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 .
Preliminary Matters
New claims 56-74 are pending and under consideration in this office action.
The instant application is a CON of 16/800,988, which is a DIV of 14/971,356. A restriction requirements was made in 14/971,356 4/12/2017 which require restriction between genetic modifying an organism by modifying an embryo and producing the organism (group I); A gene therapy that genetically modifies an organism by deliver of a gene therapy composition to the organism (group II); and a method of treating a disease (group III). The new claims are also a gene therapy and are the subject matter of group II, which was the elected group II in the 14/971,356 and the subject matter of the claimed invention in 16/800,988. Thus a double patenting rejection made between the instant application and its parent applications are proper because they are all gene therapies that would be grouped together.
Claim Rejections - 35 USC § 112
The following is a quotation of 35 U.S.C. 112(b):
(b) CONCLUSION.—The specification shall conclude with one or more claims particularly pointing out and distinctly claiming the subject matter which the inventor or a joint inventor regards as the invention.
The following is a quotation of 35 U.S.C. 112 (pre-AIA ), second paragraph:
The specification shall conclude with one or more claims particularly pointing out and distinctly claiming the subject matter which the applicant regards as his invention.
Claims 65 and 73 are rejected under 35 U.S.C. 112(b) or 35 U.S.C. 112 (pre-AIA ), second paragraph, as being indefinite for failing to particularly point out and distinctly claim the subject matter which the inventor or a joint inventor (or for applications subject to pre-AIA 35 U.S.C. 112, the applicant), regards as the invention.
Claim 65 contains the trademark/trade names Lipofectamine 2000 and Invivofectamine. Where a trademark or trade name is used in a claim as a limitation to identify or describe a particular material or product, the claim does not comply with the requirements of 35 U.S.C. 112(b) or 35 U.S.C. 112 (pre-AIA ), second paragraph. See Ex parte Simpson, 218 USPQ 1020 (Bd. App. 1982). The claim scope is uncertain since the trademark or trade name cannot be used properly to identify any particular material or product. A trademark or trade name is used to identify a source of goods, and not the goods themselves. Thus, a trademark or trade name does not identify or describe the goods associated with the trademark or trade name. In the present case, the trademark/trade name is used to identify/describe the source of a liposome and, accordingly, the identification/description is indefinite.
Claim 73 recites, “within three weeks of the intravenous injection”. Claim 74 depends upon claim 56 which only recites delivering without recitation or implication that injection, more particularly intravenous injection is occurring. As such, Claim 73 lacks sufficient antecedent basis for the above citation and renders the claims indefinite because it is not apparent to which intravenous injection the citation is intended to refer, given the base claim does not require any type of intravenous injection.
Double Patenting
The nonstatutory double patenting rejection is based on a judicially created doctrine grounded in public policy (a policy reflected in the statute) so as to prevent the unjustified or improper timewise extension of the “right to exclude” granted by a patent and to prevent possible harassment by multiple assignees. A nonstatutory double patenting rejection is appropriate where the conflicting claims are not identical, but at least one examined application claim is not patentably distinct from the reference claim(s) because the examined application claim is either anticipated by, or would have been obvious over, the reference claim(s). See, e.g., In re Berg, 140 F.3d 1428, 46 USPQ2d 1226 (Fed. Cir. 1998); In re Goodman, 11 F.3d 1046, 29 USPQ2d 2010 (Fed. Cir. 1993); In re Longi, 759 F.2d 887, 225 USPQ 645 (Fed. Cir. 1985); In re Van Ornum, 686 F.2d 937, 214 USPQ 761 (CCPA 1982); In re Vogel, 422 F.2d 438, 164 USPQ 619 (CCPA 1970); In re Thorington, 418 F.2d 528, 163 USPQ 644 (CCPA 1969).
A timely filed terminal disclaimer in compliance with 37 CFR 1.321(c) or 1.321(d) may be used to overcome an actual or provisional rejection based on nonstatutory double patenting provided the reference application or patent either is shown to be commonly owned with the examined application, or claims an invention made as a result of activities undertaken within the scope of a joint research agreement. See MPEP § 717.02 for applications subject to examination under the first inventor to file provisions of the AIA as explained in MPEP § 2159. See MPEP § 2146 et seq. for applications not subject to examination under the first inventor to file provisions of the AIA . A terminal disclaimer must be signed in compliance with 37 CFR 1.321(b).
