DETAILED CORRESPONDENCE
Status of the Application
The present application, filed on or after March 16, 2013, is being examined under the first inventor to file provisions of the AIA .
Claims 1-4, 6, 14, 18-30, 34, 36, 37, 41-43, and 45-50 are pending in the application.
Applicant's amendment to the claims, filed May 26, 2026, is acknowledged. This listing of the claims replaces all prior versions and listings of the claims.
Applicant's remarks filed May 26, 2026 in response to the non-final rejection filed February 25, 2026 are acknowledged and have been fully considered.
The text of those sections of Title 35, U.S. Code not included in this action can be found in a prior Office action.
Claim 5 has been canceled by applicant’s amendment filed May 26, 2026 and rejections previously applied to this claim are canceled.
Restriction/Election
In response to requirements for restriction/election filed September 7, 2022 and August 26, 2024, applicant elected without traverse the following subject matter in the replies filed November 7, 2022 and October 25, 2024:
Group I, pending claims 1-4, 6, 14, 18-24, 27-30, 34, 36, 37, 41-43, and 45, drawn to the technical feature of an engineered, non-naturally occurring system suitable for modifying post-translational modification sites on a protein encoded by a target RNA, a cell, and a non-human animal or plant;
Species A) a catalytically inactive (dead) Cas13 protein and a nucleotide deaminase protein;
Species 1) the ADAR protein or catalytic domain thereof comprises a mutation in amino acid L332 of an hADAR2-D amino acid sequence of the corresponding mutation in a homologous ADAR protein;
Species BB) the target sequence comprises one or more codons with a cytidine;
Species AAA) the nucleotide deaminase is an adenosine deaminase or catalytic domain thereof;
Species BBBB) the Cas13 protein is Cas13b; and
Species BBBBB) a single guide molecule is used to target the at least two or at least three phosphorylation sites of the same protein.
Claims 25, 26, and 46-50 are withdrawn from further consideration pursuant to 37 CFR 1.142(b) as being drawn to nonelected inventions, there being no allowable generic or linking claim.
Claims 4 and 36 are withdrawn from further consideration pursuant to 37 CFR 1.142(b) as being drawn to a nonelected species, there being no allowable generic or linking claim.
Claims 1-3, 6, 14, 18-24, 27-30, 34, 37, 41-43, and 45 are being examined on the merits with claims 1, 2, 6, 14, 18, and 22 are being examined only to the extent the claims read on the elected subject matter set forth above.
Priority
This application is filed under 35 U.S.C. 371 as a national stage of international application PCT/US2018/057179, filed October 23, 2018, which claims domestic priority under 35 U.S.C. 119(e) to U.S. provisional application numbers 62/576,052 and 62/643,666, filed October 23, 2017 and March 15, 2018, respectively.
Applicant’s claim for the benefit of a prior-filed application under 35 U.S.C. 119(e) or under 35 U.S.C. 120, 121, 365(c), or 386(c) is acknowledged. Applicant has not complied with one or more conditions for receiving the benefit of an earlier filing date under 35 U.S.C. 119(e) as follows:
The later-filed application must be an application for a patent for an invention which is also disclosed in the prior application (the parent or original nonprovisional application or provisional application). The disclosure of the invention in the parent application and in the later-filed application must be sufficient to comply with the requirements of 35 U.S.C. 112(a), except for the best mode requirement. See Transco Products, Inc. v. Performance Contracting, Inc., 38 F.3d 551, 32 USPQ2d 1077 (Fed. Cir. 1994).
The disclosures of the prior-filed provisional applications, U.S. provisional application numbers 62/576,052 and 62/643,666, fail to provide adequate support or enablement in the manner provided by 35 U.S.C. 112(a) for claims 1-3, 6, 14, 18-24, 27-30, 34, 37, 41-43, and 45 of this application. For example, the provisional application numbers 62/576,052 and 62/643,666 fail to provide descriptive support for all recited mutations in claim 1 (and claims dependent therefrom), e.g., K350I and L332I. Claims 1-3, 6, 14, 18-24, 27-30, 34, 37, 41-43, and 45 have an effective filing date of October 23, 2018.
Claim Objections
The objection to claim 6 is withdrawn in view of applicant’s amendment to claim 6.
Claims 1, 6, 22-24, and 30 are objected to because of the following informalities:
Claim 1 is objected to in the in recitation of “with the exception of a K350I mutation and one or more mutations selected from the group consisting of E488Q, V351G, S486A, T375S, S370C, P462A, N597I, L332I, and I398V.” One of skill in the art would have recognized that the numbering of the mutation positions is with respect to the catalytic domain of hADAR2 as taught by Supplementary Text and Figures (obtained from https://www.nature.com/articles/nsmb.3203#Sec21, 2016, 14 pages, particularly Supplementary table 1 at p. 14; cited on Form PTO-892 filed August 26, 2024). However, in the interest of improving claim form, it is suggested that the noted phrase be amended to recite (with markings to show changes) “with the exception of a K350I mutation and one or more mutations selected from the group consisting of E488Q, V351G, S486A, T375S, S370C, P462A, N597I, L332I, and I398V, wherein the amino acid numbering corresponds to the amino acid sequence of the catalytic domain of the hADAR2 protein.”
Claim 1 is also objected to in the in recitation of “is adapted to link thereto when contacted with the dead Cas13 protein or the guide molecule” and in the interest of improving claim form, it is suggested that the noted phrase be amended to recite (with markings to show changes) “is adapted to link to said dead Cas13 protein or said guide molecule
Claim 6 is objected to in the in recitation of “wherein the nucleotide deaminase:” and in the interest of improving claim form, it is suggested that the noted phrase be amended to recite (with markings to show changes) “wherein the nucleotide deaminase protein or catalytic domain thereof:.”
Claim 22 is objected to in the in recitation of “claim 1, the guide sequence” and in the interest of improving claim form, it is suggested that the noted phrase be amended to recite (with markings to show changes) “claim 1, wherein the guide sequence.”
