a targeting sequence as required by the claim. Nagy taught the use of donor template to introduce a nucleic acid into a target site. For example claim 12 of Nagy taught a method of modifying a target site using CasX, a gRNA and a donor template. As such one of ordinary skill in the art would have bene motivated to generate a composition comprising a CasX comprising the claimed sequence and a gRNA targeting PTBP1 and a template in view of the cited prior art. It is also noted that Nagy taught that the CasX nuclease further comprises a nuclear localization signal as required by claim 185.
One of ordinary skill in the art, given the teachings of Fernandes in view of Roberson and Nagy would have readily arrived at a composition comprising a gRNA targeting PTBP1 for use with the CasX protein taught by Fernandes. The person would have been motivated to further modify the composition with a donor template to insert a sequence at the target site for further modifying the target site, as design of such RNAs is routine, predictable and well documented by prior art, as shown by Roberson and Nagy.
U.S. Application No. 17/791,130
Claim 184, 186-190, 195 are provisionally rejected on the ground of nonstatutory double patenting as being unpatentable over claim 215-237 of copending Application No. 17/791,130 (reference application) in view of Roberson (BMC Genomics 20, 528 (2019); hereinafter Roberson, See PTO-892).
Although the claims at issue are not identical, they are not patentably distinct from each other because of the reasons stated below. This is a provisional nonstatutory double patenting rejection because the patentably indistinct claims have not in fact been patented.
Regarding claim 184, 186-188, 190, 195: Claim 1 of reference application is directed to a composition comprising a CRISPR nuclease and a CRISPR guide RNA. Claim 222 of reference application was directed to a CasX comprising a SEQ ID NO: 145, which is 100% identical to instant SEQ ID NO: 133 (See alignment below). Claim 226 of reference application taught that the CRISPR RNA comprises a scaffold sequence. It is noted that claims of reference application did not teach or suggest a gRNA comprising a targeting sequence that is complementary sequence to a PTBP1 gene target nucleic acid sequence. However, it would have been obvious for a person of ordinary skill in the art to arrive at a gRNA for CasX using routine experimentation. For example Roberson taught that CasX guide sites are relatively common in all their tested genomes (Roberson, p.4, col. 2, para 2). Roberson also taught a method to arrive at suitable guide sequences for CasX. For example Roberson “performed the annotations on the Washington University Center for High Performance Computing cluster. The motif location output included the location of the hit in the genome (contig, start, end) and the associated sequences.” Roberson “calculated the size of the reference genomes from their FASTA index files, determined the uniqueness of guide RNA sites amongst all editing sites, counted PAM usage, and annotated any overlaps with the exons of known genes. It is worth noting that uniqueness of a guide was determined only among editing sites. Presumably another site that matches the guide exactly, but does not have the PAM site would not be cleaved. A guide that overlaps an exon can likely be used to knockout the gene or knock-in coding variants at the exon.” (See Roberson, p. 2, para 2, as required by claims 186, 190). As such Roberson determined that arriving at a suitable gRNA for CasX is routine and systematic.
One of ordinary skill in the art, given the teachings of Roberson would have readily designed a gRNA complementary to PTBP1 for use with the CasX protein taught by reference application, as design of such RNA is routine, predictable and well documented by prior art, as shown by Roberson.