The filing of a terminal disclaimer by itself is not a complete reply to a nonstatutory double patenting (NSDP) rejection. A complete reply requires that the terminal disclaimer be accompanied by a reply requesting reconsideration of the prior Office action. Even where the NSDP rejection is provisional the reply must be complete. See MPEP § 804, subsection I.B.1. For a reply to a non-final Office action, see 37 CFR 1.111(a). For a reply to final Office action, see 37 CFR 1.113(c). A request for reconsideration while not provided for in 37 CFR 1.113(c) may be filed after final for consideration. See MPEP §§ 706.07(e) and 714.13.
The USPTO Internet website contains terminal disclaimer forms which may be used. Please visit www.uspto.gov/patent/patents-forms. The actual filing date of the application in which the form is filed determines what form (e.g., PTO/SB/25, PTO/SB/26, PTO/AIA /25, or PTO/AIA /26) should be used. A web-based eTerminal Disclaimer may be filled out completely online using web-screens. An eTerminal Disclaimer that meets all requirements is auto-processed and approved immediately upon submission. For more information about eTerminal Disclaimers, refer to www.uspto.gov/patents/apply/applying-online/eterminal-disclaimer.
Claims 56-59, 63-64, and 66 are rejected on the ground of nonstatutory double patenting as being unpatentable over claims 1-4, 9, and 14-16 of U.S. Patent No. 12,0182,275 Although the claims at issue are not identical, they are not patentably distinct from each other because the patent claims are an anticipatory species of the instant claims, rendering the instant claims obvious variants.
Regarding claim 56, a method of modifying a mammalian subject by editing in vivo a DNA target sequence in a genomic locus of interest of a hepatic cell in the mammalian subject, said method comprising in vivo delivering to the hepatic cell a a composition comprising a stable nucleic acid-lipid particle (SNALP) comprising a CRISPR-Cas system, wherein the CRISPR-Cas system comprises: I. a CRISPR-Cas system RNA comprising a guide sequence that hybridizes to the DNA target sequence, and II. a Cas9 comprising at least one nuclear localization sequence (NLS) or an mRNA encoding the Cas9, wherein the guide sequence directs sequence-specific binding of a CRISPR complex to the DNA target sequence, the CRISPR complex comprises the Cas9 complexed with the CRISPR-Cas system RNA, and wherein the CRISPR complex introduces a double-stranded break in vivo in the DNA target sequence in the genomic locus of interest of the hepatic cell which forms a targeted indel in the genomic locus of interest and produces a phenotypic change in said mammalian subject, and wherein the delivering results in greater than 20% indel formation in the genomic locus of interest of the hepatic cell. The many difference between the instant claim and patent claim is that the patent claim recites a SNALP. A SNALP is a species of liposome. Instant claim 1 also recites a PAM sequence that is not recites in patent claim 1. However, PAM structural components of a CRISP-Cas system gRNA as recited in patent claim 1. Thus, an ordinary artisan would understand that the gRNA recited in patent claim 1 would have a PAM sequence. As such, the patent claim discloses a species variant of instant claim 1.
Instant claim 1 is also rendered obvious by patent claims 15 and 16 for the rationale discussed above for patent claim 1.
Regarding claim 57, patent claim 9 specify the nucleic acid encoding Cas9 is an mRNA. Patent claim 9 does not recite “codon optimized for expression in a mammalian subject”. However, at the time of the patent means of codon optimization to optimize mammalian expression were well established in the prior art and could be predictably applied to the patent claim 9 to arrive at the limitations of instant claim 57.
Regarding claim 58, patent claim 2 specifies S. pyogenes Cas9.
Regarding claim 59, patent claim 3 specifies S. aureus Cas9.
Regarding claims 63 and 64, patent claim 4 specifies the CRISPR-Cas system RNA is a chimeric RNA (chiRNA) comprising the guide sequence fused to a tracr-mate sequence and a tracr-sequence.
Patent claim 66, patent claim 14 discloses a SNALP comprising cholesterol and PEG-lipid.