Claim 23 is objected to in the in recitation of “said adenosine deaminase protein or catalytic domain thereof, or both said dead Cas13 protein and said adenosine deaminase protein” and in the interest of improving claim form, it is suggested that the noted phrase be amended to recite (with markings to show changes) “said nucleotidenucleotide
Claim 24 is objected to in the in recitation of “claim 1, said target” and in the interest of improving claim form, it is suggested that the noted phrase be amended to recite (with markings to show changes) “claim 1, wherein said target.”
Claim 30 is objected to in the recitation of “MLK3 at S647, and ASK1 at S83, CREB at S133, FOXO1 at S256, S319, and T24, FOXO2 at S32, S253, and S315, and FOXO4 at S193, S258, and T28, and IKKa at T23;” and in the interest of improving claim form, it is suggested that the noted phrase be amended to recite (with markings to show changes) “MLK3 at S647, [[and]] ASK1 at S83, CREB at S133, FOXO1 at S256, S319, and T24, FOXO2 at S32, S253, and S315, [[and]] FOXO4 at S193, S258, and T28, and IKKa at T23;.”
Claim 30 is also objected to in the recitation of “inactivates a phosphorylation site of at least two or at least three proteins involved in the same signaling pathway;” and in the interest of improving claim form, it is suggested that the noted phrase be amended to recite (with markings to show changes) “inactivates a phosphorylation site of at least two or at least three proteins of a signaling pathway, wherein the at least two or at least three proteins are involved in the same signaling pathway;.”
Claim Rejections - 35 USC § 112(b)
The rejection of claim 6 under 35 U.S.C. 112(b) as being indefinite and confusing in the recitation of “wherein (a) is a hADAR2 catalytic domain thereof” is withdrawn in view of applicant’s amendment to claim 6 to recite “(a) is a catalytic domain of the nucleotide deaminase protein.”
Claim Rejections - 35 USC § 112(a)
The rejections of claims 1-3, 6, 14, 18-24, 27-30, 34, 37, 41-43, and 45 under 35 U.S.C. 112(a) as failing to comply with the written description and enablement requirements are withdrawn in view of applicant’s amendments to claim 1 to recite “wherein the nucleotide deaminase protein or catalytic domain thereof comprises the amino acid sequence of a human adenosine deaminase acting on RNA 2 (hADAR2) protein or catalytic domain thereof with the exception of a K350I mutation.”
Claim Rejections - 35 USC § 103
The rejection of claims 1, 2, 6, 14, 21-24, 27-30, 37, 41-43, and 45 under 35 U.S.C. 103 as being unpatentable over Yeo et al. (US 2018/0334685 A1, with priority to May 10, 2017; cited on Form PTO-892 filed September 7, 2022) in view of Zhang et al. (Sci. China Life Sci. 59:8, 2016, 3 pages; cited on Form PTO-892 filed September 7, 2022) and Radivojac et al. (Bioinformatics 24:241-247, 2008; cited on Form PTO-892 filed September 7, 2022),
the rejection of claim 3 under 35 U.S.C. 103 as being unpatentable over Yeo in view of Zhang and Radivojac as applied to claims 1, 2, 6, 14, 21-24, 27-30, 37, 41-43, and 45 above, and further in view of Kouranova et al. (Human Gene Therapy 27:464-475, 2016; cited on Form PTO-892 filed January 25, 2023),
the rejection of claims 18-20 under 35 U.S.C. 103 as being unpatentable over Yeo in view of Zhang and Radivojac as applied to claims 1, 2, 6, 14, 21-24, 27-30, 37, 41-43, and 45 above, and further in view of Abudayyeh et al. (Science 353:6299, 2016, 23 pages; cited on the IDS filed April 28, 2020), and
the rejection of claim 34 under 35 U.S.C. 103 as being unpatentable over Yeo in view of Zhang and Radivojac as applied to claims 1, 2, 6, 14, 21-24, 27-30, 37, 41-43, and 45 above, and further in view of Gao et al. (Biochem. Biophys. Res. Comm. 264:860-864, 1999; cited on Form PTO-892 filed January 25, 2023) and Carr et al. (Cell Reports 16:2618-2629, 2016; cited on Form PTO-892 filed January 25, 2023)
are withdrawn in view of applicant’s amendments to claim 1 to recite “wherein the nucleotide deaminase protein or catalytic domain thereof comprises the amino acid sequence of a human adenosine deaminase acting on RNA 2 (hADAR2) protein or catalytic domain thereof with the exception of a K350I mutation.” The cited prior art does not teach or suggest the “nucleotide deaminase protein or catalytic domain thereof” as recited in part (b) of instant claim 1.
Claim Rejections - 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.
The provisional rejection of claims 1-3, 6, 14, 18-24, 27-30, 34, 37, 41-43, and 45 on the ground of nonstatutory double patenting as being unpatentable over claims 1-3, 5, 7, 14, and 18-24 of co-pending application no. 16/756,139 (reference application) in view of Yeo et al. (US 2018/0334685 A1, with priority to May 10, 2017; cited on Form PTO-892 filed September 7, 2022; hereafter “Yeo”) and Radivojac et al. (Bioinformatics 24:241-247, 2008; cited on Form PTO-892 filed September 7, 2022; hereafter “Radivojac”) is withdrawn in view of applicant's submission of a terminal disclaimer on June 26, 2023 disclaiming the terminal portion of any patent granted on this application which would extend beyond the expiration date of any patent granted on Application Number 16/756,139.