Query 1 QEIKRINKIRRRLVKDSNTKKAGKTGPMKTLLVRVMTPDLRERLENLRKKPENIPQPISN 60
QEIKRINKIRRRLVKDSNTKKAGKTGPMKTLLVRVMTPDLRERLENLRKKPENIPQPISN
Sbjct 1 QEIKRINKIRRRLVKDSNTKKAGKTGPMKTLLVRVMTPDLRERLENLRKKPENIPQPISN 60
Query 61 TSRANLNKLLTDYTEMKKAILHVYWEEFQKDPVGLMSRVAQPASKKIDQNKLKPEMDEKG 120
TSRANLNKLLTDYTEMKKAILHVYWEEFQKDPVGLMSRVAQPASKKIDQNKLKPEMDEKG
Sbjct 61 TSRANLNKLLTDYTEMKKAILHVYWEEFQKDPVGLMSRVAQPASKKIDQNKLKPEMDEKG 120
Query 121 NLTTAGFACSQCGQPLFVYKLEQVSEKGKAYTNYFGRCNVAEHEKLILLAQLKPEKDSDE 180
NLTTAGFACSQCGQPLFVYKLEQVSEKGKAYTNYFGRCNVAEHEKLILLAQLKPEKDSDE
Sbjct 121 NLTTAGFACSQCGQPLFVYKLEQVSEKGKAYTNYFGRCNVAEHEKLILLAQLKPEKDSDE 180
Query 181 AVTYSLGKFGQRALDFYSIHVTKESTHPVKPLAQIAGNRYASGPVGKALSDACMGTIASF 240
AVTYSLGKFGQRALDFYSIHVTKESTHPVKPLAQIAGNRYASGPVGKALSDACMGTIASF
Sbjct 181 AVTYSLGKFGQRALDFYSIHVTKESTHPVKPLAQIAGNRYASGPVGKALSDACMGTIASF 240
Query 241 LSKYQDIIIEHQKVVKGNQKRLESLRELAGKENLEYPSVTLPPQPHTKEGVDAYNEVIAR 300
LSKYQDIIIEHQKVVKGNQKRLESLRELAGKENLEYPSVTLPPQPHTKEGVDAYNEVIAR
Sbjct 241 LSKYQDIIIEHQKVVKGNQKRLESLRELAGKENLEYPSVTLPPQPHTKEGVDAYNEVIAR 300
Query 301 VRMWVNLNLWQKLKLSRDDAKPLLRLKGFPSFPLVERQANEVDWWDMVCNVKKLINEKKE 360
VRMWVNLNLWQKLKLSRDDAKPLLRLKGFPSFPLVERQANEVDWWDMVCNVKKLINEKKE
Sbjct 301 VRMWVNLNLWQKLKLSRDDAKPLLRLKGFPSFPLVERQANEVDWWDMVCNVKKLINEKKE 360
Query 361 DGKVFWQNLAGYKRQEALRPYLSSEEDRKKGKKFARYQLGDLLLHLEKKHGEDWGKVYDE 420
DGKVFWQNLAGYKRQEALRPYLSSEEDRKKGKKFARYQLGDLLLHLEKKHGEDWGKVYDE
Sbjct 361 DGKVFWQNLAGYKRQEALRPYLSSEEDRKKGKKFARYQLGDLLLHLEKKHGEDWGKVYDE 420
Query 421 AWERIDKKVEGLSKHIKLEEERRSEDAQSKAALTDWLRAKASFVIEGLKEADKDEFCRCE 480
AWERIDKKVEGLSKHIKLEEERRSEDAQSKAALTDWLRAKASFVIEGLKEADKDEFCRCE
Sbjct 421 AWERIDKKVEGLSKHIKLEEERRSEDAQSKAALTDWLRAKASFVIEGLKEADKDEFCRCE 480
Query 481 LKLQKWYGDLRGKPFAIEAENSILDISGFSKQYNCAFIWQKDGVKKLNLYLIINYFKGGK 540
LKLQKWYGDLRGKPFAIEAENSILDISGFSKQYNCAFIWQKDGVKKLNLYLIINYFKGGK
Sbjct 481 LKLQKWYGDLRGKPFAIEAENSILDISGFSKQYNCAFIWQKDGVKKLNLYLIINYFKGGK 540
Query 541 LRFKKIKPEAFEANRFYTVINKKSGEIVPMEVNFNFDDPNLIILPLAFGKRQGREFIWND 600
LRFKKIKPEAFEANRFYTVINKKSGEIVPMEVNFNFDDPNLIILPLAFGKRQGREFIWND
Sbjct 541 LRFKKIKPEAFEANRFYTVINKKSGEIVPMEVNFNFDDPNLIILPLAFGKRQGREFIWND 600
Query 601 LLSLETGSLKLANGRVIEKTLYNRRTRQDEPALFVALTFERREVLDSSNIKPMNLIGVDR 660
LLSLETGSLKLANGRVIEKTLYNRRTRQDEPALFVALTFERREVLDSSNIKPMNLIGVDR
Sbjct 601 LLSLETGSLKLANGRVIEKTLYNRRTRQDEPALFVALTFERREVLDSSNIKPMNLIGVDR 660
Query 661 GENIPAVIALTDPEGCPLSRFKDSLGNPTHILRIGESYKEKQRTIQAKKEVEQRRAGGYS 720
GENIPAVIALTDPEGCPLSRFKDSLGNPTHILRIGESYKEKQRTIQAKKEVEQRRAGGYS
Sbjct 661 GENIPAVIALTDPEGCPLSRFKDSLGNPTHILRIGESYKEKQRTIQAKKEVEQRRAGGYS 720
Query 721 RKYASKAKNLADDMVRNTARDLLYYAVTQDAMLIFENLSRGFGRQGKRTFMAERQYTRME 780
RKYASKAKNLADDMVRNTARDLLYYAVTQDAMLIFENLSRGFGRQGKRTFMAERQYTRME
Sbjct 721 RKYASKAKNLADDMVRNTARDLLYYAVTQDAMLIFENLSRGFGRQGKRTFMAERQYTRME 780
Query 781 DWLTAKLAYEGLPSKTYLSKTLAQYTSKTCSNCGFTITSADYDRVLEKLKKTATGWMTTI 840
DWLTAKLAYEGLPSKTYLSKTLAQYTSKTCSNCGFTITSADYDRVLEKLKKTATGWMTTI
Sbjct 781 DWLTAKLAYEGLPSKTYLSKTLAQYTSKTCSNCGFTITSADYDRVLEKLKKTATGWMTTI 840
Query 841 NGKELKVEGQITYYNRYKRQNVVKDLSVELDRLSEESVNNDISSWTKGRSGEALSLLKKR 900
NGKELKVEGQITYYNRYKRQNVVKDLSVELDRLSEESVNNDISSWTKGRSGEALSLLKKR
Sbjct 841 NGKELKVEGQITYYNRYKRQNVVKDLSVELDRLSEESVNNDISSWTKGRSGEALSLLKKR 900
