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 .
Claims 229-232, 247-254, and 256-274 are pending.
Continued Examination Under 37 CFR 1.114
A request for continued examination under 37 CFR 1.114, including the fee set forth in 37 CFR 1.17(e), was filed in this application after final rejection. Since this application is eligible for continued examination under 37 CFR 1.114, and the fee set forth in 37 CFR 1.17(e) has been timely paid, the finality of the previous Office action has been withdrawn pursuant to 37 CFR 1.114. Applicant's submission filed on 27 March 2026 has been entered.
Status of the Application
Applicant’s response and amendment filed 27 March 2026 are acknowledged and entered. Applicant has amended Claims 229 and 248-253. Applicant has added Claims 271-274.
Response to Amendment
The NSDP rejections over App671, App425, and App969 are withdrawn in view of the claim amendments or amendments to the copending claims. All other NSDP rejections are maintained.
Claims 229-232, 247-254, and 256-274 are examined.
Arguments applicable to newly applied rejections to amended or newly presented claims are addressed below. Arguments that are no longer relevant are not addressed.
Rejections not reiterated here are withdrawn.
Claim Interpretation
Claims 231 and 252-253 recite … a defective CLRN1 gene. The Spec. discloses (p. 146 L13-16): In some embodiments of any of these methods, the mammal has been previously identified as having a defective CLRN1 gene (e.g., a CLRN1 gene having a mutation that results in a decrease in the expression and/or activity of a CLRN1 protein encoded by the gene). Therefore the claim recitation a defective CLRN1 gene is interpreted as meaning the CLRN1 gene has any mutation that results in the mammal expressing less CLRN1 gene or protein as compared with CLRN1 gene or protein expression of a mammal with a wildtype CLRN1 gene or the mutation makes the mammal’s CLRN1 protein less active as compared with CLRN1 protein expressed by a mammal expressing a wildtype CLRN1 protein.
It is noted that Claims 269-270 (which depend from Claim 264 248) are composition claims directed to a kit that comprise instructions for performing a method. The kit includes instructions for performing a method but those instructions do not add change the structure of the composition recited in Claim 232 and therefore do not provide any patentable weight to composition claims. Applicant should note that methods to any kind of treatment or methods of treating any deafness, any hearing loss, any vision loss, any Usher syndrome type III, or any retinitis pigmentosa are not enabled.
Claims 271-274 recite the nucleic acid vector comprises at least 90% or at least 95% sequence identity to SEQ ID NO 42. Those claims are interpreted as encompassing nucleic acid vectors comprising at least 90% or at least 95% sequence identity to the entire length of SEQ ID NO 42.
Claim Objections
Claim 267 is objected to for minor informalities. Claim 267 will be better if it recites: the kit of claim 264, wherein the method comprises introducing the composition into a cell of a subject wherein the subject is a mammal.
Appropriate correction is required.
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 264-270 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. These rejections are new.
A claim may be considered indefinite if the resulting claim does not clearly set forth the metes and bounds of the patent protection desired. See MPEP § 2173. In the present instance, Claims 264-270 recite both a composition (i.e., a kit comprising a composition, wherein the composition comprises…) and instructions for performing method steps. The claim(s) are considered indefinite because there is a question or doubt as to what are the metes and bounds of the claims. Method claims that depend from composition claims are not permitted.
II. PRODUCT AND PROCESS IN THE SAME CLAIM
A single claim which claims both an apparatus and the method steps of using the apparatus is indefinite under 35 U.S.C. 112(b) or pre-AIA 35 U.S.C. 112, second paragraph. See In re Katz Interactive Call Processing Patent Litigation, 639 F.3d 1303, 1318, 97 USPQ2d 1737, 1748-49 (Fed. Cir. 2011). In Katz, a claim directed to "[a] system with an interface means for providing automated voice messages…to certain of said individual callers, wherein said certain of said individual callers digitally enter data" was determined to be indefinite because the italicized claim limitation is not directed to the system, but rather to actions of the individual callers, which creates confusion as to when direct infringement occurs. Katz, 639 F.3d at 1318, 97 USPQ2d at 1749 (citing IPXL Holdings v. Amazon.com, Inc., 430 F.3d 1377, 1384, 77 USPQ2d 1140, 1145 (Fed. Cir. 2005), in which a system claim that recited "an input means" and required a user to use the input means was found to be indefinite because it was unclear "whether infringement … occurs when one creates a system that allows the user [to use the input means], or whether infringement occurs when the user actually uses the input means."); Ex parte Lyell, 17 USPQ2d 1548 (Bd. Pat. App. & Inter. 1990) (claim directed to an automatic transmission workstand and the method of using it held ambiguous and properly rejected under 35 U.S.C. 112, second paragraph).
MPEP §2173.05(p)
Similar to the case described above, these claims are indefinite because the method limitations are not directed to the kit, but rather to instructions that describe actions or potential actions of an individual in possession of the kit, which creates confusion as to when direct infringement occurs. In this case it is ambiguous whether or not the method steps on the instructions must be carried out to meet the terms of the claims.
Claims 264-270 are rejected for those reasons. Claims 265-270 are rejected because they depend from Claim 264 and fail to remedy the issues. In the interest of compact prosecution the claims are interpreted as if the instructions for performing the various methods are merely intended uses and do not add any patentable weight to the kit.
The following is a quotation of 35 U.S.C. 112(d):
(d) REFERENCE IN DEPENDENT FORMS.—Subject to subsection (e), a claim in dependent form shall contain a reference to a claim previously set forth and then specify a further limitation of the subject matter claimed. A claim in dependent form shall be construed to incorporate by reference all the limitations of the claim to which it refers.
The following is a quotation of pre-AIA 35 U.S.C. 112, fourth paragraph:
Subject to the following paragraph [i.e., the fifth paragraph of pre-AIA 35 U.S.C. 112], a claim in dependent form shall contain a reference to a claim previously set forth and then specify a further limitation of the subject matter claimed. A claim in dependent form shall be construed to incorporate by reference all the limitations of the claim to which it refers.
Claims 264-270 are rejected under 35 U.S.C. 112(d) or pre-AIA 35 U.S.C. 112, 4th paragraph, as being of improper dependent form for failing to further limit the subject matter of the claim upon which it depends, or for failing to include all the limitations of the claim upon which it depends. These rejections are new.
Claim 264 is directed to a kit comprising a composition comprising an AAV nucleic acid vector, wherein the vector comprises components (i)-(ix), wherein the kit further comprises instructions for performing a method. As discussed in §Claim Interpretation, the recitation the kit further comprises instructions for performing a method does not at all change the structure of the composition comprised by the kit. Therefore the limitation the kit further comprises instructions for performing a method fails to add any patentable weight. Claim 264 therefore fails to further limit the claim from which it depends, namely Claim 248. Similarly, Claims 265-270 all depend from Claim 264 and either describe the method of the instructions of Claim 264, or recite method steps on the instructions of Claim 264; those descriptions or steps listed on the instructions also fail to limit the structure of the composition comprised by the kit because they are merely written on instructions.
Claims 264-270 are rejected for those reasons. Claims 265-270 are rejected because they depend from Claim 264 and fail to remedy the issues.
Applicant may cancel the claim(s), amend the claim(s) to place the claim(s) in proper dependent form, rewrite the claim(s) in independent form, or present a sufficient showing that the dependent claim(s) complies with the statutory requirements.
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 229-232, 247-254, and 256-270 are rejected on the ground of nonstatutory double patenting as being unpatentable over claims 1-28 of the U.S. Patent No. 11807867 (“US867”) in view of WO900, Powell, App178, and US952. This rejection is maintained and updated in response to the claim amendments. All supporting references are of record.
Although the claims at issue are not identical, they are directed to overlapping subject matter because the instant claims recite a composition comprising an AAV nucleic acid vector wherein the vector comprises a 5’ ITR, a CMV enhancer, a CBA promoter, a chimeric intron according to SEQ ID NO 16, a 5’UTR, a coding sequence (CDS) encoding a CLRN1 protein according to SEQ ID NO 3, a 3’UTR, a polyA signal, and a 3’ITR, wherein the CDS comprises a nt sequence spanning 2 consecutive exons of CLRN1 genomic DNA and lacks an intron sequence between them; wherein the composition can comprise other components such as SEQ ID NOs 17 or 20; to the composition comprising an excipient; to an AAV2 capsid comprising the composition, to an Anc80 capsid comprising the composition; to a kit comprising the composition; and to methods of introducing it to a cochlea of a mammal that can be a human who can have been previously identified as having a defective endogenous CLRN1 gene; to methods of increasing CLRN1 expression in the ear or eye; and to methods of treating hearing or vision loss.
The US867 claims are drawn to a plurality of recombinant AAV vectors: a first vector comprising a nucleic acid sequence of SEQ ID NO 96 and a second vector comprising a nucleic acid sequence of SEQ ID NO 105 (US867), wherein each of the vectors is encapsulated by an AAV capsid having a certain serotype, wherein the capsid can be an AAV2 capsid or an Anc80 capsid; to a composition comprising the vectors, wherein the composition can be formulated for intra-cochlear administration, to a method of expressing a recombinant full-length otoferlin protein in a mammalian cell, and/or to methods of treating hearing loss by administering the vectors into the cochlea of a subject.
Both claim sets are directed to AAV vectors for treating hearing loss in a mammal or human by administering the vector to the cochlea of the mammal/human.
An artisan would not know what is US867 SEQ ID NO 96 so they would consult the US867 Spec. and SEQ listing and find (Col 184 L59-67; Col 185-195) SEQ ID NO 96 comprises two ITRs (a 5’ ITR and a 3’ITR), a CAG promoter comprising: a CMV enhancer, chicken β-actin gene sequence, and a chimeric intron. US867 SEQ ID NO 96 comprises claimed SEQ ID NOs 16 and 17 as shown by the following alignments:
US-17-816-305-96
(NOTE: this sequence has 2 duplicates in the database searched.
See complete list at the end of this report)
Sequence 96, US/17816305
Patent No. 11807867
GENERAL INFORMATION
APPLICANT: AKOUOS, INC. (en)
TITLE OF INVENTION: COMPOSITIONS AND METHODS FOR TREATING NON-AGE-ASSOCIATED HEARING IMPAIRMENT IN A HUMAN SUBJECT (en)
FILE REFERENCE: 4833.0050002
CURRENT APPLICATION NUMBER: US/17/816,305
CURRENT FILING DATE: 2022-07-29
NUMBER OF SEQ ID NOS: 110
SEQ ID NO 96
LENGTH: 4744
TYPE: DNA
FEATURE:
NAME/KEY: source
LOCATION: 1..4744
QUALIFIERS: mol_type = other DNA
organism = synthetic construct
Query Match 100.0%; Score 1013; Length 4744;
Best Local Similarity 100.0%;
Matches 1013; Conservative 0; Mismatches 0; Indels 0; Gaps 0;
Qy 1 GGAGTCGCTGCGTTGCCTTCGCCCCGTGCCCCGCTCCGCGCCGCCTCGCGCCGCCCGCCC 60 SEQ ID NO 16
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 828 GGAGTCGCTGCGTTGCCTTCGCCCCGTGCCCCGCTCCGCGCCGCCTCGCGCCGCCCGCCC 887 SEQ ID NO 96
Qy 61 CGGCTCTGACTGACCGCGTTACTCCCACAGGTGAGCGGGCGGGACGGCCCTTCTCCTCCG 120
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 888 CGGCTCTGACTGACCGCGTTACTCCCACAGGTGAGCGGGCGGGACGGCCCTTCTCCTCCG 947
Qy 121 GGCTGTAATTAGCGCTTGGTTTAATGACGGCTCGTTTCTTTTCTGTGGCTGCGTGAAAGC 180
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 948 GGCTGTAATTAGCGCTTGGTTTAATGACGGCTCGTTTCTTTTCTGTGGCTGCGTGAAAGC 1007
Qy 181 CTTAAAGGGCTCCGGGAGGGCCCTTTGTGCGGGGGGGAGCGGCTCGGGGGGTGCGTGCGT 240
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 1008 CTTAAAGGGCTCCGGGAGGGCCCTTTGTGCGGGGGGGAGCGGCTCGGGGGGTGCGTGCGT 1067
Qy 241 GTGTGTGTGCGTGGGGAGCGCCGCGTGCGGCCCGCGCTGCCCGGCGGCTGTGAGCGCTGC 300
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 1068 GTGTGTGTGCGTGGGGAGCGCCGCGTGCGGCCCGCGCTGCCCGGCGGCTGTGAGCGCTGC 1127
Qy 301 GGGCGCGGCGCGGGGCTTTGTGCGCTCCGCGTGTGCGCGAGGGGAGCGCGGCCGGGGGCG 360
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 1128 GGGCGCGGCGCGGGGCTTTGTGCGCTCCGCGTGTGCGCGAGGGGAGCGCGGCCGGGGGCG 1187
Qy 361 GTGCCCCGCGGTGCGGGGGGGCTGCGAGGGGAACAAAGGCTGCGTGCGGGGTGTGTGCGT 420
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 1188 GTGCCCCGCGGTGCGGGGGGGCTGCGAGGGGAACAAAGGCTGCGTGCGGGGTGTGTGCGT 1247
Qy 421 GGGGGGGTGAGCAGGGGGTGTGGGCGCGGCGGTCGGGCTGTAACCCCCCCCTGCACCCCC 480
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 1248 GGGGGGGTGAGCAGGGGGTGTGGGCGCGGCGGTCGGGCTGTAACCCCCCCCTGCACCCCC 1307
Qy 481 CTCCCCGAGTTGCTGAGCACGGCCCGGCTTCGGGTGCGGGGCTCCGTGCGGGGCGTGGCG 540
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 1308 CTCCCCGAGTTGCTGAGCACGGCCCGGCTTCGGGTGCGGGGCTCCGTGCGGGGCGTGGCG 1367
Qy 541 CGGGGCTCGCCGTGCCGGGCGGGGGGTGGCGGCAGGTGGGGGTGCCGGGCGGGGCGGGGC 600
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 1368 CGGGGCTCGCCGTGCCGGGCGGGGGGTGGCGGCAGGTGGGGGTGCCGGGCGGGGCGGGGC 1427
Qy 601 CGCCTCGGGCCGGGGAGGGCTCGGGGGAGGGGCGCGGCGGCCCCCGGAGCGCCGGCGGCT 660
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 1428 CGCCTCGGGCCGGGGAGGGCTCGGGGGAGGGGCGCGGCGGCCCCCGGAGCGCCGGCGGCT 1487
Qy 661 GTCGAGGCGCGGCGAGCCGCAGCCATTGCCTTTTATGGTAATCGTGCGAGAGGGCGCAGG 720
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 1488 GTCGAGGCGCGGCGAGCCGCAGCCATTGCCTTTTATGGTAATCGTGCGAGAGGGCGCAGG 1547
Qy 721 GACTTCCTTTGTCCCAAATCTGTGCGGAGCCGAAATCTGGGAGGCGCCGCCGCACCCCCT 780
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 1548 GACTTCCTTTGTCCCAAATCTGTGCGGAGCCGAAATCTGGGAGGCGCCGCCGCACCCCCT 1607
Qy 781 CTAGCGGGCGCGGGGCGAAGCGGTGCGGCGCCGGCAGGAAGGAAATGGGCGGGGAGGGCC 840
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 1608 CTAGCGGGCGCGGGGCGAAGCGGTGCGGCGCCGGCAGGAAGGAAATGGGCGGGGAGGGCC 1667
Qy 841 TTCGTGCGTCGCCGCGCCGCCGTCCCCTTCTCCCTCTCCAGCCTCGGGGCTGTCCGCGGG 900
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 1668 TTCGTGCGTCGCCGCGCCGCCGTCCCCTTCTCCCTCTCCAGCCTCGGGGCTGTCCGCGGG 1727
Qy 901 GGGACGGCTGCCTTCGGGGGGGACGGGGCAGGGCGGGGTTCGGCTTCTGGCGTGTGACCG 960
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 1728 GGGACGGCTGCCTTCGGGGGGGACGGGGCAGGGCGGGGTTCGGCTTCTGGCGTGTGACCG 1787
Qy 961 GCGGCTCTAGAGCCTCTGCTAACCATGTTCATGCCTTCTTCTTTTTCCTACAG 1013
|||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 1788 GCGGCTCTAGAGCCTCTGCTAACCATGTTCATGCCTTCTTCTTTTTCCTACAG 1840
SEQ ID NO 17
Query Match 100.0%; Score 380; DB 1; Length 4744;
Best Local Similarity 100.0%;
Matches 380; Conservative 0; Mismatches 0; Indels 0; Gaps 0;
Qy 1 GACATTGATTATTGACTAGTTATTAATAGTAATCAATTACGGGGTCATTAGTTCATAGCC 60 SEQ ID NO 17
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 168 GACATTGATTATTGACTAGTTATTAATAGTAATCAATTACGGGGTCATTAGTTCATAGCC 227 SEQ ID NO 96
Qy 61 CATATATGGAGTTCCGCGTTACATAACTTACGGTAAATGGCCCGCCTGGCTGACCGCCCA 120
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 228 CATATATGGAGTTCCGCGTTACATAACTTACGGTAAATGGCCCGCCTGGCTGACCGCCCA 287
Qy 121 ACGACCCCCGCCCATTGACGTCAATAATGACGTATGTTCCCATAGTAACGCCAATAGGGA 180
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 288 ACGACCCCCGCCCATTGACGTCAATAATGACGTATGTTCCCATAGTAACGCCAATAGGGA 347
Qy 181 CTTTCCATTGACGTCAATGGGTGGACTATTTACGGTAAACTGCCCACTTGGCAGTACATC 240
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 348 CTTTCCATTGACGTCAATGGGTGGACTATTTACGGTAAACTGCCCACTTGGCAGTACATC 407
Qy 241 AAGTGTATCATATGCCAAGTACGCCCCCTATTGACGTCAATGACGGTAAATGGCCCGCCT 300
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 408 AAGTGTATCATATGCCAAGTACGCCCCCTATTGACGTCAATGACGGTAAATGGCCCGCCT 467
Qy 301 GGCATTATGCCCAGTACATGACCTTATGGGACTTTCCTACTTGGCAGTACATCTACGTAT 360
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 468 GGCATTATGCCCAGTACATGACCTTATGGGACTTTCCTACTTGGCAGTACATCTACGTAT 527
Qy 361 TAGTCATCGCTATTACCATG 380
||||||||||||||||||||
Db 528 TAGTCATCGCTATTACCATG 547
Therefore the patented US867 claims recite elements (i), (ii), (iii), (iv), and (ix) of the claimed invention. Then the other prior art teaches the other claim elements that the US867 claims do not recite:
WO900 (¶99) teaches an rAAV vector comprising the CLRN1 cDNA including the 5’ and 3’UTRs, and teaches driving it with the chicken β-actin promoter. WO900 teaches (¶9-10) the polynucleotide (polynt) can include a sequence having SEQ ID NO 2 (which WO900 specifies comprises a 5’UTR and 3’UTR) and can be included on a vector that can be an adeno-associated viral vector (AAV) that can be used for transfecting ocular cells or cells of the inner ear. WO900 teaches (¶21) that the heterologous polynucleotide comprised in the AAV vector is flanked by at least one, and generally by two AAV inverted terminal repeat sequence (ITRs); an artisan would realize that being flanked by two ITRs refers to one ITR on either side, which is a 5’ITR and a 3’ITR. WO900 teaches (¶10-11) treating retinal cells.
WO900 SEQ ID NO 2 comprises a polynt comprising a sequence encoding the amino acid sequence of claimed SEQ ID NO 3 (which has been back-translated from AA[Wingdings font/0xE0]nucleotides). This is shown by the following sequence alignment:
RESULT 7
BDA01054
ID BDA01054 standard; cDNA; 2352 BP.
XX
AC BDA01054;
XX
DT 16-JUN-2016 (first entry)
XX
DE Human derived clarin-1 (CLRN1) polynucleotide SEQ ID NO:2.
XX
KW CLRN1 gene; auditory; clarin-1; gene therapy; hearing loss;
KW ophthalmological; ss; therapeutic; usher syndrome iii; vision disorder.
XX
OS Homo sapiens.
XX
CC PN WO2016073900-A1.
XX
CC PD 12-MAY-2016.
XX
CC PF 06-NOV-2015; 2015WO-US059546.
XX
PR 06-NOV-2014; 2014US-0076114P.
PR 08-MAY-2015; 2015US-0158846P.
XX
CC PA (UCWR ) UNIV CASE WESTERN RESERVE.
XX
CC PI Alagramam KN;
XX
DR WPI; 2016-282935/37.
XX
CC PT New polynucleotide comprising a nucleic acid sequence that includes a
CC PT cDNA coding sequence of a clarin-1 gene, useful for treating vision
CC PT and/or hearing loss associated with Usher syndrome III.
XX
CC PS Claim 9; SEQ ID NO 2; 43pp; English.
XX
CC The invention relates to a novel polynucleotide, used for treating vision
CC and/or hearing loss associated with Usher syndrome III. This
CC polynucleotide comprises a nucleic acid sequence that includes a cDNA
CC coding sequence of a clarin-1 (CLRN1) gene and a 3' untranslated region
CC (UTR) nucleic acid that is derived from the 3' UTR of the clarin-1 gene,
CC where the 3' UTR nucleic acid enhances expression of clarin-1 in a cell
CC transfected with the polynucleotide compared to a cell transfected with a
CC similar polynucleotide devoid of the 3' UTR nucleic acid. The invention
CC further claims: a nucleic acid construct comprising a polynucleotide
CC defined above; a vector for transfecting a cell, comprising a
CC polynucleotide defined above, where the transfected cell expresses clarin
CC -1; and a method of treating vision and/or hearing loss associated with
CC Usher syndrome III in a subject by administering to the ocular cells
CC and/or cells of the inner ear of the subject, a vector that promotes
CC expression of clarin-1 in the cells. The present sequence is a clarin-1
CC polynucleotide, used for treating vision and/or hearing loss associated
CC with Usher syndrome III in a subject.
XX
SQ Sequence 2352 BP; 705 A; 475 C; 484 G; 688 T; 0 U; 0 Other;
Alignment Scores:
Length: 2352
Score: 1214.00 Matches: 232
Percent Similarity: 100.0% Conservative: 0
Best Local Similarity: 100.0% Mismatches: 0
Query Match: 100.0% Indels: 0
Gaps: 0
US-17-253-658-3 (1-232) x BDA01054 (1-2352)
Qy 1 MetProSerGlnGlnLysLysIleIlePheCysMetAlaGlyValPheSerPheAlaCys 20 SEQ ID NO 3 translated[Wingdings font/0xE0]NT
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 282 ATGCCAAGCCAACAGAAGAAAATCATTTTTTGCATGGCCGGAGTGTTCAGTTTTGCATGT 341 WO900 SEQ ID NO 2
Qy 21 AlaLeuGlyValValThrAlaLeuGlyThrProLeuTrpIleLysAlaThrValLeuCys 40
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 342 GCCCTCGGAGTTGTGACAGCCTTGGGGACACCGTTGTGGATCAAAGCCACTGTCCTCTGC 401
Qy 41 LysThrGlyAlaLeuLeuValAsnAlaSerGlyGlnGluLeuAspLysPheMetGlyGlu 60
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 402 AAAACGGGAGCTCTGCTCGTCAATGCCTCAGGGCAGGAGCTGGACAAGTTTATGGGTGAA 461
Qy 61 MetGlnTyrGlyLeuPheHisGlyGluGlyValArgGlnCysGlyLeuGlyAlaArgPro 80
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 462 ATGCAGTACGGGCTTTTCCACGGAGAGGGTGTGAGGCAGTGTGGGTTGGGAGCAAGGCCC 521
Qy 81 PheArgPheSerPhePheProAspLeuLeuLysAlaIleProValSerIleHisValAsn 100
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 522 TTTCGGTTCTCATTTTTTCCAGATTTGCTCAAAGCAATCCCAGTGAGCATCCACGTCAAT 581
Qy 101 ValIleLeuPheSerAlaIleLeuIleValLeuThrMetValGlyThrAlaPhePheMet 120
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 582 GTCATTCTCTTCTCTGCCATCCTTATTGTGTTAACCATGGTGGGGACAGCCTTCTTCATG 641
Qy 121 TyrAsnAlaPheGlyLysProPheGluThrLeuHisGlyProLeuGlyLeuTyrLeuLeu 140
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 642 TACAATGCTTTTGGAAAACCTTTTGAAACTCTGCATGGTCCCCTAGGGCTGTACCTTTTG 701
Qy 141 SerPheIleSerGlySerCysGlyCysLeuValMetIleLeuPheAlaSerGluValLys 160
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 702 AGCTTCATTTCAGGCTCCTGTGGCTGTCTTGTCATGATATTGTTTGCCTCTGAAGTGAAA 761
Qy 161 IleHisHisLeuSerGluLysIleAlaAsnTyrLysGluGlyThrTyrValTyrLysThr 180
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 762 ATCCATCACCTCTCAGAAAAAATTGCAAATTATAAAGAAGGGACTTATGTCTACAAAACG 821
Qy 181 GlnSerGluLysTyrThrThrSerPheTrpValIlePhePheCysPhePheValHisPhe 200
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 822 CAAAGTGAAAAATATACCACCTCATTCTGGGTCATTTTCTTTTGCTTTTTTGTTCATTTT 881
Qy 201 LeuAsnGlyLeuLeuIleArgLeuAlaGlyPheGlnPheProPheAlaLysSerLysAsp 220
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 882 CTGAATGGGCTCCTAATACGACTTGCTGGATTTCAGTTCCCTTTTGCAAAATCTAAAGAC 941
Qy 221 AlaGluThrThrAsnValAlaAlaAspLeuMetTyr 232
||||||||||||||||||||||||||||||||||||
Db 942 GCAGAAACAACTAATGTAGCTGCAGATCTAATGTAC 977
That alignment shows that the composition of WO900 comprises SEQ ID NO 3 itself, a 5’UTR, and a 3’UTR. Those are elements (v), (vi), and (vii) of the instant claims.
Powell teaches (§Polyadenylation Signal Sequences and Upstream Enhancer) one study, in human epithelial-like cells, found that a transgene had a 2.5-fold increase in expression with … bovine growth hormone polyA (bGHpA) signal sequences compared to a minimal synthetic polyA (SPA) signal.
App178 teaches SEQ ID NO 30 which comprises a bovine growth hormone polyA signal and is 100% identical to claimed SEQ ID NO 20, as shown by the following sequence alignment:
RESULT 1
AXQ64086
(NOTE: this sequence has 272 duplicates in the database searched.
See complete list at the end of this report)
ID AXQ64086 standard; DNA; 225 BP.
XX
AC AXQ64086;
XX
DT 29-OCT-2009 (first entry)
XX
DE BGH polyA Yes1 supplementary expression cassette 3' UTR, SEQ:30 #2.
XX
KW 3'-utr; Yes1; dna cassette; gene expression; gene silencing;
KW protein production; rna interference; ss.
XX
OS Bos taurus.
OS Synthetic.
XX
CC PN US2009215178-A1.
XX
CC PD 27-AUG-2009.
XX
CC PF 22-FEB-2008; 2008US-00035437.
XX
PR 22-FEB-2008; 2008US-00035437.
XX
CC PA (TANG/) TANG Z.
XX
CC PI Tang Z;
XX
DR WPI; 2009-M96179/59.
XX
CC PT Generating cell clones with stable transgene (Gene of Interest (GOI))
CC PT expression comprises inactivation of endogenous essential genes of cell
CC PT substrate and trans-complementation of essential genes products.
XX
CC PS Example 3; SEQ ID NO 30; 9pp; English.