Regarding claims 73-74, patent claim 1 further recites wherein the delivering results in greater than 20% indel formation, which comprises the range of at least 30% indel formation as claimed.
(2) Claims 56, 59, 63, 73, and 74rejected on the ground of nonstatutory double patenting as being unpatentable over claims 1, 2, and 9 of U.S. Patent No. 10577630 in view of Conway (US 2015/0056705 A1 effectively filed:5/15/2013; of record) and Jinek (WO2013/176772 A1 effectively filed:, of record).
Regarding claim 56, patent claim 1 teaches method of modifying a mammal by editing in vivo a DNA target sequence in a genomic locus of interest of a hepatic cell in the mammal, said method comprising delivering to the hepatic cell one or more doses of a non-naturally occurring composition comprising a hepatotropic adeno-associated virus (AAV) particle comprising one or more polynucleotides encoding: I. a CRISPR-Cas system guide RNA comprising a guide sequence that hybridizes to the DNA target sequence, and II. a CRISPR enzyme, wherein the CRISPR enzyme is Staphylococcus aureus Cas9 (SaCas9), wherein the guide sequence directs sequence-specific binding of a CRISPR complex to the DNA target sequence, the CRISPR complex comprises the CRISPR enzyme complexed with the CRISPR-Cas system guide RNA, and wherein the CRISPR complex introduces a double-stranded break in vivo in the DNA target sequence in the genomic locus of interest of the hepatic cell.
Patent claim 1 does not teach that the CRISPR/Cas system is delivered by a liposome but rather an AAV vector. However Conway teaches an in vivo delivery of a nucleic acid encoding a CRISPR/Cas9 system and gRNA can be delivered by viral means, such as AAV vectors and non-viral means, such as liposomes. (p. 26, [0190]-[0191]).
Patent claim 1 also does not teaches that the Cas protein is fused to an NSL. However, Jinek teaches Jinek teaches method of modifying DNA target sequences in vivo using CRISPR/Cas systems in vivo for purposes of gene therapy. In vivo embodiments including administering a DNA-targeting RNA and site-directed modifying polypeptide directly to an individual (p. 83, [00310]; p. 66, [00261]). Jinek that the site-directed modifying polypeptide can be Cas9, such as Cas9 from S. pyogenes (p. 64, [0256]). Jinek further teaches that the site-directed modifying polypeptides can further comprises a heterologous sequence for subcellular localization, such as an NLS for targeting to the nucleus (p. 68, [0265]).
As such, it would have been obvious to an artisan of ordinary skill at the time of the patent to choose a liposome, as taught by Conway, and the use of an NSL sequence with the Cas9, as taught by Jenik in the method of modifying a mammal in vivo as taught by patent claim 1 to predictably arrive at the limitations of claim 56. The artisan would have a reasonable expectation of success because Conway teaches liposomes as a successful alternative delivery vehicle to AAV vector and means of adding an NSL sequence a Cas9 protein were known and predictable in the prior art, as demonstrated by Jenik. Thus, patent claim 1 in view of Conway and Jenik render instant claim 56 obvious.
Regarding claim 59, patent claim 1 teaches SaCas9.
Regarding claim 63, patent claim 7 teaches the CRISPR-Cas system guide RNA is a chimeric RNA (chiRNA).
Regarding claims 73 and 74, patent claim 2 teaches greater than 205 indel formation.
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.
(1) Claim(s) 56-58, 61-64, 66-68, and 70-72 is/are rejected under 35 U.S.C. 103 as being unpatentable over Conway (US 2015/0056705 A1 effectively filed:5/15/2013; of record) in view of Jinek (WO2013/176772 A1 effectively filed:, of record).