Query 901 FSHRPVQEKFVCLNCGFETHADEQAALNIARSWLFLRSQEYKKYQTNKTTGNTDKRAFVE 960
FSHRPVQEKFVCLNCGFETHADEQAALNIARSWLFLRSQEYKKYQTNKTTGNTDKRAFVE
Sbjct 901 FSHRPVQEKFVCLNCGFETHADEQAALNIARSWLFLRSQEYKKYQTNKTTGNTDKRAFVE 960
Query 961 TWQSFYRKKLKEVWKPAV 978
TWQSFYRKKLKEVWKPAV
Sbjct 961 TWQSFYRKKLKEVWKPAV 978
Regarding claim 189: Roberson taught that the CasX comprises a 4-basepair PAM: TTCN (See Roberson, p.1, col.2, para 2).
Claims 184-204 are provisionally rejected on the ground of nonstatutory double patenting as being unpatentable over claim 215-237 of copending Application No. 17/791,130 (reference application) in view of Roberson (BMC Genomics (2019); hereinafter Roberson, See PTO-892) and Ousterout et al (Nat Commun. 2015 Feb 18; See PTO-892; hereinafter “Ousterout”).
The teachings of Fernandes in view of Roberson are set forth above. Fernandes in view of Roberson did not teach a second gRNA comprising a scaffold and a targeting sequence as required by the claim. Ousterout taught that multiplex gRNA targeting to use two guide RNAs targeting the same exon or different genes are common practices in CRISPR technologies: “The versatility, efficiency and multiplexing capabilities of the CRISPR/Cas9 system enable a variety of otherwise challenging gene correction strategies. Here, we use the CRISPR/Cas9 system to restore the expression of the dystrophin gene in cells carrying dystrophin mutations that cause Duchenne muscular dystrophy (DMD). We design single or multiplexed sgRNAs to restore the dystrophin reading frame by targeting the mutational hotspot at exons 45–55 and introducing shifts within exons or deleting one or more exons.” (See Ousterout Abstract).
One of ordinary skill in the art, given the teachings of Fernandes in view of Roberson and Ousterout would have readily designed multiple gRNAs for editing same exon complementary to PTBP1 for use with the CasX protein taught by Fernandes, as design of such RNAs is routine, predictable and well documented by prior art, as shown by Roberson and Ousterout.
Claims 185, 195-196 are provisionally rejected on the ground of nonstatutory double patenting as being unpatentable over claim 215-237 of copending Application No. 17/791,130 (reference application) in view of in view of Roberson (BMC Genomics (2019); hereinafter Roberson, See PTO-892) and WO2019084148A1 (Published May 2, 2019; See PTO-892; hereinafter “Nagy”).
The teachings of Fernandes in view of Roberson are set forth above. Fernandes in view of Roberson did not teach a donor template comprising a scaffold and a targeting sequence as required by the claim. Nagy taught the use of donor template to introduce a nucleic acid into a target site. For example claim 12 of Nagy taught a method of modifying a target site using CasX, a gRNA and a donor template. As such one of ordinary skill in the art would have bene motivated to generate a composition comprising a CasX comprising the claimed sequence and a gRNA targeting PTBP1 and a template in view of the cited prior art. It is also noted that Nagy taught that the CasX nuclease further comprises a nuclear localization signal as required by claim 185.
