DETAILED ACTION
The present application is being examined under the pre-AIA first to invent provisions.
Continued Examination Under 37 CFR 1.114
A request for continued examination under 37 CFR 1.114, including the fee set forth in 37 CFR 1.17(e), was filed in this application after final rejection. Since this application is eligible for continued examination under 37 CFR 1.114, and the fee set forth in 37 CFR 1.17(e) has been timely paid, the finality of the previous Office action has been withdrawn pursuant to 37 CFR 1.114.
Claims 1-6 and 25-34 are pending and under examination.
Double Patenting rejections maintained
The rejections of claims 1-6, 25-33 and new claim 34 on the ground of nonstatutory double patenting as being unpatentable over claims 23-33, 38-41 and 43-45 of copending Application No. 14/704551 (US20150247150A1, cited previously) as applied to claim 1 above, in view of Doudna et al. (US20140068797A1, cited previously) in further view of Smith et al (Stem Cells 26:496-504, 2008) are maintained. The instant application and the copending applicant have a common assignee.
The reference Chen et al (US 2016/0017366, published January 21, 2016, effective filing date December 6, 2012, IDS) has been removed as art in view of Applicant’s Declaration under 37 USC §1.131 by each of the inventors Prashant Mali, George Church, and Luhan Yang evidencing reduction to practice of the claimed invention at least as early as before the December 6, 2012 filing date of the Chen provisional application.
Although the claims at issue are not identical, they are not patentably distinct from each other because the instant claimed invention is nearly rendered obvious over the claims of the copending application. The copending claims are directed to a composition comprising a S. pyogenes Cas9 and genus of a guide RNA sequence comprising a tracrRNA sequence that is 50 or more nucleotides in length (instant SEQ ID NO:46 comprises a tracrRNA that is more than 50 nucleotides in length). The instant claims are directed to a method of modifying a target sequence in a eukaryotic organism comprised of providing a Cas9 and a guide RNA sequence comprising SEQ ID NO:46. Regarding instant claims 7 and 25, copending claim 5 limits the Cas9 to be a nickase. Regarding instant claims 51-54, copending claims 9-10 state that Cas9 comprises a nuclear localization sequence.
Regarding the instant embodiment of a guide RNA sequence comprising the sequence of SEQ ID NO:46, “[The specification] may be used to learn the meaning of terms and interpreting the coverage of a claim." In re Basell Poliolefine Italia S.P.A., 89 USPQ2d 1030, 1036 (Fed. Cir. 2008). Thus, the specification is used as a dictionary to determine the meaning of the term guide RNA sequence. Figure 10 of the copending specification disclosed a guide RNA sequence (chiRNA (+85)), which comprises a scaffold sequence that is the same as instant SEQ ID NO:46, is the most effective guide RNA sequence to guide Cas9-mediated DNA modification (figure 10 and paragraph 0177). It would be obvious that the copending claimed composition comprising Cas9 and a genus of guide RNA sequence would include a guide RNA sequence that has been shown to be the best guide RNA sequence that functions with Cas9 to mediate DNA modifications. Further, it would be obvious that the copending claimed composition is used in a method of modifying DNA since Cas9 is a DNA nuclease. Therefore, it is obvious to a skilled artisan that the claimed composition of Zhang et al. would be used in a method of modifying a target nucleic acid sequence comprising the guide RNA sequence chiRNA (+85), which comprises a scaffold sequence that is the same as instant SEQ ID NO:46. Thus, even though the instant claims recite specificities not explicitly recited by the claims of the reference application/patent, the reference application/patent specification defines the application/patent claims as being directed to species of the instant claims (MPEP 804(II)(B)(2)(a), fifth paragraph; and non-precedential BPAI decision 2018-009106).
The copending application does not teach providing plurality of guide RNA sequences. However, this deficiency is made up in Doudna et al.
Doudna et al. teaches a method of modifying a mouse embryonic stem cell comprised of providing a C. pyogenes Cas9 and a guide RNA sequence (Example 7). Doudna et al. also teaches modifying the DNA of pluripotent stem cells comprised of Cas9 and a guide RNA sequence (paragraphs 0141 and 0142 in particular). Doudna et al. further teaches that providing a plurality of guide RNA sequences (paragraph 0271). Doudna discloses that AAV is an appropriate delivery system for the CRISPR-Cas vector system (paragraph 302). Doudna discloses Cas9 (DNA 2.0) was fused with C-terminal SV40 nuclear localization sequences (paragraph 736).
One of ordinary skill in the art at the time the invention was made would have been motivated to modify the copending method of altering a eukaryotic cell comprised of Cas9 and a guide RNA sequence of Zhang et al. to modify a human stem cell or a pluripotent stem cell comprised of Cas9 of Doudna to form a method of targeting a Cas9 protein to a plurality of target nucleic acids in a eukaryotic stem cell comprising providing a plurality of guide RNA sequences and providing a Cas9 protein with a guide RNA sequence comprising the chiRNA (+85) in order to more effective modify the DNA of a stem cell, because the copending claims are directed to a method of altering DNA comprised of Cas9 and a guide RNA sequence, including a chiRNA (+85), and Doudna et al. teaches modifying a human stem cell or pluripotent stem cell comprising a Cas9 and guide RNA sequence and showed that Cas9 and a guide RNA sequence effectively modify a human embryonic stem cell. Furthermore, the modified method of altering a stem cell can include providing a plurality of guide RNA sequences, because Doudna also teaches a method of modifying DNA with Cas9 comprised of providing a plurality of guide RNA sequences.