The provisional rejection of claims 1, 2, 6, 14, 19-24, 27-30, 37, 41-43, and 45 on the ground of nonstatutory double patenting as being unpatentable over claims 1 and 17 of co-pending application no. 17/264,340 (reference application) in view of Yeo and Radivojac,
the provisional rejection of claim 3 on the ground of nonstatutory double patenting as being unpatentable over claims 1 and 17 of co-pending application no. 17/264,340 (reference application) in view of Yeo and Radivojac as applied to claims 1, 2, 6, 14, 19-24, 27-30, 37, 41-43, and 45 above, and further in view of Kouranova et al. (Human Gene Therapy 27:464-475, 2016; cited on Form PTO-892 filed January 25, 2023; hereafter “Kouranova’), and
the provisional rejection of claim 18 on the ground of nonstatutory double patenting as being unpatentable over claims 1 and 17 of co-pending application no. 17/264,340 in view of Yeo and Radivojac as applied to claims 1, 2, 6, 14, 19-24, 27-30, 37, 41-43, and 45 above, and further in view of Abudayyeh et al. (Science 353:6299, 2016, 23 pages; cited on the IDS filed on April 28, 2020; hereafter "Abudayyeh"), and
the provisional rejection of claim 34 on the ground of nonstatutory double patenting as being unpatentable over claims 1 and 17 of co-pending application no. 17/264,340 in view of Yeo and Radivojac as applied to claims 1, 2, 6, 14, 19-24, 27-30, 37, 41-43, and 45 above, and further in view of Gao et al. (Biochem. Biophys. Res. Comm. 264:860-864, 1999; cited on Form PTO-892 filed January 25, 2023; hereafter “Gao”) and Carr et al. (Cell Reports 16:2618-2629, 2016; cited on Form PTO- 892 filed January 25, 2023)
are withdrawn in view of applicant’s amendments to claim 1 to recite “wherein the nucleotide deaminase protein or catalytic domain thereof comprises the amino acid sequence of a human adenosine deaminase acting on RNA 2 (hADAR2) protein or catalytic domain thereof with the exception of a K350I mutation and one or more mutations selected from the group consisting of E488Q, V351G, S486A, T375S, S370C, P462A, N597I, L332I, and I398V” and applicant’s argument that the claims of the reference application require E488Q and M383L mutations while instant claim 1 excludes a M383L mutation (instant remarks at p. 16, top).
Claims 1, 2, 6, 14, 21-24, 27-30, 37, 41-43, and 45 are provisionally rejected on the ground of nonstatutory double patenting as being unpatentable over claims 1-3, 7-14, 16-18, and 20 of co-pending application no. 19/677,353 (reference application) in view of Yeo and Radivojac. Although the claims at issue are not identical, they are not patentably distinct from each other.
The instant Office action is made non-final in view of this new provisional rejection, which is necessitated by applicant’s filing of the reference application on May 14, 2026. The patent term filing date of this application is the same as the patent term filing date of the reference application and applicant’s attention is directed to MPEP 804.I.B.1.(b).(ii).
The claims of the reference application recite a cell, or progeny thereof, comprising an engineered, non-naturally occurring system suitable for modifying post-translational modification sites on a protein encoded by a target RNA, comprising:
(a) a catalytically inactive (dead) Cas13 protein, or a nucleotide sequence encoding said dead Cas13 protein;
(b) an adenosine deaminase acting on RNA (ADAR) protein or catalytic domain thereof comprising cytidine deaminase activity, a mutation of E488Q, and one or more mutations selected from L332I and K350 of an hADAR2-D amino acid sequence, or one or more corresponding mutations in a homologous ADAR protein;
(c) a guide molecule comprising a guide sequence designed to have a degree of complementarity with a target sequence in the target RNA at one or more codons that comprises an adenosine or cytosine and encodes an amino acid that is post-translationally modified;
wherein said adenosine deaminase protein or catalytic domain thereof is adapted to link thereto when contacted with the dead Cas13 protein or said guide molecule, and
wherein the post-translational modification sites are not phosphorylation sites.
The differences between instant claims 1, 6, 22, and 30, and the claims of the reference application is that the claims of the reference application do not recite the instant claim 1 limitation of the codon encodes an amino acid that is post-translationally modified by phosphorylation and the limitations of claims 6, 22, and 30.
Yeo teaches editing RNAs in living cells that cause cancer (paragraph [0028)]). Radivojac teaches phosphorylation of amino acid residues serine, threonine, and tyrosine is common in cancer-associated proteins and changes in phosphorylation signaling can be due to disruption and deregulation of kinase and phosphatase function due to amino acid substitutions of kinases and phosphatases that results in changes in target phosphorylation (p. i241, column 2, middle). Radivojac teaches there is evidence that disruptions of phosphorylation are associated with cancer (p. i241, column 2, bottom) and that cancer mutation datasets were shown to have a significant enrichment for mutations that cause gain or loss of phosphorylation when compared to control datasets (p. i241, Abstract).
In view of the teachings of Yeo and Radivojac, it would have been obvious to one of ordinary skill in the art before the effective filing date to modify the system of the claims of the reference application for the guide sequence to be designed to modify one or more codons encoding a cancer-related phosphorylation site or sites. One would have been motivated to and would have had a reasonable expectation to do this because Yeo discloses editing RNAs that cause cancer and Radivojac teaches cancer mutation datasets were shown to have a significant enrichment for mutations that cause gain or loss of phosphorylation.
Regarding instant claims 2 and 41, claim 8 of the reference application recites the cell of claim 1, wherein said guide sequence comprises a non-pairing nucleotide at a position corresponding to said adenosine or cytosine resulting in a mismatch in an RNA duplex formed between the target RNA and the guide molecule and claim 20 of the reference application recites the cell of claim 1, or progeny thereof, wherein said cell comprises a hypoxanthine or a guanine in place of an adenine in said target RNA compared to a corresponding cell not subjected to the system method.