One of ordinary skill in the art, given the teachings of Fernandes in view of Roberson and Nagy would have readily arrived at a composition comprising a gRNA targeting PTBP1 for use with the CasX protein taught by Fernandes. The person would have been motivated to further modify the composition with a donor template to insert a sequence at the target site for further modifying the target site, as design of such RNAs is routine, predictable and well documented by prior art, as shown by Roberson and Nagy.
U.S. Application No. 18/568,029
Claim 184, 186-190, 195 are provisionally rejected on the ground of nonstatutory double patenting as being unpatentable over claim 1-4, 13-14, 18-20, 23, 25-31, 35, 37-39, 41-43, 45 of copending Application No. 18/568,029 (reference application) in view of Roberson (BMC Genomics 20, 528 (2019); hereinafter Roberson, See PTO-892).
Although the claims at issue are not identical, they are not patentably distinct from each other because of the reasons stated below. This is a provisional nonstatutory double patenting rejection because the patentably indistinct claims have not in fact been patented.
Regarding claim 184, 186-188, 190, 195: Claim 1 of reference application is directed to a composition comprising a CRISPR nuclease and a CRISPR guide RNA. Claim 39 of reference application was directed to a CasX comprising SEQ ID NOs: 635, 668, 892, 829, 871, 868, 828, 703, 878, 931, 928, 929, 834, which are > 90% identical to instant SEQ ID NO: 133 (See for alignment of SEQ ID NO: 635 with SEQ ID NO: 133 below). Claim 41 of reference application taught that the CRISPR RNA comprises a scaffold sequence. It is noted that claims of reference application did not teach or suggest a gRNA comprising a targeting sequence that is complementary sequence to a PTBP1 gene target nucleic acid sequence. However, it would have been obvious for a person of ordinary skill in the art to arrive at a gRNA for CasX using routine experimentation. For example Roberson taught that CasX guide sites are relatively common in all their tested genomes (Roberson, p.4, col. 2, para 2). Roberson also taught a method to arrive at suitable guide sequences for CasX. For example Roberson “performed the annotations on the Washington University Center for High Performance Computing cluster. The motif location output included the location of the hit in the genome (contig, start, end) and the associated sequences.” Roberson “calculated the size of the reference genomes from their FASTA index files, determined the uniqueness of guide RNA sites amongst all editing sites, counted PAM usage, and annotated any overlaps with the exons of known genes. It is worth noting that uniqueness of a guide was determined only among editing sites. Presumably another site that matches the guide exactly, but does not have the PAM site would not be cleaved. A guide that overlaps an exon can likely be used to knockout the gene or knock-in coding variants at the exon.” (See Roberson, p. 2, para 2, as required by claims 186, 190). As such Roberson determined that arriving at a suitable gRNA for CasX is routine and systematic.