One of ordinary skill in the art at the time the invention was made would have had a reasonable expectation of success for modifying the copending method of altering a eukaryotic cell comprised of Cas9 and a guide RNA sequence of Zhang et al. to modify a human stem cell or a pluripotent stem cell comprised of Cas9 of Doudna to form a method of modifying a human embryonic stem cell or pluripotent stem cell comprised of Cas9 and a guide RNA sequence comprising the chiRNA (+85) in order to more effective modify the DNA of a stem cell, because the copending claims are directed to a method of altering DNA comprised of Cas9 and a guide RNA sequence, including a chiRNA (+85), and Doudna et al. teaches modifying a human stem cell or pluripotent stem cell comprising a Cas9 and guide RNA sequence and showed that Cas9 and a guide RNA sequence effectively modify a human embryonic stem cell.
Neither the claims of Application No. 14/704551 nor Doudna disclose the limitation “wherein a target nucleic acid sequence of the different target nucleic acid sequences is within an AAVS 1 locus”. However, the AAVS1 locus was well known to be an optimal location for transgene integration at the time this application was filed.
Smith disclose that transgene integration at the AAVS1 site demonstrated increased expression and stability for the transgene. (page 498, 1st column to page 503, 1st column; Table 1;Abstract)
One of ordinary skill in the art would have been motivated to apply Smith’s disclosure of transgene integration at the AAVS1 site to the claims of Application No. 14/704551 and Doudna’s method of targeting a Cas9 protein to a plurality of
target nucleic acids in a eukaryotic cell comprising providing to the eukaryotic cell a plurality of guide RNA sequences complementary to the plurality of target nucleic acid sequences in the eukaryotic cell because Smith disclose that transgene integration at the AAVS1 site demonstrated increased expression and stability for the transgene. Thus, the AAVS1 site was known to be a desirable locus for the insertion of the CRISPR-Cas vector system for use in eukaryotic cells comprising a plurality of guide RNAs. Absent unexpected results it would have been obvious to have a method of targeting a Cas9 protein to a plurality of target nucleic acids in a eukaryotic cell comprising providing to the eukaryotic cell a plurality of guide RNA sequences complementary to the plurality of target nucleic acid sequences in the eukaryotic cell, wherein a target nucleic acid sequence of the plurality of target nucleic acid sequences is within an AAVS 1 locus, and providing to the eukaryotic cell a Cas9 protein that interacts with the plurality of guide RNA sequences to form guide RNA/Cas9 protein complexes bound to the plurality of target nucleic acids.
This is a provisional nonstatutory double patenting rejection because the patentably indistinct claims have not in fact been patented.
The rejections of Claims 1-6, 25-33 and new claim 34 on the ground of nonstatutory double patenting as being unpatentable over claims 1-30 of U.S. Patent No. 8871445B2, cited previously as applied to claim 1 above, and further in view of Doudna et al. (US20140068797A1, cited previously) in further view of Smith et al (Stem Cells 26:496-504, 2008, cited previously) are maintained. The instant application and U.S. Patent No. 8871445B2 have a common assignee.
The reference Chen et al (US 2016/0017366, published January 21, 2016, effective filing date December 6, 2012, IDS) has been removed as art in view of Applicant’s Declaration under 37 USC §1.131 by each of the inventors Prashant Mali, George Church, and Luhan Yang evidencing reduction to practice of the claimed invention at least as early as before the December 6, 2012 filing date of the Chen provisional application.
Although the claims at issue are not identical, they are not patentably distinct from each other because the instant claimed invention is anticipated by or nearly rendered obvious over the claims of the patent. The patented claims are directed to a method of modifying a target sequence comprising a Cas9 comprising two or more nuclear localization sequences, and a genus of a guide RNA sequence, or a composition comprising said Cas9 and a genus of a guide RNA sequence. The instant claimed method comprising a genus of Cas9 comprising a nuclear localization sequence (claims 51-54), and a guide RNA sequence comprising SEQ ID NO:46.
Regarding the instant embodiment of a guide RNA sequence comprising the sequence of SEQ ID NO:46, “[The specification] may be used to learn the meaning of terms and interpreting the coverage of a claim." In re Basell Poliolefine Italia S.P.A., 89 USPQ2d 1030, 1036 (Fed. Cir. 2008). The specification of the patent disclosed a guide RNA sequence comprising SEQ ID NO:364 (chiRNA (+85)), which comprises a scaffold sequence that is the same as instant SEQ ID NO:46, and demonstrated that it is the best guide RNA sequence to guide Cas9-mediated DNA modification (figures 18 and 19). It would be obvious that the copending claimed method of modifying DNA with Cas9 would include the guide RNA sequence that has been shown to be the best guide RNA sequence that functions with Cas9 to mediate DNA modifications. Therefore, the patented claims of Zhang et al. encompasses a method of modifying a target nucleic acid sequence comprising a guide RNA sequence comprising SEQ ID NO:364.