XX
CC The present invention relates to a method for generating cell clones with
CC stable transgene (Gene Of Interest (GOI)) expression. The method of the
CC invention comprises: (i) inactivation of endogenous essential genes of
CC cell substrate through Gene Inactivation Cassettes (GIC), (ii) trans-
CC complementation of essential gene products through Gene Supplementary
CC Cassettes (GSC), alternatively, the cassette codes for the gene product
CC that is capable of inactivating GIC function, (iii) the GOI expression
CC cassettes are preferably, physically linked to GSC to take advantage of
CC favourable selective pressure, (iv) GIC could be preferably physically
CC linked to GSC and GOI expression cassettes, where the endogenous
CC essential genes of cell substrate refer to genes or combination of genes
CC that are essential for cell survival and / or cell proliferation. The GIC
CC comprises a vector comprising a promoter operably linked to RNA
CC interference, RNAi (shRNA) / dsRNA / ribozyme molecule, or tandem repeats
CC of such transcript units, targeted to cell endogenous essential mRNA. The
CC invention provides strategies for increasing the productivity of
CC recombinant protein expression in isogenic cell-lines, and a novel
CC selection system for the improved stability and homogeneity of transgene
CC expression in isogenic cells without dependence on continuous selective
CC drugs. An example of the invention provides an essential gene knock-down
CC cassette, targeted at 3' UTR of human endogenous Yes1 gene, and a
CC supplementary Yes1 expression cassette which uses a 3' UTR from bovine
CC growth hormone (BGH) polyA. The present sequence is a bovine growth
CC hormone (BGH) polyA Yes1 supplementary expression cassette 3' UTR, used
CC in an example of the invention. Note: This version of SEQ ID 30 is given
CC in example 3, but it is not the same as the sequence referred to as SEQ
CC ID 30 (seeAXQ61560) in the sequence listing.
XX
SQ Sequence 225 BP; 41 A; 53 C; 72 G; 59 T; 0 U; 0 Other;
Query Match 100.0%; Score 225; Length 225;
Best Local Similarity 100.0%;
Matches 225; Conservative 0; Mismatches 0; Indels 0; Gaps 0;
Qy 1 CTGTGCCTTCTAGTTGCCAGCCATCTGTTGTTTGCCCCTCCCCCGTGCCTTCCTTGACCC 60 SEQ ID NO 20
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 1 CTGTGCCTTCTAGTTGCCAGCCATCTGTTGTTTGCCCCTCCCCCGTGCCTTCCTTGACCC 60 Prior art SEQ
Qy 61 TGGAAGGTGCCACTCCCACTGTCCTTTCCTAATAAAATGAGGAAATTGCATCGCATTGTC 120
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 61 TGGAAGGTGCCACTCCCACTGTCCTTTCCTAATAAAATGAGGAAATTGCATCGCATTGTC 120
Qy 121 TGAGTAGGTGTCATTCTATTCTGGGGGGTGGGGTGGGGCAGGACAGCAAGGGGGAGGATT 180
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 121 TGAGTAGGTGTCATTCTATTCTGGGGGGTGGGGTGGGGCAGGACAGCAAGGGGGAGGATT 180
Qy 181 GGGAAGACAATAGCAGGCATGCTGGGGATGCGGTGGGCTCTATGG 225
|||||||||||||||||||||||||||||||||||||||||||||
Db 181 GGGAAGACAATAGCAGGCATGCTGGGGATGCGGTGGGCTCTATGG 225
A poly-A sequence comprising SEQ ID NO 20 is component (viii) of the instant claims.
It would have been obvious to an artisan before the effective filing date of the claimed invention to modify the invention of the US867 claims with the sequence encoding CLRN1 of WO900 and the teachings about a polyA sequence of Powell and App178 for the benefits of using the US867 vectors to treat Usher syndrome and to increase transgene expression. One would have been motivated to do so with a reasonable expectation of success because Powell teaches that a bovine growth hormone polyA signal can increase transgene expression. One would have been motivated to do so with a reasonable expectation of success because WO900 teaches (¶3-4) expressing CLRN1 had known usage in treating Usher syndrome, including (¶11) for both hearing and vision losses, and it would have been a simple matter to swap the sequence encoding CLRN1 of WO900 for the sequence encoding otoferlin of the US867 claims. An artisan would know that they need only use one AAV vector to encode CLRN1 because WO900 teaches (¶99, 108-111) the entire mCLRN1 cDNA was placed on a single AAV vector, indicating the entire CLRN1 cDNA could fit on a single AAV vector. They would have been motivated to use a single vector because it is simpler to administer a single vector gene therapy than a dual vector gene therapy.
US952 teaches (Col 11 L3-15) a kit that comprises nucleic acid compounds within a container of solution and that the kit can comprise a pre-loaded syringe comprising the compounds. An artisan would have put their compounds into a kit comprising a pre-loaded syringe for the benefit of ensuring that the recipient has the exact dosage ready to administer and because doing so would have prevented any complications that arise from mixing a solution and then getting the mixed solution into a syringe.
Therefore the instant claims would have been obvious in view of the US867 claims, WO900, Powell, App178, and US952.
Claims 229-232, 247-254, and 256-270 are rejected on the ground of nonstatutory double patenting as being unpatentable over claims 1-25 of US Patent No. 12077773 (“US773”) in view of WO900, Powell, App178, and US952. This rejection is maintained and updated in response to the claim amendments. All supporting references are of record.
Although the claims at issue are not identical, they are directed to overlapping subject matter because the instant claims recite a composition comprising an AAV nucleic acid vector wherein the vector comprises a 5’ ITR, a CMV enhancer, a CBA promoter, a chimeric intron according to SEQ ID NO 16, a 5’UTR, a coding sequence (CDS) encoding a CLRN1 protein according to SEQ ID NO 3, a 3’UTR, a polyA signal, and a 3’ITR, wherein the CDS comprises a nt sequence spanning 2 consecutive exons of CLRN1 genomic DNA and lacks an intron sequence between them; wherein the composition can comprise other components such as SEQ ID NOs 17 or 20; to the composition comprising an excipient; to an AAV2 capsid comprising the composition, to an Anc80 capsid comprising the composition; to a kit comprising the composition; and to methods of introducing it to a cochlea of a mammal that can be a human who can have been previously identified as having a defective endogenous CLRN1 gene; to methods of increasing CLRN1 expression in the ear or eye; and to methods of treating hearing or vision loss.
The US773 claims are drawn to a plurality of recombinant AAV vectors: a first vector comprising a 5’ITR, a 3’ITR, a CAG promoter comprising the CMV enhancer of SEQ ID NO 98, a chicken β-actin gene sequence, and the chimeric intron of SEQ ID NO 100 and a second vector, wherein each of the vectors is encapsulated by an AAV capsid having a certain serotype, wherein the AAV vector can be an AAV2 or an Anc80; to a composition comprising the vectors, wherein the composition can be formulated for intra-cochlear administration.
Both claim sets are directed to AAV vectors for administering a gene therapy to the cochlea.
An artisan would not know what are US773 SEQ ID NOs 98 and 100 so they would consult the US773 Spec. and SEQ listing and find (Col 184 L59-67; Col 185-195) SEQ ID NO 98 comprises a CMV enhancer and SEQ ID NO 100 comprises a chimeric intron. US773 SEQ ID NO 100 comprises claimed SEQ ID NO 16 and US773 SEQ ID NO 98 comprises claimed SEQ ID NO 17 as shown by the following alignments:
US-18-485-178-100
Filing date in PALM: 2023-10-11
Sequence 100, US/18485178
Patent No. 12077773
GENERAL INFORMATION
APPLICANT: AKOUOS, INC. (en)
TITLE OF INVENTION: COMPOSITIONS AND METHODS FOR TREATING NON-AGE-ASSOCIATED HEARING IMPAIRMENT IN A HUMAN SUBJECT (en)
FILE REFERENCE: 4833.0050003
CURRENT APPLICATION NUMBER: US/18/485,178
CURRENT FILING DATE: 2023-10-11
NUMBER OF SEQ ID NOS: 110
SEQ ID NO 100
LENGTH: 1013
TYPE: DNA
FEATURE:
NAME/KEY: source
LOCATION: 1..1013
QUALIFIERS: mol_type = other DNA
organism = synthetic construct
Query Match 100.0%; Score 1013; Length 1013;
Best Local Similarity 100.0%;
Matches 1013; Conservative 0; Mismatches 0; Indels 0; Gaps 0;
Qy 1 GGAGTCGCTGCGTTGCCTTCGCCCCGTGCCCCGCTCCGCGCCGCCTCGCGCCGCCCGCCC 60 SEQ ID NO 16
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 1 GGAGTCGCTGCGTTGCCTTCGCCCCGTGCCCCGCTCCGCGCCGCCTCGCGCCGCCCGCCC 60 SEQ ID NO 100
Qy 61 CGGCTCTGACTGACCGCGTTACTCCCACAGGTGAGCGGGCGGGACGGCCCTTCTCCTCCG 120
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 61 CGGCTCTGACTGACCGCGTTACTCCCACAGGTGAGCGGGCGGGACGGCCCTTCTCCTCCG 120
Qy 121 GGCTGTAATTAGCGCTTGGTTTAATGACGGCTCGTTTCTTTTCTGTGGCTGCGTGAAAGC 180
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 121 GGCTGTAATTAGCGCTTGGTTTAATGACGGCTCGTTTCTTTTCTGTGGCTGCGTGAAAGC 180
Qy 181 CTTAAAGGGCTCCGGGAGGGCCCTTTGTGCGGGGGGGAGCGGCTCGGGGGGTGCGTGCGT 240
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 181 CTTAAAGGGCTCCGGGAGGGCCCTTTGTGCGGGGGGGAGCGGCTCGGGGGGTGCGTGCGT 240
Qy 241 GTGTGTGTGCGTGGGGAGCGCCGCGTGCGGCCCGCGCTGCCCGGCGGCTGTGAGCGCTGC 300
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 241 GTGTGTGTGCGTGGGGAGCGCCGCGTGCGGCCCGCGCTGCCCGGCGGCTGTGAGCGCTGC 300
Qy 301 GGGCGCGGCGCGGGGCTTTGTGCGCTCCGCGTGTGCGCGAGGGGAGCGCGGCCGGGGGCG 360
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 301 GGGCGCGGCGCGGGGCTTTGTGCGCTCCGCGTGTGCGCGAGGGGAGCGCGGCCGGGGGCG 360
Qy 361 GTGCCCCGCGGTGCGGGGGGGCTGCGAGGGGAACAAAGGCTGCGTGCGGGGTGTGTGCGT 420
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 361 GTGCCCCGCGGTGCGGGGGGGCTGCGAGGGGAACAAAGGCTGCGTGCGGGGTGTGTGCGT 420
Qy 421 GGGGGGGTGAGCAGGGGGTGTGGGCGCGGCGGTCGGGCTGTAACCCCCCCCTGCACCCCC 480
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 421 GGGGGGGTGAGCAGGGGGTGTGGGCGCGGCGGTCGGGCTGTAACCCCCCCCTGCACCCCC 480
Qy 481 CTCCCCGAGTTGCTGAGCACGGCCCGGCTTCGGGTGCGGGGCTCCGTGCGGGGCGTGGCG 540
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 481 CTCCCCGAGTTGCTGAGCACGGCCCGGCTTCGGGTGCGGGGCTCCGTGCGGGGCGTGGCG 540
Qy 541 CGGGGCTCGCCGTGCCGGGCGGGGGGTGGCGGCAGGTGGGGGTGCCGGGCGGGGCGGGGC 600
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 541 CGGGGCTCGCCGTGCCGGGCGGGGGGTGGCGGCAGGTGGGGGTGCCGGGCGGGGCGGGGC 600
Qy 601 CGCCTCGGGCCGGGGAGGGCTCGGGGGAGGGGCGCGGCGGCCCCCGGAGCGCCGGCGGCT 660
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 601 CGCCTCGGGCCGGGGAGGGCTCGGGGGAGGGGCGCGGCGGCCCCCGGAGCGCCGGCGGCT 660
Qy 661 GTCGAGGCGCGGCGAGCCGCAGCCATTGCCTTTTATGGTAATCGTGCGAGAGGGCGCAGG 720
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 661 GTCGAGGCGCGGCGAGCCGCAGCCATTGCCTTTTATGGTAATCGTGCGAGAGGGCGCAGG 720
Qy 721 GACTTCCTTTGTCCCAAATCTGTGCGGAGCCGAAATCTGGGAGGCGCCGCCGCACCCCCT 780
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 721 GACTTCCTTTGTCCCAAATCTGTGCGGAGCCGAAATCTGGGAGGCGCCGCCGCACCCCCT 780
Qy 781 CTAGCGGGCGCGGGGCGAAGCGGTGCGGCGCCGGCAGGAAGGAAATGGGCGGGGAGGGCC 840
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 781 CTAGCGGGCGCGGGGCGAAGCGGTGCGGCGCCGGCAGGAAGGAAATGGGCGGGGAGGGCC 840
Qy 841 TTCGTGCGTCGCCGCGCCGCCGTCCCCTTCTCCCTCTCCAGCCTCGGGGCTGTCCGCGGG 900
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 841 TTCGTGCGTCGCCGCGCCGCCGTCCCCTTCTCCCTCTCCAGCCTCGGGGCTGTCCGCGGG 900
Qy 901 GGGACGGCTGCCTTCGGGGGGGACGGGGCAGGGCGGGGTTCGGCTTCTGGCGTGTGACCG 960
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 901 GGGACGGCTGCCTTCGGGGGGGACGGGGCAGGGCGGGGTTCGGCTTCTGGCGTGTGACCG 960
Qy 961 GCGGCTCTAGAGCCTCTGCTAACCATGTTCATGCCTTCTTCTTTTTCCTACAG 1013
|||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 961 GCGGCTCTAGAGCCTCTGCTAACCATGTTCATGCCTTCTTCTTTTTCCTACAG 1013
SEQ ID NO 17
Query Match 100.0%; Score 380; DB 1; Length 381;
Best Local Similarity 100.0%;
Matches 380; Conservative 0; Mismatches 0; Indels 0; Gaps 0;
Qy 1 GACATTGATTATTGACTAGTTATTAATAGTAATCAATTACGGGGTCATTAGTTCATAGCC 60 SEQ ID NO 17
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 1 GACATTGATTATTGACTAGTTATTAATAGTAATCAATTACGGGGTCATTAGTTCATAGCC 60 SEQ ID NO 96
Qy 61 CATATATGGAGTTCCGCGTTACATAACTTACGGTAAATGGCCCGCCTGGCTGACCGCCCA 120
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 61 CATATATGGAGTTCCGCGTTACATAACTTACGGTAAATGGCCCGCCTGGCTGACCGCCCA 120
Qy 121 ACGACCCCCGCCCATTGACGTCAATAATGACGTATGTTCCCATAGTAACGCCAATAGGGA 180
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 121 ACGACCCCCGCCCATTGACGTCAATAATGACGTATGTTCCCATAGTAACGCCAATAGGGA 180
Qy 181 CTTTCCATTGACGTCAATGGGTGGACTATTTACGGTAAACTGCCCACTTGGCAGTACATC 240
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 181 CTTTCCATTGACGTCAATGGGTGGACTATTTACGGTAAACTGCCCACTTGGCAGTACATC 240
Qy 241 AAGTGTATCATATGCCAAGTACGCCCCCTATTGACGTCAATGACGGTAAATGGCCCGCCT 300
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 241 AAGTGTATCATATGCCAAGTACGCCCCCTATTGACGTCAATGACGGTAAATGGCCCGCCT 300
Qy 301 GGCATTATGCCCAGTACATGACCTTATGGGACTTTCCTACTTGGCAGTACATCTACGTAT 360
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 301 GGCATTATGCCCAGTACATGACCTTATGGGACTTTCCTACTTGGCAGTACATCTACGTAT 360
Qy 361 TAGTCATCGCTATTACCATG 380
||||||||||||||||||||
Db 361 TAGTCATCGCTATTACCATG 380
Therefore the patented US773 claims recite elements (i), (ii), (iii), (iv), and (ix) of the claimed invention. Then the other prior art teaches the other claim elements that the US773 claims do not recite:
WO900 teaches (¶99) an rAAV vector comprising the CLRN1 cDNA including the 5’ and 3’UTRs, and teaches driving it with the chicken β-actin promoter. WO900 teaches (¶9-10) the polynucleotide (polynt) can include a sequence having SEQ ID NO 2 (which it specifies comprises a 5’UTR and 3’UTR) and can be included on a vector that can be an adeno-associated viral vector (AAV) that can be used for transfecting ocular cells or cells of the inner ear. WO900 teaches (¶21) that the heterologous polynucleotide comprised in the AAV vector is flanked by at least one, and generally by two AAV inverted terminal repeat sequence (ITRs); an artisan would realize that being flanked by two ITRs refers to one ITR on either side, which is a 5’ITR and a 3’ITR. WO900 teaches (¶10-11) treating retinal cells.
WO900 SEQ ID NO 2 comprises a polynt comprising a sequence encoding the amino acid sequence of claimed SEQ ID NO 3 (which has been back-translated from AA[Wingdings font/0xE0]nucleotides). This is shown by the following sequence alignment:
RESULT 7
BDA01054
ID BDA01054 standard; cDNA; 2352 BP.
XX
AC BDA01054;
XX
DT 16-JUN-2016 (first entry)
XX
DE Human derived clarin-1 (CLRN1) polynucleotide SEQ ID NO:2.
XX
KW CLRN1 gene; auditory; clarin-1; gene therapy; hearing loss;
KW ophthalmological; ss; therapeutic; usher syndrome iii; vision disorder.
XX
OS Homo sapiens.
XX
CC PN WO2016073900-A1.
XX
CC PD 12-MAY-2016.
XX
CC PF 06-NOV-2015; 2015WO-US059546.
XX
PR 06-NOV-2014; 2014US-0076114P.
PR 08-MAY-2015; 2015US-0158846P.
XX
CC PA (UCWR ) UNIV CASE WESTERN RESERVE.
XX
CC PI Alagramam KN;
XX
DR WPI; 2016-282935/37.
XX
CC PT New polynucleotide comprising a nucleic acid sequence that includes a
CC PT cDNA coding sequence of a clarin-1 gene, useful for treating vision
CC PT and/or hearing loss associated with Usher syndrome III.
XX
CC PS Claim 9; SEQ ID NO 2; 43pp; English.
XX
CC The invention relates to a novel polynucleotide, used for treating vision
CC and/or hearing loss associated with Usher syndrome III. This
CC polynucleotide comprises a nucleic acid sequence that includes a cDNA
CC coding sequence of a clarin-1 (CLRN1) gene and a 3' untranslated region
CC (UTR) nucleic acid that is derived from the 3' UTR of the clarin-1 gene,
CC where the 3' UTR nucleic acid enhances expression of clarin-1 in a cell
CC transfected with the polynucleotide compared to a cell transfected with a
CC similar polynucleotide devoid of the 3' UTR nucleic acid. The invention
CC further claims: a nucleic acid construct comprising a polynucleotide
CC defined above; a vector for transfecting a cell, comprising a
CC polynucleotide defined above, where the transfected cell expresses clarin
CC -1; and a method of treating vision and/or hearing loss associated with
CC Usher syndrome III in a subject by administering to the ocular cells
CC and/or cells of the inner ear of the subject, a vector that promotes
CC expression of clarin-1 in the cells. The present sequence is a clarin-1
CC polynucleotide, used for treating vision and/or hearing loss associated
CC with Usher syndrome III in a subject.
XX
SQ Sequence 2352 BP; 705 A; 475 C; 484 G; 688 T; 0 U; 0 Other;
Alignment Scores:
Length: 2352
Score: 1214.00 Matches: 232
Percent Similarity: 100.0% Conservative: 0
Best Local Similarity: 100.0% Mismatches: 0
Query Match: 100.0% Indels: 0
Gaps: 0
US-17-253-658-3 (1-232) x BDA01054 (1-2352)
Qy 1 MetProSerGlnGlnLysLysIleIlePheCysMetAlaGlyValPheSerPheAlaCys 20 SEQ ID NO 3 translated[Wingdings font/0xE0]NT
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 282 ATGCCAAGCCAACAGAAGAAAATCATTTTTTGCATGGCCGGAGTGTTCAGTTTTGCATGT 341 WO900 SEQ ID NO 2
Qy 21 AlaLeuGlyValValThrAlaLeuGlyThrProLeuTrpIleLysAlaThrValLeuCys 40
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 342 GCCCTCGGAGTTGTGACAGCCTTGGGGACACCGTTGTGGATCAAAGCCACTGTCCTCTGC 401
Qy 41 LysThrGlyAlaLeuLeuValAsnAlaSerGlyGlnGluLeuAspLysPheMetGlyGlu 60
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 402 AAAACGGGAGCTCTGCTCGTCAATGCCTCAGGGCAGGAGCTGGACAAGTTTATGGGTGAA 461
Qy 61 MetGlnTyrGlyLeuPheHisGlyGluGlyValArgGlnCysGlyLeuGlyAlaArgPro 80
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 462 ATGCAGTACGGGCTTTTCCACGGAGAGGGTGTGAGGCAGTGTGGGTTGGGAGCAAGGCCC 521
Qy 81 PheArgPheSerPhePheProAspLeuLeuLysAlaIleProValSerIleHisValAsn 100
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 522 TTTCGGTTCTCATTTTTTCCAGATTTGCTCAAAGCAATCCCAGTGAGCATCCACGTCAAT 581
Qy 101 ValIleLeuPheSerAlaIleLeuIleValLeuThrMetValGlyThrAlaPhePheMet 120
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 582 GTCATTCTCTTCTCTGCCATCCTTATTGTGTTAACCATGGTGGGGACAGCCTTCTTCATG 641
Qy 121 TyrAsnAlaPheGlyLysProPheGluThrLeuHisGlyProLeuGlyLeuTyrLeuLeu 140
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 642 TACAATGCTTTTGGAAAACCTTTTGAAACTCTGCATGGTCCCCTAGGGCTGTACCTTTTG 701
Qy 141 SerPheIleSerGlySerCysGlyCysLeuValMetIleLeuPheAlaSerGluValLys 160
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 702 AGCTTCATTTCAGGCTCCTGTGGCTGTCTTGTCATGATATTGTTTGCCTCTGAAGTGAAA 761
Qy 161 IleHisHisLeuSerGluLysIleAlaAsnTyrLysGluGlyThrTyrValTyrLysThr 180
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 762 ATCCATCACCTCTCAGAAAAAATTGCAAATTATAAAGAAGGGACTTATGTCTACAAAACG 821
Qy 181 GlnSerGluLysTyrThrThrSerPheTrpValIlePhePheCysPhePheValHisPhe 200
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 822 CAAAGTGAAAAATATACCACCTCATTCTGGGTCATTTTCTTTTGCTTTTTTGTTCATTTT 881
Qy 201 LeuAsnGlyLeuLeuIleArgLeuAlaGlyPheGlnPheProPheAlaLysSerLysAsp 220
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 882 CTGAATGGGCTCCTAATACGACTTGCTGGATTTCAGTTCCCTTTTGCAAAATCTAAAGAC 941
Qy 221 AlaGluThrThrAsnValAlaAlaAspLeuMetTyr 232
||||||||||||||||||||||||||||||||||||
Db 942 GCAGAAACAACTAATGTAGCTGCAGATCTAATGTAC 977
That alignment shows that the composition of WO900 comprises SEQ ID NO 3 itself, a 5’UTR, and a 3’UTR. Those are elements (v), (vi), and (vii) of the instant claims.
Powell teaches (§Polyadenylation Signal Sequences and Upstream Enhancer) one study, in human epithelial-like cells, found that a transgene had a 2.5-fold increase in expression with … bovine growth hormone polyA (bGHpA) signal sequences compared to a minimal synthetic polyA (SPA) signal.
App178 teaches SEQ ID NO 30 which comprises a bovine growth hormone polyA signal and is 100% identical to claimed SEQ ID NO 20, as shown by the following sequence alignment:
RESULT 1
AXQ64086
(NOTE: this sequence has 272 duplicates in the database searched.
See complete list at the end of this report)
ID AXQ64086 standard; DNA; 225 BP.
XX
AC AXQ64086;
XX
DT 29-OCT-2009 (first entry)
XX
DE BGH polyA Yes1 supplementary expression cassette 3' UTR, SEQ:30 #2.
XX
KW 3'-utr; Yes1; dna cassette; gene expression; gene silencing;
KW protein production; rna interference; ss.
XX
OS Bos taurus.
OS Synthetic.
XX
CC PN US2009215178-A1.
XX
CC PD 27-AUG-2009.
XX
CC PF 22-FEB-2008; 2008US-00035437.
XX
PR 22-FEB-2008; 2008US-00035437.
XX
CC PA (TANG/) TANG Z.
XX
CC PI Tang Z;
XX
DR WPI; 2009-M96179/59.
XX
CC PT Generating cell clones with stable transgene (Gene of Interest (GOI))
CC PT expression comprises inactivation of endogenous essential genes of cell
CC PT substrate and trans-complementation of essential genes products.
XX
CC PS Example 3; SEQ ID NO 30; 9pp; English.
XX
CC The present invention relates to a method for generating cell clones with
CC stable transgene (Gene Of Interest (GOI)) expression. The method of the
CC invention comprises: (i) inactivation of endogenous essential genes of
CC cell substrate through Gene Inactivation Cassettes (GIC), (ii) trans-
CC complementation of essential gene products through Gene Supplementary
CC Cassettes (GSC), alternatively, the cassette codes for the gene product
CC that is capable of inactivating GIC function, (iii) the GOI expression
CC cassettes are preferably, physically linked to GSC to take advantage of
CC favourable selective pressure, (iv) GIC could be preferably physically
CC linked to GSC and GOI expression cassettes, where the endogenous
CC essential genes of cell substrate refer to genes or combination of genes
CC that are essential for cell survival and / or cell proliferation. The GIC
CC comprises a vector comprising a promoter operably linked to RNA
CC interference, RNAi (shRNA) / dsRNA / ribozyme molecule, or tandem repeats
CC of such transcript units, targeted to cell endogenous essential mRNA. The
CC invention provides strategies for increasing the productivity of
CC recombinant protein expression in isogenic cell-lines, and a novel
CC selection system for the improved stability and homogeneity of transgene
CC expression in isogenic cells without dependence on continuous selective
CC drugs. An example of the invention provides an essential gene knock-down
CC cassette, targeted at 3' UTR of human endogenous Yes1 gene, and a
CC supplementary Yes1 expression cassette which uses a 3' UTR from bovine
CC growth hormone (BGH) polyA. The present sequence is a bovine growth
CC hormone (BGH) polyA Yes1 supplementary expression cassette 3' UTR, used
CC in an example of the invention. Note: This version of SEQ ID 30 is given
CC in example 3, but it is not the same as the sequence referred to as SEQ
CC ID 30 (seeAXQ61560) in the sequence listing.