One of ordinary skill in the art, given the teachings of Roberson would have readily designed a gRNA complementary to PTBP1 for use with the CasX protein taught by reference application, as design of such RNA is routine, predictable and well documented by prior art, as shown by Roberson.
Query 1 QEIKRINKIRRRLVKDSNTKKAGKTGPMKTLLVRVMTPDLRERLENLRKKPENIPQPISN 60
QEIKRINKIRRRLVKDSNTKKAGKTGPMKTLLVRVMTPDLRERLENLRKKPENIPQPISN
Sbjct 1 QEIKRINKIRRRLVKDSNTKKAGKTGPMKTLLVRVMTPDLRERLENLRKKPENIPQPISN 60
Query 61 TSRANLNKLLTDYTEMKKAILHVYWEEFQKDPVGLMSRVAQPASKKIDQNKLKPEMDEKG 120
TSRANLNKLLTDYTEMKKAILHVYWEEFQKDPVGLMSRVAQPASKKIDQNKLKPEMDEKG
Sbjct 61 TSRANLNKLLTDYTEMKKAILHVYWEEFQKDPVGLMSRVAQPASKKIDQNKLKPEMDEKG 120
Query 121 NLTTAGFACSQCGQPLFVYKLEQVSEKGKAYTNYFGRCNVAEHEKLILLAQLKPEKDSDE 180
NLTTAGFACSQCGQPLFVYKLEQVSEKGKAYTNYFGRCNVAEHEKLILLAQLKPEKDSDE
Sbjct 121 NLTTAGFACSQCGQPLFVYKLEQVSEKGKAYTNYFGRCNVAEHEKLILLAQLKPEKDSDE 180
Query 181 AVTYSLGKFGQRALDFYSIHVTKESTHPVKPLAQIAGNRYASGPVGKALSDACMGTIASF 240
AVTYSLGKFGQRALDFYSIHVTKESTHPVKPLAQIAGNRYASGPVGKALSDACMGTIASF
Sbjct 181 AVTYSLGKFGQRALDFYSIHVTKESTHPVKPLAQIAGNRYASGPVGKALSDACMGTIASF 240
Query 241 LSKYQDIIIEHQKVVKGNQKRLESLRELAGKENLEYPSVTLPPQPHTKEGVDAYNEVIAR 300
LSKYQDIIIEHQKVVKGNQKRLESLRELAGKENLEYPSVTLPPQPHTKEGVDAYNEVIAR
Sbjct 241 LSKYQDIIIEHQKVVKGNQKRLESLRELAGKENLEYPSVTLPPQPHTKEGVDAYNEVIAR 300
Query 301 VRMWVNLNLWQKLKLSRDDAKPLLRLKGFPSFPLVERQANEVDWWDMVCNVKKLINEKKE 360
VRMWVNLNLWQKLKLSRDDAKPLLRLKGFPSFPLVERQANEVDWWDMVCNVKKLINEKKE
Sbjct 301 VRMWVNLNLWQKLKLSRDDAKPLLRLKGFPSFPLVERQANEVDWWDMVCNVKKLINEKKE 360
Query 361 DGKVFWQNLAGYKRQEALRPYLSSEEDRKKGKKFARYQLGDLLLHLEKKHGEDWGKVYDE 420
DGKVFWQNLAGYKRQEALRPYLSSEEDRKKGKKFARYQLGDLLLHLEKKHGEDWGKVYDE
Sbjct 361 DGKVFWQNLAGYKRQEALRPYLSSEEDRKKGKKFARYQLGDLLLHLEKKHGEDWGKVYDE 420
Query 421 AWERIDKKVEGLSKHIKLEEERRSEDAQSKAALTDWLRAKASFVIEGLKEADKDEFCRCE 480
AWERIDKKVEGLSKHIKLEEERRSEDAQSKAALTDWLRAKASFVIEGLKEADKDEFCRCE
Sbjct 421 AWERIDKKVEGLSKHIKLEEERRSEDAQSKAALTDWLRAKASFVIEGLKEADKDEFCRCE 480
Query 481 LKLQKWYGDLRGKPFAIEAENSILDISGFSKQYNCAFIWQKDGVKKLNLYLIINYFKGGK 540
LKLQKWYGDLRGKPFAIEAENSILDISGFSKQYNCAFIWQKDGVKKLNLYLIINYFKGGK
Sbjct 481 LKLQKWYGDLRGKPFAIEAENSILDISGFSKQYNCAFIWQKDGVKKLNLYLIINYFKGGK 540
Query 541 LRFKKIKPEAFEANRFYTVINKKSGEIVPMEVNFNFDDPNLIILPLAFGKRQGREFIWND 600
LRFKKIKPEAFEANRFYTVINKKSGEIVPMEVNFNFDDPNLIILPLAFGKRQGREFIWND
Sbjct 541 LRFKKIKPEAFEANRFYTVINKKSGEIVPMEVNFNFDDPNLIILPLAFGKRQGREFIWND 600
Query 601 LLSLETGSLKLANGRVIEKTLYNRRTRQDEPALFVALTFERREVLDSSNIKPMNLIGVDR 660
LLSLETGSLKLANGRVIEKTLYNRRTRQDEPALFVALTFERREVLDSSNIKPMNLIGVDR
Sbjct 601 LLSLETGSLKLANGRVIEKTLYNRRTRQDEPALFVALTFERREVLDSSNIKPMNLIGVDR 660
Query 661 GENIPAVIALTDPEGCPLSRFKDSLGNPTHILRIGESYKEKQRTIQAKKEVEQRRAGGYS 720
GENIPAVIALTDPEGCPLSRFKDSLGNPTHILRIGESYKEKQRTIQAKKEVEQRRAGGYS
Sbjct 661 GENIPAVIALTDPEGCPLSRFKDSLGNPTHILRIGESYKEKQRTIQAKKEVEQRRAGGYS 720
Query 721 RKYASKAKNLADDMVRNTARDLLYYAVTQDAMLIFENLSRGFGRQGKRTFMAERQYTRME 780
RKYASKAKNLADDMVRNTARDLLYYAVTQDAMLIFENLSRGFGRQGKRTFMAERQYTRME
Sbjct 721 RKYASKAKNLADDMVRNTARDLLYYAVTQDAMLIFENLSRGFGRQGKRTFMAERQYTRME 780
Query 781 DWLTAKLAYEGLPSKTYLSKTLAQYTSKTCSNCGFTITSADYDRVLEKLKKTATGWMTTI 840
DWLTAKLAYEGLPSKTYLSKTLAQYTSKTCSNCGFTITSADYDRVLEKLKKTATGWMTTI
Sbjct 781 DWLTAKLAYEGLPSKTYLSKTLAQYTSKTCSNCGFTITSADYDRVLEKLKKTATGWMTTI 840
Query 841 NGKELKVEGQITYYNRYKRQNVVKDLSVELDRLSEESVNNDISSWTKGRSGEALSLLKKR 900
NGKELKVEGQITYYNRYKRQNVVKDLSVELDRLSEESVNNDISSWTKGRSGEALSLLKKR
