DETAILED ACTION
Notice of Pre-AIA or AIA Status
The present application, filed on or after March 16, 2013, is being examined under the first inventor to file provisions of the AIA .
Applicant’s amendment filed on 04/10/2026 has been entered.
Claims 1, 20-21, 24-27, 29, 34-35, 38 and new claims 41-49 are pending in the present application.
Applicant’s election without traverse of Group II, drawn to a method of altering a target nucleic acid sequence of the present application, in the reply filed on 04/10/2026 is acknowledged.
Applicant also elected without traverse the following species: (i) a system comprising one or more nucleic acids encoding a single engineered CRISPR-Cas system; (ii) Cas11, Cas3, the two or more additional Cas proteins, and the at least one gRNA are encoded by different nucleic acids; (iii) two or more additional Cas proteins of Cas5, Cas7, and Cas8; (iv) target nucleic acid in a cell; and (v) introducing the system into the cell via in vivo administration to a subject.
Accordingly, claims 1 and 20-21 are withdrawn from further consideration because they are directed to a non-elected invention.
Additionally, claims 45 and 48-49 are also withdrawn from further consideration because they are drawn to non-elected species.
Therefore, claims 24-27, 29, 34-35, 38, 41-44 and 46-47 are examined on the merits herein with the above elected species.
Claim Rejections - 35 USC § 112 (Lack of Written Description)
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 24-27, 28, 34-35, 38, 41-44 and 47 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.
MPEP 2163 - 35 U.S.C. 112(a) and the first paragraph of pre-AIA 35 U.S.C. 112 require that the “specification shall contain a written description of the invention ....” This requirement is separate and distinct from the enablement requirement. Ariad Pharm., Inc. v. Eli Lilly & Co., 598 F.3d 1336, 1340, 94 USPQ2d 1161, 1167 (Fed. Cir. 2010) (en banc). Vas-Cath Inc. v. Mahurkar, 19USPQ2d 1111 (Fed. Cir. 1991), clearly states that “applicant must convey with reasonable clarity to those skilled in the art that, as of the filing date sought, he or she was in possession of the invention. The invention is, for purposes of the ‘written description’ inquiry, whatever is now claimed.” Vas-Cath Inc. v. Mahurkar, 19USPQ2d at 1117. The specification does not “clearly allow persons of ordinary skill in the art to recognize that [he or she] invented what is claimed. ”Vas-Cath Inc. v. Mahurkar, 19USPQ2d at 1116.
The instant claims encompass a method of altering a target nucleic acid sequence comprising contacting a target nucleic acid sequence (e.g., introducing into a cell in vitro, ex vivo, or in vivo containing the target nucleic acid sequence) with an engineered clustered Regularly Interspaced Short Palindromic Repeats (CRISPR)-CRISPR associated (Cas) (CRISPR-Cas) system and/or one or more nucleic acids encoding the engineered CRISPR-Cas system or a composition thereof, wherein the engineered CRISPR-Cas system comprises: (a) Cas11; (b) Cas3; (c) two or more additional Cas proteins (e.g., 2, 3, 4 or more additional Cas proteins) from a CRISPR-Associated Complex for Anti-viral Defense (Cascade) complex; and (d) at least one guide RNA (gRNA), wherein each gRNA is configured to hybridize to a portion of a target nucleic acid sequence; the same method wherein the engineered CRISPR-Cas system is derived from Neisseria lactamica (dependent claim 47).
Apart from disclosing a compact Type-IC CRISPR-Cas3 from N. lactamica (Nla CRISPR-Cas3 system) that consists of a CRISPR array and seven cas genes, including the spacer acquisition genes cas1, cas2, and cas4, the nuclease-helicase gene cas3, and the set of genes comprised of cas5, cas8 and cas7 encoding protein subunits of Cascade, and further discovering that cas8 gene of the Nla CRISPR-Cas3 system also encodes Cas11 via alternative translation initiation with the NlaCas11 is an integral part of the target recognition module Cascade for genome engineering with the Nla CRISPR-Cas3 system (see at least Examples 1-2, 4-5; and Figs. 1A, 2A, 4 and 12), the instant specification fails to provide sufficient description for other engineered CRISPR-Cas system comprising Cas11, Cas3, with any two or three additional Cas proteins from any Complex, not necessarily limited to Nla Cas5, Cas8 and Cas7, and at least one gRNA to be utilized in a method for altering a target nucleic acid sequence as claimed broadly. For example, apart from Nla Cas5, Cas8 and Cas7 which essential characteristics or elements of the two or three additional Cas proteins from a Cascade complex possess, such that the Nla CRISPR-Cas3 system is functional for altering a target nucleic acid sequence? Additionally, with respect to known CRISPR-Cas3 systems Mashimo et al (US 2020/0102580; IDS) already stated “The type I-E CRISPR-Cas3 system, which is common among type I CRISPR-Cas3 systems, cleaves DNA when a crRNA cooperates with Cas3 and Cascade (Cse1 (Cas8), Cse2 (Cas11), Cas5, Cas6, and Cas7). The type I-A system has Cascade constituent elements of Cas8a1, Csa5 (Cas11), Cas5, Cas6, and Cas7, the type I-B has Cascade constituent elements of Cas8b1, Cass, Cas6 and Cas7, the type I-C has Cascade constituent elements of Cas8c, Cas5 and Cas7, the type I-D has Cascade constituent elements of Cas10d, Csc1 (Cas5), Cas6, and Csc2 (Cas7), the type I-F has Cascade constituent elements of Csy1 (Cas8f), Csy2 (Cas5), Cas6, and Csy7 (Cas7), and the type I-G system has Cascade constituent elements Cst1 (Cas8a1), Cas5, Cas6, and Cst2 (Cas7)” (paragraph [0061]). Apparently, none of the known CRISPR-Cas3 systems has a Cascade complex containing less than three specific constituent elements. Moreover, McBride et al (Molecular Cell 80:971-979, 2020; IDS) already taught that diverse CRISPR-Cas complexes require independent translation of small and large subunits from a single gene; and they showed that internal translation to generate small subunits is widespread across diverse type I-D, I-B and I-C CRISPR-Cas systems (Abstract). McBride et al stated “Importantly, we uncover an alternative internal translational initiation site within cas10d that leads to expression of the small subunit, Cas11d. We further demonstrate that internal translation of small subunits from within cas10d or cas8 large subunit gene is conserved in type I CRISPR-Cas systems that lack a separate cas11 gene, with the exception of type I-F” (last two sentences of first paragraph on left column at page 972).