Regarding claim 56, Conway teaches methods and composition for genetic modification for example for the treatment of diseases. Genome editing is used to correct an aberrant gene or change the expression of an endogenous gene (i.e. produce a phenotypic change). One or more endogenous genes can be targeted for genomic editing including any mammalian gene(s) (See p. 2, [0015). A CRISPR/Cas system that binds to target site in a region of interest in an endogenous gene (e.g., an endogenous or safe harbor gene, or a regulatory gene or its DNA target) in a genome, wherein the CRISPR/Cas system comprises one or more engineered single guide RNAs that recognize the target gene and a functional domain (e.g., a transcriptional regulatory domain and/or a nuclease domain) (See p. 2, [0016]). Conway teaches chimeric or sgRNA can be engineered to comprise a sequence complementary to any desired target. The RNAs comprise 22 bases complementary to a target and of the form G[N19], followed by a protospacer-adjacent motif (PAM). See p. 24, [0176]. The CRISPR/Cas system as described herein may bind to and/or cleave the region of interest in a coding or non-coding region within or adjacent to the gene (See p. 2, [0017]). Gene therapy, including liver-directed gene therapy protocols and direct intramuscular injection, involving the introduction of plasmid and other vectors (e.g., AAV) encoding a functional FIX protein have been described for treatment of hemophilia B (p. 8, [0063]). The albumin gene is highly expressed in the liver. Thus, insertion of a transgene into the endogenous albumin locus using a specific nuclease results in high level expression of the protein or gene product encoded by that transgene, which may also be secreted into the blood stream The transgene can encode any protein or peptide including those providing therapeutic benefit. For example, the transgene can encode a protein involved in disorders of the blood, for example, clotting disorders, and a variety of other monogenic diseases. The transgene can be inserted into the endogenous albumin locus such that expression of the transgene is controlled by the albumin expressional control elements, resulting in liver-specific expression of the transgene encoded protein at high concentrations (p. 8, [0060]). The nucleases, polynucleotides encoding these nucleases, donor polynucleotides and compositions comprising the proteins and/or polynucleotides described herein may be delivered in vivo or ex vivo by any suitable means (p. 25, [0188]). Nucleases and/or donor constructs as described herein may also be delivered using vectors containing sequences encoding one or more of the CRISPR/Cas system(s). Any vector systems may be used including, but not limited to, plasmid vectors, DNA minicircles, retroviral vectors, lentiviral vectors, adenovirus vectors, poxvirus vectors; herpesvirus vectors and adeno-associated virus vectors, etc., and combinations thereof (p. 26, [0190]). Conventional viral and non-viral based gene transfer methods can be used to introduce nucleic acids encoding nucleases and donor constructs in cells (e.g., mammalian cells) and target tissues. Non-viral vector delivery systems include DNA plasmids, DNA minicircles, naked nucleic acid, and nucleic acid complexed with a delivery vehicle such as a liposome (i.e. lipid particles) or poloxamer (p. 26, [0191]). Methods of non-viral delivery of nucleic acids include electroporation, lipofection, microinjection, biolistics, virosomes, liposomes, immunoliposomes, polycation or lipid:nucleic acid conjugates, naked DNA, naked RNA, capped RNA, artificial virions, and agent-enhanced uptake of DNA. Sonoporation using, e.g., the Sonitron 2000 system (Rich-Mar) can also be used for delivery of nucleic acids (p. 26, [0192]). The preparation of lipid:nucleic acid complexes, including targeted liposomes such as immunolipid complexes, is well known to one of skill in the art (p. 26. [0194]). Thus, Conway expressly teaches a method of modifying a mammalian subject by editing in vivo a DNA target sequence in a genomic locus of interest of hepatic cells comprising the claimed CRISPR/Cas system to produce a phenotypic change as claimed.
Conway does not teach that the Cas 9 comprises at least one nuclear localization sequence (NLS). However, Jinek teaches method of modifying DNA target sequences in vivo using CRISPR/Cas systems in vivo for purposes of gene therapy. In vivo embodiments including administering a DNA-targeting RNA and site-directed modifying polypeptide directly to an individual (p. 83, [00310]; p. 66, [00261]). Jinek that the site-directed modifying polypeptide can be Cas9, such as Cas9 from S. pyogenes (p. 64, [0256]). Jinek further teaches that the site-directed modifying polypeptides can further comprises a heterologous sequence for subcellular localization, such as an NLS for targeting to the nucleus (p. 68, [0265]).