Regarding instant claim 14, claim 8 of the reference application recites the cell of claim 1, wherein said dead Cas13 protein is a dead Cas13a, dead Cas13b, or dead Cas13c; or wherein said dead Cas13 originates from a Cas13 according to any one of SEQ ID NO: 34-161, or
originates from a bacterial species selected from Leptotrichia shahii, L wadei F0279 (Lw2), Listeria seeligeri, Lachnospiraceae bacterium MA2020, Lachnospiraceae bacterium NK4A179, [Clostridium] aminophilum DSM 10710, Carnobacterium gallinarum DSM 4847, Paludibacter propionicigenes WB4, Listeria weihenstephanensis FSL R9-0317, Listeriaceae bacterium FSL M6- 0635, Leptotrichia wadei F0279, Rhodobacter capsulatus SB 1003, Rhodobacter capsulatus R121, Rhodobacter capsulatus DE442, Leptotrichia buccalis C-1013-b, Herbinix hemicellulosilytica, [Eubacterium] rectale, Eubacteriaceae bacterium CHKCI004, Blautia sp. Marseille-P2398, Leptotrichia sp. oral taxon 879 str. F0557, Lachnospiraceae bacterium NK4A144, Chloroflexus aggregans, Demequina aurantiaca, Thalassospira sp. TSL5-1, SAMN04487830_13920 [Pseudobutyrivibrio sp. OR37], SAMN02910398_00008 [Butyrivibrio sp. YAB3001], Leptotrichia sp. Marseille-P3007, Bacteroides ihuae, [Porphyromonadaceae bacterium KH3CP3RA], Listeria riparia, Insolitispirillum peregrinum, Bergeyella zoohelcum, Prevotella intermedia, Prevotella buccae, Porphyromonas gingivalis, Bacteroides pyogenes, Alistipes sp. ZOR0009, Prevotella sp. MA2016, Riemerella anatipestifer, Prevotella aurantiaca, Prevotella saccharolytica, [Myroides odoratimimus CCUG 10230], Capnocytophaga canimorsus, Porphyromonas gulae, Prevotella sp. P5-125, Flavobacterium branchiophilum, Myroides odoratimimus, Flavobacterium columnare, Porphyromonas sp. COT-052 OH4946, PIN17_0200 [Prevotella intermedia 17], Prevotella buccae ATCC 33574, Prevotella pallens ATCC 700821, Myroides odoratimimus CCUG 12901, Myroides odoratimimus CCUG 3837, Bergeyella zoohelcum ATCC 43767, Prevotella saccharolytica F0055, Porphyromonas gingivalis JCVI SC001, Bacteroides pyogenes F0041, Porphyromonas gingivalis F0568, Porphyromonas gingivalis F0185, Porphyromonas gingivalis W4087, Prevotella intermedia ZT, Bacteroidetes bacterium GWA2_31_9, Chryseobacterium jejuense, Chryseobacterium carnipullorum, Chryseobacterium ureilyticum, Porphyromonas gingivalis, Prevotella pallens, Myroides odoratimimus, Prevotella sp. MSX73, Paludibacter propionicigenes, Flavobacterium columnare, Psychroflexus torquis, Riemerella anatipestifer, Prevotella pleuritidis, Prevotella falsenii, Prevotella pleuritidis, Capnocytophaga cynodegmi, Prevotella sp. P5-119, Prevotella sp. P4-76, Prevotella sp. P5-60, WP_047431796, Sinomicrobium oceani, Reichenbachiella agariperforans, Fusobacterium necrophorum subsp. funduliforme ATCC 51357, Fusobacterium necrophorum DJ-2, Fusobacterium necrophorum BFTR-1, Fusobacterium necrophorum subsp. funduliforme 1_1_36S, Fusobacterium perfoetens, Fusobacterium ulcerans, Anaerosalibacter sp. ND1; or wherein said dead Cas13 protein originates from a Prevotella sp. P5-125 Cas13b, Porphyromonas gulae Cas13b, or Riemerella anatipestifer Cas13b.
Regarding claim 21, given a broadest reasonable interpretation, the recitation of "wherein said dead Cas13 is a C-terminally truncated dead Cas13b functional variant of a corresponding wild type Cas13, wherein said C-terminally truncated dead Cas13b is encoded by a nucleotide sequence originating from nt 1-984 of Prevotella sp. P5-125 Cas13b or the corresponding nt of a Cas13b orthologue or homologue" is interpreted as encompassing dCas13a, dCas13b, or dCas13c of claim 8 of the reference application.
Regarding instant claim 23, claim 14 of the reference application recites the cell of claim 1, wherein (a) said dead Cas13 protein, (b) said adenosine deaminase protein or catalytic domain thereof, or (c) both (a) and (b) comprise one or more heterologous nuclear export signal(s) (NES(s)) or nuclear localization signal(s) (NLS(s)), wherein the NES(s) are selected from an HIV Rev NES or MAPK NES, wherein the one or more NES(s), NLS(s), or both are at the C-terminus, N-terminus, or both of (a) the dead Cas13 protein, (b) the adenosine deaminase, or (c) both (a) and (b).
Regarding instant claims 24 and 42, claim 3 of the reference application recites the cell of claim 2, wherein said cell is a human or non-human animal cell, optionally wherein said cell is a therapeutic T cell, an antibody-producing B-cell, a natural killer (NK) cell, a regulatory T cell, or a tumor-infiltrating lymphocyte, optionally wherein said cell is a hepatocyte or a liver cell, and optionally wherein said cell is a hematopoietic stem cell (HSC) or a hematopoietic stem and progenitor cell (HSPC).
Regarding instant claims 27-29, in view of the recitation of “for use…” in claims 27 and 28, claims 27-29 and 34 are interpreted as reciting an intended use of the system of instant claim 1. The limitations of claims 27-29 and 34 do not further limit the structure and/or function of the system of instant claim 1.
Regarding instant claim 37, Yeo teaches the guide RNA comprises one or more modified nucleotides (paragraph [0121)).
Regarding instant claim 43, claims 16 and 17 of the reference application recite a non-human animal or a plant comprising the cell of claim 1, or a progeny thereof.