Since the prior art before the effective filing date of the present application (05/26/2021) did not provide any guidance regarding the issues discussed above as evidenced at least by the teachings of Gersbach et al (WO 2017/066497), Mashimo et al (US 2020/0102580; IDS), Ke et al (WO 2019/246555; IDS) and McBride et al (Molecular Cell 80:971-979, 2020; IDS); it is incumbent upon the present application to do so. The instant specification also fails to provide at least a sufficient number of a representative number of species for a broad genus of an engineered CRISPR-Cas system, particularly the CRISPR-Cas system derived from Neisseria lactamica, to be utilized in a method of altering a target nucleic acid sequence as claimed broadly.
The claimed invention as a whole is not adequately described if the claims require essential or critical elements which are not adequately described in the specification and which are not conventional in the art as of Applicants’ filing date. Possession may be shown by actual reduction to practice, clear depiction of the invention in a detailed drawing, or by describing the invention with sufficient relevant identifying characteristics such that a person skilled in the art would recognize that the inventor had possession of the claimed invention. Pfaff v. Wells Electronics, Inc., 48 USPQ2d 1641, 1646 (1998). The skilled artisan cannot envision the detailed structure at least of a representative number of species for a broad genus of an engineered CRISPR-Cas system, particularly the CRISPR-Cas system derived from Neisseria lactamica, to be utilized in a method of altering a target nucleic acid sequence as claimed broadly, and therefore conception is not achieved until reduction to practice has occurred, regardless of the complexity or simplicity of the method. Adequate written description requires more than a mere statement that it is part of the invention and reference to a method of isolating it. See Fiers v. Revel, 25 USPQ2d 1601, 1606 (Fed. Cir. 1993) and Amgen Inc. v. Chugai Pharmaceutical Co. Ltd., 18 USPQ2d 1016 (Fed. Cir. 1991). One cannot describe what one has not conceived. See Fiddes v. Baird, 30 USPQ2d 1481, 1483.
Applicant is reminded that Vas-Cath makes clear that the written description provision of 35 U.S.C. §112 is severable from its enablement provision (see page 1115).
Claim Rejections - 35 USC § 102
The following is a quotation of the appropriate paragraphs of 35 U.S.C. 102 that form the basis for the rejections under this section made in this Office action:
A person shall be entitled to a patent unless –
(a)(1) the claimed invention was patented, described in a printed publication, or in public use, on sale, or otherwise available to the public before the effective filing date of the claimed invention.
Claims 24-27, 29, 34-35, 38, 41-44 and 46 are rejected under 35 U.S.C. 102(a)(1) as being anticipated by Mashimo et al (US 2020/0102580; IDS).
The instant claims encompass a method of altering a target nucleic acid sequence comprising contacting a target nucleic acid sequence (e.g., introducing into a cell in vitro, ex vivo, or in vivo containing the target nucleic acid sequence) with an engineered clustered Regularly Interspaced Short Palindromic Repeats (CRISPR)-CRISPR associated (Cas) (CRISPR-Cas) system and/or one or more nucleic acids encoding the engineered CRISPR-Cas system or a composition thereof, wherein the engineered CRISPR-Cas system comprises: (a) Cas11; (b) Cas3; (c) two or more additional Cas proteins from a CRISPR-Associated Complex for Anti-viral Defense (Cascade) complex; and (d) at least one guide RNA (gRNA), wherein each gRNA is configured to hybridize to a portion of a target nucleic acid sequence.
Mashimo et al already disclosed at least a method comprising introducing a CRISPR-Cas3 system into a eukaryotic cell (e.g., animal cells, plant cells, mammalian cells such as fibroblasts, hematopoietic cells, muscle cells, liver cells), wherein the CRISPR-Cas3 system comprises: (a) a Cas3 protein, a polynucleotide encoding the protein, or an expression vector containing the polynucleotide; (b) a Cascade protein, a polynucleotide encoding the protein, or an expression vector containing the polynucleotide; and (c) a crRNA, a polynucleotide encoding the crRNA, or an expression vector containing the polynucleotide; the same method wherein a nuclear localization signal is added to the Cas3 protein and/or the Cascade protein (see at least Abstract; Summary of Invention; particularly paragraphs [0013]-[0019], [0060]-[0061], [0066]-[0074], [0085]-[0094], [0100]-[0101], [0110]-[0111]). Mashimo et al stated “The CRISPR-Cas3 system of the present invention includes all six types of type I….The type I-E CRISPR-Cas3 system, which is common among type I CRISPR-Cas3 systems, cleaves DNA when a crRNA cooperates with Cas3 and Cascade (Cse1 (Cas8), Cse2 (Cas11), Cas5, Cas6, and Cas7)….the type I-C has Cascade constituent elements of Cas8c, Cas5, and Cas7” (paragraphs [0060]-[0061]); and “[t]he CRISPR-Cas3 system causes DNA cleavages at multiple locations. Therefore, use of the CRISPR-Cas3 system of the present invention makes it possible to generate a wide range of deletion mutations ranging from one hundred to several thousands, and possibly more bases (FIGS. 3, 6, and 16 to 18)” (paragraph [0058]). Mashimo et al also taught that the polynucleotide encoding the Cas protein group (Cas3 and Cascade) is mounted on vectors of one type (of the same type), all or some of the polynucleotide encoding the Cas protein groups is mounted on separate vectors, and it is preferable that the polynucleotide encoding the Cas protein groups on six different types of vectors for expression efficiency (paragraph [0089]). Mashimo et al also stated clearly “DNA editing may be performed on DNA contained in a specific cell within an individual. Such DNA editing can be performed on, for example, a specific cell as a target among cells constituting the body of an animal or plant. No limitation is imposed on the method for introducing the molecules constituting the CRISPR-Cas3 system of the present invention into eukaryotic cells in the form of a polynucleotide or an expression vector containing the polynucleotide” [0110]-[0111]); and “In the present invention, “editing the DNA of a eukaryotic cell” may be a step in which the DNA of a eukaryotic cell is edited in vivo or in vitro….the DNA used in the above context includes not only DNA present in the nucleus of a cell but also exogenous DNA and DNA present other than the nucleus of a cell such as mitochondrial DNA” (paragraph [0104]). Examples A-1, A-2 and A-3 demonstrated exogenous CCR5 gene, endogenous CCR5 gene and endogenous EMX1 gene in HEK 239 T cells were cleaved by the above disclosed CRISPR-Cas3 system, respectively (FIGs. 1-3 and 6). With respect to the limitation of “wherein the deletion is unidirectional” in claim 26, since the CRISPR-Cas3 system of Mashimo et al is the same as that of the presently claimed invention, it is necessarily that such CRISPR-Cas3 system also generates unidirectional deletion.