As such, it would have been obvious to an artisan of ordinary skill at the time of effectively filing to modify the Cas9 protein in the method of Conway to include a heterologous NSL sequence as taught by Jinek to predictably arrive at the limitations of claim 56. The artisan would have a reasonable expectation of success because NSL sequences were commonly being added to protein sequence using long established molecular biology techniques, as those detailed in Conway and Jinek. Further, the artisan would be motivated to include a NSL sequence in the Cas9 protein because the NSL will allow for Cas9 transportation to the nucleus, which is its intended site of action. As such, Conway in view of Jinek render claim 56 obvious.
Regarding claim 57, Conway also teaches that the Cas9 in the CRISPR/Cas system can be in the form of an mRNA encoding the Cas9 ([0028]). Thus, Conway in view of Jinek renders claim 57 obvious.
Regarding claim 58, Conway teaches the Cas9 can be any Cas9, including the S. pyogenes Cas9 (p. 24-25 [0177] and [0178]). Thus Conway in view of Jinek renders claim 59 obvious.
Regarding claim 61, Conway teaches the methods and compositions of the invention also comprise fusion proteins wherein the Cas9 protein, or truncation thereof, is fused to a functional domain. In some aspects, the functional domain is an activation or a repression domain. (see [0072]).
Regarding claim 62, Conway teaches for example, with respect to a fusion polypeptide in which a Cas DNA-binding domain is fused to an activation domain, the Cas DNA-binding domain and the activation domain are in operative linkage if, in the fusion polypeptide, the Cas DNA-binding domain portion is able to bind its target site and/or its binding site, while the activation domain is able to up-regulate gene expression. When a fusion polypeptide in which a Cas DNA-binding domain is fused to a cleavage domain, the Cas DNA-binding domain and the cleavage domain are in operative linkage if, in the fusion polypeptide, the Cas DNA-binding domain portion is able to bind its target site and/or its binding site, while the cleavage domain is able to cleave DNA in the vicinity of the target site. See [0138]. The CRISPR/Cas system can also be used to inhibit gene expression. Lei et al (see, (2013) Cell, 152, (5): 1173-1183) have shown that a catalytically dead Cas9 lacking endonuclease activity, when coexpressed with a guide RNA, generates a DNA recognition complex that can specifically interfere with transcriptional elongation, RNA polymerase binding, or transcription factor binding. This system, called CRISPR interference (CRISPRi), can efficiently repress expression of targeted genes. See [0158].
Regarding claims 63-64, Conway teaches that in some embodiments a chimeric RNA is constructed where an engineered mature crRNA (conferring target specificity) is fused to a tracrRNA (supplying interaction with the Cas9) to crease a chimeric cr-RNA-tracrRNA hybrid (also termed a single guide RNA). See p. 24, [0175]. Therefore, Conway in view of Jinek renders claim 63 obvious for reasons discussed above.
Regarding claim 66, Conway teaches a SNALP, ionizable and cationic lipids as discussed above. Thus Conway in view of Jinek render claim 66 for reasons discussed above.
Regarding claim 70, Conway teaches as noted above, insertion of an exogenous sequence (also called a "donor sequence" or "donor" or "transgene"), for example for correction of a mutant gene or for increased expression of a wild-type gene. It will be readily apparent that the donor sequence is typically not identical to the genomic sequence where it is placed. A donor sequence can contain a non-homologous sequence flanked by two regions of homology to allow for efficient HDR at the location of interest. See [0181]
Regarding claim 71, Conway teaches that the terms “subject” and “patient” are used interchangeably and refer to mammals such as human patients ([0142]). Thus Conway in view of Jinek render claim.
Regarding claim 72, Conway teaches gene therapy vectors can be delivered in vivo by administration to an individual subject typically by systemic administration (e.g., intravenous, intraperitoneal, intramuscular, subdermal or intracranial infusion ([0205]). Thus, Conway in view of Jinek renders claim 72 obvious for reasons discussed above.