Regarding patented claims 18-30, it would be obvious that the patented composition is used in a method for modifying a target nucleic acid as shown by the claimed methods that are recited in patented claims 1-17. Thus, even though the instant claims recite specificities not explicitly recited by the claims of the reference application/patent, the reference application/patent specification defines the application/patent claims as being directed to species of the instant claims (MPEP 804(II)(B)(2)(a), fifth paragraph; and non-precedential BPAI decision 2018-009106).
The patented claims are silent for providing plurality of guide RNA sequences. However, this deficiency is made up in Doudna et al.
Doudna et al. teaches a method of modifying a mouse embryonic stem cell comprised of providing a Cas9 and a guide RNA sequence (Example 7). Doudna et al. also teaches modifying the DNA of pluripotent stem cells comprised of Cas9 and a guide RNA sequence (paragraphs 0141 and 0142 in particular). Doudna et al. further teaches that providing a plurality of guide RNA sequences (paragraph 0271). Doudna discloses that AAV is an appropriate delivery system for the CRISPR-Cas vector system (paragraph 302). Doudna discloses Cas9 (DNA 2.0) was fused with C-terminal SV40 nuclear localization sequences (paragraph 736).
One of ordinary skill in the art at the time the invention was made would have been motivated to modify the copending method of altering a eukaryotic cell comprised of Cas9 and a guide RNA sequence of Zhang et al. to modify a human stem cell or a pluripotent stem cell comprised of Cas9 of Doudna to form a method of targeting a Cas9 protein to a plurality of target nucleic acids in a eukaryotic stem cell comprising providing a plurality of guide RNA sequences and providing a Cas9 protein with a guide RNA sequence comprising the chiRNA (+85) in order to more effective modify the DNA of a stem cell, because the copending claims are directed to a method of altering DNA comprised of Cas9 and a guide RNA sequence, including a chiRNA (+85), and Doudna et al. teaches modifying a human stem cell or pluripotent stem cell comprising a Cas9 and guide RNA sequence and showed that Cas9 and a guide RNA sequence effectively modify a human embryonic stem cell. Furthermore, the modified method of altering a stem cell can include providing a plurality of guide RNA sequences, because Doudna also teaches a method of modifying DNA with Cas9 comprised of providing a plurality of guide RNA sequences.
One of ordinary skill in the art at the time the invention was made would have had a reasonable expectation of success for modifying the copending method of altering a eukaryotic cell comprised of Cas9 and a guide RNA sequence of Zhang et al. to modify a human stem cell or a pluripotent stem cell comprised of Cas9 of Doudna to form a method of modifying a human embryonic stem cell or pluripotent stem cell comprised of Cas9 and a guide RNA sequence comprising the chiRNA (+85) in order to more effective modify the DNA of a stem cell, because the copending claims are directed to a method of altering DNA comprised of Cas9 and a guide RNA sequence, including a chiRNA (+85), and Doudna et al. teaches modifying a human stem cell or pluripotent stem cell comprising a Cas9 and guide RNA sequence and showed that Cas9 and a guide RNA sequence effectively modify a human embryonic stem cell.
Neither the claims of U.S. Patent No. 8871445B2 nor Doudna disclose “wherein a target nucleic acid sequence of the different target nucleic acid sequences is within an AAVS 1 locus”. However, the AAVS1 locus was well known to be an optimal location for transgene integration at the time this application was filed.
Smith disclose that transgene integration at the AAVS1 site demonstrated increased expression and stability for the transgene. (page 498, 1st column to page 503, 1st column; Table 1;Abstract).
One of ordinary skill in the art would have been motivated to apply Smith’s disclosure of transgene integration at the AAVS1 site to the claims of U.S. Patent No. 8871445B2 and Doudna’s method of targeting a Cas9 protein to a plurality of target nucleic acids in a eukaryotic cell comprising providing to the eukaryotic cell a plurality of guide RNA sequences complementary to the plurality of target nucleic acid sequences in the eukaryotic cell because Smith disclose that transgene integration at the AAVS1 site demonstrated increased expression and stability for the transgene. Thus, the AAVS1 site was known to be a desirable locus for the insertion of the CRISPR-Cas vector system for use in eukaryotic cells comprising a plurality of guide RNAs. Absent unexpected results it would have been obvious to have a method of targeting a Cas9 protein to a plurality of target nucleic acids in a eukaryotic cell comprising providing to the eukaryotic cell a plurality of guide RNA sequences complementary to the plurality of target nucleic acid sequences in the eukaryotic cell, wherein a target nucleic acid sequence of the plurality of target nucleic acid sequences is within an AAVS1 locus, and providing to the eukaryotic cell a Cas9 protein that interacts with the plurality of guide RNA sequences to form guide RNA/Cas9 protein complexes bound to the plurality of target nucleic acids.