Sbjct 841 NGKELKVEGQITYYNRYKRQNVVKDLSVELDRLSEESVNNDISSWTKGRSGEALSLLKKR 900
Query 901 FSHRPVQEKFVCLNCGFETHADEQAALNIARSWLFLRSQEYKKYQTNKTTGNTDKRAFVE 960
FSHRPVQEKFVCLNCGFETHADEQAALNIARSWLFLRSQEYKKYQTNKTTGNTDKRAFVE
Sbjct 901 FSHRPVQEKFVCLNCGFETHADEQAALNIARSWLFLRSQEYKKYQTNKTTGNTDKRAFVE 960
Query 961 TWQSFYRKKLKEVWKPAV 978
TWQSFYRKKLKEVWKPAV
Sbjct 961 TWQSFYRKKLKEVWKPAV 978
Regarding claim 189: Roberson taught that the CasX comprises a 4-basepair PAM: TTCN (See Roberson, p.1, col.2, para 2).
Claims 184-204 are provisionally rejected on the ground of nonstatutory double patenting as being unpatentable over claim 1-4, 13-14, 18-20, 23, 25-31, 35, 37-39, 41-43, 45 of copending Application No. 18/568,029 in view of Roberson (BMC Genomics (2019); hereinafter Roberson, See PTO-892) and Ousterout et al (Nat Commun. 2015 Feb 18; See PTO-892; hereinafter “Ousterout”).
The teachings of Fernandes in view of Roberson are set forth above. Fernandes in view of Roberson did not teach a second gRNA comprising a scaffold and a targeting sequence as required by the claim. Ousterout taught that multiplex gRNA targeting to use two guide RNAs targeting the same exon or different genes are common practices in CRISPR technologies: “The versatility, efficiency and multiplexing capabilities of the CRISPR/Cas9 system enable a variety of otherwise challenging gene correction strategies. Here, we use the CRISPR/Cas9 system to restore the expression of the dystrophin gene in cells carrying dystrophin mutations that cause Duchenne muscular dystrophy (DMD). We design single or multiplexed sgRNAs to restore the dystrophin reading frame by targeting the mutational hotspot at exons 45–55 and introducing shifts within exons or deleting one or more exons.” (See Ousterout Abstract).
One of ordinary skill in the art, given the teachings of Fernandes in view of Roberson and Ousterout would have readily designed multiple gRNAs for editing same exon complementary to PTBP1 for use with the CasX protein taught by Fernandes, as design of such RNAs is routine, predictable and well documented by prior art, as shown by Roberson and Ousterout.
Claims 185, 195-196 are provisionally rejected on the ground of nonstatutory double patenting as being unpatentable over 1-4, 13-14, 18-20, 23, 25-31, 35, 37-39, 41-43, 45 of copending Application No. 18/568,029 in view of in view of Roberson (BMC Genomics (2019); hereinafter Roberson, See PTO-892) and WO2019084148A1 (Published May 2, 2019; See PTO-892; hereinafter “Nagy”).
The teachings of Fernandes in view of Roberson are set forth above. Fernandes in view of Roberson did not teach a donor template comprising a scaffold and a targeting sequence as required by the claim. Nagy taught the use of donor template to introduce a nucleic acid into a target site. For example claim 12 of Nagy taught a method of modifying a target site using CasX, a gRNA and a donor template. As such one of ordinary skill in the art would have bene motivated to generate a composition comprising a CasX comprising the claimed sequence and a gRNA targeting PTBP1 and a template in view of the cited prior art. It is also noted that Nagy taught that the CasX nuclease further comprises a nuclear localization signal as required by claim 185.