The combination of prior art cited above in all rejections under 35 U.S.C. 103 satisfies the factual inquiries as set forth in Graham v. John Deere Co., 383 U.S. 1, 148 USPQ 459 (1966). Once this has been accomplished the holdings in KSR can be applied (KSR International Co. v. Teleflex Inc. (KSR), 550 U.S. 389, 82 USPQ2d 1385 (2007): "Exemplary rationales that may support a conclusion of obviousness include: (A) Combining prior art elements according to known methods to yield predictable results; (B) Simple substitution of one known element for another to obtain predictable results; (C) Use of known technique to improve similar devices (methods, or products) in the same way; (D) Applying a known technique to a known device (method, or product) ready for improvement to yield predictable results; (E) "Obvious to try" - choosing from a finite number of identified, predictable solutions, with a reasonable expectation of success; (F) Known work in one field of endeavor may prompt variations of it for use in either the same field or a different one based on design incentives or other market forces if the variations are predictable to one of ordinary skill in the art; (G) Some teaching, suggestion, or motivation in the prior art that would have led one of ordinary skill to modify the prior art reference or to combine prior art reference teachings to arrive at the claimed invention."
In the present situation, rationales A and G are applicable. The claimed method was known in the art at the time of filing as indicated by Conway in view of Jinek. Thus, the teachings of the cited prior art in the obviousness rejection above provide the requisite teachings and motivations with a clear, reasonable expectation. The cited prior art meets the criteria set forth in both Graham and KSR.
(2) Claim(s) 66-69 is/are rejected under 35 U.S.C. 103 as being unpatentable over Conway (US 2015/0056705 A1 effectively filed:5/15/2013; of record) in view of Jinek (WO2013/176772 A1 of record) and David (David et al. Pharmacological Research 62:100-114, 2010).
Conway in view of Jinek teach the limitations of claims as discussed above. To reiterate Conway teaches liposomes and contemplates the use of SNALPs to deliver the components of the CRISPR-Cas9 coding sequences. Conway in view of Jinek does not teach ionizable or cationic lipid (Claim 66), such as DLinDAP, DLinDMA, DLinKDMA, or DLinkDMA (claim 67), a neutral helper lipid (claim 66), such as DSPC (claim 68), a PEG-lipid or cholesterol (claim 66), such as PEG-C-MCA, PEG-S-DMG, or PEG-C-DOMG (claim 69).
However, David teaches a complex formulation was successfully used on cynomolgus monkeys, targeting apolipoprotein B (apoB) to the liver. The liposomes were composed of distearoyl-glycero-phosphatidylcholine (DSPC), dilinoleyloxy-dimethyl-aminopropane (DLinDMA), methoxypolyethyleneglycol-carbamoyl-dimyristyloxy-propylamine (PEG-c-DMA), and cholesterol. These liposomes complexed with siRNA are called stable nucleic acid lipid particles (SNALP). David also teaches Different studies have been carried out with these complexes. These particles were used on cynomolgus monkeys after preliminary tests on mice. They chose apoB as an endogenous gene target and potential therapeutic target for hypercholesterolemia. Their SNALP had a size between 77 and 83 nm, a polydispersity range of 0.09–0.15, and encapsulation efficiencies between 92 and 97%. The results showed that the silencing effect of SNALP-formulated siRNA represented more than a 100-fold improvement in potency compared with systemic administration of cholesterol-conjugated siApoB. See page 104, col 2, middle paragraph to page 106, col 2, second to last paragraph).
Thus, it would have been obvious to an artisan of ordinary skill at the time of effectively filing to choose one of the SNALPs comprising a cholesterol and a PEG-lipid as taught by David as the SNALP used in the method of in vivo gene editing taught by Conway in view of Jinek to predictably arrive at the invention of new claim 75. The artisan would have a reasonable expectation of success in utilizing the SNALP of David with the nucleic acid sequences for delivery in Conway because David teaches that these SNALP effectively deliver the payload of the SNALP to cells the liver in vivo. Further, the artisan would be motivated to use such SNALP taught by David because David teaches significant improvement in potency compared to other systemic administrations that soles have cholesterol conjugates. Thus Conway in view of Jinek and Davide render new claim 66-69 obvious.