The rejections of claims 1-6, 25-33 and new claim 34 on the ground of nonstatutory double patenting as being unpatentable over claims 1-21, 29 and 30 of U.S. Patent No. 8906616B2, cited previously, as applied to claim 1 above in view of Doudna et al. (US20140068797A1, cited previously) in further view of Smith et al (Stem Cells 26:496-504, 2008, cited previously) are maintained. The instant application and U.S. Patent No. 8906616B2 have a common assignee.
The reference Chen et al (US 2016/0017366, published January 21, 2016, effective filing date December 6, 2012, IDS) has been removed as art in view of Applicant’s Declaration under 37 USC §1.131 by each of the inventors Prashant Mali, George Church, and Luhan Yang evidencing reduction to practice of the claimed invention at least as early as before the December 6, 2012 filing date of the Chen provisional application.
Although the claims at issue are not identical, they are not patentably distinct from each other because the instant claimed invention is anticipated by or nearly rendered obvious over the claims of the patent. The patented claims are directed to a method of modifying a target sequence comprising a Cas9 and a genus of a guide RNA sequence (claims 29 and 30), or a composition comprising a Cas9 and a genus of a guide RNA sequence (claims 1-21). The instant claimed method comprising a genus of Cas9 comprising a nuclear localization sequence (claims 51-54), and a guide RNA sequence comprising SEQ ID NO:46.
Regarding the instant embodiment of a guide RNA sequence comprising the sequence of SEQ ID NO:46, “[The specification] may be used to learn the meaning of terms and interpreting the coverage of a claim." In re Basell Poliolefine Italia S.P.A., 89 USPQ2d 1030, 1036 (Fed. Cir. 2008). Thus, the specification is used as a dictionary to determine the meaning of the term guide RNA sequence. The specification of the patent disclosed a guide RNA sequence comprising SEQ ID NO:153 (chiRNA (+85)), which is comprised of 85 nucleotides wild type S. pyogenes Cas9 tracrRNA (figure 10; example 4). Guide RNA sequence comprising SEQ ID NO:153 has the same scaffold sequence that is the same as instant SEQ ID NO:46. Furthermore, Zhang et al. demonstrated that it is the best guide RNA sequence to guide Cas9-mediated DNA modification (figures 10 and 11). Therefore, patented claims 29 and 30 encompasses a method of modifying a target nucleic acid sequence comprising a guide RNA sequence comprising SEQ ID NO:153.
Regarding patented claims 1-21, it would be obvious that the patented composition is used in a method for modifying a target nucleic acid as shown by the claimed methods that are recited in patented claims 29 and 30. Patent claim 8, limits the tracr RNA sequence to comprise at least nucleotides 1-85 of the corresponding wild type S. pyogenes Cas9 tracRNA. The specification is used as a dictionary to determine the meaning of the term “at least nucleotides 1-85 of the corresponding wild type S. pyogenes Cas9 tracRNA”. The specification of the patent disclosed a guide RNA sequence comprising SEQ ID NO:153, which is comprised of 85 nucleotides wild type S. pyogenes Cas9 tracRNA (figure 10; example 4). Guide RNA sequence comprising SEQ ID NO:153 has the same scaffold sequence that is the same as instant SEQ ID NO:46.
Thus, even though the instant claims recite specificities not explicitly recited by the claims of the reference application/patent, the reference application/patent specification defines the application/patent claims as being directed to species of the instant claims (MPEP 804(II)(B)(2)(a), fifth paragraph; and non-precedential BPAI decision 2018-009106).
The patented claims are silent that the eukaryotic cell is a stem cell, and providing plurality of guide RNA sequences. However, this deficiency is made up in Doudna et al.
Doudna et al. teaches a method of modifying a mouse embryonic stem cell comprised of providing a Cas9 and a guide RNA sequence (Example 7). Doudna et al. also teaches modifying the DNA of pluripotent stem cells comprised of Cas9 and a guide RNA sequence (paragraphs 0141 and 0142 in particular). Doudna et al. further teaches that providing a plurality of guide RNA sequences (paragraph 0271). Doudna discloses that AAV is an appropriate delivery system for the CRISPR-Cas vector system (paragraph 302). Doudna discloses Cas9 (DNA 2.0) was fused with C-terminal SV40 nuclear localization sequences (paragraph 736).
One of ordinary skill in the art at the time the invention was made would have been motivated to modify the copending method of altering a eukaryotic cell comprised of Cas9 and a guide RNA sequence of Zhang et al. to modify a human stem cell or a pluripotent stem cell comprised of Cas9 of Doudna to form a method of targeting a Cas9 protein to a plurality of target nucleic acids in a eukaryotic stem cell comprising providing a plurality of guide RNA sequences and providing a Cas9 protein with a guide RNA sequence comprising the chiRNA (+85) in order to more effective modify the DNA of a stem cell, because the copending claims are directed to a method of altering DNA comprised of Cas9 and a guide RNA sequence, including a chiRNA (+85), and Doudna et al. teaches modifying a human stem cell or pluripotent stem cell comprising a Cas9 and guide RNA sequence and showed that Cas9 and a guide RNA sequence effectively modify a human embryonic stem cell. Furthermore, the modified method of altering a stem cell can include providing a plurality of guide RNA sequences, because Doudna also teaches a method of modifying DNA with Cas9 comprised of providing a plurality of guide RNA sequences.