Regarding instant claim 45, claim 18 of the reference application recites the cell of claim 1 for use in therapy, optionally wherein the therapy is cell therapy.
Therefore, claims of this application are unpatentable over claims of the reference application. This is a provisional nonstatutory double patenting rejection because the patentably indistinct claims have not in fact been patented.
Claim 3 is provisionally rejected on the ground of nonstatutory double patenting as being unpatentable over claims 1-3, 7-14, 16-18, and 20 of co-pending application no. 19/677,353 (reference application) in view of Yeo and Radivojac as applied to claims 1, 2, 6, 14, 21-24, 27-30, 37, 41-43, and 45 above, and further in view of Kouranova. Although the claims at issue are not identical, they are not patentably distinct from each other.
The claims of the reference application do not recite the limitations of claim 3 of this application.
Regarding instant claim 3 of this application, the reference of Kouranova teaches that the components of CRISPR can be delivered into cells as a precomplexed ribonucleoprotein particle (p. 465, column 2, top). Kouranova teaches a method for RNP complex formation (p. 466, column 1, middle). Kouranova teaches benefits to delivering CRISPR components by RNP including fewer off-target modifications (p. 465, column 1, top) and RNP is the only format that is reliably active in cells (p. 474, column 2). According to Kouranova, the RNPs are the most convenient and efficient delivery method for cultured cell lines (p. 464, Abstract). Kouranova teaches delivery of the RNP into cells by cationic lipid transfection or via a nanoparticle (p. 12, paragraph bridging columns 1-2).
In view of the teachings of Kouranova, it would have been obvious to one of ordinary skill in the art before the effective filing date to modify the claims of the reference application to deliver a RNP by cationic lipid transfection or via a nanoparticle. One would have been motivated to and would have had a reasonable expectation of success to do this because Kouranova taught the benefits of RNP delivery and taught RNP delivery by cationic lipid transfection or via a nanoparticle.
Therefore, claim 3 of this application are unpatentable over claims of the reference application. This is a provisional nonstatutory double patenting rejection because the patentably indistinct claims have not in fact been patented.
Claims 18-20 are provisionally rejected on the ground of nonstatutory double patenting as being unpatentable over claims 1-3, 7-14, 16-18, and 20 of co-pending application no. 19/677,353 (reference application) in view of Yeo and Radivojac as applied to claims 1, 2, 6, 14, 21-24, 27-30, 37, 41-43, and 45 above, and further in view of Abudayyeh.
The claims of the reference application do not recite the limitations of claims 18-20 of this application.
Regarding instant claim 18, Abudayyeh teaches that Leptotrichia shahii C2c2 (C2c2 is otherwise known in the prior art as Cas13a) comprises two HEPN domains (p. 2, bottom) and that alanine substitution of the catalytic residues R597 and R1278 of the HEPN domain converted C2c2 into an inactive programmable RNA-binding protein (dC2c2) (paragraph bridging pp. 5-6; p. 9, top). R597 and R1278 of Leptotrichia shahii C2c2 HEPN domain are considered to correspond to R474 and R1046 of Leptotrichia wadei C2c2 HEPN domain.
In view of the teachings of Abudayyeh, it would have been obvious to one of ordinary skill in the art before the effective filing date for a Leptotrichia shahii dCas13a comprising alanine substitutions of the HEPN domain catalytic residues R597 and R1278. One would have been motivated to and would have had a reasonable expectation of success for a Leptotrichia shahii dCas13a comprising alanine substitutions of the HEPN domain catalytic residues R597 and R1278 because the claims of the reference application recite a dead Cas13a and Abudayyeh taught that alanine substitution of any of the four predicted HEPN domain catalytic residues converted Leptotrichia shahii Cas13a into dCas13a.
Regarding instant claims 19 and 20, Yeo further discloses the guide RNA forms an A-C mismatch with a target RNA (paragraph [0066]). Abudayyeh teaches that Cas13a is guided by a single crRNA (p. 1, Abstract) with a spacer of at least 22 nucleotides that is complementary to the target ssRNA and a double repeat longer than 24 nucleotides (p. 6, bottom). Abudayyeh teaches that Cas13a is tolerant to single mismatches across the spacer (p. 7, top).
In view of the further teachings of Abudayyeh, it would have been obvious to one of ordinary skill in the art before the effective filing date for a guide RNA comprising a non-pairing cytosine with the 5' end of the guide sequence being 20-30 nucleotides. One would have been motivated to and would have had a reasonable expectation of success for a guide RNA comprising a non-pairing cytosine with the 5' end of the guide sequence being 20-30 nucleotides because Yeo disclosed a guide RNA that forms an A-C mismatch with a target RNA and Abudayyeh taught Cas13a is guided by a single crRNA with a spacer of at least 22 nucleotides that is complementary to the target ssRNA and a double repeat longer than 24 nucleotides and Cas13a is tolerant to single mismatches across the spacer.
Therefore, claims of this application are unpatentable over claims of the reference application. This is a provisional nonstatutory double patenting rejection because the patentably indistinct claims have not in fact been patented.
Claim 34 is provisionally rejected on the ground of nonstatutory double patenting as being unpatentable over claims 1-3, 7-14, 16-18, and 20 of co-pending application no. 19/677,353 (reference application) in view of Yeo and Radivojac as applied to claims 1, 2, 6, 14, 21-24, 27-30, 37, 41-43, and 45 above, and further in view of Gao and Carr. Although the claims at issue are not identical, they are not patentably distinct from each other.
The claims of the reference application do not recite the limitations of claim 34 of this application.