The combination of prior art cited above in all rejections under 35 U.S.C. 103 satisfies the factual inquiries as set forth in Graham v. John Deere Co., 383 U.S. 1, 148 USPQ 459 (1966). Once this has been accomplished the holdings in KSR can be applied (KSR International Co. v. Teleflex Inc. (KSR), 550 U.S. 389, 82 USPQ2d 1385 (2007): "Exemplary rationales that may support a conclusion of obviousness include: (A) Combining prior art elements according to known methods to yield predictable results; (B) Simple substitution of one known element for another to obtain predictable results; (C) Use of known technique to improve similar devices (methods, or products) in the same way; (D) Applying a known technique to a known device (method, or product) ready for improvement to yield predictable results; (E) "Obvious to try" - choosing from a finite number of identified, predictable solutions, with a reasonable expectation of success; (F) Known work in one field of endeavor may prompt variations of it for use in either the same field or a different one based on design incentives or other market forces if the variations are predictable to one of ordinary skill in the art; (G) Some teaching, suggestion, or motivation in the prior art that would have led one of ordinary skill to modify the prior art reference or to combine prior art reference teachings to arrive at the claimed invention."
In the present situation, rationales A, B, E and G are applicable. The claimed method was known in the art at the time of filing as indicated by Conway in view of Jinek and David. Thus, the teachings of the cited prior art in the obviousness rejection above provide the requisite teachings and motivations with a clear, reasonable expectation. The cited prior art meets the criteria set forth in both Graham and KSR.
(3) Claim(s) 65 is/are rejected under 35 U.S.C. 103 as being unpatentable over Conway (US 2015/0056705 A1 effectively filed:5/15/2013; of record) in view of Jinek (WO2013/176772 A1 of record) and Patra (Patra International Journal of Bio-resource and Stress Management 2011, 2(3):313-319).
Conway in view of Jinek teaches the claim as discussed above. Conway in view of Jinek does not teach Lipofectamine 2000. However, before the effective filing date of the instant application, Patra teaches that lipofectamine 2000 was a cationic liposome used to effectively deliver nucleic acid payloads specifically to liver cells (abstract on page 313).
As such, it would have been obvious to an artisan of ordinary skill before the time of effective filing to use the species of liposome, Lipofectamine 2000, as taught by Patra, in the gene editing method of Conway in view of Jinek to predicably arrive at the limitations of the claim. An artisan was have had a reasonable expectation of success because Patra teaches that Lipofectamine 2000 was an established and available liposome used for transfection of liver cells. Further, the artisan would have been motivated to use Lipofectamine 2000 because Patra teaches that is effectively and specifically targets liver cells. As such, Conway in view of Jinek and Patra render claim 65 obvious.
(4) Claim(s) 65 is/are rejected under 35 U.S.C. 103 as being unpatentable over Conway (US 2015/0056705 A1 effectively filed:5/15/2013; of record) in view of Jinek (WO2013/176772 A1 of record) and Markowitz (Markowitz et al. Molecular Therapy 17(supplement 1):S391, abstract 1028, 2009).
Conway in view of Jinek teaches the claim as discussed above. Conway in view of Jinek does not teach Invivofectamine. However, before the effective filing date of the instant application, Markowitz teaches currently, siRNAs for therapeutics have been limited to diseases in which the tissue is easily accessible for local delivery. In this study, we have developed a new delivery reagent (Invivofectamine™) for systemic or local delivery of siRNA in vivo. After a single intravenous injection (low pressure) of Stealth™RNAi complexed with Invivofectamine ™, we observed more than 70% knockdown in Liver, Kidney, Lung, and Spleen. The knockdown was dose dependent and can be detected in liver as early as 6 hours post injection. We also demonstrated more that 70% of knock down of at least 3 different target genes (PPIB, MAPK1 and RRM1) after a single intratumoral injection in HCT166 xenograft tumors. Additionally, the Invivofectamine™- Stealth™RNAi complex did not trigger an IFN response or liver toxicity (ALT and AST measurements). The ease of use, effi cacy, and low toxicity of Invivofectamine™ complexed with Stealth™RNAi make it the best choice for successful in vivo experiments. See abstract
As such, it would have been obvious to an artisan of ordinary skill before the time of effective filing to use the species of liposome, Invivofectamine, as taught by Markowitz, in the gene editing method of Conway in view of Jinek to predicably arrive at the limitations of the claim. An artisan was have had a reasonable expectation of success because Marktowitz teaches that Invivofectamine was an established and available liposome used for transfection of liver. Further, the artisan would have been motivated to use Invivofectamine because Markowitz teaches that is targets liver and it is the best choice for successful in vivo experiments. As such, Conway in view of Jinek and Patra render claim 65 obvious.