One of ordinary skill in the art at the time the invention was made would have had a reasonable expectation of success for modifying the copending method of altering a eukaryotic cell comprised of Cas9 and a guide RNA sequence of Zhang et al. to modify a human stem cell or a pluripotent stem cell comprised of Cas9 of Doudna to form a method of modifying a human embryonic stem cell or pluripotent stem cell comprised of Cas9 and a guide RNA sequence comprising the chiRNA (+85) in order to more effective modify the DNA of a stem cell, because the copending claims are directed to a method of altering DNA comprised of Cas9 and a guide RNA sequence, including a chiRNA (+85), and Doudna et al. teaches modifying a human stem cell or pluripotent stem cell comprising a Cas9 and guide RNA sequence and showed that Cas9 and a guide RNA sequence effectively modify a human embryonic stem cell.
Neither the claims of U.S. Patent No. 8906616B2 nor Doudna disclose “wherein a target nucleic acid sequence of the different target nucleic acid sequences is within an AAVS 1 locus”. However, the AAVS1 locus was well known to be an optimal location for transgene integration at the time this application was filed.
Smith disclose that transgene integration at the AAVS1 site demonstrated increased expression and stability for the transgene. (page 498, 1st column to page 503, 1st column; Table 1;Abstract)
One of ordinary skill in the art would have been motivated to apply Smith’s disclosure of transgene integration at the AAVS1 site to the claims of U.S. Patent No. 8906616B2 and Doudna’s method of targeting a Cas9 protein to a plurality of target nucleic acids in a eukaryotic cell comprising providing to the eukaryotic cell a plurality of guide RNA sequences complementary to the plurality of target nucleic acid sequences in the eukaryotic cell because Smith disclose that transgene integration at the AAVS1 site demonstrated increased expression and stability for the transgene. Thus, the AAVS1 site was known to be a desirable locus for the insertion of the CRISPR-Cas vector system for use in eukaryotic cells comprising a plurality of guide RNAs. Absent unexpected results it would have been obvious to have a method of targeting a Cas9 protein to a plurality of target nucleic acids in a eukaryotic cell comprising providing to the eukaryotic cell a plurality of guide RNA sequences complementary to the plurality of target nucleic acid sequences in the eukaryotic cell, wherein a target nucleic acid sequence of the plurality of target nucleic acid sequences is within an AAVS 1 locus, and providing to the eukaryotic cell a Cas9 protein that interacts with the plurality of guide RNA sequences to form guide RNA/Cas9 protein complexes bound to the plurality of target nucleic acids.
The rejections of claims 1-6, 25-33 and new claim 34 on the ground of nonstatutory double patenting as being unpatentable over claims 1-30 of U.S. Patent No. 8932814B2, cited previously, as applied to claim 1 above in view of Doudna et al. (US20140068797A1, cited previously) in further view of Smith et al (Stem Cells 26:496-504, 2008, cited previously) are maintained. The instant application and U.S. Patent No. 8932814B2 have a common assignee.
The reference Chen et al (US 2016/0017366, published January 21, 2016, effective filing date December 6, 2012, IDS) has been removed as art in view of Applicant’s Declaration under 37 USC §1.131 by each of the inventors Prashant Mali, George Church, and Luhan Yang evidencing reduction to practice of the claimed invention at least as early as before the December 6, 2012 filing date of the Chen provisional application.
Although the claims at issue are not identical, they are not patentably distinct from each other because the instant claimed invention is nearly rendered obvious over the claims of the patent. The patented claims are directed to a method of modifying a target sequence comprising a Cas9 comprising a mutation in the catalytic domain and a nuclear localization sequence, and a genus of a guide RNA sequence, or a composition comprising said Cas9 and a genus of a guide RNA sequence. The instant claimed method comprising a genus of Cas9 and a nuclear localization sequence (claims 51-54), and a guide RNA sequence comprising SEQ ID NO:46. The instant claimed method comprising a genus of Cas9 encompasses a Cas9 mutant.
Regarding the instant embodiment of a guide RNA sequence comprising the sequence of SEQ ID NO:46, “[The specification] may be used to learn the meaning of terms and interpreting the coverage of a claim." In re Basell Poliolefine Italia S.P.A., 89 USPQ2d 1030, 1036 (Fed. Cir. 2008). Thus, the specification is used as a dictionary to determine the meaning of the term guide RNA sequences. The specification of the patent disclosed a guide RNA sequence comprising SEQ ID NO:366 (chiRNA(+85), which comprises a scaffold sequence that is the same as instant SEQ ID NO:46, and demonstrated that it is the best guide RNA sequence to guide Cas9-mediated DNA modification (figures 18 and 19). It would be obvious that the copending claimed method of modifying DNA with Cas9 would include the guide RNA sequence that has been shown to be the best guide RNA sequence that functions with Cas9 to mediate DNA modifications. Therefore, the patented claims of Zhang et al. encompass a method of modifying a target nucleic acid sequence comprising a guide RNA sequence comprising SEQ ID NO:366.