Regarding instant claim 34, Gao teaches that tumors with MDM2 amplification or overexpression typically contain the wild-type p53 and that loss of p53 function in tumors has been associated with drug resistance and poor prognosis (p. 860, column 2). Carr teaches that ATM phosphorylation of Mdm2-S394 is required for robust p53 activation (p. 2618, Abstract) and that failure to induce a robust p53 response translates to increased spontaneous lymphomagenesis (p. 2619, column 1). Carr teaches that Mdm-S394A mice are resistant to IR-induced lymphomagenesis (p. 2622, column 2) and that inhibiting Mdm2-S394 phosphorylation during radiation exposure or chemotherapy would ameliorate bone marrow failure and prevent the development of secondary hematological malignancies (p. 2618, Abstract).
In view of the teachings of Gao and Carr, it would have been obvious to one of ordinary skill in the art before the effective filing date for the guide RNA of the claims of the reference application to be designed to substitute the codon encoding S394 of Mdm with A. One would have been motivated to and would have had a reasonable expectation of success to do this because Yeo teaches editing RNAs in living cells that cause cancer and Carr teaches that Mdm-S394A mice are resistant to IR-induced lymphomagenesis and teaches inhibiting Mdm2-S394 phosphorylation during radiation exposure or chemotherapy would ameliorate bone marrow failure and prevent the development of secondary hematological malignancies.
Therefore, claims of this application are unpatentable over claims of the reference application. This is a provisional nonstatutory double patenting rejection because the patentably indistinct claims have not in fact been patented.
Conclusion
Status of the claims:
Claims 1-4, 6, 14, 18-30, 34, 36, 37, 41-43, and 45-50 are pending in the application.
Claims 4, 25, 26, 36, and 46-50 are withdrawn from consideration.
Claims 1-3, 6, 14, 18-24, 27-30, 34, 37, 41-43, and 45 are rejected.
No claim is in condition for allowance.
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APPENDIX
(Currently Amended) An engineered, non-naturally occurring system suitable for modifying post-translational phosphorylation sites on a protein encoded by a target RNA, comprising:
(a) a catalytically inactive (dead) Cas13 protein, or a polynucleotide comprising a nucleotide sequence encoding said dead Cas13 protein;
(b) a nucleotide deaminase protein or catalytic domain thereof, or a polynucleotide comprising a nucleotide sequence encoding said nucleotide deaminase protein or catalytic domain thereof, wherein the nucleotide deaminase protein or catalytic domain thereof comprises the amino acid sequence of a human adenosine deaminase acting on RNA2 (hADAR2) protein or catalytic domain thereof with the exception of a K350I mutation and one or more mutations selected from the group consisting of E488Q, V351G, S486A, T375S, S370C, P462A, N597I, L332I, and I398V, wherein the amino acid numbering corresponds to the amino acid sequence of the catalytic domain of the hADAR2 protein; and
(c) a guide molecule comprising a guide sequence designed to have a degree of complementarity with a target sequence in the target RNA at one or more codons that comprises an adenosine or cytosine and encodes an amino acid that is post-translationally modified by phosphorylation,
wherein said nucleotide deaminase protein or catalytic domain thereof is covalently or non-covalently linked to said dead Cas13 protein or said guide molecule, or is adapted to link thereto when contacted with the dead Cas13 protein or the guide molecule.
(Previously Presented) The system of claim 1, wherein said guide sequence comprises a non-pairing nucleotide at a position corresponding to said adenosine or cytosine resulting in a mismatch in an RNA duplex formed between the target RNA and the guide molecule.
(Original) The system of claim 1, wherein the system comprises a particle delivery system comprising a ribonucleoprotein complex comprising (a), (b), and (c) encapsulated within or otherwise attached to a delivery particle, the delivery particle further optionally comprising a tissue-specific, cell-specific, and/or cell compartment-specific targeting molecule.
(Currently Amended) The system of claim 1, wherein the system comprises a vector system comprising one or more vectors comprising:
a first regulatory element operably linked to the[[a]]
a second regulatory element operably linked to the nucleotide sequence encoding said dead Cas13 protein; and
a nucleotide sequence encoding the nucleotide deaminase protein or catalytic domain thereof operably linked to
wherein if said nucleotide sequence encoding the nucleotide deaminase protein or catalytic domain thereof is operably linked to the third regulatory element, said nucleotide deaminase protein or catalytic domain thereof is adapted to link to said guide molecule or said dead Cas13 protein after expression; and
wherein components (i), (ii) and (iii) are located on the same or different vectors of the system, optionally wherein said first, second, and/or third regulatory element is an inducible promoter.
(Canceled)
(Currently Amended) The system of claim 1, wherein the nucleotide deaminase protein or catalytic domain thereof:
is the[[a]] catalytic domain of the nucleotide deaminase protein;
is delivered together with a uracil glycosylase inhibitor (UGI), where said UGI is covalently linked to said nucleotide deaminase protein or catalytic domain thereof and/or said catalytically inactive Cas13 protein;
is fused to N- or C-terminus of said dead Cas13 protein, optionally by a linker, optionally wherein said linker is selected from the group consisting of SEQ ID NO: 1-11
is linked to an adaptor protein and said guide molecule or said dead Cas13 protein comprises an aptamer sequence capable of binding to said adaptor protein, wherein said adaptor protein is selected from MS2, PP7, Qß, F2, GA, fr, JP501, M12, R17, BZ13, JP34, JP500, KU1, M11, MX1, TW18, VK, SP, FI, ID2, NL95, TW19, AP205, ΦCb5, ΦCb8r, ΦCb12r, ΦCb23r, 7s, and PRR1;
is inserted into an internal loop of said dead Cas13 protein; or
(f) any combination of (a)-(e).