Accordingly, the teachings of Mashimo et al meet every limitation of the instant claims. Therefore, the reference anticipates the instant claims.
Claims 24-27, 29, 34-35, 38, 41-44 and 46 are rejected under 35 U.S.C. 102(a)(1) as being anticipated by Ke et al (WO 2019/246555; IDS).
Ke et al already disclosed at least a method of modifying DNA in eukaryotic cells (e.g., in vitro cell culture and ex vivo) by introducing into the eukaryotic cells: (i) a combination of proteins comprising Cas3, Cse1/CasA (Cas8), Cse2/CasB (Cas11), Cas7/CasC, Cas5e/CasD and Cas6e/CasE, each comprising an amino acid sequence that is at least 85% homologous across its entire length to a Thermobifida Fusca (T. fusca) protein; (ii) a guide RNA (a targeting RNA) comprising a sequence that is complementary to a targeted site in a segment of the DNA, the targeted site comprising a spacer sequence; and (iii) allowing the combination of the proteins and the guide RNA to modify the DNA by nicking, causing a double stranded break (DSB), and/or unidirectional deleting of a single strand of the DNA; the same method wherein long deletion such as up to 100 kb are introduced (e.g., a deletion upstream of a targeted site that comprises a deletion of from about 500 base pairs to about 100,000 base pairs) (Abstract; Summary; particularly paragraphs [0005]-[006], [009]-[0010], [0042]-0043], [0052]-[0053], [0061]-[0062 and [0064]-[0065]]; and Figures 1 and 16). Ke et al also taught that any of the above enzyme or other protein is introduced into eukaryotic cells as an RNA encoding the protein that is expressed once introduced into the cells, or an expression vector encoding the protein that is expressed in the cells; and that these components can be provided on the same or different polynucleotides, such as plasmids (paragraphs [0035], [0040] and [0062]). Ke et al also disclosed that the targeting RNA is complementary to a sequence in a chromosome of a eukaryotic cell, or to a dsDNA extrachromosomal element, such as a dsDNA viral genome (paragraph [0058]); and eukaryotic cells include embryonic stem cells or adult stem cells such as neural stem cells, hematopoietic stem cells, and the cells are mammalian cells such as human or non-human mammalian cells (paragraph [0064]). Ke et al stated “In embodiments, an essential functional group may be added to Cas3 to aid in visualization, localization, or to confer new activity or other properties to Cas3” (second last sentence of paragraph [0075]); and “In embodiments, the disclosure includes obtaining cells from an individual, modifying the cells ex vivo using a Type I CRISPR system as described herein, and reintroducing the cells or their progeny into the individual” (paragraph [0065]). Examples demonstrated that T. fusca Type I-E CRISPR-Cas successfully genome edited hESC dual-reporter line bearing EGFP and tdTomata at the DNMT3B locus via RNA-guided gene disruption of the EGFP reporter gene or the tdTomato reporter gene.
Accordingly, the teachings of Ke et al meet every limitation of the instant claims. Therefore, the reference anticipates the instant claims.
Claim Rejections - 35 USC § 103
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.
Claims 24, 35 and 38 (elected embodiment of in vivo administration to a subject) are rejected under 35 U.S.C. 103 as being unpatentable over Ke et al (WO 2019/246555; IDS) in view of Gersbach et al (WO 2017/066497).
Ke et al already disclosed at least a method of modifying DNA in eukaryotic cells (e.g., in vitro cell culture and ex vivo) by introducing into the eukaryotic cells: (i) a combination of proteins comprising Cas3, Cse1/CasA (Cas8), Cse2/CasB (Cas11), Cas7/CasC, Cas5e/CasD and Cas6e/CasE, each comprising an amino acid sequence that is at least 85% homologous across its entire length to a Thermobifida Fusca (T. fusca) protein; (ii) a guide RNA (a targeting RNA) comprising a sequence that is complementary to a targeted site in a segment of the DNA, the targeted site comprising a spacer sequence; and (iii) allowing the combination of the proteins and the guide RNA to modify the DNA by nicking, causing a double stranded break (DSB), and/or unidirectional deleting of a single strand of the DNA; the same method wherein long deletion such as up to 100 kb are introduced (e.g., a deletion upstream of a targeted site that comprises a deletion of from about 500 base pairs to about 100,000 base pairs) (Abstract; Summary; particularly paragraphs [0005]-[006], [009]-[0010], [0042]-0043], [0052]-[0053], [0061]-[0062 and [0064]-[0065]]; and Figures 1 and 16). Ke et al also taught that any of the above enzyme or other protein is introduced into eukaryotic cells as an RNA encoding the protein that is expressed once introduced into the cells, or an expression vector encoding the protein that is expressed in the cells; and that these components can be provided on the same or different polynucleotides, such as plasmids (paragraphs [0035], [0040] and [0062]). Ke et al also disclosed that the targeting RNA is complementary to a sequence in a chromosome of a eukaryotic cell, or to a dsDNA extrachromosomal element, such as a dsDNA viral genome (paragraph [0058]); and eukaryotic cells include embryonic stem cells or adult stem cells such as neural stem cells, hematopoietic stem cells, and the cells are mammalian cells such as human or non-human mammalian cells (paragraph [0064]). Ke et al stated “In embodiments, an essential functional group may be added to Cas3 to aid in visualization, localization, or to confer new activity or other properties to Cas3” (second last sentence of paragraph [0075]); and “In embodiments, the disclosure includes obtaining cells from an individual, modifying the cells ex vivo using a Type I CRISPR system as described herein, and reintroducing the cells or their progeny into the individual” (paragraph [0065]). Examples demonstrated that T. fusca Type I-E CRISPR-Cas successfully genome edited hESC dual-reporter line bearing EGFP and tdTomata at the DNMT3B locus via RNA-guided gene disruption of the EGFP reporter gene or the tdTomato reporter gene.
Ke et al did not teach specifically a method of altering a target nucleic acid sequence comprising contacting a target nucleic acid sequence in a cell by introducing the disclosed CRISPR-Cas3 system into the cell via in vivo administration to a subject.