One of ordinary skill in the art, given the teachings of Fernandes in view of Roberson and Nagy would have readily arrived at a composition comprising a gRNA targeting PTBP1 for use with the CasX protein taught by Fernandes. The person would have been motivated to further modify the composition with a donor template to insert a sequence at the target site for further modifying the target site, as design of such RNAs is routine, predictable and well documented by prior art, as shown by Roberson and Nagy.
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 185-199 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.
CasX variants
Claim 184 is directed to a CasX variant protein and a guide RNA where the CasX variant comprises all sequences 90% identical to SEQ ID NO: 133 and any gRNA with targeting sequence that is complementary to PTBP1.
Applicant’s claims allows for substitutions of 97 different amino acids in the 978 amino acid long SEQ ID NO: 133 and encompasses
978
C
97
×
10
97
=
9.6
×
10
259
different polypeptides if only substitution mutations were considered. It is also pointed out that the wording of the claim encompasses deletions, and insertions, taking the number of mutants even higher. It is noted that the specification is restricted to CasX variants comprising SEQ ID NOs: 59, 72-99, 101-148, and 43662-43907 i.e. 323 different polypeptides. The specification did not point to any general region or residues where mutations would be tolerated, or not tolerated. Nor did the specification teach or identify any conserved structural motifs that are key to identification of amino acids that are important to maintain the function and/or structure. It is submitted that there is not enough disclosure in the specification to arrive at the claimed number of polynucleotides.
For the reasons elucidated above, Applicants were not in possession of the full scope of the claimed invention at the time of filing of the instant invention.
Similar rejection applies to claim 198.
Claims 185-196 inherit the rejection due to their dependency on claim 184.
Scaffold sequences
Claim 194 requires a scaffold sequence having 70% sequence identity to a sequence of SEQ ID NO: 43577.
The specification clearly defines a scaffold sequence of SEQ ID NO: 43577. However, the specification is deficient in identifying scaffolds that are less that which are 100% identical to SEQ ID NO: 43577 but still retain the scaffold sequence. (See [0149]). It is understood by a person of ordinary skill in the art that the structure of scaffold is important for binding for CasX. For example, Liu et al (Nature 2019, See PTO-892; hereinafter “Liu”) disclosed from eight cryo-electron microscopy structures of CasX in different states of assembly with its guide RNA and double-stranded DNA substrates that an extensive RNA scaffold and a domain are required for DNA unwinding. (See Liu Abstract). Liu taught that “‘scaffold’ stem interacts with the helical II domain” (See Liu p. 221, col. 2, para 2). Liu further taught that alterations to the triplex or the scaffold stem diminished CasX activity in vivo. (See Liu p. 221, col. 2, para 2). The specification fails to identify any nucleic acids that are key for maintenance of CasX binding and retention of activity. The specification only provides SEQ ID NO: 43577. As such it is submitted that the specification lacks adequate description for any scaffold sequence that is 70% identical to SEQ ID NO: 43577.
The Application is determined to be lacking description for a scaffold sequence having 70% sequence identity to a sequence of SEQ ID NO: 43577.
Similar rejections apply to claims 197 and 199.
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.
Claim 199 is rejected under 35 U.S.C. 112(b) or 35 U.S.C. 112 (pre-AIA ), second paragraph, as failing to set forth 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.
Claim 199 is directed to a CasX variant protein comprises an amino acid sequence selected from the group consisting of SEQ ID NOs: 43577, or a sequence having at least 90% sequence identity thereto and a gRNA scaffold and a targeting sequence comprises a sequence having at least 70% sequence identity to a sequence of SEQ ID NOs: 43577. It is unclear if SEQ ID NO: 43577 is a sequence of gRNA scaffold and a targeting region or a CasX variant. For the sake of compact prosecution, it is assumed that the CasX variant is SEQ ID NO: 133 or a sequence with 90% identity thereof.
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 200-204 are rejected under 35 U.S.C. 103 as being unpatentable over Roberson (BMC Genomics 20, 528 (2019); hereinafter "Roberson" See PTO-892), and Zhou et al (Cell. 2020 Apr 30; See PTO-892; Hereinafter "Zhou" See PTO-892) in view of Liu (Nature. 2019 Feb; See PTO-892; hereinafter "Liu").