XX
SQ Sequence 225 BP; 41 A; 53 C; 72 G; 59 T; 0 U; 0 Other;
Query Match 100.0%; Score 225; Length 225;
Best Local Similarity 100.0%;
Matches 225; Conservative 0; Mismatches 0; Indels 0; Gaps 0;
Qy 1 CTGTGCCTTCTAGTTGCCAGCCATCTGTTGTTTGCCCCTCCCCCGTGCCTTCCTTGACCC 60 SEQ ID NO 20
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 1 CTGTGCCTTCTAGTTGCCAGCCATCTGTTGTTTGCCCCTCCCCCGTGCCTTCCTTGACCC 60 Prior art SEQ
Qy 61 TGGAAGGTGCCACTCCCACTGTCCTTTCCTAATAAAATGAGGAAATTGCATCGCATTGTC 120
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 61 TGGAAGGTGCCACTCCCACTGTCCTTTCCTAATAAAATGAGGAAATTGCATCGCATTGTC 120
Qy 121 TGAGTAGGTGTCATTCTATTCTGGGGGGTGGGGTGGGGCAGGACAGCAAGGGGGAGGATT 180
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 121 TGAGTAGGTGTCATTCTATTCTGGGGGGTGGGGTGGGGCAGGACAGCAAGGGGGAGGATT 180
Qy 181 GGGAAGACAATAGCAGGCATGCTGGGGATGCGGTGGGCTCTATGG 225
|||||||||||||||||||||||||||||||||||||||||||||
Db 181 GGGAAGACAATAGCAGGCATGCTGGGGATGCGGTGGGCTCTATGG 225
A poly-A sequence comprising SEQ ID NO 20 is component (viii) of the instant claims.
It would have been obvious to an artisan before the effective filing date of the claimed invention to modify the invention of the US773 claims with the sequence encoding CLRN1 of WO900 and the teachings about a polyA sequence of Powell and App178 for the benefits of using the US773 vectors to treat Usher syndrome and to increase transgene expression. One would have been motivated to do so with a reasonable expectation of success because Powell teaches that a bovine growth hormone polyA signal can increase transgene expression. One would have been motivated to do so with a reasonable expectation of success because WO900 teaches (¶3-4) expressing CLRN1 had known usage in treating Usher syndrome, including (¶11) for both hearing and vision losses, and it would have been a simple matter to swap the sequence encoding CLRN1 of WO900 for the sequence encoding otoferlin of the US773 claims. An artisan would know that they need only use one AAV vector to encode CLRN1 because WO900 teaches (¶99, 108-111) the entire CLRN1 cDNA was placed on a single AAV vector, indicating the entire CLRN1 cDNA could fit on a single AAV vector. They would have been motivated to use a single vector because it is simpler to administer a single vector gene therapy than a dual vector gene therapy.
US952 teaches (Col 11 L3-15) a kit that comprises nucleic acid compounds within a container of solution and that the kit can comprise a pre-loaded syringe comprising the compounds. An artisan would have put their compounds into a kit comprising a pre-loaded syringe for the benefit of ensuring that the recipient has the exact dosage ready to administer and because doing so would have prevented any complications that arise from mixing a solution and then getting the mixed solution into a syringe.
Therefore the instant claims would have been obvious in view of the US773 claims, WO900, Powell, App178, and US952.
Claims 229-232, 247-254, and 256-270 are rejected on the ground of nonstatutory double patenting as being unpatentable over claims 1-26 of the U.S. Patent No. 12305191 (“US191”) in view of WO900, Powell, App178, and US952. This rejection is maintained and updated in response to the claim amendments. All supporting references are of record.
Although the claims at issue are not identical, they are directed to overlapping subject matter because the instant claims recite a composition comprising an AAV nucleic acid vector wherein the vector comprises a 5’ ITR, a CMV enhancer, a CBA promoter, a chimeric intron according to SEQ ID NO 16, a 5’UTR, a coding sequence (CDS) encoding a CLRN1 protein according to SEQ ID NO 3, a 3’UTR, a polyA signal, and a 3’ITR, wherein the CDS comprises a nt sequence spanning 2 consecutive exons of CLRN1 genomic DNA and lacks an intron sequence between them; wherein the composition can comprise other components such as SEQ ID NOs 17 or 20; to the composition comprising an excipient; to an AAV2 capsid comprising the composition, to an Anc80 capsid comprising the composition; to a kit comprising the composition; and to methods of introducing it to a cochlea of a mammal that can be a human who can have been previously identified as having a defective endogenous CLRN1 gene; to methods of increasing CLRN1 expression in the ear or eye; and to methods of treating hearing or vision loss.
The US191 claims are drawn to a plurality of recombinant AAV vectors: a first vector comprising a 5’ITR, a 3’ITR, a CAG promoter comprising SEQ ID NO 61, and a second vector, wherein each of the vectors is encapsulated by an AAV capsid having a certain serotype, wherein the capsid can be an AAV2 capsid or an Anc80 capsid; to a composition comprising the vectors, wherein the composition can be formulated for intra-cochlear administration.
Both claim sets are directed to AAV vectors for administering a gene therapy to the cochlea.
An artisan would not know what is US191 SEQ ID NO 61 so they would consult the US191 Spec. and SEQ listing and find (Col 81 L30-35; Col 184 L10-20) SEQ ID NO 61 comprises a CAG promoter comprising: a CMV enhancer, chicken β-actin gene sequence, and a chimeric intron. US191 SEQ ID NO 61 comprises claimed SEQ ID NOs 16 and 17 as shown by the following alignments:
US-18-777-787-61
Filing date in PALM: 2024-07-19
Sequence 61, US/18777787
Patent No. 12305191
GENERAL INFORMATION
APPLICANT: AKOUOS, INC. (en)
TITLE OF INVENTION: COMPOSITIONS AND METHODS FOR TREATING NON-AGE-ASSOCIATED HEARING IMPAIRMENT IN A HUMAN SUBJECT (en)
FILE REFERENCE: 4833.0050004
CURRENT APPLICATION NUMBER: US/18/777,787
CURRENT FILING DATE: 2024-07-19
NUMBER OF SEQ ID NOS: 110
SEQ ID NO 61
LENGTH: 1671
TYPE: DNA
FEATURE:
NAME/KEY: source
LOCATION: 1..1671
QUALIFIERS: mol_type = other DNA
organism = synthetic construct
ALIGNMENT:
Query Match 100.0%; Score 1013; Length 1671;
Best Local Similarity 100.0%;
Matches 1013; Conservative 0; Mismatches 0; Indels 0; Gaps 0;
Qy 1 GGAGTCGCTGCGTTGCCTTCGCCCCGTGCCCCGCTCCGCGCCGCCTCGCGCCGCCCGCCC 60 SEQ ID NO 16
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 659 GGAGTCGCTGCGTTGCCTTCGCCCCGTGCCCCGCTCCGCGCCGCCTCGCGCCGCCCGCCC 718 SEQ ID NO 61
Qy 61 CGGCTCTGACTGACCGCGTTACTCCCACAGGTGAGCGGGCGGGACGGCCCTTCTCCTCCG 120
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 719 CGGCTCTGACTGACCGCGTTACTCCCACAGGTGAGCGGGCGGGACGGCCCTTCTCCTCCG 778
Qy 121 GGCTGTAATTAGCGCTTGGTTTAATGACGGCTCGTTTCTTTTCTGTGGCTGCGTGAAAGC 180
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 779 GGCTGTAATTAGCGCTTGGTTTAATGACGGCTCGTTTCTTTTCTGTGGCTGCGTGAAAGC 838
Qy 181 CTTAAAGGGCTCCGGGAGGGCCCTTTGTGCGGGGGGGAGCGGCTCGGGGGGTGCGTGCGT 240
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 839 CTTAAAGGGCTCCGGGAGGGCCCTTTGTGCGGGGGGGAGCGGCTCGGGGGGTGCGTGCGT 898
Qy 241 GTGTGTGTGCGTGGGGAGCGCCGCGTGCGGCCCGCGCTGCCCGGCGGCTGTGAGCGCTGC 300
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 899 GTGTGTGTGCGTGGGGAGCGCCGCGTGCGGCCCGCGCTGCCCGGCGGCTGTGAGCGCTGC 958
Qy 301 GGGCGCGGCGCGGGGCTTTGTGCGCTCCGCGTGTGCGCGAGGGGAGCGCGGCCGGGGGCG 360
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 959 GGGCGCGGCGCGGGGCTTTGTGCGCTCCGCGTGTGCGCGAGGGGAGCGCGGCCGGGGGCG 1018
Qy 361 GTGCCCCGCGGTGCGGGGGGGCTGCGAGGGGAACAAAGGCTGCGTGCGGGGTGTGTGCGT 420
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 1019 GTGCCCCGCGGTGCGGGGGGGCTGCGAGGGGAACAAAGGCTGCGTGCGGGGTGTGTGCGT 1078
Qy 421 GGGGGGGTGAGCAGGGGGTGTGGGCGCGGCGGTCGGGCTGTAACCCCCCCCTGCACCCCC 480
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 1079 GGGGGGGTGAGCAGGGGGTGTGGGCGCGGCGGTCGGGCTGTAACCCCCCCCTGCACCCCC 1138
Qy 481 CTCCCCGAGTTGCTGAGCACGGCCCGGCTTCGGGTGCGGGGCTCCGTGCGGGGCGTGGCG 540
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 1139 CTCCCCGAGTTGCTGAGCACGGCCCGGCTTCGGGTGCGGGGCTCCGTGCGGGGCGTGGCG 1198
Qy 541 CGGGGCTCGCCGTGCCGGGCGGGGGGTGGCGGCAGGTGGGGGTGCCGGGCGGGGCGGGGC 600
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 1199 CGGGGCTCGCCGTGCCGGGCGGGGGGTGGCGGCAGGTGGGGGTGCCGGGCGGGGCGGGGC 1258
Qy 601 CGCCTCGGGCCGGGGAGGGCTCGGGGGAGGGGCGCGGCGGCCCCCGGAGCGCCGGCGGCT 660
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 1259 CGCCTCGGGCCGGGGAGGGCTCGGGGGAGGGGCGCGGCGGCCCCCGGAGCGCCGGCGGCT 1318
Qy 661 GTCGAGGCGCGGCGAGCCGCAGCCATTGCCTTTTATGGTAATCGTGCGAGAGGGCGCAGG 720
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 1319 GTCGAGGCGCGGCGAGCCGCAGCCATTGCCTTTTATGGTAATCGTGCGAGAGGGCGCAGG 1378
Qy 721 GACTTCCTTTGTCCCAAATCTGTGCGGAGCCGAAATCTGGGAGGCGCCGCCGCACCCCCT 780
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 1379 GACTTCCTTTGTCCCAAATCTGTGCGGAGCCGAAATCTGGGAGGCGCCGCCGCACCCCCT 1438
Qy 781 CTAGCGGGCGCGGGGCGAAGCGGTGCGGCGCCGGCAGGAAGGAAATGGGCGGGGAGGGCC 840
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 1439 CTAGCGGGCGCGGGGCGAAGCGGTGCGGCGCCGGCAGGAAGGAAATGGGCGGGGAGGGCC 1498
Qy 841 TTCGTGCGTCGCCGCGCCGCCGTCCCCTTCTCCCTCTCCAGCCTCGGGGCTGTCCGCGGG 900
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 1499 TTCGTGCGTCGCCGCGCCGCCGTCCCCTTCTCCCTCTCCAGCCTCGGGGCTGTCCGCGGG 1558
Qy 901 GGGACGGCTGCCTTCGGGGGGGACGGGGCAGGGCGGGGTTCGGCTTCTGGCGTGTGACCG 960
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 1559 GGGACGGCTGCCTTCGGGGGGGACGGGGCAGGGCGGGGTTCGGCTTCTGGCGTGTGACCG 1618
Qy 961 GCGGCTCTAGAGCCTCTGCTAACCATGTTCATGCCTTCTTCTTTTTCCTACAG 1013
|||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 1619 GCGGCTCTAGAGCCTCTGCTAACCATGTTCATGCCTTCTTCTTTTTCCTACAG 1671
SEQ ID NO 17
Query Match 100.0%; Score 380; DB 1; Length 1671;
Best Local Similarity 100.0%;
Matches 380; Conservative 0; Mismatches 0; Indels 0; Gaps 0;
Qy 1 GACATTGATTATTGACTAGTTATTAATAGTAATCAATTACGGGGTCATTAGTTCATAGCC 60 SEQ ID NO 17
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 1 GACATTGATTATTGACTAGTTATTAATAGTAATCAATTACGGGGTCATTAGTTCATAGCC 60 SEQ ID NO 61
Qy 61 CATATATGGAGTTCCGCGTTACATAACTTACGGTAAATGGCCCGCCTGGCTGACCGCCCA 120
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 61 CATATATGGAGTTCCGCGTTACATAACTTACGGTAAATGGCCCGCCTGGCTGACCGCCCA 120
Qy 121 ACGACCCCCGCCCATTGACGTCAATAATGACGTATGTTCCCATAGTAACGCCAATAGGGA 180
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 121 ACGACCCCCGCCCATTGACGTCAATAATGACGTATGTTCCCATAGTAACGCCAATAGGGA 180
Qy 181 CTTTCCATTGACGTCAATGGGTGGACTATTTACGGTAAACTGCCCACTTGGCAGTACATC 240
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 181 CTTTCCATTGACGTCAATGGGTGGACTATTTACGGTAAACTGCCCACTTGGCAGTACATC 240
Qy 241 AAGTGTATCATATGCCAAGTACGCCCCCTATTGACGTCAATGACGGTAAATGGCCCGCCT 300
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 241 AAGTGTATCATATGCCAAGTACGCCCCCTATTGACGTCAATGACGGTAAATGGCCCGCCT 300
Qy 301 GGCATTATGCCCAGTACATGACCTTATGGGACTTTCCTACTTGGCAGTACATCTACGTAT 360
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 301 GGCATTATGCCCAGTACATGACCTTATGGGACTTTCCTACTTGGCAGTACATCTACGTAT 360
Qy 361 TAGTCATCGCTATTACCATG 380
||||||||||||||||||||
Db 361 TAGTCATCGCTATTACCATG 380
Therefore the patented US191 claims recite elements (i), (ii), (iii), (iv), and (ix) of the claimed invention. Then the other prior art teaches the other claim elements that the US191 claims do not recite:
WO900 teaches (¶99) an rAAV vector comprising the CLRN1 cDNA including the 5’ and 3’UTRs, and teaches driving it with the chicken β-actin promoter. WO900 teaches (¶9-10) the polynucleotide (polynt) can include a sequence having SEQ ID NO 2 (which it specifies comprises a 5’UTR and 3’UTR) and can be included on a vector that can be an adeno-associated viral vector (AAV) that can be used for transfecting ocular cells or cells of the inner ear. WO900 teaches (¶21) that the heterologous polynucleotide comprised in the AAV vector is flanked by at least one, and generally by two AAV inverted terminal repeat sequence (ITRs); an artisan would realize that being flanked by two ITRs refers to one ITR on either side, which is a 5’ITR and a 3’ITR. WO900 teaches (¶10-11) treating retinal cells.
WO900 SEQ ID NO 2 comprises a polynt comprising a sequence encoding the amino acid sequence of claimed SEQ ID NO 3 (which has been back-translated from AA[Wingdings font/0xE0]nucleotides). This is shown by the following sequence alignment:
RESULT 7
BDA01054
ID BDA01054 standard; cDNA; 2352 BP.
XX
AC BDA01054;
XX
DT 16-JUN-2016 (first entry)
XX
DE Human derived clarin-1 (CLRN1) polynucleotide SEQ ID NO:2.
XX
KW CLRN1 gene; auditory; clarin-1; gene therapy; hearing loss;
KW ophthalmological; ss; therapeutic; usher syndrome iii; vision disorder.
XX
OS Homo sapiens.
XX
CC PN WO2016073900-A1.
XX
CC PD 12-MAY-2016.
XX
CC PF 06-NOV-2015; 2015WO-US059546.
XX
PR 06-NOV-2014; 2014US-0076114P.
PR 08-MAY-2015; 2015US-0158846P.
XX
CC PA (UCWR ) UNIV CASE WESTERN RESERVE.
XX
CC PI Alagramam KN;
XX
DR WPI; 2016-282935/37.
XX
CC PT New polynucleotide comprising a nucleic acid sequence that includes a
CC PT cDNA coding sequence of a clarin-1 gene, useful for treating vision
CC PT and/or hearing loss associated with Usher syndrome III.
XX
CC PS Claim 9; SEQ ID NO 2; 43pp; English.
XX
CC The invention relates to a novel polynucleotide, used for treating vision
CC and/or hearing loss associated with Usher syndrome III. This
CC polynucleotide comprises a nucleic acid sequence that includes a cDNA
CC coding sequence of a clarin-1 (CLRN1) gene and a 3' untranslated region
CC (UTR) nucleic acid that is derived from the 3' UTR of the clarin-1 gene,
CC where the 3' UTR nucleic acid enhances expression of clarin-1 in a cell
CC transfected with the polynucleotide compared to a cell transfected with a
CC similar polynucleotide devoid of the 3' UTR nucleic acid. The invention
CC further claims: a nucleic acid construct comprising a polynucleotide
CC defined above; a vector for transfecting a cell, comprising a
CC polynucleotide defined above, where the transfected cell expresses clarin
CC -1; and a method of treating vision and/or hearing loss associated with
CC Usher syndrome III in a subject by administering to the ocular cells
CC and/or cells of the inner ear of the subject, a vector that promotes
CC expression of clarin-1 in the cells. The present sequence is a clarin-1
CC polynucleotide, used for treating vision and/or hearing loss associated
CC with Usher syndrome III in a subject.
XX
SQ Sequence 2352 BP; 705 A; 475 C; 484 G; 688 T; 0 U; 0 Other;
Alignment Scores:
Length: 2352
Score: 1214.00 Matches: 232
Percent Similarity: 100.0% Conservative: 0
Best Local Similarity: 100.0% Mismatches: 0
Query Match: 100.0% Indels: 0
Gaps: 0
US-17-253-658-3 (1-232) x BDA01054 (1-2352)
Qy 1 MetProSerGlnGlnLysLysIleIlePheCysMetAlaGlyValPheSerPheAlaCys 20 SEQ ID NO 3 translated[Wingdings font/0xE0]NT
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 282 ATGCCAAGCCAACAGAAGAAAATCATTTTTTGCATGGCCGGAGTGTTCAGTTTTGCATGT 341 WO900 SEQ ID NO 2
Qy 21 AlaLeuGlyValValThrAlaLeuGlyThrProLeuTrpIleLysAlaThrValLeuCys 40
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 342 GCCCTCGGAGTTGTGACAGCCTTGGGGACACCGTTGTGGATCAAAGCCACTGTCCTCTGC 401
Qy 41 LysThrGlyAlaLeuLeuValAsnAlaSerGlyGlnGluLeuAspLysPheMetGlyGlu 60
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 402 AAAACGGGAGCTCTGCTCGTCAATGCCTCAGGGCAGGAGCTGGACAAGTTTATGGGTGAA 461
Qy 61 MetGlnTyrGlyLeuPheHisGlyGluGlyValArgGlnCysGlyLeuGlyAlaArgPro 80
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 462 ATGCAGTACGGGCTTTTCCACGGAGAGGGTGTGAGGCAGTGTGGGTTGGGAGCAAGGCCC 521
Qy 81 PheArgPheSerPhePheProAspLeuLeuLysAlaIleProValSerIleHisValAsn 100
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 522 TTTCGGTTCTCATTTTTTCCAGATTTGCTCAAAGCAATCCCAGTGAGCATCCACGTCAAT 581
Qy 101 ValIleLeuPheSerAlaIleLeuIleValLeuThrMetValGlyThrAlaPhePheMet 120
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 582 GTCATTCTCTTCTCTGCCATCCTTATTGTGTTAACCATGGTGGGGACAGCCTTCTTCATG 641
Qy 121 TyrAsnAlaPheGlyLysProPheGluThrLeuHisGlyProLeuGlyLeuTyrLeuLeu 140
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 642 TACAATGCTTTTGGAAAACCTTTTGAAACTCTGCATGGTCCCCTAGGGCTGTACCTTTTG 701
Qy 141 SerPheIleSerGlySerCysGlyCysLeuValMetIleLeuPheAlaSerGluValLys 160
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 702 AGCTTCATTTCAGGCTCCTGTGGCTGTCTTGTCATGATATTGTTTGCCTCTGAAGTGAAA 761
Qy 161 IleHisHisLeuSerGluLysIleAlaAsnTyrLysGluGlyThrTyrValTyrLysThr 180
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 762 ATCCATCACCTCTCAGAAAAAATTGCAAATTATAAAGAAGGGACTTATGTCTACAAAACG 821
Qy 181 GlnSerGluLysTyrThrThrSerPheTrpValIlePhePheCysPhePheValHisPhe 200
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 822 CAAAGTGAAAAATATACCACCTCATTCTGGGTCATTTTCTTTTGCTTTTTTGTTCATTTT 881
Qy 201 LeuAsnGlyLeuLeuIleArgLeuAlaGlyPheGlnPheProPheAlaLysSerLysAsp 220
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 882 CTGAATGGGCTCCTAATACGACTTGCTGGATTTCAGTTCCCTTTTGCAAAATCTAAAGAC 941
Qy 221 AlaGluThrThrAsnValAlaAlaAspLeuMetTyr 232
||||||||||||||||||||||||||||||||||||
Db 942 GCAGAAACAACTAATGTAGCTGCAGATCTAATGTAC 977
That alignment shows that the composition of WO900 comprises SEQ ID NO 3 itself, a 5’UTR, and a 3’UTR. Those are elements (v), (vi), and (vii) of the instant claims.
Powell teaches (§Polyadenylation Signal Sequences and Upstream Enhancer) one study, in human epithelial-like cells, found that a transgene had a 2.5-fold increase in expression with … bovine growth hormone polyA (bGHpA) signal sequences compared to a minimal synthetic polyA (SPA) signal.
App178 teaches SEQ ID NO 30 which comprises a bovine growth hormone polyA signal and is 100% identical to claimed SEQ ID NO 20, as shown by the following sequence alignment:
RESULT 1
AXQ64086
(NOTE: this sequence has 272 duplicates in the database searched.
See complete list at the end of this report)
ID AXQ64086 standard; DNA; 225 BP.
XX
AC AXQ64086;
XX
DT 29-OCT-2009 (first entry)
XX
DE BGH polyA Yes1 supplementary expression cassette 3' UTR, SEQ:30 #2.
XX
KW 3'-utr; Yes1; dna cassette; gene expression; gene silencing;
KW protein production; rna interference; ss.
XX
OS Bos taurus.
OS Synthetic.
XX
CC PN US2009215178-A1.
XX
CC PD 27-AUG-2009.
XX
CC PF 22-FEB-2008; 2008US-00035437.
XX
PR 22-FEB-2008; 2008US-00035437.
XX
CC PA (TANG/) TANG Z.
XX
CC PI Tang Z;
XX
DR WPI; 2009-M96179/59.
XX
CC PT Generating cell clones with stable transgene (Gene of Interest (GOI))
CC PT expression comprises inactivation of endogenous essential genes of cell
CC PT substrate and trans-complementation of essential genes products.
XX
CC PS Example 3; SEQ ID NO 30; 9pp; English.
XX
CC The present invention relates to a method for generating cell clones with
CC stable transgene (Gene Of Interest (GOI)) expression. The method of the
CC invention comprises: (i) inactivation of endogenous essential genes of
CC cell substrate through Gene Inactivation Cassettes (GIC), (ii) trans-
CC complementation of essential gene products through Gene Supplementary
CC Cassettes (GSC), alternatively, the cassette codes for the gene product
CC that is capable of inactivating GIC function, (iii) the GOI expression
CC cassettes are preferably, physically linked to GSC to take advantage of
CC favourable selective pressure, (iv) GIC could be preferably physically
CC linked to GSC and GOI expression cassettes, where the endogenous
CC essential genes of cell substrate refer to genes or combination of genes
CC that are essential for cell survival and / or cell proliferation. The GIC
CC comprises a vector comprising a promoter operably linked to RNA
CC interference, RNAi (shRNA) / dsRNA / ribozyme molecule, or tandem repeats
CC of such transcript units, targeted to cell endogenous essential mRNA. The
CC invention provides strategies for increasing the productivity of
CC recombinant protein expression in isogenic cell-lines, and a novel
CC selection system for the improved stability and homogeneity of transgene
CC expression in isogenic cells without dependence on continuous selective
CC drugs. An example of the invention provides an essential gene knock-down
CC cassette, targeted at 3' UTR of human endogenous Yes1 gene, and a
CC supplementary Yes1 expression cassette which uses a 3' UTR from bovine
CC growth hormone (BGH) polyA. The present sequence is a bovine growth
CC hormone (BGH) polyA Yes1 supplementary expression cassette 3' UTR, used
CC in an example of the invention. Note: This version of SEQ ID 30 is given
CC in example 3, but it is not the same as the sequence referred to as SEQ
CC ID 30 (seeAXQ61560) in the sequence listing.
XX
SQ Sequence 225 BP; 41 A; 53 C; 72 G; 59 T; 0 U; 0 Other;
Query Match 100.0%; Score 225; Length 225;
Best Local Similarity 100.0%;
Matches 225; Conservative 0; Mismatches 0; Indels 0; Gaps 0;
Qy 1 CTGTGCCTTCTAGTTGCCAGCCATCTGTTGTTTGCCCCTCCCCCGTGCCTTCCTTGACCC 60 SEQ ID NO 20
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 1 CTGTGCCTTCTAGTTGCCAGCCATCTGTTGTTTGCCCCTCCCCCGTGCCTTCCTTGACCC 60 Prior art SEQ
Qy 61 TGGAAGGTGCCACTCCCACTGTCCTTTCCTAATAAAATGAGGAAATTGCATCGCATTGTC 120
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 61 TGGAAGGTGCCACTCCCACTGTCCTTTCCTAATAAAATGAGGAAATTGCATCGCATTGTC 120
Qy 121 TGAGTAGGTGTCATTCTATTCTGGGGGGTGGGGTGGGGCAGGACAGCAAGGGGGAGGATT 180
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 121 TGAGTAGGTGTCATTCTATTCTGGGGGGTGGGGTGGGGCAGGACAGCAAGGGGGAGGATT 180
Qy 181 GGGAAGACAATAGCAGGCATGCTGGGGATGCGGTGGGCTCTATGG 225
|||||||||||||||||||||||||||||||||||||||||||||
Db 181 GGGAAGACAATAGCAGGCATGCTGGGGATGCGGTGGGCTCTATGG 225
A poly-A sequence comprising SEQ ID NO 20 is component (viii) of the instant claims.
It would have been obvious to an artisan before the effective filing date of the claimed invention to modify the invention of the US191 claims with the sequence encoding CLRN1 of WO900 and the teachings about a polyA sequence of Powell and App178 for the benefits of using the US191 vectors to treat Usher syndrome and to increase transgene expression. One would have been motivated to do so with a reasonable expectation of success because Powell teaches that a bovine growth hormone polyA signal can increase transgene expression. One would have been motivated to do so with a reasonable expectation of success because WO900 teaches (¶3-4) expressing CLRN1 had known usage in treating Usher syndrome, including (¶11) for both hearing and vision losses, and it would have been a simple matter to swap the sequence encoding CLRN1 of WO900 for the sequence encoding otoferlin of US191. An artisan would know that they need only use one AAV vector to encode CLRN1 because WO900 teaches (¶99, 108-111) the entire mCLRN1 cDNA was placed on a single AAV vector, indicating the entire CLRN1 cDNA could fit on a single AAV vector. They would have been motivated to use a single vector because it is simpler to administer a single vector gene therapy than a dual vector gene therapy.
US952 teaches (Col 11 L3-15) a kit that comprises nucleic acid compounds within a container of solution and that the kit can comprise a pre-loaded syringe comprising the compounds. An artisan would have put their compounds into a kit comprising a pre-loaded syringe for the benefit of ensuring that the recipient has the exact dosage ready to administer and because doing so would have prevented any complications that arise from mixing a solution and then getting the mixed solution into a syringe.
Therefore the instant claims would have been obvious in view of the US191 claims, WO900, Powell, App178, and US952.