Before the effective filing date of the present application (05/26/2021), Gersbach et al already taught a method for treating a viral infection in a subject (e.g., a mammal such as cow, pig, cat, dog, non-human primate and a human), the method comprises administering to the subject an effective amount of (A) (i) at least one nucleic acid construct encoding polypeptides of a Type I CRISPR-Cas system (e.g., Type I-E, Type I-C); and (ii) a CRISPR array comprising at least one spacer sequence that is complementary to a target DNA on the chromosome or extrachromosomal element; or (B) a protein-RNA complex comprising polypeptides of a Type I CRISPR-Cas system and a CRISPR array comprising at least one spacer sequence that is complementary to a target DNA on the chromosome or extrachromosomal element; and (C) a template comprising a single stranded DNA sequence or a double stranded DNA sequence and an intervening sequence having zero nucleotides or base pairs, respectively, wherein the target DNA is DNA of a virus infecting the subject (see at least Abstract; Summary; particularly paragraphs [0019]-[0020], [00180], [00198]-[00207], [00323]-[[00326], [00374]-[00389]; Examples and Figs. 1C, 2-9).
Accordingly, it would have been obvious for an ordinary skilled artisan before the effective filing date of the present application to modify a method of altering a target nucleic acid sequence in a cell of Ke et al by also introducing the disclosed CRISPR-Cas3 system into the cell via in vivo administration to a subject; in light of the teachings of Gersbach et al as presented above.
An ordinary skilled artisan would have been motivated to carry out the above modification because Gersbach et al already taught at least a method for treating a viral infection in a subject (e.g., a mammal such as cow, pig, cat, dog, non-human primate and a human), the method comprises administering to the subject an effective amount of (i) at least one nucleic acid construct encoding polypeptides of a Type I CRISPR-Cas system (e.g., Type I-E, Type I-C); and (ii) a CRISPR array comprising at least one spacer sequence that is complementary to a target DNA on the chromosome or extrachromosomal element; wherein the target DNA is DNA of a virus infecting the subject.
An ordinary skilled artisan would have a reasonable expectation of success in light of the teachings of Ke et al and Gersbach et al; coupled with a high level of skill of an ordinary skilled artisan in the relevant art.
The modified method resulting from the combined teachings of Ke et al and Gersbach et al as set forth above is indistinguishable from and encompassed by the method of the presently claimed invention.
Therefore, the claimed invention as a whole was prima facie obvious in the absence of evidence to the contrary.
Claims 24-27, 29, 34-35, 38, 41-44 and 46-47 are rejected under 35 U.S.C. 103 as being obvious over Zhang et al (WO 2021/247301; IDS) in view of McBride et al (Molecular Cell 80:971-979, 2020; IDS) and Mashimo et al (US 2020/0102580; IDS).
The applied reference has a common joint Inventor with the instant application. Based upon the earlier effectively filed date of the reference, it constitutes prior art under 35 U.S.C. 102(a)(2).
Zhang et al already disclosed a method of altering a target DNA sequence (e.g., a genomic DNA sequence) in a host cell, the method comprises introducing into the host cell containing the target DNA sequence: (a) a synthetic guide RNA sequence that is complementary to a target DNA sequence in the host cell (e.g., wherein the target genomic DNA sequence encodes at least one gene product); and (b) a combination of two or more Neisseria lactamica (Nla) proteins selected from Cas3, Cas5, Cas8c, and Cas7; wherein the guide RNA sequence and the combination of two or more Neisseria lactamica protein induce cleavage of one or both strands in the target DNA sequence, thereby altering the target DNA sequence (Abstract; Summary; particularly paragraphs [0022], [0046]-[0052], and Examples). Figure 6A is a schematic of the miniature type I-C CRISPR-Cas locus from N. lactamica, with cas1, cas2 and cas4, cas7, cas8, cas5, and cas3. Zhang et al also taught that nucleic acid sequences encoding the various components of the Nla CRISPR-Cas3 system may be introduced into host cells as part of a vector (e.g., a plasmid, episome, cosmid, viral vector or phage) (paragraphs [0058]-[0059], [0062]). Zhang et al further taught that each of nucleic acid sequences encoding Cas7, Cas8c, Cas5, and Cas3 proteins may be codon-optimized and/or modified to include an appropriate nuclear localization signal (NLS) or purification tag, and expressed in separate plasmids; alternatively, the Cascade proteins Cas7, Cas8c, and Cas5 may be expressed from a single plasmid, with the Cas3 protein expressed on a different plasmid; while the crRNA may also be expressed separately via an RNA polymerase III promoter (paragraphs [0050]-[0051]). Zhang et al also taught that the Nla CRISPR-Cas3 system introduces a long range and unidirectional genomic DNA deletion upstream of the PAM without prominent off-target activity, and the deletion of the target genomic DNA sequence comprises from about 500 nucleotides to about 100,000 nucleotides (paragraph [0052]).
Zhang et al did not teach specifically a method of altering a target nucleic acid sequence in a host cell using a combination of Neisseria lactamica proteins comprised of Cas3, Cas5, Cas8c and Cas7 that further containing Cas11; and contacting a target nucleic acid sequence in a host cell by introducing the engineered Nla Type I-C CRISPR-Cas3 system into the host cell via in vivo administration to a subject.
Before the effective filing date of the present application (05/26/2021), McBride et al already taught that diverse CRISPR-Cas complexes require independent translation of small and large subunits from a single gene; and they showed that internal translation to generate small subunits is widespread across diverse type I-D, I-B and I-C CRISPR-Cas systems (Abstract). McBride et al stated “Importantly, we uncover an alternative internal translational initiation site within cas10d that leads to expression of the small subunit, Cas11d. We further demonstrate that internal translation of small subunits from within cas10d or cas8 large subunit gene is conserved in type I CRISPR-Cas systems that lack a separate cas11 gene, with the exception of type I-F” (last two sentences of first paragraph on left column at page 972). McBride et al further taught that similar to Cas11 small subunit (Cse2) from the type I-E system that is important for the interaction of Cascade with DNA through stabilization of the R-loop formed during complex with target DNA, Cas11 d is required for specific binding of the type I-D Cascade complex to target dsDNA (paragraph bridging right column at page 974 and left column at page 975). McBride et al also stated “In contrast to the type I-D system, Cas8 is the large subunit in all other type I systems. Analysis of large subunit proteins revealed conservation of a potential translation start site near the C terminus in both type I-B and type I-C systems (Figure 4D, Data S3 and S4). Using both in silico predictions and translation reporter assays, we demonstrated that these regions within cas8 supported translation initiation in representatives of type I-B and I-C systems (Figure 4E). The predicted mass of these small subunits ranged between 12-17 kDa and their sequence showed some similarity within their respective system type, but low compared to other Cas11 proteins” (left column, last paragraph continues to first paragraph on right column at page 975).