(Canceled)
14. (Previously Presented) The system of claim 1, wherein said dead Cas13 protein is dead Cas13a, dead Cas13b, or dead Cas13c, wherein said dead Cas13 originates from a Cas13 according to any one of SEQ ID NO: 34-161, or according to SEQIDNO: 892, SEQID NO: 763, SEQ IDNO: 891, SEQIDNO: 890, SEQIDNO: 889, SEQIDNO: 888, SEQIDNO: 768, SEQ ID NO: 887, SEQ ID NO: 156, SEQ ID NO: 159, SEQ ID NO: 155, SEQ ID NO: 886, SEQ ID NO: 46, SEQ IDNO: 42, SEQ ID NO: 48, SEQ ID NO: 34, SEQ ID NO: 35, SEQ ID NO: 36, SEQ ID NO: 37, SEQ ID NO: 38, SEQ ID NO: 39, SEQ ID NO: 40, SEQ ID NO: 41, SEQ ID NO: 42, SEQ ID NO: 44, SEQ ID NO: 45, SEQ ID NO: 45, SEQ ID NO: 49, SEQ ID NO: 50, SEQ ID NO: 51, SEQ IDNO: 52, SEQ IDNO: 53, SEQ ID NO: 541, SEQID NO: 67, SEQ ID NO: 68, SEQ ID NO: 69, SEQ ID NO: 72, SEQ ID NO: 74, SEQ ID NO: 75, SEQ ID NO: 76, SEQ ID NO: 77, SEQ ID NO: 79, SEQ ID NO: 80, SEQ ID NO: 81, SEQ ID NO: 82, SEQID NO: 83, SEQIDNO: 86, SEQID NO: 88, SEQID NO: 885, SEQIDNO: 156, SEQID NO: 157, SEQ ID NO: 158, SEQID NO: 159, SEQID NO: 160, or SEQ ID NO: 161;
or originates from a bacterial species selected from Leptotrichia shahii, Leptotrichia wadei F0279 (Lw2), Listeria seeligeri, Lachnospiraceae bacterium MA2020, Lachnospiraceae bacterium NK4A179, Clostridium aminophilum DSM 10710, Carnobacterium gallinarum DSM 4847, Paludibacter propionicigenes WB4, Listeria weihenstephanensis FSL R9-0317, Listeriaceae bacterium FSL M6-0635, Rhodobacter capsulatus SB 1003, Rhodobacter capsulatus R121, Rhodobacter capsulatus DE442, Leptotrichia buccalis C-1013-b, Herbinix hemicellulosilytica, Eubacterium rectale, Eubacteriaceae bacterium CHKCI004, Blautia sp. Marseille-P2398, Leptotrichia sp. oral taxon 879 str. F0557, Lachnospiraceae bacterium NK4A144, Chloroflexus aggregans, Demequina aurantiaca, Thalassospira sp. TSL5-1, SAMN04487830_13920 [Pseudobutyrivibrio sp. OR37], SAMN02910398_00008 [Butyrivibrio sp. YAB3001], Leptotrichia sp. Marseille-P3007, Bacteroides ihuae, [Porphyromonadaceae bacterium KH3CP3RA], Listeria riparia, Insolitispirillum peregrinum, Bergeyella zoohelcum, Prevotella intermedia, Prevotella buccae, Porphyromonas gingivalis, Bacteroides pyogenes, Alistipes sp. ZOR0009, Prevotella sp. MA2016, Riemerella anatipestifer, Prevotella aurantiaca, Prevotella saccharolytica, Myroides odoratimimus CCUG 10230, Capnocytophaga canimorsus, Porphyromonas gulae, Prevotella sp. P5-125, Flavobacterium branchiophilum, Myroides odoratimimus, Flavobacterium columnare, Porphyromonas sp. COT-052 OH4946, PIN17_0200 [Prevotella intermedia 17], StegatellaSegatella buccae strain VPI D3A-6, Prevotella pallens strain NCTC 13042, Myroides odoratimimus CCUG 12901, Myroides odoratimimus CCUG 3837, Bergeyella zoohelcum strain NCTC 11660, Prevotella saccharolytica F0055, Porphyromonas gingivalis JCVI SC001, Bacteroides pyogenes F0041, Porphyromonas gingivalis F0568, Porphyromonas gingivalis F0185, Porphyromonas gingivalis W4087, Prevotella intermedia ZT, Bacteroidetes bacterium GWA2_31_9, Chryseobacterium jejuense, Chryseobacterium carnipullorum, Chryseobacterium ureilyticum, Porphyromonas gingivalis, Prevotella pallens, Myroides odoratimimus, Prevotella sp. MSX73, Paludibacter propionicigenes, Flavobacterium columnare, Psychroflexus torquis, Riemerella anatipestifer, Prevotella falsenii, Prevotella pleuritidis, Capnocytophaga cynodegmi, Prevotella sp. P5-119, Prevotella sp. P4-76, Prevotella sp. P5-60, WP_047431796, Sinomicrobium oceani, Reichenbachiella agariperforans, Fusobacterium necrophorum subsp. funduliforme strain JCM 3724, Fusobacterium necrophorum DJ-2, Fusobacterium necrophorum BFTR-1, Fusobacterium necrophorum subsp. funduliforme 1_1_36S, Fusobacterium perfoetens, Fusobacterium ulcerans, Anaerosalibacter sp. ND1; or
wherein said dead Cas13 protein originates from Prevotella sp. P5-125 Cas13b, Porphyromonas gulae Cas13b, or Riemerella anatipestifer Cas13b.
15-17. (Canceled)
18. (Previously Presented) The system of claim 1, wherein said dead Cas13 protein is a Cas13a protein and said Cas13a comprises one or more mutations in one or both of two HEPN domains at position R474 and R1046 of Cas13a protein originating from Leptotrichia wadei or amino acid positions corresponding thereto of a Casl3a ortholog; or
wherein said dead Cas13 protein is a Cas13b protein and said Cas13b comprises a mutation in one or more of positions R116, H121, R1177, H1182 of Cas13b protein originating from Bergeyella zoohelcum strain according to SEQ ID No. 95 or amino acid positions corresponding thereto of a Cas13b ortholog, or
wherein said Cas13 protein is a Cas13b protein and said Cas13b comprises a mutation in one or more of positions R128, H133, R1053, H1058 of a Cas13b protein originating from Prevotella sp. P5-125 or amino acid positions corresponding thereto of a Cas13b ortholog.