Regarding claim 200-202 and 204: Roberson was directed to use of CasX gRNA for treatment of diseases, for example, Roberson disclosed that “major concern for human gene-editing, however, is the possibility of introducing new genetic lesions through off-target activity of the editing enzyme. This has led to a general consensus that germline correction of a disease-causing variant in humans via Cas9 knock-in is not advisable at this time, and triggered intense research into ways to reduce off-target editing for clinical use. One mechanism of reducing off-target effects would be to use an endonuclease with a longer PAM sequence. One recently identified RNA-guided genome editing endonuclease from Deltaproteobacteria is CasX (DpbCasX), tentatively designated as Cas12e.” As such Roberson disclosed the advantages of using CasX for gene editing in disease pathologies. As disclosed above, Roberson also disclosed a method of selecting a gRNA for appropriate targeting of a gene. Briefly, Roberson “performed the annotations on the Washington University Center for High Performance Computing cluster. The motif location output included the location of the hit in the genome (contig, start, end) and the associated sequences.” Roberson “calculated the size of the reference genomes from their FASTA index files, determined the uniqueness of guide RNA sites amongst all editing sites, counted PAM usage, and annotated any overlaps with the exons of known genes. It is worth noting that uniqueness of a guide was determined only among editing sites. Presumably another site that matches the guide exactly, but does not have the PAM site would not be cleaved. A guide that overlaps an exon can likely be used to knockout the gene or knock-in coding variants at the exon.” (See Roberson, p. 2, para 2, as required by claims 186, 190). As such Roberson determined that arriving at a suitable gRNA for CasX is routine and systematic. Roberson did not specifically teach targeting PTBP1. However, it was known at the time of filing that PTBP1 was implicated in neurological diseases and cancer. For example, Zhou taught that downregulation of a single RNA-binding protein, polypyrimidine tract-binding protein 1 (Ptbp1), using in vivo viral delivery of a recently developed RNA-targeting CRISPR system CasRx, resulted in the conversion of Müller glia into retinal ganglion cells (RGCs) with a high efficiency, leading to the alleviation of disease symptoms associated with RGC loss. (See Zhou Abstract). As such a person of ordinary skill in the art would have been motivated to choose PTBP1 as a target for gene editing. Further it is noted that Roberson taught methods to select gRNA for CasX. A person of ordinary skill in the art would have found it predictable and routine to combine teachings of Zhou with Roberson to arrive at a method of treating a neurological disease using CasX-gRNA system. The person would also be motivated to arrive at a guide sequence as required by claim 204. It is further noted that as enumerated above, Liu taught the importance of scaffold for interacting with CasX (“‘scaffold’ stem interacts with the helical II domain” (See Liu p. 221, col. 2, para 2)). As such one or ordinary skill in the art would be motivated to include a scaffold sequence in the guide RNA. It is noted that the claimed invention can be easily arrived at using routine systematic and predictable experimentation.
Thus, administering a composition comprising a CasX variant and a PTBP1-targeting gRNA to treat a PTBP1-related disease would have been obvious to a person of ordinary skill in the art at the time of the invention. The claimed method therefore lacks patentable distinctness over the prior art.
Claim 203 are rejected under 35 U.S.C. 103 as being unpatentable over Roberson (BMC Genomics 20, 528 (2019); hereinafter "Roberson" See PTO-892), and Bielli et al (Transl Androl Urol. 2018 Dec; See PTO-892; Hereinafter "Bielli") in view of Liu (Nature. 2019 Feb; See PTO-892; hereinafter "Liu").
Regarding claim 203: The teachings of Roberson in view of Zhou are stated above. The cited prior art did not teach implication of PTBP1 in cancer. Bielli taught that “depletion of PTBP1 strongly limited bladder cancer cell malignancy, it is possible that targeting PTBP1, or its splicing program, will represent the basis for the development of novel therapeutics strategies to treat NMIBC.” (See Bielli S766, col. 2, para 2). As such a person of ordinary skill in the art would have been motivated to use a gRNA targeting PTBP1 for treatment of cancer.
Thus, administering a composition comprising a CasX variant and a PTBP1-targeting gRNA to treat a PTBP1-related cancer would have been obvious to a person of ordinary skill in the art at the time of the invention. The claimed method therefore lacks patentable distinctness over the prior art.
Conclusion
Claims 184-199 appear free of art in view of sequence search results, but lack written description and have double patenting issues. No prior art appears to render Claims 184-199 obvious or unpatentable in view of sequence search results.
No claim is allowed.
Any inquiry concerning this communication or earlier communications from the examiner should be directed to JAGAMYA VIJAYARAGHAVAN whose telephone number is (703)756-5934. The examiner can normally be reached 9:00a-5:00p.
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/JAGAMYA NMN VIJAYARAGHAVAN/ Examiner, Art Unit 1633
/EVELYN Y PYLA/Primary Examiner, Art Unit 1633
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