Additionally, Mashimo et al already disclosed at least a method comprising introducing a CRISPR-Cas3 system into a eukaryotic cell (e.g., animal cells, plant cells, mammalian cells such as fibroblasts, hematopoietic cells, muscle cells, liver cells), wherein the CRISPR-Cas3 system comprises: (a) a Cas3 protein, a polynucleotide encoding the protein, or an expression vector containing the polynucleotide; (b) a Cascade protein, a polynucleotide encoding the protein, or an expression vector containing the polynucleotide; and (c) a crRNA, a polynucleotide encoding the crRNA, or an expression vector containing the polynucleotide; the same method wherein a nuclear localization signal is added to the Cas3 protein and/or the Cascade protein (see at least Abstract; Summary of Invention; particularly paragraphs [0013]-[0019], [0060]-[0061], [0066]-[0074], [0085]-[0094], [0100]-[0101], [0110]-[0111]). Mashimo et al stated “The CRISPR-Cas3 system of the present invention includes all six types of type I….The type I-E CRISPR-Cas3 system, which is common among type I CRISPR-Cas3 systems, cleaves DNA when a crRNA cooperates with Cas3 and Cascade (Cse1 (Cas8), Cse2 (Cas11), Cas5, Cas6, and Cas7)….the type I-C has Cascade constituent elements of Cas8c, Cas5, and Cas7” (paragraphs [0060]-[0061]); and “[t]he CRISPR-Cas3 system causes DNA cleavages at multiple locations. Therefore, use of the CRISPR-Cas3 system of the present invention makes it possible to generate a wide range of deletion mutations ranging from one hundred to several thousands, and possibly more bases (FIGS. 3, 6, and 16 to 18)” (paragraph [0058]). Mashimo et al also taught that the polynucleotide encoding the Cas protein group (Cas3 and Cascade) is mounted on vectors of one type (of the same type), all or some of the polynucleotide encoding the Cas protein groups is mounted on separate vectors, and it is preferable that the polynucleotide encoding the Cas protein groups on six different types of vectors for expression efficiency (paragraph [0089]). Mashimo et al also stated clearly “DNA editing may be performed on DNA contained in a specific cell within an individual. Such DNA editing can be performed on, for example, a specific cell as a target among cells constituting the body of an animal or plant. No limitation is imposed on the method for introducing the molecules constituting the CRISPR-Cas3 system of the present invention into eukaryotic cells in the form of a polynucleotide or an expression vector containing the polynucleotide” [0110]-[0111]); and “In the present invention, “editing the DNA of a eukaryotic cell” may be a step in which the DNA of a eukaryotic cell is edited in vivo or in vitro….the DNA used in the above context includes not only DNA present in the nucleus of a cell but also exogenous DNA and DNA present other than the nucleus of a cell such as mitochondrial DNA” (paragraph [0104]). Examples A-1, A-2 and A-3 demonstrated exogenous CCR5 gene, endogenous CCR5 gene and endogenous EMX1 gene in HEK 239 T cells were cleaved by the above disclosed CRISPR-Cas3 system, respectively (FIGs. 1-3 and 6).
Accordingly, it would have been obvious for an ordinary skilled artisan before the effective filing date of the present application to modify a method of altering a target nucleic acid sequence in a host cell of Zhang et al by also further including Nla Cas 11 protein into the combination of Neisseria lactamica proteins Cas3, Cas5, Cas8c and Cas7, wherein the Cas11 protein is derived from the same cas8c gene via alternative translation initiation, as well as introducing the modified disclosed Nla Type I-C CRISPR-Cas3 system into the host cell via in vivo administration to a subject; in light of the teachings of McBride et al and Mashimo et al as presented above.
An ordinary skilled artisan would have been motivated to carry out the above modifications because: (i) McBride et al already taught that internal translation of small subunits from within cas10d or cas8 large subunit gene is conserved in type I CRISPR-Cas systems that lack a separate cas11 gene, and that Cas11 plays an important role in the interaction of Cascade with target DNA; and (ii) Mashimo et al also taught at least a method comprising introducing a CRISPR-Cas3 system into a eukaryotic cell in vitro and/or in vivo (in an individual).
An ordinary skilled artisan would have a reasonable expectation of success in light of the teachings of Zhang et al, McBride et al and Mashimo et al; coupled with a high level of skill of an ordinary skilled artisan in the relevant art.
The modified method resulting from the combined teachings of Zhang et al, McBride et al and Mashimo et al as set forth above is indistinguishable from and encompassed by the method of the presently claimed invention.
Therefore, the claimed invention as a whole was prima facie obvious in the absence of evidence to the contrary.
This rejection under 35 U.S.C. 103 might be overcome by: (1) a showing under 37 CFR 1.130(a) that the subject matter disclosed in the reference was obtained directly or indirectly from the inventor or a joint inventor of this application and is thus not prior art in accordance with 35 U.S.C.102(b)(2)(A); (2) a showing under 37 CFR 1.130(b) of a prior public disclosure under 35 U.S.C. 102(b)(2)(B); or (3) a statement pursuant to 35 U.S.C. 102(b)(2)(C) establishing that, not later than the effective filing date of the claimed invention, the subject matter disclosed and the claimed invention were either owned by the same person or subject to an obligation of assignment to the same person or subject to a joint research agreement. See generally MPEP § 717.02.
Double Patenting
The nonstatutory double patenting rejection is based on a judicially created doctrine grounded in public policy (a policy reflected in the statute) so as to prevent the unjustified or improper timewise extension of the “right to exclude” granted by a patent and to prevent possible harassment by multiple assignees. A nonstatutory double patenting rejection is appropriate where the conflicting claims are not identical, but at least one examined application claim is not patentably distinct from the reference claim(s) because the examined application claim is either anticipated by, or would have been obvious over, the reference claim(s). See, e.g., In re Berg, 140 F.3d 1428, 46 USPQ2d 1226 (Fed. Cir. 1998); In re Goodman, 11 F.3d 1046, 29 USPQ2d 2010 (Fed. Cir. 1993); In re Longi, 759 F.2d 887, 225 USPQ 645 (Fed. Cir. 1985); In re Van Ornum, 686 F.2d 937, 214 USPQ 761 (CCPA 1982); In re Vogel, 422 F.2d 438, 164 USPQ 619 (CCPA 1970); In re Thorington, 418 F.2d 528, 163 USPQ 644 (CCPA 1969).