Claims 229-232, 247-254, and 256-270 are provisionally rejected on the ground of nonstatutory double patenting as being unpatentable over claims 1, 44, 55, 58-61, 90-91, 93-95, 97-101, 107-117 of copending Application No. 17628266 (reference application; “App266”) in view of Powell, WO900, App178, and US952. This rejection is maintained and updated in response to the claim amendments. All supporting references are of record.
Although the claims at issue are not identical, they are not patentably distinct from each other because both claim sets are directed to methods and compositions of gene therapies for expressing a gene of interest in the inner ear to treat hearing loss. The instant claims recite a composition comprising an AAV nucleic acid vector wherein the vector comprises a 5’ ITR, a CMV enhancer, a CBA promoter, a chimeric intron, a 5’UTR, a coding sequence (CDS) encoding a CLRN1 protein according to SEQ ID NO 3, a 3’UTR, a polyA signal, and a 3’ITR, wherein the CDS comprises a nt sequence spanning 2 consecutive exons of CLRN1 genomic DNA and lacks an intron sequence between them; wherein the composition can comprise other components such as SEQ ID NOs 16-17 or 20; to the composition comprising an excipient; to an AAV2 capsid comprising the composition, to an Anc80 capsid comprising the composition; to a kit comprising the composition; and to methods of introducing it to a cochlea of a mammal that can be a human who can have been previously identified as having a defective endogenous CLRN1 gene; to methods of increasing CLRN1 expression in the ear or eye; and to methods of treating hearing or vision loss.
The App266 claims are very broad and recite a construct comprising a promoter that can be a chicken β-actin promoter, a chimeric intron comprising SEQ ID NO 19 (i.e., claimed SEQ ID NO 16), a CVM enhancer comprising SEQ ID NO 17, a 5’UTR and a 3’UTR, two AAV ITRs flanking the coding sequence of an NDP protein, and a kit for using the construct to treat hearing loss. App266 claim 1 recites that the coding sequence encodes NDP protein. App266 claims 105 and 106 recite an AAV2 capsid or Anc80 capsid comprising the construct.
Both claim sets are directed to constructs for gene expression in the ear, wherein the constructs comprise the same elements including a chimeric intron comprising SEQ ID NO 16 and a CVM enhancer comprising SEQ ID NO 17. App266 SEQ ID NO 17 is identical to claimed SEQ ID NO 17:
US-17-628-266-17
Query Match 100.0%; Score 380; DB 1; Length 381;
Best Local Similarity 100.0%;
Matches 380; Conservative 0; Mismatches 0; Indels 0; Gaps 0;
Qy 1 GACATTGATTATTGACTAGTTATTAATAGTAATCAATTACGGGGTCATTAGTTCATAGCC 60 SEQ ID NO 17
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 1 GACATTGATTATTGACTAGTTATTAATAGTAATCAATTACGGGGTCATTAGTTCATAGCC 60 App266 SEQ 17
Qy 61 CATATATGGAGTTCCGCGTTACATAACTTACGGTAAATGGCCCGCCTGGCTGACCGCCCA 120
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 61 CATATATGGAGTTCCGCGTTACATAACTTACGGTAAATGGCCCGCCTGGCTGACCGCCCA 120
Qy 121 ACGACCCCCGCCCATTGACGTCAATAATGACGTATGTTCCCATAGTAACGCCAATAGGGA 180
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 121 ACGACCCCCGCCCATTGACGTCAATAATGACGTATGTTCCCATAGTAACGCCAATAGGGA 180
Qy 181 CTTTCCATTGACGTCAATGGGTGGACTATTTACGGTAAACTGCCCACTTGGCAGTACATC 240
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 181 CTTTCCATTGACGTCAATGGGTGGACTATTTACGGTAAACTGCCCACTTGGCAGTACATC 240
Qy 241 AAGTGTATCATATGCCAAGTACGCCCCCTATTGACGTCAATGACGGTAAATGGCCCGCCT 300
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 241 AAGTGTATCATATGCCAAGTACGCCCCCTATTGACGTCAATGACGGTAAATGGCCCGCCT 300
Qy 301 GGCATTATGCCCAGTACATGACCTTATGGGACTTTCCTACTTGGCAGTACATCTACGTAT 360
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 301 GGCATTATGCCCAGTACATGACCTTATGGGACTTTCCTACTTGGCAGTACATCTACGTAT 360
Qy 361 TAGTCATCGCTATTACCATG 380
||||||||||||||||||||
Db 361 TAGTCATCGCTATTACCATG 380
App266 SEQ ID NO 19 is identical to claimed SEQ ID NO 16:
RESULT 1
US-17-628-266-19
Query Match 100.0%; Score 1013; DB 1; Length 1040;
Best Local Similarity 100.0%;
Matches 1013; Conservative 0; Mismatches 0; Indels 0; Gaps 0;
Qy 1 GGAGTCGCTGCGTTGCCTTCGCCCCGTGCCCCGCTCCGCGCCGCCTCGCGCCGCCCGCCC 60 SEQ ID NO 16
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 1 GGAGTCGCTGCGTTGCCTTCGCCCCGTGCCCCGCTCCGCGCCGCCTCGCGCCGCCCGCCC 60 App266 SEQ 19
Qy 61 CGGCTCTGACTGACCGCGTTACTCCCACAGGTGAGCGGGCGGGACGGCCCTTCTCCTCCG 120
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 61 CGGCTCTGACTGACCGCGTTACTCCCACAGGTGAGCGGGCGGGACGGCCCTTCTCCTCCG 120
Qy 121 GGCTGTAATTAGCGCTTGGTTTAATGACGGCTCGTTTCTTTTCTGTGGCTGCGTGAAAGC 180
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 121 GGCTGTAATTAGCGCTTGGTTTAATGACGGCTCGTTTCTTTTCTGTGGCTGCGTGAAAGC 180
Qy 181 CTTAAAGGGCTCCGGGAGGGCCCTTTGTGCGGGGGGGAGCGGCTCGGGGGGTGCGTGCGT 240
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 181 CTTAAAGGGCTCCGGGAGGGCCCTTTGTGCGGGGGGGAGCGGCTCGGGGGGTGCGTGCGT 240
Qy 241 GTGTGTGTGCGTGGGGAGCGCCGCGTGCGGCCCGCGCTGCCCGGCGGCTGTGAGCGCTGC 300
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 241 GTGTGTGTGCGTGGGGAGCGCCGCGTGCGGCCCGCGCTGCCCGGCGGCTGTGAGCGCTGC 300
Qy 301 GGGCGCGGCGCGGGGCTTTGTGCGCTCCGCGTGTGCGCGAGGGGAGCGCGGCCGGGGGCG 360
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 301 GGGCGCGGCGCGGGGCTTTGTGCGCTCCGCGTGTGCGCGAGGGGAGCGCGGCCGGGGGCG 360
Qy 361 GTGCCCCGCGGTGCGGGGGGGCTGCGAGGGGAACAAAGGCTGCGTGCGGGGTGTGTGCGT 420
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 361 GTGCCCCGCGGTGCGGGGGGGCTGCGAGGGGAACAAAGGCTGCGTGCGGGGTGTGTGCGT 420
Qy 421 GGGGGGGTGAGCAGGGGGTGTGGGCGCGGCGGTCGGGCTGTAACCCCCCCCTGCACCCCC 480
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 421 GGGGGGGTGAGCAGGGGGTGTGGGCGCGGCGGTCGGGCTGTAACCCCCCCCTGCACCCCC 480
Qy 481 CTCCCCGAGTTGCTGAGCACGGCCCGGCTTCGGGTGCGGGGCTCCGTGCGGGGCGTGGCG 540
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 481 CTCCCCGAGTTGCTGAGCACGGCCCGGCTTCGGGTGCGGGGCTCCGTGCGGGGCGTGGCG 540
Qy 541 CGGGGCTCGCCGTGCCGGGCGGGGGGTGGCGGCAGGTGGGGGTGCCGGGCGGGGCGGGGC 600
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 541 CGGGGCTCGCCGTGCCGGGCGGGGGGTGGCGGCAGGTGGGGGTGCCGGGCGGGGCGGGGC 600
Qy 601 CGCCTCGGGCCGGGGAGGGCTCGGGGGAGGGGCGCGGCGGCCCCCGGAGCGCCGGCGGCT 660
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 601 CGCCTCGGGCCGGGGAGGGCTCGGGGGAGGGGCGCGGCGGCCCCCGGAGCGCCGGCGGCT 660
Qy 661 GTCGAGGCGCGGCGAGCCGCAGCCATTGCCTTTTATGGTAATCGTGCGAGAGGGCGCAGG 720
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 661 GTCGAGGCGCGGCGAGCCGCAGCCATTGCCTTTTATGGTAATCGTGCGAGAGGGCGCAGG 720
Qy 721 GACTTCCTTTGTCCCAAATCTGTGCGGAGCCGAAATCTGGGAGGCGCCGCCGCACCCCCT 780
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 721 GACTTCCTTTGTCCCAAATCTGTGCGGAGCCGAAATCTGGGAGGCGCCGCCGCACCCCCT 780
Qy 781 CTAGCGGGCGCGGGGCGAAGCGGTGCGGCGCCGGCAGGAAGGAAATGGGCGGGGAGGGCC 840
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 781 CTAGCGGGCGCGGGGCGAAGCGGTGCGGCGCCGGCAGGAAGGAAATGGGCGGGGAGGGCC 840
Qy 841 TTCGTGCGTCGCCGCGCCGCCGTCCCCTTCTCCCTCTCCAGCCTCGGGGCTGTCCGCGGG 900
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 841 TTCGTGCGTCGCCGCGCCGCCGTCCCCTTCTCCCTCTCCAGCCTCGGGGCTGTCCGCGGG 900
Qy 901 GGGACGGCTGCCTTCGGGGGGGACGGGGCAGGGCGGGGTTCGGCTTCTGGCGTGTGACCG 960
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 901 GGGACGGCTGCCTTCGGGGGGGACGGGGCAGGGCGGGGTTCGGCTTCTGGCGTGTGACCG 960
Qy 961 GCGGCTCTAGAGCCTCTGCTAACCATGTTCATGCCTTCTTCTTTTTCCTACAG 1013
|||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 961 GCGGCTCTAGAGCCTCTGCTAACCATGTTCATGCCTTCTTCTTTTTCCTACAG 1013
Therefore the App266 claims recite elements (i), (ii), (iii), (iv), (v), (vii) and (ix) of the claimed invention. Then the other prior art teaches the other claim elements that the App266 claims do not recite:
The App266 claims recite the construct encodes a different protein than CLRN1, but WO900 (¶99) teaches an rAAV vector comprising the CLRN1 cDNA. WO900 teaches (¶9-10) the polynucleotide (polynt) can include a sequence having SEQ ID NO 2 (which it specifies comprises a 5’UTR and 3’UTR) and can be included on a vector that can be an adeno-associated viral vector (AAV) that can be used for transfecting ocular cells or cells of the inner ear.
WO900 SEQ ID NO 2 comprises a polynt comprising a sequence encoding the amino acid sequence of claimed SEQ ID NO 3 (which has been back-translated from AA[Wingdings font/0xE0]nucleotides). This is shown by the following sequence alignment:
RESULT 7
BDA01054
ID BDA01054 standard; cDNA; 2352 BP.
XX
AC BDA01054;
XX
DT 16-JUN-2016 (first entry)
XX
DE Human derived clarin-1 (CLRN1) polynucleotide SEQ ID NO:2.
XX
KW CLRN1 gene; auditory; clarin-1; gene therapy; hearing loss;
KW ophthalmological; ss; therapeutic; usher syndrome iii; vision disorder.
XX
OS Homo sapiens.
XX
CC PN WO2016073900-A1.
XX
CC PD 12-MAY-2016.
XX
CC PF 06-NOV-2015; 2015WO-US059546.
XX
PR 06-NOV-2014; 2014US-0076114P.
PR 08-MAY-2015; 2015US-0158846P.
XX
CC PA (UCWR ) UNIV CASE WESTERN RESERVE.
XX
CC PI Alagramam KN;
XX
DR WPI; 2016-282935/37.
XX
CC PT New polynucleotide comprising a nucleic acid sequence that includes a
CC PT cDNA coding sequence of a clarin-1 gene, useful for treating vision
CC PT and/or hearing loss associated with Usher syndrome III.
XX
CC PS Claim 9; SEQ ID NO 2; 43pp; English.
XX
CC The invention relates to a novel polynucleotide, used for treating vision
CC and/or hearing loss associated with Usher syndrome III. This
CC polynucleotide comprises a nucleic acid sequence that includes a cDNA
CC coding sequence of a clarin-1 (CLRN1) gene and a 3' untranslated region
CC (UTR) nucleic acid that is derived from the 3' UTR of the clarin-1 gene,
CC where the 3' UTR nucleic acid enhances expression of clarin-1 in a cell
CC transfected with the polynucleotide compared to a cell transfected with a
CC similar polynucleotide devoid of the 3' UTR nucleic acid. The invention
CC further claims: a nucleic acid construct comprising a polynucleotide
CC defined above; a vector for transfecting a cell, comprising a
CC polynucleotide defined above, where the transfected cell expresses clarin
CC -1; and a method of treating vision and/or hearing loss associated with
CC Usher syndrome III in a subject by administering to the ocular cells
CC and/or cells of the inner ear of the subject, a vector that promotes
CC expression of clarin-1 in the cells. The present sequence is a clarin-1
CC polynucleotide, used for treating vision and/or hearing loss associated
CC with Usher syndrome III in a subject.
XX
SQ Sequence 2352 BP; 705 A; 475 C; 484 G; 688 T; 0 U; 0 Other;
Alignment Scores:
Length: 2352
Score: 1214.00 Matches: 232
Percent Similarity: 100.0% Conservative: 0
Best Local Similarity: 100.0% Mismatches: 0
Query Match: 100.0% Indels: 0
Gaps: 0
US-17-253-658-3 (1-232) x BDA01054 (1-2352)
Qy 1 MetProSerGlnGlnLysLysIleIlePheCysMetAlaGlyValPheSerPheAlaCys 20 SEQ ID NO 3 translated[Wingdings font/0xE0]NT
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 282 ATGCCAAGCCAACAGAAGAAAATCATTTTTTGCATGGCCGGAGTGTTCAGTTTTGCATGT 341 WO900 SEQ ID NO 2
Qy 21 AlaLeuGlyValValThrAlaLeuGlyThrProLeuTrpIleLysAlaThrValLeuCys 40
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 342 GCCCTCGGAGTTGTGACAGCCTTGGGGACACCGTTGTGGATCAAAGCCACTGTCCTCTGC 401
Qy 41 LysThrGlyAlaLeuLeuValAsnAlaSerGlyGlnGluLeuAspLysPheMetGlyGlu 60
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 402 AAAACGGGAGCTCTGCTCGTCAATGCCTCAGGGCAGGAGCTGGACAAGTTTATGGGTGAA 461
Qy 61 MetGlnTyrGlyLeuPheHisGlyGluGlyValArgGlnCysGlyLeuGlyAlaArgPro 80
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 462 ATGCAGTACGGGCTTTTCCACGGAGAGGGTGTGAGGCAGTGTGGGTTGGGAGCAAGGCCC 521
Qy 81 PheArgPheSerPhePheProAspLeuLeuLysAlaIleProValSerIleHisValAsn 100
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 522 TTTCGGTTCTCATTTTTTCCAGATTTGCTCAAAGCAATCCCAGTGAGCATCCACGTCAAT 581
Qy 101 ValIleLeuPheSerAlaIleLeuIleValLeuThrMetValGlyThrAlaPhePheMet 120
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 582 GTCATTCTCTTCTCTGCCATCCTTATTGTGTTAACCATGGTGGGGACAGCCTTCTTCATG 641
Qy 121 TyrAsnAlaPheGlyLysProPheGluThrLeuHisGlyProLeuGlyLeuTyrLeuLeu 140
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 642 TACAATGCTTTTGGAAAACCTTTTGAAACTCTGCATGGTCCCCTAGGGCTGTACCTTTTG 701
Qy 141 SerPheIleSerGlySerCysGlyCysLeuValMetIleLeuPheAlaSerGluValLys 160
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 702 AGCTTCATTTCAGGCTCCTGTGGCTGTCTTGTCATGATATTGTTTGCCTCTGAAGTGAAA 761
Qy 161 IleHisHisLeuSerGluLysIleAlaAsnTyrLysGluGlyThrTyrValTyrLysThr 180
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 762 ATCCATCACCTCTCAGAAAAAATTGCAAATTATAAAGAAGGGACTTATGTCTACAAAACG 821
Qy 181 GlnSerGluLysTyrThrThrSerPheTrpValIlePhePheCysPhePheValHisPhe 200
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 822 CAAAGTGAAAAATATACCACCTCATTCTGGGTCATTTTCTTTTGCTTTTTTGTTCATTTT 881
Qy 201 LeuAsnGlyLeuLeuIleArgLeuAlaGlyPheGlnPheProPheAlaLysSerLysAsp 220
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 882 CTGAATGGGCTCCTAATACGACTTGCTGGATTTCAGTTCCCTTTTGCAAAATCTAAAGAC 941
Qy 221 AlaGluThrThrAsnValAlaAlaAspLeuMetTyr 232
||||||||||||||||||||||||||||||||||||
Db 942 GCAGAAACAACTAATGTAGCTGCAGATCTAATGTAC 977
That alignment shows that the composition of WO900 comprises element (vi) of the instant claims. WO900 teaches (¶10-11) treating retinal cells.
Powell teaches (§Polyadenylation Signal Sequences and Upstream Enhancer) one study, in human epithelial-like cells, found that a transgene had a 2.5-fold increase in expression with … bovine growth hormone polyA (bGHpA) signal sequences compared to a minimal synthetic polyA (SPA) signal.
App178 teaches SEQ ID NO 30 which comprises a bovine growth hormone polyA signal and is 100% identical to claimed SEQ ID NO 20, as shown by the following sequence alignment:
RESULT 1
AXQ64086
(NOTE: this sequence has 272 duplicates in the database searched.
See complete list at the end of this report)
ID AXQ64086 standard; DNA; 225 BP.
XX
AC AXQ64086;
XX
DT 29-OCT-2009 (first entry)
XX
DE BGH polyA Yes1 supplementary expression cassette 3' UTR, SEQ:30 #2.
XX
KW 3'-utr; Yes1; dna cassette; gene expression; gene silencing;
KW protein production; rna interference; ss.
XX
OS Bos taurus.
OS Synthetic.
XX
CC PN US2009215178-A1.
XX
CC PD 27-AUG-2009.
XX
CC PF 22-FEB-2008; 2008US-00035437.
XX
PR 22-FEB-2008; 2008US-00035437.
XX
CC PA (TANG/) TANG Z.
XX
CC PI Tang Z;
XX
DR WPI; 2009-M96179/59.
XX
CC PT Generating cell clones with stable transgene (Gene of Interest (GOI))
CC PT expression comprises inactivation of endogenous essential genes of cell
CC PT substrate and trans-complementation of essential genes products.
XX
CC PS Example 3; SEQ ID NO 30; 9pp; English.
XX
CC The present invention relates to a method for generating cell clones with
CC stable transgene (Gene Of Interest (GOI)) expression. The method of the
CC invention comprises: (i) inactivation of endogenous essential genes of
CC cell substrate through Gene Inactivation Cassettes (GIC), (ii) trans-
CC complementation of essential gene products through Gene Supplementary
CC Cassettes (GSC), alternatively, the cassette codes for the gene product
CC that is capable of inactivating GIC function, (iii) the GOI expression
CC cassettes are preferably, physically linked to GSC to take advantage of
CC favourable selective pressure, (iv) GIC could be preferably physically
CC linked to GSC and GOI expression cassettes, where the endogenous
CC essential genes of cell substrate refer to genes or combination of genes
CC that are essential for cell survival and / or cell proliferation. The GIC
CC comprises a vector comprising a promoter operably linked to RNA
CC interference, RNAi (shRNA) / dsRNA / ribozyme molecule, or tandem repeats
CC of such transcript units, targeted to cell endogenous essential mRNA. The
CC invention provides strategies for increasing the productivity of
CC recombinant protein expression in isogenic cell-lines, and a novel
CC selection system for the improved stability and homogeneity of transgene
CC expression in isogenic cells without dependence on continuous selective
CC drugs. An example of the invention provides an essential gene knock-down
CC cassette, targeted at 3' UTR of human endogenous Yes1 gene, and a
CC supplementary Yes1 expression cassette which uses a 3' UTR from bovine
CC growth hormone (BGH) polyA. The present sequence is a bovine growth
CC hormone (BGH) polyA Yes1 supplementary expression cassette 3' UTR, used
CC in an example of the invention. Note: This version of SEQ ID 30 is given
CC in example 3, but it is not the same as the sequence referred to as SEQ
CC ID 30 (seeAXQ61560) in the sequence listing.
XX
SQ Sequence 225 BP; 41 A; 53 C; 72 G; 59 T; 0 U; 0 Other;
Query Match 100.0%; Score 225; Length 225;
Best Local Similarity 100.0%;
Matches 225; Conservative 0; Mismatches 0; Indels 0; Gaps 0;
Qy 1 CTGTGCCTTCTAGTTGCCAGCCATCTGTTGTTTGCCCCTCCCCCGTGCCTTCCTTGACCC 60 SEQ ID NO 20
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 1 CTGTGCCTTCTAGTTGCCAGCCATCTGTTGTTTGCCCCTCCCCCGTGCCTTCCTTGACCC 60 Prior art SEQ
Qy 61 TGGAAGGTGCCACTCCCACTGTCCTTTCCTAATAAAATGAGGAAATTGCATCGCATTGTC 120
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 61 TGGAAGGTGCCACTCCCACTGTCCTTTCCTAATAAAATGAGGAAATTGCATCGCATTGTC 120
Qy 121 TGAGTAGGTGTCATTCTATTCTGGGGGGTGGGGTGGGGCAGGACAGCAAGGGGGAGGATT 180
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 121 TGAGTAGGTGTCATTCTATTCTGGGGGGTGGGGTGGGGCAGGACAGCAAGGGGGAGGATT 180
Qy 181 GGGAAGACAATAGCAGGCATGCTGGGGATGCGGTGGGCTCTATGG 225
|||||||||||||||||||||||||||||||||||||||||||||
Db 181 GGGAAGACAATAGCAGGCATGCTGGGGATGCGGTGGGCTCTATGG 225
The App266 claims do not recite a kit that comprises a pre-loaded syringe. However, US952 teaches (Col 11 L3-15) a kit that comprises nucleic acid compounds within a container of solution and that the kit can comprise a pre-loaded syringe comprising the compounds. An artisan would have put their compounds into a kit comprising a pre-loaded syringe for the benefit of ensuring that the recipient has the exact dosage ready to administer and because doing so would have prevented any complications that arise from mixing a solution and then getting the mixed solution into a syringe.
Therefore it would have been obvious to use WO900’s SEQ ID NO 2 with the expression construct of App266 in order to express CLRN1. An artisan would have known that using WO900’s sequence and teachings with the invention recited in the App266 claims and modified by the teachings of Powell, App178, and US952 would have provided a benefit of treating hearing or vision loss because WO900 teaches that (¶11). Using the bovine growth hormone polyA signal of App178 would have been of benefit based on the teachings of Powell. Packaging it into a pre-loaded syringe would also have been of benefit as taught by US952. There is no reason why the invention of the App266 claims are exclusively for expression of secreted proteins. Using WO900’s sequence and teachings with the invention recited in the App266 claims and modified by the teachings of Powell, App178, and US952 would have produced the instant invention.
This is a provisional nonstatutory double patenting rejection.
Claims 229-232, 247-254, and 256-270 are rejected on the ground of nonstatutory double patenting as being unpatentable over claims 1-2, 4-6, 8-9, and 11-13 of US Pat. No. 12365726 (reference application; “US726”) in view of WO900 and US952. This rejection is maintained and updated in response to the claim amendments. All supporting references are of record.
Although the claims at issue are not identical, they are not patentably distinct from each other because both claim sets are directed to methods and compositions of gene therapies for expressing a gene of interest in the inner ear to treat hearing loss. The instant claims recite a composition comprising an AAV nucleic acid vector wherein the vector comprises a 5’ ITR, a CMV enhancer, a CBA promoter, a chimeric intron, a 5’UTR, a coding sequence (CDS) encoding a CLRN1 protein according to SEQ ID NO 3, a 3’UTR, a polyA signal, and a 3’ITR, wherein the CDS comprises a nt sequence spanning 2 consecutive exons of CLRN1 genomic DNA and lacks an intron sequence between them; wherein the composition can comprise other components such as SEQ ID NOs 16-17 or 20; to the composition comprising an excipient; to an AAV2 capsid comprising the composition, to an Anc80 capsid comprising the composition; to a kit comprising the composition; and to methods of introducing it to a cochlea of a mammal that can be a human who can have been previously identified as having a defective endogenous CLRN1 gene; to methods of increasing CLRN1 expression in the ear or eye; and to methods of treating hearing or vision loss.
The US726claims recite an AAV particle comprising a nucleic acid construct according to SEQ ID NO 91 or 92 and an AAV capsid, wherein the capsid can be an AAV2 capsid or an Anc80 capsid; and a kit and composition comprising the particle. An artisan would not know what are SEQ ID NO 91 or 92 but they would consult the Spec. (¶29, ) and SEQ listing and find that those SEQ ID NOs comprise a 5’ITR, a CMV enhancer comprising claimed SEQ ID NO 17, a CBA promoter, a chimeric intron according claimed SEQ ID NO 16, a coding sequence, and a 3’ITR.