Regarding patented claims 13, 25, 26 and 30, it would be obvious that the patented composition is used in a method for modifying a target nucleic acid as shown by the claimed methods that are recited in patented claims 1-12, 14-24, 28 and 29.
Thus, even though the instant claims recite specificities not explicitly recited by the claims of the reference application/patent, the reference application/patent specification defines the application/patent claims as being directed to species of the instant claims (MPEP 804(II)(B)(2)(a), fifth paragraph; and non-precedential BPAI decision 2018-009106).
The patented claims are silent that the eukaryotic cell is a stem cell, and providing plurality of guide RNA sequences. However, this deficiency is made up in Doudna et al.
Doudna et al. teaches a method of modifying a mouse embryonic stem cell comprised of providing a Cas9 and a guide RNA sequence (Example 7). Doudna et al. also teaches modifying the DNA of pluripotent stem cells comprised of Cas9 and a guide RNA sequence (paragraphs 0141 and 0142 in particular). Doudna et al. further teaches that providing a plurality of guide RNA sequences (paragraph 0271). Doudna discloses that AAV is an appropriate delivery system for the CRISPR-Cas vector system (paragraph 302). Doudna discloses Cas9 (DNA 2.0) was fused with C-terminal SV40 nuclear localization sequences (paragraph 736).
One of ordinary skill in the art at the time the invention was made would have been motivated to modify the copending method of altering a eukaryotic cell comprised of Cas9 and a guide RNA sequence of Zhang et al. to modify a human stem cell or a pluripotent stem cell comprised of Cas9 of Doudna to form a method of targeting a Cas9 protein to a plurality of target nucleic acids in a eukaryotic stem cell comprising providing a plurality of guide RNA sequences and providing a Cas9 protein with a guide RNA sequence comprising the chiRNA (+85) in order to more effective modify the DNA of a stem cell, because the copending claims are directed to a method of altering DNA comprised of Cas9 and a guide RNA sequence, including a chiRNA (+85), and Doudna et al. teaches modifying a human stem cell or pluripotent stem cell comprising a Cas9 and guide RNA sequence and showed that Cas9 and a guide RNA sequence effectively modify a human embryonic stem cell. Furthermore, the modified method of altering a stem cell can include providing a plurality of guide RNA sequences, because Doudna also teaches a method of modifying DNA with Cas9 comprised of providing a plurality of guide RNA sequences.
One of ordinary skill in the art at the time the invention was made would have had a reasonable expectation of success for modifying the copending method of altering a eukaryotic cell comprised of Cas9 and a guide RNA sequence of Zhang et al. to modify a human stem cell or a pluripotent stem cell comprised of Cas9 of Doudna to to form a method of targeting a Cas9 protein to a plurality of target nucleic acids in a eukaryotic stem cell comprising providing a plurality of guide RNA sequences and providing a Cas9 protein with a guide RNA sequence comprising the chiRNA (+85) in order to more effective modify the DNA of a stem cell, because the copending claims are directed to a method of altering DNA comprised of Cas9 and a guide RNA sequence, including a chiRNA (+85), and Doudna et al. teaches modifying a human stem cell or pluripotent stem cell comprising a Cas9 and guide RNA sequence and showed that Cas9 and a guide RNA sequence effectively modify a human embryonic stem cell.
Neither the claims of U.S. Patent No. 8932814B2 nor Doudna disclose “wherein a target nucleic acid sequence of the different target nucleic acid sequences is within an AAVS 1 locus”. However, the AAVS1 locus was well known to be an optimal location for transgene integration at the time this application was filed.
Smith disclose that transgene integration at the AAVS1 site demonstrated increased expression and stability for the transgene. (page 498, 1st column to page 503, 1st column; Table 1;Abstract)
One of ordinary skill in the art would have been motivated to apply Smith’s disclosure of transgene integration at the AAVS1 site to the claims of U.S. Patent No. 8932814B2 and Doudna’s method of targeting a Cas9 protein to a plurality of target nucleic acids in a eukaryotic cell comprising providing to the eukaryotic cell a plurality of guide RNA sequences complementary to the plurality of target nucleic acid sequences in the eukaryotic cell because Smith disclose that transgene integration at the AAVS1 site demonstrated increased expression and stability for the transgene. Thus, the AAVS1 site was known to be a desirable locus for the insertion of the CRISPR-Cas vector system for use in eukaryotic cells comprising a plurality of guide RNAs. Absent unexpected results it would have been obvious to have a method of targeting a Cas9 protein to a plurality of target nucleic acids in a eukaryotic cell comprising providing to the eukaryotic cell a plurality of guide RNA sequences complementary to the plurality of target nucleic acid sequences in the eukaryotic cell, wherein a target nucleic acid sequence of the plurality of target nucleic acid sequences is within an AAVS 1 locus, and providing to the eukaryotic cell a Cas9 protein that interacts with the plurality of guide RNA sequences to form guide RNA/Cas9 protein complexes bound to the plurality of target nucleic acids.