A timely filed terminal disclaimer in compliance with 37 CFR 1.321(c) or 1.321(d) may be used to overcome an actual or provisional rejection based on nonstatutory double patenting provided the reference application or patent either is shown to be commonly owned with the examined application, or claims an invention made as a result of activities undertaken within the scope of a joint research agreement. See MPEP § 717.02 for applications subject to examination under the first inventor to file provisions of the AIA as explained in MPEP § 2159. See MPEP § 2146 et seq. for applications not subject to examination under the first inventor to file provisions of the AIA . A terminal disclaimer must be signed in compliance with 37 CFR 1.321(b).
The USPTO Internet website contains terminal disclaimer forms which may be used. Please visit www.uspto.gov/patent/patents-forms. The filing date of the application in which the form is filed determines what form (e.g., PTO/SB/25, PTO/SB/26, PTO/AIA /25, or PTO/AIA /26) should be used. A web-based eTerminal Disclaimer may be filled out completely online using web-screens. An eTerminal Disclaimer that meets all requirements is auto-processed and approved immediately upon submission. For more information about eTerminal Disclaimers, refer to www.uspto.gov/patents/process/file/efs/guidance/eTD-info-I.jsp.
Claims 24-27, 34-35, 43-44 and 46 are rejected on the ground of nonstatutory double patenting as being unpatentable over claims 1-15 of U.S. Patent No. 12,188,015.
Although the claims at issue are not identical, they are not patentably distinct from each other because a method of modifying DNA in eukaryotic cells, the method comprising introducing into the eukaryotic cells (e.g., a population of eukaryotic cells in an in vitro cell culture; dependent claims 3-4): (i) a combination of proteins comprising Cas3, Cse1/CasA (Cas8), Cse2/CasB (Cas11), Cas7/CasC, Cas5e/CasD and Cas6e/CasE, each comprising an amino acid sequence that is at least 85% homologous across its entire length to a Thermobifida Fusca (T. fusca) protein, wherein the Cas3 protein comprises the sequence of SEQ ID NO:1 or a sequence that is at least 85% homologous across it entire length to the sequence of SEQ ID NO:1, wherein the sequence of the Cse2/CasB protein comprises or a sequence that is at least 85-99% homologous across the entire length sequence of SEQ ID NO:2, wherein the sequence that is at least 85-99% homologous to the sequence of SEQ ID NO:2 comprises an amino acid at position 23 of SEQ ID NO:2 that is not an N, and wherein the modification of the DNA is performed at a temperature of about 370C; (ii) a guide RNA (a targeting RNA) comprising a sequence that is complementary to a targeted site in a segment of the DNA, the targeted site comprising a spacer sequence; and (iii) allowing the combination of the proteins and the guide RNA to modify the DNA by nicking, causing a double stranded break (DS), and/or unidirectional deleting of a single strand of the DNA (e.g., a deletion of from about 500 nucleotides to about 100,000 nucleotides; dependent claim 6), wherein the targeted site is not modified, and wherein the DNA is comprised by a chromosome or an extrachromosomal element; the same method wherein at least one of the proteins is introduced into the eukaryotic cells by expression from an expression vector, or by introducing into the eukaryotic cells mRNA encoding the at least one protein; dependent claim 11) in independent claims 1-15 of U.S. Patent No. 12,188,015 anticipates a method of altering a target nucleic acid sequence in the application being examined and, therefore, a patent to the genus would, necessarily, extend the rights of the species or sub- should the genus issue as a patent after the species of sub-genus.
Claims 24, 29, 35, 38 and 41-42 are rejected on the ground of nonstatutory double patenting as being unpatentable over claims 1-15 of U.S. Patent No. 12,188,015 in view of Mashimo et al (US 2020/0102580; IDS).
Claims 1-15 of U.S. Patent No. 12,188,015 encompass a method of modifying DNA in eukaryotic cells, the method comprising introducing into the eukaryotic cells (e.g., a population of eukaryotic cells in an in vitro cell culture; dependent claims 3-4): (i) a combination of proteins comprising Cas3, Cse1/CasA (Cas8), Cse2/CasB (Cas11), Cas7/CasC, Cas5e/CasD and Cas6e/CasE, each comprising an amino acid sequence that is at least 85% homologous across its entire length to a Thermobifida Fusca (T. fusca) protein, wherein the Cas3 protein comprises the sequence of SEQ ID NO:1 or a sequence that is at least 85% homologous across it entire length to the sequence of SEQ ID NO:1, wherein the sequence of the Cse2/CasB protein comprises or a sequence that is at least 85-99% homologous across the entire length sequence of SEQ ID NO:2, wherein the sequence that is at least 85-99% homologous to the sequence of SEQ ID NO:2 comprises an amino acid at position 23 of SEQ ID NO:2 that is not an N, and wherein the modification of the DNA is performed at a temperature of about 370C; (ii) a guide RNA (a targeting RNA) comprising a sequence that is complementary to a targeted site in a segment of the DNA, the targeted site comprising a spacer sequence; and (iii) allowing the combination of the proteins and the guide RNA to modify the DNA by nicking, causing a double stranded break (DS), and/or unidirectional deleting of a single strand of the DNA (e.g., a deletion of from about 500 nucleotides to about 100,000 nucleotides; dependent claim 6), wherein the targeted site is not modified, and wherein the DNA is comprised by a chromosome or an extrachromosomal element; the same method wherein at least one of the proteins is introduced into the eukaryotic cells by expression from an expression vector, or by introducing into the eukaryotic cells mRNA encoding the at least one protein; dependent claim 11).
The claims of the present application differ from claims 1-15 of U.S. Patent No. 12,188,015 in reciting specifically “one or more nucleic acids encoding the engineered CRISPR-Cas system” (an embodiment of claim 24); “the targeting nucleic acid sequence encodes a gene product” (claim 29); “wherein introducing the system into the cell comprises an in vivo administration or transplantation of ex vivo treated cells comprising the system to a subject” (claim 38); “wherein Cas11, Cas3, the two or more additional Cas proteins, and the at least one gRNA are encoded by a single nucleic acid or different nucleic acids” (claim 41); and “wherein at least one or all of Cas11, Cas3, and the two or more additional Cas proteins comprise a nuclear localization sequence or a tag” (claim 42).