Both claim sets are directed to AAV constructs for gene expression, wherein the constructs comprise the same elements including a chimeric intron comprising SEQ ID NO 16 and a CVM enhancer comprising SEQ ID NO 17 and a polyA sequence comprising SEQ ID NO 20. US726 SEQ ID NOs 91 and 92 comprise regions identical to claimed SEQ ID NOs 17, 16, and 20:
RESULT 1
US-18-134-095-91
Query Match 100.0%; Score 380; DB 1; Length 3847;
Best Local Similarity 100.0%;
Matches 380; Conservative 0; Mismatches 0; Indels 0; Gaps 0;
Qy 1 GACATTGATTATTGACTAGTTATTAATAGTAATCAATTACGGGGTCATTAGTTCATAGCC 60 SEQ ID NO 17
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 168 GACATTGATTATTGACTAGTTATTAATAGTAATCAATTACGGGGTCATTAGTTCATAGCC 227 US726 SEQ 91
Qy 61 CATATATGGAGTTCCGCGTTACATAACTTACGGTAAATGGCCCGCCTGGCTGACCGCCCA 120
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 228 CATATATGGAGTTCCGCGTTACATAACTTACGGTAAATGGCCCGCCTGGCTGACCGCCCA 287
Qy 121 ACGACCCCCGCCCATTGACGTCAATAATGACGTATGTTCCCATAGTAACGCCAATAGGGA 180
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 288 ACGACCCCCGCCCATTGACGTCAATAATGACGTATGTTCCCATAGTAACGCCAATAGGGA 347
Qy 181 CTTTCCATTGACGTCAATGGGTGGACTATTTACGGTAAACTGCCCACTTGGCAGTACATC 240
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 348 CTTTCCATTGACGTCAATGGGTGGACTATTTACGGTAAACTGCCCACTTGGCAGTACATC 407
Qy 241 AAGTGTATCATATGCCAAGTACGCCCCCTATTGACGTCAATGACGGTAAATGGCCCGCCT 300
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 408 AAGTGTATCATATGCCAAGTACGCCCCCTATTGACGTCAATGACGGTAAATGGCCCGCCT 467
Qy 301 GGCATTATGCCCAGTACATGACCTTATGGGACTTTCCTACTTGGCAGTACATCTACGTAT 360
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 468 GGCATTATGCCCAGTACATGACCTTATGGGACTTTCCTACTTGGCAGTACATCTACGTAT 527
Qy 361 TAGTCATCGCTATTACCATG 380
||||||||||||||||||||
Db 528 TAGTCATCGCTATTACCATG 547
SEQ ID NO 16:
RESULT 1
US-18-134-095-91
Query Match 100.0%; Score 1013; DB 1; Length 3847;
Best Local Similarity 100.0%;
Matches 1013; Conservative 0; Mismatches 0; Indels 0; Gaps 0;
Qy 1 GGAGTCGCTGCGTTGCCTTCGCCCCGTGCCCCGCTCCGCGCCGCCTCGCGCCGCCCGCCC 60 SEQ ID NO 16
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 828 GGAGTCGCTGCGTTGCCTTCGCCCCGTGCCCCGCTCCGCGCCGCCTCGCGCCGCCCGCCC 887 US726 SEQ 91
Qy 61 CGGCTCTGACTGACCGCGTTACTCCCACAGGTGAGCGGGCGGGACGGCCCTTCTCCTCCG 120
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 888 CGGCTCTGACTGACCGCGTTACTCCCACAGGTGAGCGGGCGGGACGGCCCTTCTCCTCCG 947
Qy 121 GGCTGTAATTAGCGCTTGGTTTAATGACGGCTCGTTTCTTTTCTGTGGCTGCGTGAAAGC 180
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 948 GGCTGTAATTAGCGCTTGGTTTAATGACGGCTCGTTTCTTTTCTGTGGCTGCGTGAAAGC 1007
Qy 181 CTTAAAGGGCTCCGGGAGGGCCCTTTGTGCGGGGGGGAGCGGCTCGGGGGGTGCGTGCGT 240
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 1008 CTTAAAGGGCTCCGGGAGGGCCCTTTGTGCGGGGGGGAGCGGCTCGGGGGGTGCGTGCGT 1067
Qy 241 GTGTGTGTGCGTGGGGAGCGCCGCGTGCGGCCCGCGCTGCCCGGCGGCTGTGAGCGCTGC 300
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 1068 GTGTGTGTGCGTGGGGAGCGCCGCGTGCGGCCCGCGCTGCCCGGCGGCTGTGAGCGCTGC 1127
Qy 301 GGGCGCGGCGCGGGGCTTTGTGCGCTCCGCGTGTGCGCGAGGGGAGCGCGGCCGGGGGCG 360
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 1128 GGGCGCGGCGCGGGGCTTTGTGCGCTCCGCGTGTGCGCGAGGGGAGCGCGGCCGGGGGCG 1187
Qy 361 GTGCCCCGCGGTGCGGGGGGGCTGCGAGGGGAACAAAGGCTGCGTGCGGGGTGTGTGCGT 420
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 1188 GTGCCCCGCGGTGCGGGGGGGCTGCGAGGGGAACAAAGGCTGCGTGCGGGGTGTGTGCGT 1247
Qy 421 GGGGGGGTGAGCAGGGGGTGTGGGCGCGGCGGTCGGGCTGTAACCCCCCCCTGCACCCCC 480
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 1248 GGGGGGGTGAGCAGGGGGTGTGGGCGCGGCGGTCGGGCTGTAACCCCCCCCTGCACCCCC 1307
Qy 481 CTCCCCGAGTTGCTGAGCACGGCCCGGCTTCGGGTGCGGGGCTCCGTGCGGGGCGTGGCG 540
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 1308 CTCCCCGAGTTGCTGAGCACGGCCCGGCTTCGGGTGCGGGGCTCCGTGCGGGGCGTGGCG 1367
Qy 541 CGGGGCTCGCCGTGCCGGGCGGGGGGTGGCGGCAGGTGGGGGTGCCGGGCGGGGCGGGGC 600
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 1368 CGGGGCTCGCCGTGCCGGGCGGGGGGTGGCGGCAGGTGGGGGTGCCGGGCGGGGCGGGGC 1427
Qy 601 CGCCTCGGGCCGGGGAGGGCTCGGGGGAGGGGCGCGGCGGCCCCCGGAGCGCCGGCGGCT 660
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 1428 CGCCTCGGGCCGGGGAGGGCTCGGGGGAGGGGCGCGGCGGCCCCCGGAGCGCCGGCGGCT 1487
Qy 661 GTCGAGGCGCGGCGAGCCGCAGCCATTGCCTTTTATGGTAATCGTGCGAGAGGGCGCAGG 720
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 1488 GTCGAGGCGCGGCGAGCCGCAGCCATTGCCTTTTATGGTAATCGTGCGAGAGGGCGCAGG 1547
Qy 721 GACTTCCTTTGTCCCAAATCTGTGCGGAGCCGAAATCTGGGAGGCGCCGCCGCACCCCCT 780
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 1548 GACTTCCTTTGTCCCAAATCTGTGCGGAGCCGAAATCTGGGAGGCGCCGCCGCACCCCCT 1607
Qy 781 CTAGCGGGCGCGGGGCGAAGCGGTGCGGCGCCGGCAGGAAGGAAATGGGCGGGGAGGGCC 840
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 1608 CTAGCGGGCGCGGGGCGAAGCGGTGCGGCGCCGGCAGGAAGGAAATGGGCGGGGAGGGCC 1667
Qy 841 TTCGTGCGTCGCCGCGCCGCCGTCCCCTTCTCCCTCTCCAGCCTCGGGGCTGTCCGCGGG 900
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 1668 TTCGTGCGTCGCCGCGCCGCCGTCCCCTTCTCCCTCTCCAGCCTCGGGGCTGTCCGCGGG 1727
Qy 901 GGGACGGCTGCCTTCGGGGGGGACGGGGCAGGGCGGGGTTCGGCTTCTGGCGTGTGACCG 960
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 1728 GGGACGGCTGCCTTCGGGGGGGACGGGGCAGGGCGGGGTTCGGCTTCTGGCGTGTGACCG 1787
Qy 961 GCGGCTCTAGAGCCTCTGCTAACCATGTTCATGCCTTCTTCTTTTTCCTACAG 1013
|||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 1788 GCGGCTCTAGAGCCTCTGCTAACCATGTTCATGCCTTCTTCTTTTTCCTACAG 1840
SEQ ID NO 20:
RESULT 1
US-18-134-095-92
Query Match 100.0%; Score 225; DB 1; Length 3845;
Best Local Similarity 100.0%;
Matches 225; Conservative 0; Mismatches 0; Indels 0; Gaps 0;
Qy 1 CTGTGCCTTCTAGTTGCCAGCCATCTGTTGTTTGCCCCTCCCCCGTGCCTTCCTTGACCC 60 SEQ ID NO 20
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 3438 CTGTGCCTTCTAGTTGCCAGCCATCTGTTGTTTGCCCCTCCCCCGTGCCTTCCTTGACCC 3497 US726 SEQ 92
Qy 61 TGGAAGGTGCCACTCCCACTGTCCTTTCCTAATAAAATGAGGAAATTGCATCGCATTGTC 120
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 3498 TGGAAGGTGCCACTCCCACTGTCCTTTCCTAATAAAATGAGGAAATTGCATCGCATTGTC 3557
Qy 121 TGAGTAGGTGTCATTCTATTCTGGGGGGTGGGGTGGGGCAGGACAGCAAGGGGGAGGATT 180
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 3558 TGAGTAGGTGTCATTCTATTCTGGGGGGTGGGGTGGGGCAGGACAGCAAGGGGGAGGATT 3617
Qy 181 GGGAAGACAATAGCAGGCATGCTGGGGATGCGGTGGGCTCTATGG 225
|||||||||||||||||||||||||||||||||||||||||||||
Db 3618 GGGAAGACAATAGCAGGCATGCTGGGGATGCGGTGGGCTCTATGG 3662
Therefore the US726 claims recite elements (i), (ii), (iii), (iv), (viii), and (ix) of the claimed invention. Then the other prior art teaches the other claim elements that the US726 claims do not recite, including a sequence encoding CLRN1:
WO900 teaches (¶99) an rAAV vector comprising the CLRN1 cDNA including the 5’ and 3’UTRs, and teaches driving it with the chicken β-actin promoter. WO900 teaches (¶9-10) the polynucleotide (polynt) can include a sequence having SEQ ID NO 2 (which it specifies comprises a 5’UTR and 3’UTR) and can be included on a vector that can be an adeno-associated viral vector (AAV) that can be used for transfecting ocular cells or cells of the inner ear. WO900 teaches (¶21) that the heterologous polynucleotide comprised in the AAV vector is flanked by at least one, and generally by two AAV inverted terminal repeat sequence (ITRs); an artisan would realize that being flanked by two ITRs refers to one ITR on either side, which is a 5’ITR and a 3’ITR.
WO900 SEQ ID NO 2 comprises a polynt comprising a sequence encoding the amino acid sequence of claimed SEQ ID NO 3 (which has been back-translated from AA[Wingdings font/0xE0]nucleotides). This is shown by the following sequence alignment:
RESULT 7
BDA01054
ID BDA01054 standard; cDNA; 2352 BP.
XX
AC BDA01054;
XX
DT 16-JUN-2016 (first entry)
XX
DE Human derived clarin-1 (CLRN1) polynucleotide SEQ ID NO:2.
XX
KW CLRN1 gene; auditory; clarin-1; gene therapy; hearing loss;
KW ophthalmological; ss; therapeutic; usher syndrome iii; vision disorder.
XX
OS Homo sapiens.
XX
CC PN WO2016073900-A1.
XX
CC PD 12-MAY-2016.
XX
CC PF 06-NOV-2015; 2015WO-US059546.
XX
PR 06-NOV-2014; 2014US-0076114P.
PR 08-MAY-2015; 2015US-0158846P.
XX
CC PA (UCWR ) UNIV CASE WESTERN RESERVE.
XX
CC PI Alagramam KN;
XX
DR WPI; 2016-282935/37.
XX
CC PT New polynucleotide comprising a nucleic acid sequence that includes a
CC PT cDNA coding sequence of a clarin-1 gene, useful for treating vision
CC PT and/or hearing loss associated with Usher syndrome III.
XX
CC PS Claim 9; SEQ ID NO 2; 43pp; English.
XX
CC The invention relates to a novel polynucleotide, used for treating vision
CC and/or hearing loss associated with Usher syndrome III. This
CC polynucleotide comprises a nucleic acid sequence that includes a cDNA
CC coding sequence of a clarin-1 (CLRN1) gene and a 3' untranslated region
CC (UTR) nucleic acid that is derived from the 3' UTR of the clarin-1 gene,
CC where the 3' UTR nucleic acid enhances expression of clarin-1 in a cell
CC transfected with the polynucleotide compared to a cell transfected with a
CC similar polynucleotide devoid of the 3' UTR nucleic acid. The invention
CC further claims: a nucleic acid construct comprising a polynucleotide
CC defined above; a vector for transfecting a cell, comprising a
CC polynucleotide defined above, where the transfected cell expresses clarin
CC -1; and a method of treating vision and/or hearing loss associated with
CC Usher syndrome III in a subject by administering to the ocular cells
CC and/or cells of the inner ear of the subject, a vector that promotes
CC expression of clarin-1 in the cells. The present sequence is a clarin-1
CC polynucleotide, used for treating vision and/or hearing loss associated
CC with Usher syndrome III in a subject.
XX
SQ Sequence 2352 BP; 705 A; 475 C; 484 G; 688 T; 0 U; 0 Other;
Alignment Scores:
Length: 2352
Score: 1214.00 Matches: 232
Percent Similarity: 100.0% Conservative: 0
Best Local Similarity: 100.0% Mismatches: 0
Query Match: 100.0% Indels: 0
Gaps: 0
US-17-253-658-3 (1-232) x BDA01054 (1-2352)
Qy 1 MetProSerGlnGlnLysLysIleIlePheCysMetAlaGlyValPheSerPheAlaCys 20 SEQ ID NO 3 translated[Wingdings font/0xE0]NT
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 282 ATGCCAAGCCAACAGAAGAAAATCATTTTTTGCATGGCCGGAGTGTTCAGTTTTGCATGT 341 WO900 SEQ ID NO 2
Qy 21 AlaLeuGlyValValThrAlaLeuGlyThrProLeuTrpIleLysAlaThrValLeuCys 40
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 342 GCCCTCGGAGTTGTGACAGCCTTGGGGACACCGTTGTGGATCAAAGCCACTGTCCTCTGC 401
Qy 41 LysThrGlyAlaLeuLeuValAsnAlaSerGlyGlnGluLeuAspLysPheMetGlyGlu 60
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 402 AAAACGGGAGCTCTGCTCGTCAATGCCTCAGGGCAGGAGCTGGACAAGTTTATGGGTGAA 461
Qy 61 MetGlnTyrGlyLeuPheHisGlyGluGlyValArgGlnCysGlyLeuGlyAlaArgPro 80
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 462 ATGCAGTACGGGCTTTTCCACGGAGAGGGTGTGAGGCAGTGTGGGTTGGGAGCAAGGCCC 521
Qy 81 PheArgPheSerPhePheProAspLeuLeuLysAlaIleProValSerIleHisValAsn 100
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 522 TTTCGGTTCTCATTTTTTCCAGATTTGCTCAAAGCAATCCCAGTGAGCATCCACGTCAAT 581
Qy 101 ValIleLeuPheSerAlaIleLeuIleValLeuThrMetValGlyThrAlaPhePheMet 120
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 582 GTCATTCTCTTCTCTGCCATCCTTATTGTGTTAACCATGGTGGGGACAGCCTTCTTCATG 641
Qy 121 TyrAsnAlaPheGlyLysProPheGluThrLeuHisGlyProLeuGlyLeuTyrLeuLeu 140
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 642 TACAATGCTTTTGGAAAACCTTTTGAAACTCTGCATGGTCCCCTAGGGCTGTACCTTTTG 701
Qy 141 SerPheIleSerGlySerCysGlyCysLeuValMetIleLeuPheAlaSerGluValLys 160
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 702 AGCTTCATTTCAGGCTCCTGTGGCTGTCTTGTCATGATATTGTTTGCCTCTGAAGTGAAA 761
Qy 161 IleHisHisLeuSerGluLysIleAlaAsnTyrLysGluGlyThrTyrValTyrLysThr 180
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 762 ATCCATCACCTCTCAGAAAAAATTGCAAATTATAAAGAAGGGACTTATGTCTACAAAACG 821
Qy 181 GlnSerGluLysTyrThrThrSerPheTrpValIlePhePheCysPhePheValHisPhe 200
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 822 CAAAGTGAAAAATATACCACCTCATTCTGGGTCATTTTCTTTTGCTTTTTTGTTCATTTT 881
Qy 201 LeuAsnGlyLeuLeuIleArgLeuAlaGlyPheGlnPheProPheAlaLysSerLysAsp 220
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 882 CTGAATGGGCTCCTAATACGACTTGCTGGATTTCAGTTCCCTTTTGCAAAATCTAAAGAC 941
Qy 221 AlaGluThrThrAsnValAlaAlaAspLeuMetTyr 232
||||||||||||||||||||||||||||||||||||
Db 942 GCAGAAACAACTAATGTAGCTGCAGATCTAATGTAC 977
That alignment shows that the composition of WO900 comprises SEQ ID NO 3 itself, a 5’UTR, and a 3’UTR. Those are elements (v), (vi), and (vii) of the instant claims. WO900 teaches (¶10-11) treating retinal cells.
The US726 claims do not recite a kit that comprises a pre-loaded syringe. However, US952 teaches (Col 11 L3-15) a kit that comprises nucleic acid compounds within a container of solution and that the kit can comprise a pre-loaded syringe comprising the compounds. An artisan would have put their compounds into a kit comprising a pre-loaded syringe for the benefit of ensuring that the recipient has the exact dosage ready to administer and because doing so would have prevented any complications that arise from mixing a solution and then getting the mixed solution into a syringe.
Therefore it would have been obvious to use WO900’s SEQ ID NO 2 with the AAV particle of US726 in order to express CLRN1. An artisan would have known that using WO900’s sequence and teachings with the invention recited in the US726 claims and modified by the teachings of WO900 and US952 would have provided a benefit of treating hearing or vision loss because WO900 teaches that (¶11), and it would have been a simple matter to swap the sequence encoding CLRN1 of WO900 for the sequence encoding a VEGF antibody of the US726 claims. Packaging it into a pre-loaded syringe would also have been of benefit as taught by US952. Using WO900’s sequence and teachings with the invention recited in the US726 claims and modified by the teachings of US952 would have produced the instant invention.
Therefore the instant claims would have been obvious in view of the US726 claims, WO900, and US952.
Claims 229-232, 247-254, and 256-270 are provisionally rejected on the ground of nonstatutory double patenting as being unpatentable over claims 103-127 of copending Application No. 18696131 (reference application; “App131”) in view of Powell, WO900, Landegger (et al. 2017. A synthetic AAV vector enables safe and efficient gene transfer to the mammalian inner ear. Nat. Biotechnol. 35[3]:280-286, “Landegger”, of record on IDS), App178, and US952. This rejection is maintained and updated in response to the claim amendments. All supporting references are of record.
Although the claims at issue are not identical, they are not patentably distinct from each other because both claim sets are directed to methods and compositions of gene therapies for expressing a gene of interest in the inner ear to treat hearing loss. The instant claims recite a composition comprising an AAV nucleic acid vector wherein the vector comprises a 5’ ITR, a CMV enhancer, a CBA promoter, a chimeric intron, a 5’UTR, a coding sequence (CDS) encoding a CLRN1 protein according to SEQ ID NO 3, a 3’UTR, a polyA signal, and a 3’ITR, wherein the CDS comprises a nt sequence spanning 2 consecutive exons of CLRN1 genomic DNA and lacks an intron sequence between them; wherein the composition can comprise other components such as SEQ ID NOs 16-17 or 20; to the composition comprising an excipient; to an AAV2 capsid comprising the composition, to an Anc80 capsid comprising the composition; to a kit comprising the composition; and to methods of introducing it to a cochlea of a mammal that can be a human who can have been previously identified as having a defective endogenous CLRN1 gene; to methods of increasing CLRN1 expression in the ear or eye; and to methods of treating hearing or vision loss.
The App131 claims recite a composition comprising a construct, wherein the construct comprises a coding sequence encoding Kv7.4 protein and can comprise SEQ ID NO 333, an AAV particle comprising the construct, and methods of administering the AAV to a cochlea. An artisan would not know what is SEQ ID NO 333 but they would consult the SEQ listing and find that it comprises a 5’ITR, a CMV enhancer comprising claimed SEQ ID NO 17, a CBA promoter, a chimeric intron according claimed SEQ ID NO 16, a coding sequence, and a 3’ITR.
Both claim sets are directed to constructs for gene expression in the cochlea, wherein the constructs comprise the same elements including a chimeric intron comprising SEQ ID NO 19 and a CVM enhancer comprising SEQ ID NO 17. App131 SEQ ID NO 333 comprises regions identical to claimed SEQ ID NOs 17 and 16:
US-18-696-131A-333
Query Match 100.0%; Score 380; DB 1; Length 3405;
Best Local Similarity 100.0%;
Matches 380; Conservative 0; Mismatches 0; Indels 0; Gaps 0;
Qy 1 GACATTGATTATTGACTAGTTATTAATAGTAATCAATTACGGGGTCATTAGTTCATAGCC 60 SEQ ID NO 17
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 145 GACATTGATTATTGACTAGTTATTAATAGTAATCAATTACGGGGTCATTAGTTCATAGCC 204 App131 SEQ 333
Qy 61 CATATATGGAGTTCCGCGTTACATAACTTACGGTAAATGGCCCGCCTGGCTGACCGCCCA 120
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 205 CATATATGGAGTTCCGCGTTACATAACTTACGGTAAATGGCCCGCCTGGCTGACCGCCCA 264
Qy 121 ACGACCCCCGCCCATTGACGTCAATAATGACGTATGTTCCCATAGTAACGCCAATAGGGA 180
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 265 ACGACCCCCGCCCATTGACGTCAATAATGACGTATGTTCCCATAGTAACGCCAATAGGGA 324
Qy 181 CTTTCCATTGACGTCAATGGGTGGACTATTTACGGTAAACTGCCCACTTGGCAGTACATC 240
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 325 CTTTCCATTGACGTCAATGGGTGGACTATTTACGGTAAACTGCCCACTTGGCAGTACATC 384
Qy 241 AAGTGTATCATATGCCAAGTACGCCCCCTATTGACGTCAATGACGGTAAATGGCCCGCCT 300
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 385 AAGTGTATCATATGCCAAGTACGCCCCCTATTGACGTCAATGACGGTAAATGGCCCGCCT 444
Qy 301 GGCATTATGCCCAGTACATGACCTTATGGGACTTTCCTACTTGGCAGTACATCTACGTAT 360
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 445 GGCATTATGCCCAGTACATGACCTTATGGGACTTTCCTACTTGGCAGTACATCTACGTAT 504
Qy 361 TAGTCATCGCTATTACCATG 380
||||||||||||||||||||
Db 505 TAGTCATCGCTATTACCATG 524
SEQ ID NO 16:
US-18-696-131A-333
Query Match 100.0%; Score 1013; DB 1; Length 3405;
Best Local Similarity 100.0%;
Matches 1013; Conservative 0; Mismatches 0; Indels 0; Gaps 0;
Qy 1 GGAGTCGCTGCGTTGCCTTCGCCCCGTGCCCCGCTCCGCGCCGCCTCGCGCCGCCCGCCC 60 SEQ ID NO 16
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 803 GGAGTCGCTGCGTTGCCTTCGCCCCGTGCCCCGCTCCGCGCCGCCTCGCGCCGCCCGCCC 862 App131 SEQ 333
Qy 61 CGGCTCTGACTGACCGCGTTACTCCCACAGGTGAGCGGGCGGGACGGCCCTTCTCCTCCG 120
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 863 CGGCTCTGACTGACCGCGTTACTCCCACAGGTGAGCGGGCGGGACGGCCCTTCTCCTCCG 922
Qy 121 GGCTGTAATTAGCGCTTGGTTTAATGACGGCTCGTTTCTTTTCTGTGGCTGCGTGAAAGC 180
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 923 GGCTGTAATTAGCGCTTGGTTTAATGACGGCTCGTTTCTTTTCTGTGGCTGCGTGAAAGC 982
Qy 181 CTTAAAGGGCTCCGGGAGGGCCCTTTGTGCGGGGGGGAGCGGCTCGGGGGGTGCGTGCGT 240
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 983 CTTAAAGGGCTCCGGGAGGGCCCTTTGTGCGGGGGGGAGCGGCTCGGGGGGTGCGTGCGT 1042
Qy 241 GTGTGTGTGCGTGGGGAGCGCCGCGTGCGGCCCGCGCTGCCCGGCGGCTGTGAGCGCTGC 300
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 1043 GTGTGTGTGCGTGGGGAGCGCCGCGTGCGGCCCGCGCTGCCCGGCGGCTGTGAGCGCTGC 1102
Qy 301 GGGCGCGGCGCGGGGCTTTGTGCGCTCCGCGTGTGCGCGAGGGGAGCGCGGCCGGGGGCG 360
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 1103 GGGCGCGGCGCGGGGCTTTGTGCGCTCCGCGTGTGCGCGAGGGGAGCGCGGCCGGGGGCG 1162
Qy 361 GTGCCCCGCGGTGCGGGGGGGCTGCGAGGGGAACAAAGGCTGCGTGCGGGGTGTGTGCGT 420
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 1163 GTGCCCCGCGGTGCGGGGGGGCTGCGAGGGGAACAAAGGCTGCGTGCGGGGTGTGTGCGT 1222
Qy 421 GGGGGGGTGAGCAGGGGGTGTGGGCGCGGCGGTCGGGCTGTAACCCCCCCCTGCACCCCC 480
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 1223 GGGGGGGTGAGCAGGGGGTGTGGGCGCGGCGGTCGGGCTGTAACCCCCCCCTGCACCCCC 1282
Qy 481 CTCCCCGAGTTGCTGAGCACGGCCCGGCTTCGGGTGCGGGGCTCCGTGCGGGGCGTGGCG 540
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 1283 CTCCCCGAGTTGCTGAGCACGGCCCGGCTTCGGGTGCGGGGCTCCGTGCGGGGCGTGGCG 1342
Qy 541 CGGGGCTCGCCGTGCCGGGCGGGGGGTGGCGGCAGGTGGGGGTGCCGGGCGGGGCGGGGC 600
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 1343 CGGGGCTCGCCGTGCCGGGCGGGGGGTGGCGGCAGGTGGGGGTGCCGGGCGGGGCGGGGC 1402
Qy 601 CGCCTCGGGCCGGGGAGGGCTCGGGGGAGGGGCGCGGCGGCCCCCGGAGCGCCGGCGGCT 660
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 1403 CGCCTCGGGCCGGGGAGGGCTCGGGGGAGGGGCGCGGCGGCCCCCGGAGCGCCGGCGGCT 1462
Qy 661 GTCGAGGCGCGGCGAGCCGCAGCCATTGCCTTTTATGGTAATCGTGCGAGAGGGCGCAGG 720
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 1463 GTCGAGGCGCGGCGAGCCGCAGCCATTGCCTTTTATGGTAATCGTGCGAGAGGGCGCAGG 1522
Qy 721 GACTTCCTTTGTCCCAAATCTGTGCGGAGCCGAAATCTGGGAGGCGCCGCCGCACCCCCT 780
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 1523 GACTTCCTTTGTCCCAAATCTGTGCGGAGCCGAAATCTGGGAGGCGCCGCCGCACCCCCT 1582
Qy 781 CTAGCGGGCGCGGGGCGAAGCGGTGCGGCGCCGGCAGGAAGGAAATGGGCGGGGAGGGCC 840
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 1583 CTAGCGGGCGCGGGGCGAAGCGGTGCGGCGCCGGCAGGAAGGAAATGGGCGGGGAGGGCC 1642
Qy 841 TTCGTGCGTCGCCGCGCCGCCGTCCCCTTCTCCCTCTCCAGCCTCGGGGCTGTCCGCGGG 900
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 1643 TTCGTGCGTCGCCGCGCCGCCGTCCCCTTCTCCCTCTCCAGCCTCGGGGCTGTCCGCGGG 1702
Qy 901 GGGACGGCTGCCTTCGGGGGGGACGGGGCAGGGCGGGGTTCGGCTTCTGGCGTGTGACCG 960
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 1703 GGGACGGCTGCCTTCGGGGGGGACGGGGCAGGGCGGGGTTCGGCTTCTGGCGTGTGACCG 1762
Qy 961 GCGGCTCTAGAGCCTCTGCTAACCATGTTCATGCCTTCTTCTTTTTCCTACAG 1013
|||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 1763 GCGGCTCTAGAGCCTCTGCTAACCATGTTCATGCCTTCTTCTTTTTCCTACAG 1815
Therefore the App131 claims recite elements (i), (ii), (iii), (iv), and (ix) of the claimed invention. Then the other prior art teaches the other claim elements that the App131 claims do not recite, including a sequence encoding CLRN1:
WO900 teaches an rAAV vector comprising the CLRN1 cDNA including the 5’ and 3’UTRs, and teaches driving it with the chicken β-actin promoter. WO900 teaches (¶9-10) the polynucleotide (polynt) can include a sequence having SEQ ID NO 2 (which it specifies comprises a 5’UTR and 3’UTR) and can be included on a vector that can be an adeno-associated viral vector (AAV) that can be used for transfecting ocular cells or cells of the inner ear. WO900 teaches (¶21) that the heterologous polynucleotide comprised in the AAV vector is flanked by at least one, and generally by two AAV inverted terminal repeat sequence (ITRs); an artisan would realize that being flanked by two ITRs refers to one ITR on either side, which is a 5’ITR and a 3’ITR. WO900 teaches (¶10-11) treating retinal cells and (¶72) AAV2.