19. (Previously Presented) The system of claim 2, said guide sequence comprises a non-pairing Cytosine at a position corresponding to said adenosine resulting in an A-C mismatch in the RNA duplex formed between the target RNA and guide molecule wherein said guide sequence has a length of from about 20 to about 53 nucleotides (nt), or from about 25 to about 53 nt, or from about 29 to about 53 nt, or from about 40 to about 50 nt capable of forming said RNA duplex with said target sequence.
20. (Previously Presented) The system of claim 19, wherein the distance between said non-pairing Cytosine and the 5' end of said guide sequence is 20-30 nucleotides.
21. (Previously Presented) The system of claim 1, wherein said dead Cas13 is a C-terminally truncated dead Cas13b functional variant of a corresponding wild type Cas13, wherein said C-terminally truncated dead Cas13b is encoded by a nucleotide sequence originating from nt 1-984 of Prevotella sp. P5-125 Cas13b or the corresponding nt of a Cas13b orthologue or homologue.
22. (Currently Amended) The system of claim 1, wherein the guide sequence comprises more than one mismatch
23. (Currently Amended) The system of claim 1, wherein said dead Cas13 protein, said nucleotidenucleotidenucleotide
24. (Currently Amended) The system of claim 1, wherein said target RNA is within a eukaryotic cell selected from a human cell, or a non-human animal cell, or a plant cell.
25. (Previously Presented) A method of modifying post-translational phosphorylation sites on a protein encoded by a target RNA comprising:
contacting the target RNA with the system of claim 1.
26. (Currently Amended) The method of claim 25, wherein (a), (b), and (c) in the system of claim 1 are delivered to the target RNA
27. (Previously Presented) The system of claim 1, for use in prophylactic or therapeutic treatment, wherein said target RNA is within a human or animal.
28. (Previously Presented) The system of claim 1, for use in a treatment or prevention of a disease by inhibiting activation of pathological activation of cell signaling mediated by post translational modification, wherein the post-translational modification is a phosphorylation.
29. (Previously Presented) The system of claim 28, wherein said disease is selected from cancer, immunodeficiency diseases or disorders, infectious disease, inflammatory disorders, and neurodegenerative diseases and disorders.
30. (Currently Amended) The system of claim 1, wherein said modifying changes an encoded amino acid from a serine, threonine, or tyrosine to an amino acid that cannot be phosphorylated;
inactivates a phosphorylation site of a protein involved in MDM2-p53 signaling pathway, PI3K-Akt signaling pathways, Ras signaling pathways, GPCR signaling pathway, Wnt signaling pathway, Hippo signaling pathway, TGFa signaling pathway, NF-kB signaling pathway, Notch signaling pathway, Hedgehog signaling pathway, and/or cell-cycle signaling pathway;
inactivates a phosphorylation site of a protein involved in MDM2-p53 signaling pathway and PI3K-Akt signaling pathway, wherein the phosphorylation site is on MDM2 at S166, S190, S240, S242, S246, S260, S386, S395, S407, T419, S425, and/or S439, Akt at S473 and/or T308, or MDM4 at S96, Y99, S296, S342, S367, and/or S403;
inactivates a phosphorylation site of: IκBα at S32 and/or S36, NIK at T599, p100 at S866, S870, S872, Notch1 at S2152, Raf-1 at S43, S259, S338, and/or Y341, ß-catenin at S33, S37, S45, and /or T41, BAD at S122 and/or S136, GSK-3ß at S9, RelA(p65) at S910, YAP at S61, S109, S127, S164, S381, and/or S384, or TAZ at S66, S89, S117, and/or S311, YAP at S127, Caspase-9 at S196, MLK3 at S647, [[and]] ASK1 at S83, CREB at S133, FOXO1 at S256, S319, and T24, FOXO2 at S32, S253, and S315, [[and]] FOXO4 at S193, S258, and T28, and IKKa at T23;
inactivates at least two or at least three phosphorylation sites of the same protein;
inactivates a phosphorylation site of at least two or at least three proteins of a signaling pathway, wherein the at least two or at least three proteins are involved in the same signaling pathway;
modulates at least two or at least three different signaling pathways selected from Akt MDM2 signaling pathway, Ras signaling pathways, GPCR signaling pathway, Wnt signaling pathway, Hippo signaling pathway, TGFß signaling pathway, NF- kB signaling pathway, Notch signaling pathway, Hedgehog signaling pathway, and/or cell-cycle signaling pathway; or
modulates at least one p53-dependent signaling pathway and at least one p53-independent signaling pathway.
31-33. (Canceled)
34. (Previously Presented) The system of claim 28, wherein the disease is a p53 wild type lymphoma.
35. (Canceled)
36. (Currently Amended) The system of claim 1, wherein at least two or at least three different guide molecules are used to target [[the]] at least two or at least three phosphorylation sites of the same protein.
37. (Previously Presented) The system of claim 1, wherein a single guide molecule is used to target at least two or at least three phosphorylation sites on the same protein encoded by the target RNA.
38-40. (Canceled)
41. (Previously Presented) A cell comprising the system of claim 1, wherein the cell comprises, in a target RNA, an (a) inosine or guanosine in place of an adenosine, (b) a uracil in place of a cytosine, or (c) both (a) and (b).
42. (Previously Presented) The cell of claim 41, wherein said cell is a eukaryotic cell, wherein the eukaryotic cell is a human cell, or non-human animal cell, or a plant cell, and wherein the human cell or non-human animal cell is a therapeutic T cell or an antibody-producing B-cell.
43. (Previously Presented) A non-human animal or plant comprising said cell of claim 41.
44. (Canceled)
45. (Previously Presented) The cell according to claim 41 for use in therapy, wherein the therapy is a cell therapy.
46-50. (Canceled)