Before the effective filing date of the present application (05/26/2021), Mashimo et al already disclosed at least a method comprising introducing a CRISPR-Cas3 system into a eukaryotic cell (e.g., animal cells, plant cells, mammalian cells such as fibroblasts, hematopoietic cells, muscle cells, liver cells), wherein the CRISPR-Cas3 system comprises: (a) a Cas3 protein, a polynucleotide encoding the protein, or an expression vector containing the polynucleotide; (b) a Cascade protein, a polynucleotide encoding the protein, or an expression vector containing the polynucleotide; and (c) a crRNA, a polynucleotide encoding the crRNA, or an expression vector containing the polynucleotide; the same method wherein a nuclear localization signal is added to the Cas3 protein and/or the Cascade protein (see at least Abstract; Summary of Invention; particularly paragraphs [0013]-[0019], [0060]-[0061], [0066]-[0074], [0085]-[0094], [0100]-[0101], [0110]-[0111]). Mashimo et al stated “The CRISPR-Cas3 system of the present invention includes all six types of type I….The type I-E CRISPR-Cas3 system, which is common among type I CRISPR-Cas3 systems, cleaves DNA when a crRNA cooperates with Cas3 and Cascade (Cse1 (Cas8), Cse2 (Cas11), Cas5, Cas6, and Cas7)….the type I-C has Cascade constituent elements of Cas8c, Cas5, and Cas7” (paragraphs [0060]-[0061]); and “[t]he CRISPR-Cas3 system causes DNA cleavages at multiple locations. Therefore, use of the CRISPR-Cas3 system of the present invention makes it possible to generate a wide range of deletion mutations ranging from one hundred to several thousands, and possibly more bases (FIGS. 3, 6, and 16 to 18)” (paragraph [0058]). Mashimo et al also taught that the polynucleotide encoding the Cas protein group (Cas3 and Cascade) is mounted on vectors of one type (of the same type), all or some of the polynucleotide encoding the Cas protein groups is mounted on separate vectors, and it is preferable that the polynucleotide encoding the Cas protein groups on six different types of vectors for expression efficiency (paragraph [0089]). Mashimo et al also stated clearly “DNA editing may be performed on DNA contained in a specific cell within an individual. Such DNA editing can be performed on, for example, a specific cell as a target among cells constituting the body of an animal or plant. No limitation is imposed on the method for introducing the molecules constituting the CRISPR-Cas3 system of the present invention into eukaryotic cells in the form of a polynucleotide or an expression vector containing the polynucleotide” [0110]-[0111]); and “In the present invention, “editing the DNA of a eukaryotic cell” may be a step in which the DNA of a eukaryotic cell is edited in vivo or in vitro….the DNA used in the above context includes not only DNA present in the nucleus of a cell but also exogenous DNA and DNA present other than the nucleus of a cell such as mitochondrial DNA” (paragraph [0104]). Examples A-1, A-2 and A-3 demonstrated exogenous CCR5 gene, endogenous CCR5 gene and endogenous EMX1 gene in HEK 239 T cells were cleaved by the above disclosed CRISPR-Cas3 system, respectively (FIGs. 1-3 and 6).
Accordingly, it would have been obvious for an ordinary skilled artisan before the effective filing date of the present application to modify a method of modifying DNA in eukaryotic cells in claims 1-15 of U.S. Patent No. 12,188,015 by also having the recited features in claims of the present application, in light of the teachings of Mashimo et al as presented above.
An ordinary skilled artisan would have been motivated to carry out the above modifications because Mashimo et al already taught at least a method comprising introducing a CRISPR-Cas3 system into a eukaryotic cell in vitro and/or in vivo (in an individual) having the recited features in claims of the present application.
An ordinary skilled artisan would have a reasonable expectation of success in light of claims 1-15 of U.S. Patent No. 12,188,015 along with the teachings of Mashimo et al, coupled with a high level of skill for an ordinary skilled artisan in the relevant art.
The modified method resulting from claims 1-15 of U.S. Patent No. 12,188,015 along with the teachings of Mashimo et al is indistinguishable and encompassed by the presently claimed invention.
Therefore, the claimed invention as a whole was prima facie obvious in the absence of evidence to the contrary.
Claims 24-27, 29, 34-35, 38, 41-44 and 46-47 are rejected on the ground of nonstatutory double patenting as being unpatentable over claims 1-19 of U.S. Patent No. 12,630,846 in view of McBride et al (Molecular Cell 80:971-979, 2020; IDS) and Mashimo et al (US 2020/0102580; IDS).
Claims 1-19 of U.S. Patent No. 12,630,846 encompass a method of altering a target DNA sequence, which method comprises introducing to a target DNA sequence: (a) a synthetic guide RNA sequence that is complementary to a target DNA sequence in a host cell (e.g., a eukaryotic cell, a human cell; dependent claims 16-17); and a combination of Neisseria lactamica proteins Cas3, Cas5, Cas8c, and Cas7, including introducing the synthetic guide RNA sequence into the host cell as part for a first vector and one or more nucleic acid sequences encoding the N. Lactamica proteins into the host cell as part of a second vector, wherein the first and second vector are different (dependent claims 2 and 11)
The claims of the present application differ from claims 1-19 of U.S. Patent No. 12,630,846 in reciting specifically “the engineered CRISPR-Cas system comprises (a) Cas 11” (independent claim 24); “wherein introducing the system into the cell comprises an in vivo administration or transplantation of ex vivo treated cells comprising the system to a subject” (claim 38); and “wherein at least one or all of Cas11, Cas3, and the two or more additional Cas proteins comprise a nuclear localization sequence or a tag” (claim 42).
Before the effective filing date of the present application (05/26/2021), McBride et al already taught that diverse CRISPR-Cas complexes require independent translation of small and large subunits from a single gene; and they showed that internal translation to generate small subunits is widespread across diverse type I-D, I-B and I-C CRISPR-Cas systems (Abstract). McBride et al stated “Importantly, we uncover an alternative internal translational initiation site within cas10d that leads to expression of the small subunit, Cas11d. We further demonstrate that internal translation of small subunits from within cas10d or cas8 large subunit gene is conserved in type I CRISPR-Cas systems that lack a separate cas11 gene, with the exception of type I-F” (last two sentences of first paragraph on left column at page 972). McBride et al further taught that similar to Cas11 small subunit (Cse2) from the type I-E system that is important for the interaction of Cascade with DNA through stabilization of the R-loop formed during complex with target DNA, Cas11 d is required for specific binding of the type I-D Cascade complex to target dsDNA (paragraph bridging right column at page 974 and left column at page 975). McBride et al also stated “In contrast to the type I-D system, Cas8 is the large subunit in all other type I systems. Analysis of large subunit proteins revealed conservation of a potential translation start site near the C terminus in both type I-B and type I-C systems (Figure 4D, Data S3 and S4). Using both in silico predictions and translation reporter assays, we demonstrated that these regions within cas8 supported translation initiation in representatives of type I-B and I-C systems (Figure 4E). The predicted mass of these small subunits ranged between 12-17 kDa and their sequence showed some similarity within their respective system type, but low compared to other Cas11 proteins” (left column, last paragraph continues to first paragraph on right column at page 975).