WO900 SEQ ID NO 2 comprises a polynt comprising a sequence encoding the amino acid sequence of claimed SEQ ID NO 3 (which has been back-translated from AA[Wingdings font/0xE0]nucleotides). This is shown by the following sequence alignment:
RESULT 7
BDA01054
ID BDA01054 standard; cDNA; 2352 BP.
XX
AC BDA01054;
XX
DT 16-JUN-2016 (first entry)
XX
DE Human derived clarin-1 (CLRN1) polynucleotide SEQ ID NO:2.
XX
KW CLRN1 gene; auditory; clarin-1; gene therapy; hearing loss;
KW ophthalmological; ss; therapeutic; usher syndrome iii; vision disorder.
XX
OS Homo sapiens.
XX
CC PN WO2016073900-A1.
XX
CC PD 12-MAY-2016.
XX
CC PF 06-NOV-2015; 2015WO-US059546.
XX
PR 06-NOV-2014; 2014US-0076114P.
PR 08-MAY-2015; 2015US-0158846P.
XX
CC PA (UCWR ) UNIV CASE WESTERN RESERVE.
XX
CC PI Alagramam KN;
XX
DR WPI; 2016-282935/37.
XX
CC PT New polynucleotide comprising a nucleic acid sequence that includes a
CC PT cDNA coding sequence of a clarin-1 gene, useful for treating vision
CC PT and/or hearing loss associated with Usher syndrome III.
XX
CC PS Claim 9; SEQ ID NO 2; 43pp; English.
XX
CC The invention relates to a novel polynucleotide, used for treating vision
CC and/or hearing loss associated with Usher syndrome III. This
CC polynucleotide comprises a nucleic acid sequence that includes a cDNA
CC coding sequence of a clarin-1 (CLRN1) gene and a 3' untranslated region
CC (UTR) nucleic acid that is derived from the 3' UTR of the clarin-1 gene,
CC where the 3' UTR nucleic acid enhances expression of clarin-1 in a cell
CC transfected with the polynucleotide compared to a cell transfected with a
CC similar polynucleotide devoid of the 3' UTR nucleic acid. The invention
CC further claims: a nucleic acid construct comprising a polynucleotide
CC defined above; a vector for transfecting a cell, comprising a
CC polynucleotide defined above, where the transfected cell expresses clarin
CC -1; and a method of treating vision and/or hearing loss associated with
CC Usher syndrome III in a subject by administering to the ocular cells
CC and/or cells of the inner ear of the subject, a vector that promotes
CC expression of clarin-1 in the cells. The present sequence is a clarin-1
CC polynucleotide, used for treating vision and/or hearing loss associated
CC with Usher syndrome III in a subject.
XX
SQ Sequence 2352 BP; 705 A; 475 C; 484 G; 688 T; 0 U; 0 Other;
Alignment Scores:
Length: 2352
Score: 1214.00 Matches: 232
Percent Similarity: 100.0% Conservative: 0
Best Local Similarity: 100.0% Mismatches: 0
Query Match: 100.0% Indels: 0
Gaps: 0
US-17-253-658-3 (1-232) x BDA01054 (1-2352)
Qy 1 MetProSerGlnGlnLysLysIleIlePheCysMetAlaGlyValPheSerPheAlaCys 20 SEQ ID NO 3 translated[Wingdings font/0xE0]NT
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 282 ATGCCAAGCCAACAGAAGAAAATCATTTTTTGCATGGCCGGAGTGTTCAGTTTTGCATGT 341 WO900 SEQ ID NO 2
Qy 21 AlaLeuGlyValValThrAlaLeuGlyThrProLeuTrpIleLysAlaThrValLeuCys 40
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 342 GCCCTCGGAGTTGTGACAGCCTTGGGGACACCGTTGTGGATCAAAGCCACTGTCCTCTGC 401
Qy 41 LysThrGlyAlaLeuLeuValAsnAlaSerGlyGlnGluLeuAspLysPheMetGlyGlu 60
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 402 AAAACGGGAGCTCTGCTCGTCAATGCCTCAGGGCAGGAGCTGGACAAGTTTATGGGTGAA 461
Qy 61 MetGlnTyrGlyLeuPheHisGlyGluGlyValArgGlnCysGlyLeuGlyAlaArgPro 80
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 462 ATGCAGTACGGGCTTTTCCACGGAGAGGGTGTGAGGCAGTGTGGGTTGGGAGCAAGGCCC 521
Qy 81 PheArgPheSerPhePheProAspLeuLeuLysAlaIleProValSerIleHisValAsn 100
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 522 TTTCGGTTCTCATTTTTTCCAGATTTGCTCAAAGCAATCCCAGTGAGCATCCACGTCAAT 581
Qy 101 ValIleLeuPheSerAlaIleLeuIleValLeuThrMetValGlyThrAlaPhePheMet 120
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 582 GTCATTCTCTTCTCTGCCATCCTTATTGTGTTAACCATGGTGGGGACAGCCTTCTTCATG 641
Qy 121 TyrAsnAlaPheGlyLysProPheGluThrLeuHisGlyProLeuGlyLeuTyrLeuLeu 140
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 642 TACAATGCTTTTGGAAAACCTTTTGAAACTCTGCATGGTCCCCTAGGGCTGTACCTTTTG 701
Qy 141 SerPheIleSerGlySerCysGlyCysLeuValMetIleLeuPheAlaSerGluValLys 160
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 702 AGCTTCATTTCAGGCTCCTGTGGCTGTCTTGTCATGATATTGTTTGCCTCTGAAGTGAAA 761
Qy 161 IleHisHisLeuSerGluLysIleAlaAsnTyrLysGluGlyThrTyrValTyrLysThr 180
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 762 ATCCATCACCTCTCAGAAAAAATTGCAAATTATAAAGAAGGGACTTATGTCTACAAAACG 821
Qy 181 GlnSerGluLysTyrThrThrSerPheTrpValIlePhePheCysPhePheValHisPhe 200
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 822 CAAAGTGAAAAATATACCACCTCATTCTGGGTCATTTTCTTTTGCTTTTTTGTTCATTTT 881
Qy 201 LeuAsnGlyLeuLeuIleArgLeuAlaGlyPheGlnPheProPheAlaLysSerLysAsp 220
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 882 CTGAATGGGCTCCTAATACGACTTGCTGGATTTCAGTTCCCTTTTGCAAAATCTAAAGAC 941
Qy 221 AlaGluThrThrAsnValAlaAlaAspLeuMetTyr 232
||||||||||||||||||||||||||||||||||||
Db 942 GCAGAAACAACTAATGTAGCTGCAGATCTAATGTAC 977
That alignment shows that the composition of WO900 comprises SEQ ID NO 3 itself, a 5’UTR, and a 3’UTR. Those are elements (v), (vi), and (vii) of the instant claims.
Landegger teaches (§Abstract) an Anc80 vector for transgene delivery to the cochlea. Landegger teaches the vector is well tolerated and targets outer hair cells at high rates.
Powell teaches (§Polyadenylation Signal Sequences and Upstream Enhancer) one study, in human epithelial-like cells, found that a transgene had a 2.5-fold increase in expression with … bovine growth hormone polyA (bGHpA) signal sequences compared to a minimal synthetic polyA (SPA) signal.
App178 teaches SEQ ID NO 30 which comprises a bovine growth hormone polyA signal and is 100% identical to claimed SEQ ID NO 20, as shown by the following sequence alignment:
RESULT 1
AXQ64086
(NOTE: this sequence has 272 duplicates in the database searched.
See complete list at the end of this report)
ID AXQ64086 standard; DNA; 225 BP.
XX
AC AXQ64086;
XX
DT 29-OCT-2009 (first entry)
XX
DE BGH polyA Yes1 supplementary expression cassette 3' UTR, SEQ:30 #2.
XX
KW 3'-utr; Yes1; dna cassette; gene expression; gene silencing;
KW protein production; rna interference; ss.
XX
OS Bos taurus.
OS Synthetic.
XX
CC PN US2009215178-A1.
XX
CC PD 27-AUG-2009.
XX
CC PF 22-FEB-2008; 2008US-00035437.
XX
PR 22-FEB-2008; 2008US-00035437.
XX
CC PA (TANG/) TANG Z.
XX
CC PI Tang Z;
XX
DR WPI; 2009-M96179/59.
XX
CC PT Generating cell clones with stable transgene (Gene of Interest (GOI))
CC PT expression comprises inactivation of endogenous essential genes of cell
CC PT substrate and trans-complementation of essential genes products.
XX
CC PS Example 3; SEQ ID NO 30; 9pp; English.
XX
CC The present invention relates to a method for generating cell clones with
CC stable transgene (Gene Of Interest (GOI)) expression. The method of the
CC invention comprises: (i) inactivation of endogenous essential genes of
CC cell substrate through Gene Inactivation Cassettes (GIC), (ii) trans-
CC complementation of essential gene products through Gene Supplementary
CC Cassettes (GSC), alternatively, the cassette codes for the gene product
CC that is capable of inactivating GIC function, (iii) the GOI expression
CC cassettes are preferably, physically linked to GSC to take advantage of
CC favourable selective pressure, (iv) GIC could be preferably physically
CC linked to GSC and GOI expression cassettes, where the endogenous
CC essential genes of cell substrate refer to genes or combination of genes
CC that are essential for cell survival and / or cell proliferation. The GIC
CC comprises a vector comprising a promoter operably linked to RNA
CC interference, RNAi (shRNA) / dsRNA / ribozyme molecule, or tandem repeats
CC of such transcript units, targeted to cell endogenous essential mRNA. The
CC invention provides strategies for increasing the productivity of
CC recombinant protein expression in isogenic cell-lines, and a novel
CC selection system for the improved stability and homogeneity of transgene
CC expression in isogenic cells without dependence on continuous selective
CC drugs. An example of the invention provides an essential gene knock-down
CC cassette, targeted at 3' UTR of human endogenous Yes1 gene, and a
CC supplementary Yes1 expression cassette which uses a 3' UTR from bovine
CC growth hormone (BGH) polyA. The present sequence is a bovine growth
CC hormone (BGH) polyA Yes1 supplementary expression cassette 3' UTR, used
CC in an example of the invention. Note: This version of SEQ ID 30 is given
CC in example 3, but it is not the same as the sequence referred to as SEQ
CC ID 30 (seeAXQ61560) in the sequence listing.
XX
SQ Sequence 225 BP; 41 A; 53 C; 72 G; 59 T; 0 U; 0 Other;
Query Match 100.0%; Score 225; Length 225;
Best Local Similarity 100.0%;
Matches 225; Conservative 0; Mismatches 0; Indels 0; Gaps 0;
Qy 1 CTGTGCCTTCTAGTTGCCAGCCATCTGTTGTTTGCCCCTCCCCCGTGCCTTCCTTGACCC 60 SEQ ID NO 20
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 1 CTGTGCCTTCTAGTTGCCAGCCATCTGTTGTTTGCCCCTCCCCCGTGCCTTCCTTGACCC 60 Prior art SEQ
Qy 61 TGGAAGGTGCCACTCCCACTGTCCTTTCCTAATAAAATGAGGAAATTGCATCGCATTGTC 120
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 61 TGGAAGGTGCCACTCCCACTGTCCTTTCCTAATAAAATGAGGAAATTGCATCGCATTGTC 120
Qy 121 TGAGTAGGTGTCATTCTATTCTGGGGGGTGGGGTGGGGCAGGACAGCAAGGGGGAGGATT 180
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 121 TGAGTAGGTGTCATTCTATTCTGGGGGGTGGGGTGGGGCAGGACAGCAAGGGGGAGGATT 180
Qy 181 GGGAAGACAATAGCAGGCATGCTGGGGATGCGGTGGGCTCTATGG 225
|||||||||||||||||||||||||||||||||||||||||||||
Db 181 GGGAAGACAATAGCAGGCATGCTGGGGATGCGGTGGGCTCTATGG 225
A poly-A sequence comprising SEQ ID NO 20 is component (viii) of the instant claims.
The App131 claims do not recite a kit that comprises a pre-loaded syringe. However, US952 teaches (Col 11 L3-15) a kit that comprises nucleic acid compounds within a container of solution and that the kit can comprise a pre-loaded syringe comprising the compounds. An artisan would have put their compounds into a kit comprising a pre-loaded syringe for the benefit of ensuring that the recipient has the exact dosage ready to administer and because doing so would have prevented any complications that arise from mixing a solution and then getting the mixed solution into a syringe.
Therefore it would have been obvious to use WO900’s SEQ ID NO 2 with the expression construct of App131 in order to express CLRN1. An artisan would have known that using WO900’s sequence and teachings with the invention recited in the App131 claims and modified by the teachings of Powell, App178, and US952 would have provided a benefit of treating hearing or vision loss because WO900 teaches that (¶11), and it would have been a simple matter to swap the sequence encoding CLRN1 of WO900 for the sequence encoding a Kv7.4 protein of the App131 claims. Using the bovine growth hormone polyA signal of App178 would have been of benefit based on the teachings of Powell. It would have been obvious to use Landegger’s Anc80 vector because it is well tolerated. Packaging it into a pre-loaded syringe would also have been of benefit as taught by US952. Using WO900’s sequence and teachings with the invention recited in the App131 claims and modified by the teachings of Landegger, Powell, App178, and US952 would have produced the invention of the instant claims.
Therefore the instant claims would have been obvious in view of the App131 claims, WO900, Landegger, Powell, App178, and US952.
This is a provisional nonstatutory double patenting rejection.
Claims 229-232, 247-254, and 256-274 are provisionally rejected on the ground of nonstatutory double patenting as being unpatentable over claims 1, 10-11, 13, 15-16, 38-44, 46-47, and 51-62 of copending Application No. 18269307 (reference application; “App307”; of record) in view of US Patent No. 8980952, issued 17 March 2015 (“US952”). This rejection is maintained and updated in response to the claim amendments. All references are of record.
Although the claims at issue are not identical, they are not patentably distinct from each other because the instant claims recite a composition comprising an AAV nucleic acid vector wherein the vector comprises a 5’ ITR, a CMV enhancer, a CBA promoter, a chimeric intron according to SEQ ID NO 16, a 5’UTR, a coding sequence (CDS) encoding a CLRN1 protein according to SEQ ID NO 3, a 3’UTR, a polyA signal, and a 3’ITR, wherein the CDS comprises a nt sequence spanning 2 consecutive exons of CLRN1 genomic DNA and lacks an intron sequence between them; wherein the composition can comprise other components such as SEQ ID NOs 17 or 20; to the composition comprising an excipient; to an AAV2 capsid comprising the composition, to an Anc80 capsid comprising the composition; to a kit comprising the composition; and to methods of introducing it to a cochlea of a mammal that can be a human who can have been previously identified as having a defective endogenous CLRN1 gene; to methods of increasing CLRN1 expression in the ear or eye; and to methods of treating hearing or vision loss.
The App307 claims are drawn to a gene therapy comprising an AAV particle comprising a 5’ ITR, a CMV enhancer, a CBA promoter, a chimeric intron, a 5’UTR, a coding sequence (CDS) encoding a CLRN1 protein according to SEQ ID NO 10, a 3’UTR, a polyA signal, and a 3’ITR, wherein the CLRN1 protein can have SEQ ID NO 10, can have a polyA signal, CMV enhancer, or chimeric intron according to SEQ ID NOs 44, 38, or 39; wherein the particle can comprise an AAV capsid and the capsid can be an Anc80 capsid or an AAV2 capsid, and to methods of treating vision or hearing loss, including (Claim 59) administering to a retinal cell. The App307 claims recite SEQ ID NO 64 (Claim 11) and SEQ ID NO 68 (Claim 62). Both claim sets are drawn to gene therapies for treating hearing and vision loss by administering a gene therapy encoding a CLRN1 protein.
Claimed SEQ ID NO 3 is the same as App307 SEQ ID NO 10 (recited in App307 Claim 1), as shown by the following alignment:
RESULT 1
US-18-269-307-10
Query Match 100.0%; Score 1214; DB 1; Length 232;
Best Local Similarity 100.0%;
Matches 232; Conservative 0; Mismatches 0; Indels 0; Gaps 0;
Qy 1 MPSQQKKIIFCMAGVFSFACALGVVTALGTPLWIKATVLCKTGALLVNASGQELDKFMGE 60 SEQ ID NO 3
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 1 MPSQQKKIIFCMAGVFSFACALGVVTALGTPLWIKATVLCKTGALLVNASGQELDKFMGE 60 App307 SEQ 10
Qy 61 MQYGLFHGEGVRQCGLGARPFRFSFFPDLLKAIPVSIHVNVILFSAILIVLTMVGTAFFM 120
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 61 MQYGLFHGEGVRQCGLGARPFRFSFFPDLLKAIPVSIHVNVILFSAILIVLTMVGTAFFM 120
Qy 121 YNAFGKPFETLHGPLGLYLLSFISGSCGCLVMILFASEVKIHHLSEKIANYKEGTYVYKT 180
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 121 YNAFGKPFETLHGPLGLYLLSFISGSCGCLVMILFASEVKIHHLSEKIANYKEGTYVYKT 180
Qy 181 QSEKYTTSFWVIFFCFFVHFLNGLLIRLAGFQFPFAKSKDAETTNVAADLMY 232
||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 181 QSEKYTTSFWVIFFCFFVHFLNGLLIRLAGFQFPFAKSKDAETTNVAADLMY 232
Claimed SEQ ID NO 20 is identical to App307 SEQ ID NO 44 (recited in App307 Claim 47), as shown by the following alignment:
RESULT 1
US-17-253-658-20
Query Match 100.0%; Score 225; DB 1; Length 225;
Best Local Similarity 100.0%;
Matches 225; Conservative 0; Mismatches 0; Indels 0; Gaps 0;
Qy 1 CTGTGCCTTCTAGTTGCCAGCCATCTGTTGTTTGCCCCTCCCCCGTGCCTTCCTTGACCC 60 SEQ ID NO 20
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 1 CTGTGCCTTCTAGTTGCCAGCCATCTGTTGTTTGCCCCTCCCCCGTGCCTTCCTTGACCC 60 App307 SEQ 44
Qy 61 TGGAAGGTGCCACTCCCACTGTCCTTTCCTAATAAAATGAGGAAATTGCATCGCATTGTC 120
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 61 TGGAAGGTGCCACTCCCACTGTCCTTTCCTAATAAAATGAGGAAATTGCATCGCATTGTC 120
Qy 121 TGAGTAGGTGTCATTCTATTCTGGGGGGTGGGGTGGGGCAGGACAGCAAGGGGGAGGATT 180
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 121 TGAGTAGGTGTCATTCTATTCTGGGGGGTGGGGTGGGGCAGGACAGCAAGGGGGAGGATT 180
Qy 181 GGGAAGACAATAGCAGGCATGCTGGGGATGCGGTGGGCTCTATGG 225
|||||||||||||||||||||||||||||||||||||||||||||
Db 181 GGGAAGACAATAGCAGGCATGCTGGGGATGCGGTGGGCTCTATGG 225
Claimed SEQ ID NO 17 is the same as App307 SEQ ID NO 38 (recited in App307 Claim 41), as shown by the following alignment:
RESULT 1
US-18-269-307-38
Query Match 100.0%; Score 380; DB 1; Length 381;
Best Local Similarity 100.0%;
Matches 380; Conservative 0; Mismatches 0; Indels 0; Gaps 0;
Qy 1 GACATTGATTATTGACTAGTTATTAATAGTAATCAATTACGGGGTCATTAGTTCATAGCC 60 SEQ ID NO 17
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 1 GACATTGATTATTGACTAGTTATTAATAGTAATCAATTACGGGGTCATTAGTTCATAGCC 60 App307 SEQ 38
Qy 61 CATATATGGAGTTCCGCGTTACATAACTTACGGTAAATGGCCCGCCTGGCTGACCGCCCA 120
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 61 CATATATGGAGTTCCGCGTTACATAACTTACGGTAAATGGCCCGCCTGGCTGACCGCCCA 120
Qy 121 ACGACCCCCGCCCATTGACGTCAATAATGACGTATGTTCCCATAGTAACGCCAATAGGGA 180
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 121 ACGACCCCCGCCCATTGACGTCAATAATGACGTATGTTCCCATAGTAACGCCAATAGGGA 180
Qy 181 CTTTCCATTGACGTCAATGGGTGGACTATTTACGGTAAACTGCCCACTTGGCAGTACATC 240
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 181 CTTTCCATTGACGTCAATGGGTGGACTATTTACGGTAAACTGCCCACTTGGCAGTACATC 240
Qy 241 AAGTGTATCATATGCCAAGTACGCCCCCTATTGACGTCAATGACGGTAAATGGCCCGCCT 300
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 241 AAGTGTATCATATGCCAAGTACGCCCCCTATTGACGTCAATGACGGTAAATGGCCCGCCT 300
Qy 301 GGCATTATGCCCAGTACATGACCTTATGGGACTTTCCTACTTGGCAGTACATCTACGTAT 360
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 301 GGCATTATGCCCAGTACATGACCTTATGGGACTTTCCTACTTGGCAGTACATCTACGTAT 360
Qy 361 TAGTCATCGCTATTACCATG 380
||||||||||||||||||||
Db 361 TAGTCATCGCTATTACCATG 380
Claimed SEQ ID NO 16 is the same as App307 SEQ ID NO 39 (recited in App307 Claim 43), as shown by the following alignment:
US-18-269-307-39
Filing date in PALM: 2023-06-23
Sequence 39, US/18269307
Publication No. US20240139344A1
GENERAL INFORMATION
APPLICANT: AKOUOS, INC.
TITLE OF INVENTION: COMPOSITIONS AND METHODS FOR TREATING CLRN1-ASSOCIATED HEARING
TITLE OF INVENTION: LOSS AND/OR VISION LOSS
FILE REFERENCE: 2013615-0214
CURRENT APPLICATION NUMBER: US/18/269,307
CURRENT FILING DATE: 2023-06-23
PRIOR APPLICATION NUMBER: 63/131,413
PRIOR FILING DATE: 2020-12-29
NUMBER OF SEQ ID NOS: 71
SEQ ID NO 39
LENGTH: 1013
TYPE: DNA
ORGANISM: Artificial Sequence
FEATURE:
NAME/KEY: source
OTHER INFORMATION: /note="Description of Artificial Sequence: SyntheticRESULT 1
ALIGNMENT:
Query Match 100.0%; Score 1013; Length 1013;
Best Local Similarity 100.0%;
Matches 1013; Conservative 0; Mismatches 0; Indels 0; Gaps 0;
Qy 1 GGAGTCGCTGCGTTGCCTTCGCCCCGTGCCCCGCTCCGCGCCGCCTCGCGCCGCCCGCCC 60 SEQ ID NO 16
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 1 GGAGTCGCTGCGTTGCCTTCGCCCCGTGCCCCGCTCCGCGCCGCCTCGCGCCGCCCGCCC 60 App307 SEQ 39
Qy 61 CGGCTCTGACTGACCGCGTTACTCCCACAGGTGAGCGGGCGGGACGGCCCTTCTCCTCCG 120
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 61 CGGCTCTGACTGACCGCGTTACTCCCACAGGTGAGCGGGCGGGACGGCCCTTCTCCTCCG 120
Qy 121 GGCTGTAATTAGCGCTTGGTTTAATGACGGCTCGTTTCTTTTCTGTGGCTGCGTGAAAGC 180
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 121 GGCTGTAATTAGCGCTTGGTTTAATGACGGCTCGTTTCTTTTCTGTGGCTGCGTGAAAGC 180
Qy 181 CTTAAAGGGCTCCGGGAGGGCCCTTTGTGCGGGGGGGAGCGGCTCGGGGGGTGCGTGCGT 240
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 181 CTTAAAGGGCTCCGGGAGGGCCCTTTGTGCGGGGGGGAGCGGCTCGGGGGGTGCGTGCGT 240
Qy 241 GTGTGTGTGCGTGGGGAGCGCCGCGTGCGGCCCGCGCTGCCCGGCGGCTGTGAGCGCTGC 300
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 241 GTGTGTGTGCGTGGGGAGCGCCGCGTGCGGCCCGCGCTGCCCGGCGGCTGTGAGCGCTGC 300
Qy 301 GGGCGCGGCGCGGGGCTTTGTGCGCTCCGCGTGTGCGCGAGGGGAGCGCGGCCGGGGGCG 360
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 301 GGGCGCGGCGCGGGGCTTTGTGCGCTCCGCGTGTGCGCGAGGGGAGCGCGGCCGGGGGCG 360
Qy 361 GTGCCCCGCGGTGCGGGGGGGCTGCGAGGGGAACAAAGGCTGCGTGCGGGGTGTGTGCGT 420
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 361 GTGCCCCGCGGTGCGGGGGGGCTGCGAGGGGAACAAAGGCTGCGTGCGGGGTGTGTGCGT 420
Qy 421 GGGGGGGTGAGCAGGGGGTGTGGGCGCGGCGGTCGGGCTGTAACCCCCCCCTGCACCCCC 480
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 421 GGGGGGGTGAGCAGGGGGTGTGGGCGCGGCGGTCGGGCTGTAACCCCCCCCTGCACCCCC 480
Qy 481 CTCCCCGAGTTGCTGAGCACGGCCCGGCTTCGGGTGCGGGGCTCCGTGCGGGGCGTGGCG 540
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 481 CTCCCCGAGTTGCTGAGCACGGCCCGGCTTCGGGTGCGGGGCTCCGTGCGGGGCGTGGCG 540
Qy 541 CGGGGCTCGCCGTGCCGGGCGGGGGGTGGCGGCAGGTGGGGGTGCCGGGCGGGGCGGGGC 600
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 541 CGGGGCTCGCCGTGCCGGGCGGGGGGTGGCGGCAGGTGGGGGTGCCGGGCGGGGCGGGGC 600
Qy 601 CGCCTCGGGCCGGGGAGGGCTCGGGGGAGGGGCGCGGCGGCCCCCGGAGCGCCGGCGGCT 660
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 601 CGCCTCGGGCCGGGGAGGGCTCGGGGGAGGGGCGCGGCGGCCCCCGGAGCGCCGGCGGCT 660
Qy 661 GTCGAGGCGCGGCGAGCCGCAGCCATTGCCTTTTATGGTAATCGTGCGAGAGGGCGCAGG 720
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 661 GTCGAGGCGCGGCGAGCCGCAGCCATTGCCTTTTATGGTAATCGTGCGAGAGGGCGCAGG 720
Qy 721 GACTTCCTTTGTCCCAAATCTGTGCGGAGCCGAAATCTGGGAGGCGCCGCCGCACCCCCT 780
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 721 GACTTCCTTTGTCCCAAATCTGTGCGGAGCCGAAATCTGGGAGGCGCCGCCGCACCCCCT 780
Qy 781 CTAGCGGGCGCGGGGCGAAGCGGTGCGGCGCCGGCAGGAAGGAAATGGGCGGGGAGGGCC 840
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 781 CTAGCGGGCGCGGGGCGAAGCGGTGCGGCGCCGGCAGGAAGGAAATGGGCGGGGAGGGCC 840
Qy 841 TTCGTGCGTCGCCGCGCCGCCGTCCCCTTCTCCCTCTCCAGCCTCGGGGCTGTCCGCGGG 900
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 841 TTCGTGCGTCGCCGCGCCGCCGTCCCCTTCTCCCTCTCCAGCCTCGGGGCTGTCCGCGGG 900
Qy 901 GGGACGGCTGCCTTCGGGGGGGACGGGGCAGGGCGGGGTTCGGCTTCTGGCGTGTGACCG 960
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 901 GGGACGGCTGCCTTCGGGGGGGACGGGGCAGGGCGGGGTTCGGCTTCTGGCGTGTGACCG 960
Qy 961 GCGGCTCTAGAGCCTCTGCTAACCATGTTCATGCCTTCTTCTTTTTCCTACAG 1013
|||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 961 GCGGCTCTAGAGCCTCTGCTAACCATGTTCATGCCTTCTTCTTTTTCCTACAG 1013
The backtranslation of claimed SEQ ID NO 3 is identical App307 SEQ ID NO 19 (recited in App307 Claim 51), as shown by the following alignment:
RESULT 1
US-18-269-307-19
Query Match 100.0%; Score 696; DB 1; Length 696;
Best Local Similarity 100.0%;
Matches 696; Conservative 0; Mismatches 0; Indels 0; Gaps 0;
Qy 1 ATGCCTAGCCAGCAGAAGAAAATCATCTTCTGCATGGCCGGCGTGTTCAGCTTCGCCTGT 60 SEQ #3 transl[Wingdings font/0xE0]NT
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 1 ATGCCTAGCCAGCAGAAGAAAATCATCTTCTGCATGGCCGGCGTGTTCAGCTTCGCCTGT 60 App307 SEQ 19
Qy 61 GCTCTGGGAGTTGTGACAGCCCTGGGAACCCCTCTGTGGATCAAAGCCACAGTGCTGTGC 120
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 61 GCTCTGGGAGTTGTGACAGCCCTGGGAACCCCTCTGTGGATCAAAGCCACAGTGCTGTGC 120
Qy 121 AAGACAGGCGCCCTGCTGGTTAATGCCTCTGGCCAAGAGCTGGACAAGTTCATGGGCGAG 180
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 121 AAGACAGGCGCCCTGCTGGTTAATGCCTCTGGCCAAGAGCTGGACAAGTTCATGGGCGAG 180
Qy 181 ATGCAGTACGGCCTGTTCCATGGCGAAGGCGTCAGACAGTGTGGCCTGGGAGCCAGACCT 240
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 181 ATGCAGTACGGCCTGTTCCATGGCGAAGGCGTCAGACAGTGTGGCCTGGGAGCCAGACCT 240
Qy 241 TTCAGATTCAGCTTCTTCCCAGACCTGCTGAAGGCTATCCCCGTGTCCATCCACGTGAAC 300
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 241 TTCAGATTCAGCTTCTTCCCAGACCTGCTGAAGGCTATCCCCGTGTCCATCCACGTGAAC 300
Qy 301 GTGATCCTGTTCAGCGCCATCCTGATCGTGCTGACAATGGTCGGAACCGCCTTCTTCATG 360
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 301 GTGATCCTGTTCAGCGCCATCCTGATCGTGCTGACAATGGTCGGAACCGCCTTCTTCATG 360
Qy 361 TACAACGCCTTCGGCAAGCCCTTCGAGACACTGCATGGACCTCTGGGCCTGTACCTGCTG 420
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 361 TACAACGCCTTCGGCAAGCCCTTCGAGACACTGCATGGACCTCTGGGCCTGTACCTGCTG 420
Qy 421 AGCTTTATCAGCGGCAGCTGTGGCTGCCTGGTCATGATTCTGTTCGCCAGCGAAGTGAAG 480
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 421 AGCTTTATCAGCGGCAGCTGTGGCTGCCTGGTCATGATTCTGTTCGCCAGCGAAGTGAAG 480
Qy 481 ATCCACCACCTGAGCGAGAAGATCGCCAACTACAAAGAGGGCACCTACGTCTACAAGACC 540
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 481 ATCCACCACCTGAGCGAGAAGATCGCCAACTACAAAGAGGGCACCTACGTCTACAAGACC 540
Qy 541 CAGTCCGAGAAGTACACCACCAGCTTTTGGGTTATCTTCTTCTGTTTCTTCGTGCACTTC 600
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 541 CAGTCCGAGAAGTACACCACCAGCTTTTGGGTTATCTTCTTCTGTTTCTTCGTGCACTTC 600
Qy 601 CTGAACGGCCTGCTGATCAGACTGGCCGGCTTCCAGTTTCCATTCGCCAAGAGCAAGGAC 660
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 601 CTGAACGGCCTGCTGATCAGACTGGCCGGCTTCCAGTTTCCATTCGCCAAGAGCAAGGAC 660
Qy 661 GCCGAAACCACAAACGTGGCCGCCGATCTGATGTAC 696
||||||||||||||||||||||||||||||||||||
Db 661 GCCGAAACCACAAACGTGGCCGCCGATCTGATGTAC 696
Claimed SEQ ID NO 42 is at least 90% and at least 95% identical to App307 SEQ ID NO 68 (recited in App307 Claim 62), as shown by the following alignment:
US-18-269-307-68
Sequence 68, US/18269307
GENERAL INFORMATION
APPLICANT: AKOUOS, INC.