(5) Claim(s) 60 is/are rejected under 35 U.S.C. 103 as being unpatentable over Conway (US 2015/0056705 A1 effectively filed:5/15/2013; of record) in view of Jinek (WO2013/176772 A1 of record) and Jinek2 (US2016/0446961 effectively filed 5/25/2012).
Conway in view of Jinek teaches the claim as discussed above. They do not teach that the Cas9 proteins is a nickase comprising a mutation in D10A, E762A, H840A, N854A, N863A, or D986A.
However Jinek2 teaches in some embodiments, the modified form of the Cas9/Csn1 polypeptide is a D10A (aspartate to alanine at amino acid position 10 of SEQ ID NO:8) mutation (or the corresponding mutation of any of the proteins set forth as SEQ ID NOs:1-256 and 795-1346) that can cleave the complementary strand of the target DNA but has reduced ability to cleave the non-complementary strand of the target DNA (thus resulting in a single strand break (SSB) instead of a DSB; see FIG. 11). In some embodiments, the modified form of the Cas9/Csn1 polypeptide is a H840A (histidine to alanine at amino acid position 840 of SEQ ID NO:8) mutation (or the corresponding mutation of any of the proteins set forth as SEQ ID NOs:1-256 and 795-1346) that can cleave the non-complementary strand of the target DNA but has reduced ability to cleave the complementary strand of the target DNA (thus resulting in a single strand break (SSB) instead of a DSB; see FIG. 11). The use of the D10A or H840A variant of Cas9 (or the corresponding mutations in any of the proteins set forth as SEQ ID NOs:1-256 and 795-1346) can alter the expected biological outcome because the non-homologous end joining (NHEJ) is much more likely to occur when DSBs are present as opposed to SSBs. Thus, in some cases where one wishes to reduce the likelihood of DSB (and therefore reduce the likelihood of NHEJ), a D10A or H840A variant of Cas9 can be used. Other residues can be mutated to achieve the same effect (i.e. inactivate one or the other nuclease portions). As non-limiting examples, residues D10, G12, G17, E762, H840, N854, N863, H982, H983, A984, D986, and/or A987 (or the corresponding mutations of any of the proteins set forth as SEQ ID NOs:1-256 and 795-1346) can be altered (i.e., substituted) (see FIG. 3, FIG. 5, FIG. 11A, and Table 1 for more information regarding the conservation of Cas9 amino acid residues). Also, mutations other than alanine substitutions are suitable. In some embodiments when a site-directed polypeptide (e.g., site-directed modifying polypeptide) has reduced catalytic activity (e.g., when a Cas9 protein has a D10, G12, G17, E762, H840, N854, N863, H982, H983, A984, D986, and/or a A987 mutation, e.g., D10A, G12A, G17A, E762A, H840A, N854A, N863A, H982A, H983A, A984A, and/or D986A), the polypeptide can still bind to target DNA in a site-specific manner (because it is still guided to a target DNA sequence by a DNA-targeting RNA) as long as it retains the ability to interact with the DNA-targeting RNA. See [0262].
As such, it would have been obvious to an artisan of ordinary skill before the time of effective filing to use any one of the claimed Cas9 mutant forms, taught by Jinek2, in the gene editing method of Conway in view of Jinek to predictable arrive at the limitations of claim 60. An artisan would have a reasonable expectation of success because Jinek2 teaches that these mutants effective modify genomic DNA sequences as discussed above. Further, the artisan would be motivated to one of the Cas9 mutant of Jinek because it results in SSB as opposed to DSB and therefore are less likely to gene edit by NHEJ.
No claims are allowed.
Any inquiry concerning this communication or earlier communications from the examiner should be directed to MARCIA STEPHENS NOBLE whose telephone number is (571)272-5545. The examiner can normally be reached M-F 9-5:30.
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MARCIA S. NOBLE
Primary Examiner
Art Unit 1632
/MARCIA S NOBLE/Primary Examiner, Art Unit 1632
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