Additionally, Mashimo et al already disclosed at least a method comprising introducing a CRISPR-Cas3 system into a eukaryotic cell (e.g., animal cells, plant cells, mammalian cells such as fibroblasts, hematopoietic cells, muscle cells, liver cells), wherein the CRISPR-Cas3 system comprises: (a) a Cas3 protein, a polynucleotide encoding the protein, or an expression vector containing the polynucleotide; (b) a Cascade protein, a polynucleotide encoding the protein, or an expression vector containing the polynucleotide; and (c) a crRNA, a polynucleotide encoding the crRNA, or an expression vector containing the polynucleotide; the same method wherein a nuclear localization signal is added to the Cas3 protein and/or the Cascade protein (see at least Abstract; Summary of Invention; particularly paragraphs [0013]-[0019], [0060]-[0061], [0066]-[0074], [0085]-[0094], [0100]-[0101], [0110]-[0111]). Mashimo et al stated “The CRISPR-Cas3 system of the present invention includes all six types of type I….The type I-E CRISPR-Cas3 system, which is common among type I CRISPR-Cas3 systems, cleaves DNA when a crRNA cooperates with Cas3 and Cascade (Cse1 (Cas8), Cse2 (Cas11), Cas5, Cas6, and Cas7)….the type I-C has Cascade constituent elements of Cas8c, Cas5, and Cas7” (paragraphs [0060]-[0061]); and “[t]he CRISPR-Cas3 system causes DNA cleavages at multiple locations. Therefore, use of the CRISPR-Cas3 system of the present invention makes it possible to generate a wide range of deletion mutations ranging from one hundred to several thousands, and possibly more bases (FIGS. 3, 6, and 16 to 18)” (paragraph [0058]). Mashimo et al also taught that the polynucleotide encoding the Cas protein group (Cas3 and Cascade) is mounted on vectors of one type (of the same type), all or some of the polynucleotide encoding the Cas protein groups is mounted on separate vectors, and it is preferable that the polynucleotide encoding the Cas protein groups on six different types of vectors for expression efficiency (paragraph [0089]). Mashimo et al also stated clearly “DNA editing may be performed on DNA contained in a specific cell within an individual. Such DNA editing can be performed on, for example, a specific cell as a target among cells constituting the body of an animal or plant. No limitation is imposed on the method for introducing the molecules constituting the CRISPR-Cas3 system of the present invention into eukaryotic cells in the form of a polynucleotide or an expression vector containing the polynucleotide” [0110]-[0111]); and “In the present invention, “editing the DNA of a eukaryotic cell” may be a step in which the DNA of a eukaryotic cell is edited in vivo or in vitro….the DNA used in the above context includes not only DNA present in the nucleus of a cell but also exogenous DNA and DNA present other than the nucleus of a cell such as mitochondrial DNA” (paragraph [0104]). Examples A-1, A-2 and A-3 demonstrated exogenous CCR5 gene, endogenous CCR5 gene and endogenous EMX1 gene in HEK 239 T cells were cleaved by the above disclosed CRISPR-Cas3 system, respectively (FIGs. 1-3 and 6).
Accordingly, it would have been obvious for an ordinary skilled artisan before the effective filing date of the present application to modify a method of modifying DNA in eukaryotic cells in claims 1-19 of U.S. Patent No. 12,630,846 by also including Cas 11 protein into a combination of Neisseria lactamica proteins Cas3, Cas5, Cas8c and Cas7, wherein the Cas11 protein is derived from the same cas8c gene via alternative translation initiation, along with other recited features in claims of the present application, in light of the teachings of McBride et al and Mashimo et al as presented above.
An ordinary skilled artisan would have been motivated to carry out the above modifications because: (i) McBride et al already taught that internal translation of small subunits from within cas10d or cas8 large subunit gene is conserved in type I CRISPR-Cas systems that lack a separate cas11 gene, and that Cas11 plays an important role in the interaction of Cascade with target DNA; and (ii) Mashimo et al also taught at least a method comprising introducing a CRISPR-Cas3 system into a eukaryotic cell in vitro and/or in vivo (in an individual) having the other recited features in claims of the present application.
An ordinary skilled artisan would have a reasonable expectation of success in light of claims 1-19 of U.S. Patent No. 12,630,846 along with the teachings of McBride et al and Mashimo et al, coupled with a high level of skill for an ordinary skilled artisan in the relevant art.
The modified method resulting from claims 1-19 of U.S. Patent No. 12,630,846 along with the teachings of McBride et al and Mashimo et al is indistinguishable and encompassed by the presently claimed invention.
Therefore, the claimed invention as a whole was prima facie obvious in the absence of evidence to the contrary.
The prior art made of record and not relied upon is considered pertinent to applicant's disclosure.
1. Mashimo et al (US 11,807,869 and US 12, 371,713) already disclosed a method for cleaving endogenous DNA in a non-human animal or plant comprising introducing a CRISPR-Cas3 system that can cleave endogenous DNA in a nonhuman animal or plant, wherein the CRISPR-Cas3 system is a Type I-E or Type I-G CRISPR-Cas3 system (see issued claims).
2. Leon et al (WO 2020/257715) disclosed methods and compositions for generating deletions, inducing recombination, and for modulating gene expression in cells in vitro, ex vivo or in vivo using a Pseudomonas aeruginosa I-C CRISPR-Cas3 system, wherein the I-C CRISPR-Cas3 system comprises Cas3, Cas5, Cas7 and Cas8 proteins, or polynucleotides encoding the same (see at least Abstract; Brief Summary of the Invention; particularly paragraphs [0006], [0015]-[0016], [0018]-[0021] and [0123]-[0125]).
Conclusions
No claim is allowed.
Any inquiry concerning this communication or earlier communications from the examiner should be directed to Quang Nguyen, Ph.D., at (571) 272-0776.
If attempts to reach the examiner by telephone are unsuccessful, the examiner’s SPE, James Douglas (Doug) Schultz, Ph.D., may be reached at (571) 272-0763.
To aid in correlating any papers for this application, all further correspondence regarding this application should be directed to Group Art Unit 1631; Central Fax No. (571) 273-8300.
Any inquiry of a general nature or relating to the status of this application or proceeding should be directed to (571) 272-0547.
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/QUANG NGUYEN/
Primary Examiner, Art Unit 1631
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