TITLE OF INVENTION: COMPOSITIONS AND METHODS FOR TREATING CLRN1-ASSOCIATED HEARING
TITLE OF INVENTION: LOSS AND/OR VISION LOSS
FILE REFERENCE: 2013615-0214
CURRENT APPLICATION NUMBER: US/18/269,307
CURRENT FILING DATE: 2023-06-23
PRIOR APPLICATION NUMBER: 63/131,413
PRIOR FILING DATE: 2020-12-29
NUMBER OF SEQ ID NOS: 71
SEQ ID NO 68
LENGTH: 4653
TYPE: DNA
ORGANISM: Artificial Sequence
FEATURE:
NAME/KEY: source
OTHER INFORMATION: /note="Description of Artificial Sequence: Synthetic
polynucleotide"
Query Match 96.5%; Score 4444.2; Length 4653;
Best Local Similarity 98.5%;
Matches 4552; Conservative 0; Mismatches 33; Indels 38; Gaps 5;
Qy 12 CTGCGCGCTCGCTCGCTCACTGAGGCC-----------GCCCGGGCGTCGGGCGACCTTT 60 SEQ ID NO 42
||||||||||||||||||||||||||| | || || || || ||||
Db 16 CTGCGCGCTCGCTCGCTCACTGAGGCCGGGCGACCAAAGGTCGCCCGACGCCCGGGCTTT 75 SEQ ID NO 68
Qy 61 GGTCGCCCGGCCTCAGTGAGCGAGCGAGCGCGCAGAGAGGGAGTGGCCAACTCCATCACT 120
| || |||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 76 GCCCGGGCGGCCTCAGTGAGCGAGCGAGCGCGCAGAGAGGGAGTGGCCAACTCCATCACT 135
Qy 121 AGGGGTTCCT--------GCGGCCGCACGCGTGACATTGATTATTGACTAGTTATTAATA 172
|||||||||| ||||||||||||||||||||||||||||||||||||||||||
Db 136 AGGGGTTCCTTTGTCGACGCGGCCGCACGCGTGACATTGATTATTGACTAGTTATTAATA 195
Qy 173 GTAATCAATTACGGGGTCATTAGTTCATAGCCCATATATGGAGTTCCGCGTTACATAACT 232
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 196 GTAATCAATTACGGGGTCATTAGTTCATAGCCCATATATGGAGTTCCGCGTTACATAACT 255
Qy 233 TACGGTAAATGGCCCGCCTGGCTGACCGCCCAACGACCCCCGCCCATTGACGTCAATAAT 292
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 256 TACGGTAAATGGCCCGCCTGGCTGACCGCCCAACGACCCCCGCCCATTGACGTCAATAAT 315
Qy 293 GACGTATGTTCCCATAGTAACGCCAATAGGGACTTTCCATTGACGTCAATGGGTGGACTA 352
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 316 GACGTATGTTCCCATAGTAACGCCAATAGGGACTTTCCATTGACGTCAATGGGTGGACTA 375
Qy 353 TTTACGGTAAACTGCCCACTTGGCAGTACATCAAGTGTATCATATGCCAAGTACGCCCCC 412
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 376 TTTACGGTAAACTGCCCACTTGGCAGTACATCAAGTGTATCATATGCCAAGTACGCCCCC 435
Qy 413 TATTGACGTCAATGACGGTAAATGGCCCGCCTGGCATTATGCCCAGTACATGACCTTATG 472
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 436 TATTGACGTCAATGACGGTAAATGGCCCGCCTGGCATTATGCCCAGTACATGACCTTATG 495
Qy 473 GGACTTTCCTACTTGGCAGTACATCTACGTATTAGTCATCGCTATTACCATGGGTCGAGG 532
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 496 GGACTTTCCTACTTGGCAGTACATCTACGTATTAGTCATCGCTATTACCATGGGTCGAGG 555
Qy 533 TGAGCCCCACGTTCTGCTTCACTCTCCCCATCTCCCCCCCCTCCCCACCCCCAATTTTGT 592
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 556 TGAGCCCCACGTTCTGCTTCACTCTCCCCATCTCCCCCCCCTCCCCACCCCCAATTTTGT 615
Qy 593 ATTTATTTATTTTTTAATTATTTTGTGCAGCGATGGGGGC--GGGGGGGGGGGGGGCGCG 650
|||||||||||||||||||||||||||||||||||||||| ||||||||||||||||||
Db 616 ATTTATTTATTTTTTAATTATTTTGTGCAGCGATGGGGGCGGGGGGGGGGGGGGGGCGCG 675
Qy 651 CGCCAGGCGGGGCGGGGCGGGGCGAGGGGCGGGGCGGGGCGAGGCGGAGAGGTGCGGCGG 710
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 676 CGCCAGGCGGGGCGGGGCGGGGCGAGGGGCGGGGCGGGGCGAGGCGGAGAGGTGCGGCGG 735
Qy 711 CAGCCAATCAGAGCGGCGCGCTCCGAAAGTTTCCTTTTATGGCGAGGCGGCGGCGGCGGC 770
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 736 CAGCCAATCAGAGCGGCGCGCTCCGAAAGTTTCCTTTTATGGCGAGGCGGCGGCGGCGGC 795
Qy 771 GGCCCTATAAAAAGCGAAGCGCGCGGCGGGCGGGAGTCGCTGCGTTGCCTTCGCCCCGTG 830
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 796 GGCCCTATAAAAAGCGAAGCGCGCGGCGGGCGGGAGTCGCTGCGTTGCCTTCGCCCCGTG 855
Qy 831 CCCCGCTCCGCGCCGCCTCGCGCCGCCCGCCCCGGCTCTGACTGACCGCGTTACTCCCAC 890
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 856 CCCCGCTCCGCGCCGCCTCGCGCCGCCCGCCCCGGCTCTGACTGACCGCGTTACTCCCAC 915
Qy 891 AGGTGAGCGGGCGGGACGGCCCTTCTCCTCCGGGCTGTAATTAGCGCTTGGTTTAATGAC 950
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 916 AGGTGAGCGGGCGGGACGGCCCTTCTCCTCCGGGCTGTAATTAGCGCTTGGTTTAATGAC 975
Qy 951 GGCTCGTTTCTTTTCTGTGGCTGCGTGAAAGCCTTAAAGGGCTCCGGGAGGGCCCTTTGT 1010
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 976 GGCTCGTTTCTTTTCTGTGGCTGCGTGAAAGCCTTAAAGGGCTCCGGGAGGGCCCTTTGT 1035
Qy 1011 GCGGGGGGGAGCGGCTCGGGGGGTGCGTGCGTGTGTGTGTGCGTGGGGAGCGCCGCGTGC 1070
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 1036 GCGGGGGGGAGCGGCTCGGGGGGTGCGTGCGTGTGTGTGTGCGTGGGGAGCGCCGCGTGC 1095
Qy 1071 GGCCCGCGCTGCCCGGCGGCTGTGAGCGCTGCGGGCGCGGCGCGGGGCTTTGTGCGCTCC 1130
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 1096 GGCCCGCGCTGCCCGGCGGCTGTGAGCGCTGCGGGCGCGGCGCGGGGCTTTGTGCGCTCC 1155
Qy 1131 GCGTGTGCGCGAGGGGAGCGCGGCCGGGGGCGGTGCCCCGCGGTGCGGGGGGGCTGCGAG 1190
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 1156 GCGTGTGCGCGAGGGGAGCGCGGCCGGGGGCGGTGCCCCGCGGTGCGGGGGGGCTGCGAG 1215
Qy 1191 GGGAACAAAGGCTGCGTGCGGGGTGTGTGCGTGGGGGGGTGAGCAGGGGGTGTGGGCGCG 1250
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 1216 GGGAACAAAGGCTGCGTGCGGGGTGTGTGCGTGGGGGGGTGAGCAGGGGGTGTGGGCGCG 1275
Qy 1251 GCGGTCGGGCTGTAACCCCCCCCTGCACCCCCCTCCCCGAGTTGCTGAGCACGGCCCGGC 1310
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 1276 GCGGTCGGGCTGTAACCCCCCCCTGCACCCCCCTCCCCGAGTTGCTGAGCACGGCCCGGC 1335
Qy 1311 TTCGGGTGCGGGGCTCCGTGCGGGGCGTGGCGCGGGGCTCGCCGTGCCGGGCGGGGGGTG 1370
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 1336 TTCGGGTGCGGGGCTCCGTGCGGGGCGTGGCGCGGGGCTCGCCGTGCCGGGCGGGGGGTG 1395
Qy 1371 GCGGCAGGTGGGGGTGCCGGGCGGGGCGGGGCCGCCTCGGGCCGGGGAGGGCTCGGGGGA 1430
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 1396 GCGGCAGGTGGGGGTGCCGGGCGGGGCGGGGCCGCCTCGGGCCGGGGAGGGCTCGGGGGA 1455
Qy 1431 GGGGCGCGGCGGCCCCCGGAGCGCCGGCGGCTGTCGAGGCGCGGCGAGCCGCAGCCATTG 1490
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 1456 GGGGCGCGGCGGCCCCCGGAGCGCCGGCGGCTGTCGAGGCGCGGCGAGCCGCAGCCATTG 1515
Qy 1491 CCTTTTATGGTAATCGTGCGAGAGGGCGCAGGGACTTCCTTTGTCCCAAATCTGTGCGGA 1550
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 1516 CCTTTTATGGTAATCGTGCGAGAGGGCGCAGGGACTTCCTTTGTCCCAAATCTGTGCGGA 1575
Qy 1551 GCCGAAATCTGGGAGGCGCCGCCGCACCCCCTCTAGCGGGCGCGGGGCGAAGCGGTGCGG 1610
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 1576 GCCGAAATCTGGGAGGCGCCGCCGCACCCCCTCTAGCGGGCGCGGGGCGAAGCGGTGCGG 1635
Qy 1611 CGCCGGCAGGAAGGAAATGGGCGGGGAGGGCCTTCGTGCGTCGCCGCGCCGCCGTCCCCT 1670
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 1636 CGCCGGCAGGAAGGAAATGGGCGGGGAGGGCCTTCGTGCGTCGCCGCGCCGCCGTCCCCT 1695
Qy 1671 TCTCCCTCTCCAGCCTCGGGGCTGTCCGCGGGGGGACGGCTGCCTTCGGGGGGGACGGGG 1730
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 1696 TCTCCCTCTCCAGCCTCGGGGCTGTCCGCGGGGGGACGGCTGCCTTCGGGGGGGACGGGG 1755
Qy 1731 CAGGGCGGGGTTCGGCTTCTGGCGTGTGACCGGCGGCTCTAGAGCCTCTGCTAACCATGT 1790
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 1756 CAGGGCGGGGTTCGGCTTCTGGCGTGTGACCGGCGGCTCTAGAGCCTCTGCTAACCATGT 1815
Qy 1791 TCATGCCTTCTTCTTTTTCCTACAGCTCCTGGGCAACGTGCTGGTTATTGTGACCGGTAG 1850
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 1816 TCATGCCTTCTTCTTTTTCCTACAGCTCCTGGGCAACGTGCTGGTTATTGTGACCGGTAG 1875
Qy 1851 GAGATACTTGAAGGCAGTTTGAAAGACTTGTTTTACAGATTCTTAGTCCAAAGATTTCCA 1910
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 1876 GAGATACTTGAAGGCAGTTTGAAAGACTTGTTTTACAGATTCTTAGTCCAAAGATTTCCA 1935
Qy 1911 ATTAGGGAGAAGAAGCAGCAGAAAAGGAGAAAAGCCAAGTATGAGTGATGATGAGGCCTT 1970
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 1936 ATTAGGGAGAAGAAGCAGCAGAAAAGGAGAAAAGCCAAGTATGAGTGATGATGAGGCCTT 1995
Qy 1971 CATCTACTGACATTTAACCTGGCGAGAACCGTCGATGGTGAAGTTGCCTTTTCAGCTGGG 2030
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 1996 CATCTACTGACATTTAACCTGGCGAGAACCGTCGATGGTGAAGTTGCCTTTTCAGCTGGG 2055
Qy 2031 AGCTGTCCGTTCAGCTTCCGTAATAAATGCAGTCAAAGAGGCAGTCCCTTCCCATTGCTC 2090
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 2056 AGCTGTCCGTTCAGCTTCCGTAATAAATGCAGTCAAAGAGGCAGTCCCTTCCCATTGCTC 2115
Qy 2091 ACAAAGGTCTTGTTTTTGAACCTCGCCCTCACAGAAGCCGTTTCTCATCGCCACCATGCC 2150
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 2116 ACAAAGGTCTTGTTTTTGAACCTCGCCCTCACAGAAGCCGTTTCTCATCGCCACCATGCC 2175
Qy 2151 TAGCCAGCAGAAGAAAATCATCTTCTGCATGGCCGGCGTGTTCAGCTTCGCCTGTGCTCT 2210
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 2176 TAGCCAGCAGAAGAAAATCATCTTCTGCATGGCCGGCGTGTTCAGCTTCGCCTGTGCTCT 2235
Qy 2211 GGGAGTTGTGACAGCCCTGGGAACCCCTCTGTGGATCAAAGCCACAGTGCTGTGCAAGAC 2270
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 2236 GGGAGTTGTGACAGCCCTGGGAACCCCTCTGTGGATCAAAGCCACAGTGCTGTGCAAGAC 2295
Qy 2271 AGGCGCCCTGCTGGTTAATGCCTCTGGCCAAGAGCTGGACAAGTTCATGGGCGAGATGCA 2330
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 2296 AGGCGCCCTGCTGGTTAATGCCTCTGGCCAAGAGCTGGACAAGTTCATGGGCGAGATGCA 2355
Qy 2331 GTACGGCCTGTTCCATGGCGAAGGCGTCAGACAGTGTGGCCTGGGAGCCAGACCTTTCAG 2390
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 2356 GTACGGCCTGTTCCATGGCGAAGGCGTCAGACAGTGTGGCCTGGGAGCCAGACCTTTCAG 2415
Qy 2391 ATTCAGCTTCTTCCCAGACCTGCTGAAGGCTATCCCCGTGTCCATCCACGTGAACGTGAT 2450
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 2416 ATTCAGCTTCTTCCCAGACCTGCTGAAGGCTATCCCCGTGTCCATCCACGTGAACGTGAT 2475
Qy 2451 CCTGTTCAGCGCCATCCTGATCGTGCTGACAATGGTCGGAACCGCCTTCTTCATGTACAA 2510
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 2476 CCTGTTCAGCGCCATCCTGATCGTGCTGACAATGGTCGGAACCGCCTTCTTCATGTACAA 2535
Qy 2511 CGCCTTCGGCAAGCCCTTCGAGACACTGCATGGACCTCTGGGCCTGTACCTGCTGAGCTT 2570
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 2536 CGCCTTCGGCAAGCCCTTCGAGACACTGCATGGACCTCTGGGCCTGTACCTGCTGAGCTT 2595
Qy 2571 TATCAGCGGCAGCTGTGGCTGCCTGGTCATGATTCTGTTCGCCAGCGAAGTGAAGATCCA 2630
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 2596 TATCAGCGGCAGCTGTGGCTGCCTGGTCATGATTCTGTTCGCCAGCGAAGTGAAGATCCA 2655
Qy 2631 CCACCTGAGCGAGAAGATCGCCAACTACAAAGAGGGCACCTACGTCTACAAGACCCAGTC 2690
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 2656 CCACCTGAGCGAGAAGATCGCCAACTACAAAGAGGGCACCTACGTCTACAAGACCCAGTC 2715
Qy 2691 CGAGAAGTACACCACCAGCTTTTGGGTTATCTTCTTCTGTTTCTTCGTGCACTTCCTGAA 2750
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 2716 CGAGAAGTACACCACCAGCTTTTGGGTTATCTTCTTCTGTTTCTTCGTGCACTTCCTGAA 2775
Qy 2751 CGGCCTGCTGATCAGACTGGCCGGCTTCCAGTTTCCATTCGCCAAGAGCAAGGACGCCGA 2810
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 2776 CGGCCTGCTGATCAGACTGGCCGGCTTCCAGTTTCCATTCGCCAAGAGCAAGGACGCCGA 2835
Qy 2811 AACCACAAACGTGGCCGCCGATCTGATGTACTAAGAGCTCAAGGCAAACCTTTCTATAAT 2870
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 2836 AACCACAAACGTGGCCGCCGATCTGATGTACTAAGAGCTCAAGGCAAACCTTTCTATAAT 2895
Qy 2871 TTTACAAGGGAGTAGACTTGCTTTGGTCACTTTTAGATGTGGTTAATTTTGCATATCCTT 2930
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 2896 TTTACAAGGGAGTAGACTTGCTTTGGTCACTTTTAGATGTGGTTAATTTTGCATATCCTT 2955
Qy 2931 TTAGTCTGCATATATTAAAGCATCAGGACCCTTCGTGACAATGTTTACAAATTACGTACT 2990
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 2956 TTAGTCTGCATATATTAAAGCATCAGGACCCTTCGTGACAATGTTTACAAATTACGTACT 3015
Qy 2991 AAGGATACAGGCTGGAAAGTAAGGGAAGCAGAAGGAAGGCTTTGAAAAGTTGTTTTATCT 3050
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 3016 AAGGATACAGGCTGGAAAGTAAGGGAAGCAGAAGGAAGGCTTTGAAAAGTTGTTTTATCT 3075
Qy 3051 GGTGGGAAATTGCTTGACCCAGGTAGTCAAAGGCAGTTGACTAGAATCGACAAATTGTTA 3110
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 3076 GGTGGGAAATTGCTTGACCCAGGTAGTCAAAGGCAGTTGACTAGAATCGACAAATTGTTA 3135
Qy 3111 CTCCATATATATATA------------TGTGTGTGTGTGTGTGTAAGATGTCTTCCTATC 3158
||||||||||||||| |||||||||||||||||||||||||||||||||
Db 3136 CTCCATATATATATATGTGTGTGTGTGTGTGTGTGTGTGTGTGTAAGATGTCTTCCTATC 3195
Qy 3159 AAAAAGATATCAAAGGCACATGGAATATATTTTAATAAAAACAAATAATATCTCTAATAT 3218
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 3196 AAAAAGATATCAAAGGCACATGGAATATATTTTAATAAAAACAAATAATATCTCTAATAT 3255
Qy 3219 ATCCACACATTTGTTGCCAGATTTCAGAAAACTGAGCTGCAATCGCTTTCCTAAAACAGT 3278
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 3256 ATCCACACATTTGTTGCCAGATTTCAGAAAACTGAGCTGCAATCGCTTTCCTAAAACAGT 3315
Qy 3279 AGTGTATTAAATGAACATCTATAAAATGTATCAACACACATTTTAAAAAATTTGTTTAAA 3338
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 3316 AGTGTATTAAATGAACATCTATAAAATGTATCAACACACATTTTAAAAAATTTGTTTAAA 3375
Qy 3339 GTATACTCTTAGGCCAGGCGTGGTGACTCACACCTGTAATTCCAGCACTTCAGGAGGCCA 3398
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 3376 GTATACTCTTAGGCCAGGCGTGGTGACTCACACCTGTAATTCCAGCACTTCAGGAGGCCA 3435
Qy 3399 AGGTGGGAAGATCATTTGAGTTCAGGAGTTCGAGTTACAGTCTGGGCAATAAAGTGAGAC 3458
|||||||||||||||||||||||||||||||||||||||| |||||||||||||||||||
Db 3436 AGGTGGGAAGATCATTTGAGTTCAGGAGTTCGAGTTACAGCCTGGGCAATAAAGTGAGAC 3495
Qy 3459 CCTGTCACTAACAAAATTAAAAAATAAAATAAATATAAAATATAGGCTTTAAAAAAGCAT 3518
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 3496 CCTGTCACTAACAAAATTAAAAAATAAAATAAATATAAAATATAGGCTTTAAAAAAGCAT 3555
Qy 3519 AGTCTTATTAACCATGTCTGTTGGTCAAAATCTGCAAACTCTAAAAGAAGAAAAGAAGAA 3578
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 3556 AGTCTTATTAACCATGTCTGTTGGTCAAAATCTGCAAACTCTAAAAGAAGAAAAGAAGAA 3615
Qy 3579 AAAACCAACGTTAGGGTATTTTTCCTCCCGTGCCTGAGTCCCAATTACATTCACGACAGT 3638
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 3616 AAAACCAACGTTAGGGTATTTTTCCTCCCGTGCCTGAGTCCCAATTACATTCACGACAGT 3675
Qy 3639 ACTTTCAATGAACATAATTGTTAGGACCACTGAGGAATCATGAAAAATGATCTCTGCTTA 3698
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 3676 ACTTTCAATGAACATAATTGTTAGGACCACTGAGGAATCATGAAAAATGATCTCTGCTTA 3735
Qy 3699 GTACATTTGATGCAAAATGACTTATTAGGGGCTGTTTTTCTAGCTATAGTGTCTCGAGTA 3758
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 3736 GTACATTTGATGCAAAATGACTTATTAGGGGCTGTTTTTCTAGCTATAGTGTCTCGAGTA 3795
Qy 3759 CTAATATGCAATTATGAAAATTATATTAAATCTGGGATTATGACGGTATCACTGTATCAT 3818
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 3796 CTAATATGCAATTATGAAAATTATATTAAATCTGGGATTATGACGGTATCACTGTATCAT 3855
Qy 3819 CTTGGTCTTGTTCTGGCTGTCACCAAGCATGACCCAGGTCAACTTTTTTTTTCCCCTGAA 3878
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 3856 CTTGGTCTTGTTCTGGCTGTCACCAAGCATGACCCAGGTCAACTTTTTTTTTCCCCTGAA 3915
Qy 3879 TTACCCATCAAATTGATCTGCAGCTGACTAAAGGCCACAGCTGAGCCTGGAACTGACCCT 3938
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 3916 TTACCCATCAAATTGATCTGCAGCTGACTAAAGGCCACAGCTGAGCCTGGAACTGACCCT 3975
Qy 3939 TCCTTCATCCTCAACCTGCTGTCCTCCAGAAAGCACCAAGGAAAAAGCAGAGAATGACAG 3998
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 3976 TCCTTCATCCTCAACCTGCTGTCCTCCAGAAAGCACCAAGGAAAAAGCAGAGAATGACAG 4035
Qy 3999 CAAACAGATCACTAGGCCTCTGACCACAGGTGCTGAGTACTCAGCAGCCCTCATATAATA 4058
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 4036 CAAACAGATCACTAGGCCTCTGACCACAGGTGCTGAGTACTCAGCAGCCCTCATATAATA 4095
Qy 4059 GGTTTGAAAGTACTCCTTAAAATAAAACACTGTTTCCCTTTGGAACTATTTACAAGGATG 4118
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 4096 GGTTTGAAAGTACTCCTTAAAATAAAACACTGTTTCCCTTTGGAACTATTTACAAGGATG 4155
Qy 4119 AAACAACCGTATACCTGAGAAATAACTTGCTCTGGTGTCAATTCGCTATTCGCCAGCAGA 4178
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 4156 AAACAACCGTATACCTGAGAAATAACTTGCTCTGGTGTCAATTCGCTATTCGCCAGCAGA 4215
Qy 4179 CATCAGAACACACCGAGTTTCCAGATGCTCTGTGCCTTCTAGTTGCCAGCCATCTGTTGT 4238
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 4216 CATCAGAACACACCGAGTTTCCAGATGCTCTGTGCCTTCTAGTTGCCAGCCATCTGTTGT 4275
Qy 4239 TTGCCCCTCCCCCGTGCCTTCCTTGACCCTGGAAGGTGCCACTCCCACTGTCCTTTCCTA 4298
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 4276 TTGCCCCTCCCCCGTGCCTTCCTTGACCCTGGAAGGTGCCACTCCCACTGTCCTTTCCTA 4335
Qy 4299 ATAAAATGAGGAAATTGCATCGCATTGTCTGAGTAGGTGTCATTCTATTCTGGGGGGTGG 4358
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 4336 ATAAAATGAGGAAATTGCATCGCATTGTCTGAGTAGGTGTCATTCTATTCTGGGGGGTGG 4395
Qy 4359 GGTGGGGCAGGACAGCAAGGGGGAGGATTGGGAAGACAATAGCAGGCATGCTGGGGATGC 4418
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 4396 GGTGGGGCAGGACAGCAAGGGGGAGGATTGGGAAGACAATAGCAGGCATGCTGGGGATGC 4455
Qy 4419 GGTGGGCTCTATGGAAGCTTGAATTCAGCTGACGTGCCTCGGACCG-----CTAGGAACC 4473
|||||||||||||||||||||||||||||||||||||||||||||| |||||||
Db 4456 GGTGGGCTCTATGGAAGCTTGAATTCAGCTGACGTGCCTCGGACCGTCCTAGGAGGAACC 4515
Qy 4474 CCTAGTGATGGAGTTGGCCACTCCCTCTCTGCGCGCTCGCTCGCTCACTGAGGCCGGGCG 4533
|||||||||||||||||||||||||||||||||||||||||||||||||||||||| ||
Db 4516 CCTAGTGATGGAGTTGGCCACTCCCTCTCTGCGCGCTCGCTCGCTCACTGAGGCCGCCCG 4575
Qy 4534 ACCAAAGGTCGCCCGACGCCCGGGCTTTGCCCGGGCGGCCTCAGTGAGCGAGCGAGCGCG 4593
||||| || || || || ||||| || |||||||||||||||||||||||||
Db 4576 GGCAAAGCCCGGGCGTCGGGCGACCTTTGGTCGCCCGGCCTCAGTGAGCGAGCGAGCGCG 4635
Qy 4594 CAG 4596
|||
Db 4636 CAG 4638
The App307 claims do not recite that the kit (App307 Claim 14) comprises a pre-loaded syringe. However, US952 teaches (Col 11 L3-15) a kit that comprises nucleic acid compounds within a container of solution and that the kit can comprise a pre-loaded syringe comprising the compounds. An artisan would have put their compounds into a kit comprising a pre-loaded syringe for the benefit of ensuring that the recipient has the exact dosage ready to administer and because doing so would have prevented any complications that arise from mixing a solution and then getting the mixed solution into a syringe.