Applicant argues that as previously that the Examiner is prohibited from using the
Zhang ODP references as prior art in determining obviousness of Applicant's claimed subject matter.
In response, as discussed previously, even though the instant claims recite specificities not explicitly recited by the claims of the reference application/patent, the reference application/patent specification defines the application/patent claims as being directed to species of the instant claims (MPEP 804(II)(B)(2)(a), fifth paragraph; and non-precedential BPAI decision 2018-009106).
In response to Applicant’s argument that The "[d]etermination of obviousness cannot be based on the hindsight combination of components selectively culled from the prior art to fit the parameters of the patented invention, it must be recognized that any judgment on obviousness is in a sense necessarily a reconstruction based upon hindsight reasoning. But so long as it takes into account only knowledge which was within the level of ordinary skill at the time the claimed invention was made, and does not include knowledge gleaned only from the applicant's disclosure, such a reconstruction is proper. See In re McLaughlin, 443 F.2d 1392, 170 USPQ 209 (CCPA 1971). As discussed below, there is ample motivation to combine the references independent of the inherent feature.
Applicant argues that the Examiner has identified no evidence that one of skill reading Zhang's claims would be directed to the AAVS1 locus specifically, out of many possible targets within the human genome. Applicant argues that neither Zhang nor Doudna provides any direction to select the AAVS1 locus, out of the many possible locations in the genome that may be targeted by gRNA. Applicant argues that Smith provides no direction that a transgene can be inserted into the AAVS 1 locus by any system other than its AAV2 system. The only disclosure of targeting the AAVS1 locus using a Cas9/gRNA system is applicant's disclosure. Applicant argues that all the Examiner has done is to review claim 1 and piece together the prior art using impermissible hindsight reconstruction to identify the AAVS1 locus. This is evident
because the art discloses that the AAVS1 locus can accommodate trans gene insertion by using a system completely different from the claimed Cas9/gRNA system. Applicant argues that no hint is provided of a Cas9-gRNA system. The Examiner has identified no reason why one of skill would have selected the AAVS1 locus, as opposed to any other location within the genome. Applicant argues that the Examiner has cherry picked the prior art that uses a very different system and has alleged motivation based solely on
impermissible hindsight reconstruction.
Applicant further argues that Smith is unrelated to a CRISPR-Cas system. Smith teaches transgene insertion that is based on AAV2 technology. Specifically, Smith teaches that the essential requirements for integration at the AAVS1 locus include the viral inverted terminal repeats (ITRs), viral REP78/68 integrase and the AAV2 p5 promoter.
Applicant argues that the Examiner states that one of skill would be motivated "because Smith disclose that trans gene integration at the AAVS1 site demonstrated increased expression and stability for the transgene." Applicant argues that this result is achieved precisely using the drastically different AAV2 technology. Applicant argues that there is no evidence presented by the Examiner that the claimed Cas9/gRNA system is analogous to the AAV2 technology, or that such would function, or would be expected to function similarly to achieve transgene integration at the AAVS1 locus with increased expression and stability, as with the AAV2 system.
Applicant also argue there is, however, no evidence to support that the AAVS1 site was known to be a desirable locus for the insertion of CRISPR-Cas vector system. Applicant argues that there is no prior art disclosing that a CRISPR-Cas system was known to be inserted at the AAVS1 site. Applicant argues that there is no evidence that one of skill would have considered inserting a CRISPR-Cas system at the AAVS1 site, as opposed to any other possible transgene. Applicant argues that the AAV1 site was merely taught in Smith as a site for transgene insertion based on AAV vector technology which requires the viral inverted terminal repeats (ITRs), viral REP78/68 integrase, as well as the AAV2 p5 promoter.
Applicant’s arguments have been considered but are not persuasive. Doudna disclose that donor sequences can be introduced as naked nucleic acid, as nucleic acid complexed with an agent such as a liposome or poloxamer, or can be delivered by viruses (e.g., adenovirus, AAV), as described above for nucleic acids encoding a DNA-targeting RNA and/or site-directed modifying polypeptide and/or donor polynucleotide (paragraph 302). As evidenced by the Addgene vector guide AAV2 is the most commonly used serotype for AAV vector construction (Addgene adeno-associated viral (AAV) vector guide, page 5, 1st paragraph, downloaded October 8, 2025). Application No. 14/704551 (US20150247150A1), U.S. Patent No. 8871445B2, U.S. Patent No. 8906616B2 , U.S. Patent No. 8932814B2, the primary references in the ODP rejections discussed above, all disclose the use of adeno-associated viruses for targeting a Cas9 protein to a target nucleic acid in a eukaryotic cell.
Given that the use of AAV as a viral vector delivery system was well known, given that AAV2 is the most commonly used serotype for AAV vector construction, given that Doudna discloses that AAV is an appropriate delivery system for the CRISPR-Cas vector system, absent unexpected results it would have been obvious to combine the claims of Application No. 14/704551 (US20150247150A1), U.S. Patent No. 8871445B2, U.S. Patent No. 8906616B2 , U.S. Patent No. 8932814B2, and Doudna’s method of targeting a Cas9 protein to a plurality of target nucleic acids in a eukaryotic cell comprising providing to the eukaryotic cell a plurality of guide RNA sequences complementary to the plurality of target nucleic acid sequences in the eukaryotic cell with Smith’s disclosure of transgene integration at the AAVS1 site to have a method of targeting a Cas9 protein to a plurality of target nucleic acids in a eukaryotic cell comprising providing to the eukaryotic cell a plurality of guide RNA sequences complementary to the plurality of target nucleic acid sequences in the eukaryotic cell, wherein a target nucleic acid sequence of the plurality of target nucleic acid sequences is within an AAVS1 locus, and providing to the eukaryotic cell a Cas9 protein that interacts with the plurality of guide RNA sequences to form guide RNA/Cas9 protein complexes bound to the plurality of target nucleic acids.
Further, given that the methods of gene manipulation and transfection of adeno-associated vectors into eukaryotic cells to induce recombination were well known at the time the application was filed one of ordinary skill would have had a reasonable expectation of success in targeting the AAVS1 locus using a CRISPR-Cas transgene system. Applicant has not sufficiently described that there was not a reasonable expectation of success.
In response to Applicant’s argument Smith is unrelated to a CRISPR-Cas system one cannot show nonobviousness by attacking references individually where the rejections are based on combinations of references. See In re Keller, 642 F.2d 413, 208 USPQ 871 (CCPA 1981); In re Merck & Co., 800 F.2d 1091, 231 USPQ 375 (Fed. Cir. 1986). Smith disclose a viral vector delivery system for inserting transgenes within the genome of a stem cell. Smith disclose that transgene integration at the AAVS1 site in stem cells demonstrated increased expression and stability for the transgene
It appears that Applicant is arguing that Smith is nonanalogous art. MPEP 2141.01(a) I recites that a reference is analogous art to the claimed invention if: (1) the reference is from the same field of endeavor as the claimed invention (even if it addresses a different problem); or (2) the reference is reasonably pertinent to the problem faced by the inventor (even if it is not in the same field of endeavor as the claimed invention). See Bigio, 381 F.3d at 1325, 72 USPQ2d at 1212. Smith disclose a commonly used viral vector delivery system. Doudna disclose that donor sequences can be delivered by viruses (e.g., adenovirus, AAV). The specification of Application No. 14/704551 (US20150247150A1), U.S. Patent No. 8871445B2, U.S. Patent No. 8906616B2 and U.S. Patent No. 8932814B2, the primary references in the ODP rejections discussed above, all disclose the use of adeno-associated viruses for targeting a Cas9 protein to a target nucleic acid in a eukaryotic cell. Thus, Applicant has not sufficiently demonstrated why Smith is nonanalogous art.
In response to Applicant’s argument that all the Examiner has done is to review claim 1 and piece together the prior art using impermissible hindsight reconstruction to identify the AAVS 1 locus, all the Applicant has done is to insert a commonly used site-directed insertion site into claim 1 and argued that it would not be obvious to use that particular insertion site. Absent unexpected results as to why this particular site-directed insertion site would have it, as discussed above it would have been obvious to use the AAVS1 insertion site as described by Smith. Smith disclose that transgene integration at the AAVS1 site demonstrated increased expression and stability for the transgene.
In response to Applicant’s argument that there is no evidence presented by the Examiner that the claimed Cas9/gRNA system is analogous to the AAV2 technology, or that such would function, or would be expected to function similarly to achieve transgene integration at the AAVS1 locus with increased expression and stability, as with the AAV2 system, the fact that disclose that transgene integration at the AAVS1 site demonstrated increased expression and stability for the transgene and that Doudna discloses that AAV is an appropriate delivery system for the CRISPR-Cas vector system it would have been obvious to use the viral vector delivery system described in Smith.
In response to Applicant’s argument that there is no evidence to support that the AAVS1 site was known to be a desirable locus for the insertion of CRISPR-Cas vector system, given that the AAV2 viral vector delivery system is a common delivery system and the advantages of using the AAV2 delivery system as described in Smith it would have been obvious to use the AAV2 viral vector delivery system for insertion of the CRISPR-Cas transgene into the AAVS1 locus. Applicant has not described any unexpected results demonstrating that the AAVS1 locus was superior for insertion of the CRISPR-Cas transgene compared to other locus.
NEW REJECTIONS:
Claim Rejections - 35 USC § 112
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 66-70 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.
There is not support in the specification as filed for the limitation “wherein the Cas9 enzyme includes an SV40 nuclear localization signal”. The specification only disclose “RNA-guided gene targeting in human cells involves co-expression of the Cas9 protein bearing a C-terminus SV40 nuclear localization signal with one or more guide RNAs (gRNAs) expressed from the human U6 polymerase III promoter”.
Summary
Claims 1-6 and 25-34 stand rejected
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/MARK HALVORSON/ Primary Examiner, Art Unit 1646