Therefore the instant claims would have been obvious in view of App307 claims and US952, and the methods of the instant claims could not be used without the composition and methods of App307 claims and US952. The App307 claims encompass the invention of the instant claims.
This is a provisional nonstatutory double patenting rejection because the patentably indistinct claims have not in fact been patented.
Claims 229-232, 247-254, and 259-270 are provisionally rejected on the ground of nonstatutory double patenting as being unpatentable over claims 44, 49-56, 58-61, 66-77 of copending Application No. 19098662 (“App662”) in view of WO900, Powell, and US952. This rejection is maintained and updated in response to the claim amendments. All supporting references are of record.
Although the claims at issue are not identical, they are directed to overlapping subject matter because the instant claims recite a composition comprising an AAV nucleic acid vector wherein the vector comprises a 5’ ITR, a CMV enhancer, a CBA promoter, a chimeric intron according to SEQ ID NO 16, a 5’UTR, a coding sequence (CDS) encoding a CLRN1 protein according to SEQ ID NO 3, a 3’UTR, a polyA signal, and a 3’ITR, wherein the CDS comprises a nt sequence spanning 2 consecutive exons of CLRN1 genomic DNA and lacks an intron sequence between them; wherein the composition can comprise other components such as SEQ ID NOs 17 or 20; to the composition comprising an excipient; to an AAV2 capsid comprising the composition, to an Anc80 capsid comprising the composition; to a kit comprising the composition; and to methods of introducing it to a cochlea of a mammal that can be a human who can have been previously identified as having a defective endogenous CLRN1 gene; to methods of increasing CLRN1 expression in the ear or eye; and to methods of treating hearing or vision loss.
The App662 claims are drawn to a plurality of recombinant AAV vectors: a first vector comprising a 5’ITR, a 3’ITR, a chimeric intron comprising SEQ ID NO 61 (Claims 51 and 68), a CAG promoter comprising SEQ ID NO 61 (Claims 50 and 67), and a second vector that can comprise a bovine polyA signal, wherein each of the vectors is encapsulated by an AAV capsid having a certain serotype, wherein the capsid can be an AAV2 or Anc80 capsid, to a composition comprising the vectors, wherein the composition can be formulated for intra-cochlear administration.
Both claim sets are directed to AAV vectors for administering a gene therapy to the cochlea.
An artisan would not know what is App662 SEQ ID NOs 100 or 61 so they would consult the App662 Spec. and SEQ listing and find (p. 121; SEQ listing) SEQ ID NO 61 comprises a CAG promoter comprising: a CMV enhancer, chicken β-actin gene sequence, and a chimeric intron; and App662 SEQ ID NO 100 is identical to claimed SEQ ID NO 16 (see alignment below). App662 SEQ ID NO 61 comprises claimed SEQ ID NOs 16 and 17 as shown by the following alignments:
US-19-098-662-61
Filing date in PALM: N/A
Sequence 61, US/19098662
GENERAL INFORMATION
APPLICANT: AKOUOS, INC. (en)
TITLE OF INVENTION: COMPOSITIONS AND METHODS FOR TREATING NON-AGE-ASSOCIATED HEARING IMPAIRMENT IN A HUMAN SUBJECT (en)
FILE REFERENCE: 4833.0050005
CURRENT APPLICATION NUMBER: US/19/098,662
CURRENT FILING DATE: 2025-04-02
NUMBER OF SEQ ID NOS: 110
SEQ ID NO 61
LENGTH: 1671
TYPE: DNA
FEATURE:
NAME/KEY: source
LOCATION: 1..1671
QUALIFIERS: mol_type = other DNA
organism = synthetic construct
ALIGNMENT:
Query Match 100.0%; Score 1013; Length 1671;
Best Local Similarity 100.0%;
Matches 1013; Conservative 0; Mismatches 0; Indels 0; Gaps 0;
Qy 1 GGAGTCGCTGCGTTGCCTTCGCCCCGTGCCCCGCTCCGCGCCGCCTCGCGCCGCCCGCCC 60 SEQ ID NO 16
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 659 GGAGTCGCTGCGTTGCCTTCGCCCCGTGCCCCGCTCCGCGCCGCCTCGCGCCGCCCGCCC 718 SEQ ID NO 61
Qy 61 CGGCTCTGACTGACCGCGTTACTCCCACAGGTGAGCGGGCGGGACGGCCCTTCTCCTCCG 120
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 719 CGGCTCTGACTGACCGCGTTACTCCCACAGGTGAGCGGGCGGGACGGCCCTTCTCCTCCG 778
Qy 121 GGCTGTAATTAGCGCTTGGTTTAATGACGGCTCGTTTCTTTTCTGTGGCTGCGTGAAAGC 180
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 779 GGCTGTAATTAGCGCTTGGTTTAATGACGGCTCGTTTCTTTTCTGTGGCTGCGTGAAAGC 838
Qy 181 CTTAAAGGGCTCCGGGAGGGCCCTTTGTGCGGGGGGGAGCGGCTCGGGGGGTGCGTGCGT 240
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 839 CTTAAAGGGCTCCGGGAGGGCCCTTTGTGCGGGGGGGAGCGGCTCGGGGGGTGCGTGCGT 898
Qy 241 GTGTGTGTGCGTGGGGAGCGCCGCGTGCGGCCCGCGCTGCCCGGCGGCTGTGAGCGCTGC 300
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 899 GTGTGTGTGCGTGGGGAGCGCCGCGTGCGGCCCGCGCTGCCCGGCGGCTGTGAGCGCTGC 958
Qy 301 GGGCGCGGCGCGGGGCTTTGTGCGCTCCGCGTGTGCGCGAGGGGAGCGCGGCCGGGGGCG 360
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 959 GGGCGCGGCGCGGGGCTTTGTGCGCTCCGCGTGTGCGCGAGGGGAGCGCGGCCGGGGGCG 1018
Qy 361 GTGCCCCGCGGTGCGGGGGGGCTGCGAGGGGAACAAAGGCTGCGTGCGGGGTGTGTGCGT 420
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 1019 GTGCCCCGCGGTGCGGGGGGGCTGCGAGGGGAACAAAGGCTGCGTGCGGGGTGTGTGCGT 1078
Qy 421 GGGGGGGTGAGCAGGGGGTGTGGGCGCGGCGGTCGGGCTGTAACCCCCCCCTGCACCCCC 480
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 1079 GGGGGGGTGAGCAGGGGGTGTGGGCGCGGCGGTCGGGCTGTAACCCCCCCCTGCACCCCC 1138
Qy 481 CTCCCCGAGTTGCTGAGCACGGCCCGGCTTCGGGTGCGGGGCTCCGTGCGGGGCGTGGCG 540
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 1139 CTCCCCGAGTTGCTGAGCACGGCCCGGCTTCGGGTGCGGGGCTCCGTGCGGGGCGTGGCG 1198
Qy 541 CGGGGCTCGCCGTGCCGGGCGGGGGGTGGCGGCAGGTGGGGGTGCCGGGCGGGGCGGGGC 600
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 1199 CGGGGCTCGCCGTGCCGGGCGGGGGGTGGCGGCAGGTGGGGGTGCCGGGCGGGGCGGGGC 1258
Qy 601 CGCCTCGGGCCGGGGAGGGCTCGGGGGAGGGGCGCGGCGGCCCCCGGAGCGCCGGCGGCT 660
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 1259 CGCCTCGGGCCGGGGAGGGCTCGGGGGAGGGGCGCGGCGGCCCCCGGAGCGCCGGCGGCT 1318
Qy 661 GTCGAGGCGCGGCGAGCCGCAGCCATTGCCTTTTATGGTAATCGTGCGAGAGGGCGCAGG 720
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 1319 GTCGAGGCGCGGCGAGCCGCAGCCATTGCCTTTTATGGTAATCGTGCGAGAGGGCGCAGG 1378
Qy 721 GACTTCCTTTGTCCCAAATCTGTGCGGAGCCGAAATCTGGGAGGCGCCGCCGCACCCCCT 780
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 1379 GACTTCCTTTGTCCCAAATCTGTGCGGAGCCGAAATCTGGGAGGCGCCGCCGCACCCCCT 1438
Qy 781 CTAGCGGGCGCGGGGCGAAGCGGTGCGGCGCCGGCAGGAAGGAAATGGGCGGGGAGGGCC 840
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 1439 CTAGCGGGCGCGGGGCGAAGCGGTGCGGCGCCGGCAGGAAGGAAATGGGCGGGGAGGGCC 1498
Qy 841 TTCGTGCGTCGCCGCGCCGCCGTCCCCTTCTCCCTCTCCAGCCTCGGGGCTGTCCGCGGG 900
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 1499 TTCGTGCGTCGCCGCGCCGCCGTCCCCTTCTCCCTCTCCAGCCTCGGGGCTGTCCGCGGG 1558
Qy 901 GGGACGGCTGCCTTCGGGGGGGACGGGGCAGGGCGGGGTTCGGCTTCTGGCGTGTGACCG 960
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 1559 GGGACGGCTGCCTTCGGGGGGGACGGGGCAGGGCGGGGTTCGGCTTCTGGCGTGTGACCG 1618
Qy 961 GCGGCTCTAGAGCCTCTGCTAACCATGTTCATGCCTTCTTCTTTTTCCTACAG 1013
|||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 1619 GCGGCTCTAGAGCCTCTGCTAACCATGTTCATGCCTTCTTCTTTTTCCTACAG 1671
SEQ ID NO 17
Query Match 100.0%; Score 380; DB 1; Length 1671;
Best Local Similarity 100.0%;
Matches 380; Conservative 0; Mismatches 0; Indels 0; Gaps 0;
Qy 1 GACATTGATTATTGACTAGTTATTAATAGTAATCAATTACGGGGTCATTAGTTCATAGCC 60 SEQ ID NO 17
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 1 GACATTGATTATTGACTAGTTATTAATAGTAATCAATTACGGGGTCATTAGTTCATAGCC 60 SEQ ID NO 61
Qy 61 CATATATGGAGTTCCGCGTTACATAACTTACGGTAAATGGCCCGCCTGGCTGACCGCCCA 120
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 61 CATATATGGAGTTCCGCGTTACATAACTTACGGTAAATGGCCCGCCTGGCTGACCGCCCA 120
Qy 121 ACGACCCCCGCCCATTGACGTCAATAATGACGTATGTTCCCATAGTAACGCCAATAGGGA 180
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 121 ACGACCCCCGCCCATTGACGTCAATAATGACGTATGTTCCCATAGTAACGCCAATAGGGA 180
Qy 181 CTTTCCATTGACGTCAATGGGTGGACTATTTACGGTAAACTGCCCACTTGGCAGTACATC 240
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 181 CTTTCCATTGACGTCAATGGGTGGACTATTTACGGTAAACTGCCCACTTGGCAGTACATC 240
Qy 241 AAGTGTATCATATGCCAAGTACGCCCCCTATTGACGTCAATGACGGTAAATGGCCCGCCT 300
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 241 AAGTGTATCATATGCCAAGTACGCCCCCTATTGACGTCAATGACGGTAAATGGCCCGCCT 300
Qy 301 GGCATTATGCCCAGTACATGACCTTATGGGACTTTCCTACTTGGCAGTACATCTACGTAT 360
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 301 GGCATTATGCCCAGTACATGACCTTATGGGACTTTCCTACTTGGCAGTACATCTACGTAT 360
Qy 361 TAGTCATCGCTATTACCATG 380
||||||||||||||||||||
Db 361 TAGTCATCGCTATTACCATG 380
US-19-098-662-100
Query Match 100.0%; Score 1013; DB 1; Length 1013;
Best Local Similarity 100.0%;
Matches 1013; Conservative 0; Mismatches 0; Indels 0; Gaps 0;
Qy 1 GGAGTCGCTGCGTTGCCTTCGCCCCGTGCCCCGCTCCGCGCCGCCTCGCGCCGCCCGCCC 60 SEQ ID NO 16
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 1 GGAGTCGCTGCGTTGCCTTCGCCCCGTGCCCCGCTCCGCGCCGCCTCGCGCCGCCCGCCC 60 SEQ ID NO 100
Qy 61 CGGCTCTGACTGACCGCGTTACTCCCACAGGTGAGCGGGCGGGACGGCCCTTCTCCTCCG 120
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 61 CGGCTCTGACTGACCGCGTTACTCCCACAGGTGAGCGGGCGGGACGGCCCTTCTCCTCCG 120
Qy 121 GGCTGTAATTAGCGCTTGGTTTAATGACGGCTCGTTTCTTTTCTGTGGCTGCGTGAAAGC 180
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 121 GGCTGTAATTAGCGCTTGGTTTAATGACGGCTCGTTTCTTTTCTGTGGCTGCGTGAAAGC 180
Qy 181 CTTAAAGGGCTCCGGGAGGGCCCTTTGTGCGGGGGGGAGCGGCTCGGGGGGTGCGTGCGT 240
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 181 CTTAAAGGGCTCCGGGAGGGCCCTTTGTGCGGGGGGGAGCGGCTCGGGGGGTGCGTGCGT 240
Qy 241 GTGTGTGTGCGTGGGGAGCGCCGCGTGCGGCCCGCGCTGCCCGGCGGCTGTGAGCGCTGC 300
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 241 GTGTGTGTGCGTGGGGAGCGCCGCGTGCGGCCCGCGCTGCCCGGCGGCTGTGAGCGCTGC 300
Qy 301 GGGCGCGGCGCGGGGCTTTGTGCGCTCCGCGTGTGCGCGAGGGGAGCGCGGCCGGGGGCG 360
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 301 GGGCGCGGCGCGGGGCTTTGTGCGCTCCGCGTGTGCGCGAGGGGAGCGCGGCCGGGGGCG 360
Qy 361 GTGCCCCGCGGTGCGGGGGGGCTGCGAGGGGAACAAAGGCTGCGTGCGGGGTGTGTGCGT 420
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 361 GTGCCCCGCGGTGCGGGGGGGCTGCGAGGGGAACAAAGGCTGCGTGCGGGGTGTGTGCGT 420
Qy 421 GGGGGGGTGAGCAGGGGGTGTGGGCGCGGCGGTCGGGCTGTAACCCCCCCCTGCACCCCC 480
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 421 GGGGGGGTGAGCAGGGGGTGTGGGCGCGGCGGTCGGGCTGTAACCCCCCCCTGCACCCCC 480
Qy 481 CTCCCCGAGTTGCTGAGCACGGCCCGGCTTCGGGTGCGGGGCTCCGTGCGGGGCGTGGCG 540
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 481 CTCCCCGAGTTGCTGAGCACGGCCCGGCTTCGGGTGCGGGGCTCCGTGCGGGGCGTGGCG 540
Qy 541 CGGGGCTCGCCGTGCCGGGCGGGGGGTGGCGGCAGGTGGGGGTGCCGGGCGGGGCGGGGC 600
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 541 CGGGGCTCGCCGTGCCGGGCGGGGGGTGGCGGCAGGTGGGGGTGCCGGGCGGGGCGGGGC 600
Qy 601 CGCCTCGGGCCGGGGAGGGCTCGGGGGAGGGGCGCGGCGGCCCCCGGAGCGCCGGCGGCT 660
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 601 CGCCTCGGGCCGGGGAGGGCTCGGGGGAGGGGCGCGGCGGCCCCCGGAGCGCCGGCGGCT 660
Qy 661 GTCGAGGCGCGGCGAGCCGCAGCCATTGCCTTTTATGGTAATCGTGCGAGAGGGCGCAGG 720
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 661 GTCGAGGCGCGGCGAGCCGCAGCCATTGCCTTTTATGGTAATCGTGCGAGAGGGCGCAGG 720
Qy 721 GACTTCCTTTGTCCCAAATCTGTGCGGAGCCGAAATCTGGGAGGCGCCGCCGCACCCCCT 780
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 721 GACTTCCTTTGTCCCAAATCTGTGCGGAGCCGAAATCTGGGAGGCGCCGCCGCACCCCCT 780
Qy 781 CTAGCGGGCGCGGGGCGAAGCGGTGCGGCGCCGGCAGGAAGGAAATGGGCGGGGAGGGCC 840
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 781 CTAGCGGGCGCGGGGCGAAGCGGTGCGGCGCCGGCAGGAAGGAAATGGGCGGGGAGGGCC 840
Qy 841 TTCGTGCGTCGCCGCGCCGCCGTCCCCTTCTCCCTCTCCAGCCTCGGGGCTGTCCGCGGG 900
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 841 TTCGTGCGTCGCCGCGCCGCCGTCCCCTTCTCCCTCTCCAGCCTCGGGGCTGTCCGCGGG 900
Qy 901 GGGACGGCTGCCTTCGGGGGGGACGGGGCAGGGCGGGGTTCGGCTTCTGGCGTGTGACCG 960
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 901 GGGACGGCTGCCTTCGGGGGGGACGGGGCAGGGCGGGGTTCGGCTTCTGGCGTGTGACCG 960
Qy 961 GCGGCTCTAGAGCCTCTGCTAACCATGTTCATGCCTTCTTCTTTTTCCTACAG 1013
|||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 961 GCGGCTCTAGAGCCTCTGCTAACCATGTTCATGCCTTCTTCTTTTTCCTACAG 1013
Furthermore, App662 Claims 49 (and others) recite a polyA sequence that has SEQ ID NO 108. That is 100% identical to claimed SEQ ID NO 20 as shown by the following alignment:
RESULT 1
US-19-098-662-108
Query Match 100.0%; Score 225; DB 1; Length 225;
Best Local Similarity 100.0%;
Matches 225; Conservative 0; Mismatches 0; Indels 0; Gaps 0;
Qy 1 CTGTGCCTTCTAGTTGCCAGCCATCTGTTGTTTGCCCCTCCCCCGTGCCTTCCTTGACCC 60
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 1 CTGTGCCTTCTAGTTGCCAGCCATCTGTTGTTTGCCCCTCCCCCGTGCCTTCCTTGACCC 60
Qy 61 TGGAAGGTGCCACTCCCACTGTCCTTTCCTAATAAAATGAGGAAATTGCATCGCATTGTC 120
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 61 TGGAAGGTGCCACTCCCACTGTCCTTTCCTAATAAAATGAGGAAATTGCATCGCATTGTC 120
Qy 121 TGAGTAGGTGTCATTCTATTCTGGGGGGTGGGGTGGGGCAGGACAGCAAGGGGGAGGATT 180
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 121 TGAGTAGGTGTCATTCTATTCTGGGGGGTGGGGTGGGGCAGGACAGCAAGGGGGAGGATT 180
Qy 181 GGGAAGACAATAGCAGGCATGCTGGGGATGCGGTGGGCTCTATGG 225
|||||||||||||||||||||||||||||||||||||||||||||
Db 181 GGGAAGACAATAGCAGGCATGCTGGGGATGCGGTGGGCTCTATGG 225
Therefore the copending App662 claims recite elements (i), (ii), (iii), (iv), (viii), and (ix) of the claimed invention. Then the other prior art teaches the other claim elements that the App662 claims do not recite:
WO900 teaches an rAAV vector comprising the CLRN1 cDNA including the 5’ and 3’UTRs. WO900 teaches (¶9-10) the polynucleotide (polynt) can include a sequence having SEQ ID NO 2 (which it specifies comprises a 5’UTR and 3’UTR) and can be included on a vector that can be an adeno-associated viral vector (AAV) that can be used for transfecting ocular cells or cells of the inner ear. WO900 teaches (¶21) that the heterologous polynucleotide comprised in the AAV vector is flanked by at least one, and generally by two AAV inverted terminal repeat sequence (ITRs); an artisan would realize that being flanked by two ITRs refers to one ITR on either side, which is a 5’ITR and a 3’ITR. WO900 teaches (¶10-11) treating retinal cells.
WO900 SEQ ID NO 2 comprises a polynt comprising a sequence encoding the amino acid sequence of claimed SEQ ID NO 3 (which has been back-translated from AA[Wingdings font/0xE0]nucleotides). This is shown by the following sequence alignment:
RESULT 7
BDA01054
ID BDA01054 standard; cDNA; 2352 BP.
XX
AC BDA01054;
XX
DT 16-JUN-2016 (first entry)
XX
DE Human derived clarin-1 (CLRN1) polynucleotide SEQ ID NO:2.
XX
KW CLRN1 gene; auditory; clarin-1; gene therapy; hearing loss;
KW ophthalmological; ss; therapeutic; usher syndrome iii; vision disorder.
XX
OS Homo sapiens.
XX
CC PN WO2016073900-A1.
XX
CC PD 12-MAY-2016.
XX
CC PF 06-NOV-2015; 2015WO-US059546.
XX
PR 06-NOV-2014; 2014US-0076114P.
PR 08-MAY-2015; 2015US-0158846P.
XX
CC PA (UCWR ) UNIV CASE WESTERN RESERVE.
XX
CC PI Alagramam KN;
XX
DR WPI; 2016-282935/37.
XX
CC PT New polynucleotide comprising a nucleic acid sequence that includes a
CC PT cDNA coding sequence of a clarin-1 gene, useful for treating vision
CC PT and/or hearing loss associated with Usher syndrome III.
XX
CC PS Claim 9; SEQ ID NO 2; 43pp; English.
XX
CC The invention relates to a novel polynucleotide, used for treating vision
CC and/or hearing loss associated with Usher syndrome III. This
CC polynucleotide comprises a nucleic acid sequence that includes a cDNA
CC coding sequence of a clarin-1 (CLRN1) gene and a 3' untranslated region
CC (UTR) nucleic acid that is derived from the 3' UTR of the clarin-1 gene,
CC where the 3' UTR nucleic acid enhances expression of clarin-1 in a cell
CC transfected with the polynucleotide compared to a cell transfected with a
CC similar polynucleotide devoid of the 3' UTR nucleic acid. The invention
CC further claims: a nucleic acid construct comprising a polynucleotide
CC defined above; a vector for transfecting a cell, comprising a
CC polynucleotide defined above, where the transfected cell expresses clarin
CC -1; and a method of treating vision and/or hearing loss associated with
CC Usher syndrome III in a subject by administering to the ocular cells
CC and/or cells of the inner ear of the subject, a vector that promotes
CC expression of clarin-1 in the cells. The present sequence is a clarin-1
CC polynucleotide, used for treating vision and/or hearing loss associated
CC with Usher syndrome III in a subject.
XX
SQ Sequence 2352 BP; 705 A; 475 C; 484 G; 688 T; 0 U; 0 Other;
Alignment Scores:
Length: 2352
Score: 1214.00 Matches: 232
Percent Similarity: 100.0% Conservative: 0
Best Local Similarity: 100.0% Mismatches: 0
Query Match: 100.0% Indels: 0
Gaps: 0
US-17-253-658-3 (1-232) x BDA01054 (1-2352)
Qy 1 MetProSerGlnGlnLysLysIleIlePheCysMetAlaGlyValPheSerPheAlaCys 20 SEQ ID NO 3 translated[Wingdings font/0xE0]NT
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 282 ATGCCAAGCCAACAGAAGAAAATCATTTTTTGCATGGCCGGAGTGTTCAGTTTTGCATGT 341 WO900 SEQ ID NO 2
Qy 21 AlaLeuGlyValValThrAlaLeuGlyThrProLeuTrpIleLysAlaThrValLeuCys 40
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 342 GCCCTCGGAGTTGTGACAGCCTTGGGGACACCGTTGTGGATCAAAGCCACTGTCCTCTGC 401
Qy 41 LysThrGlyAlaLeuLeuValAsnAlaSerGlyGlnGluLeuAspLysPheMetGlyGlu 60
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 402 AAAACGGGAGCTCTGCTCGTCAATGCCTCAGGGCAGGAGCTGGACAAGTTTATGGGTGAA 461
Qy 61 MetGlnTyrGlyLeuPheHisGlyGluGlyValArgGlnCysGlyLeuGlyAlaArgPro 80
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 462 ATGCAGTACGGGCTTTTCCACGGAGAGGGTGTGAGGCAGTGTGGGTTGGGAGCAAGGCCC 521
Qy 81 PheArgPheSerPhePheProAspLeuLeuLysAlaIleProValSerIleHisValAsn 100
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 522 TTTCGGTTCTCATTTTTTCCAGATTTGCTCAAAGCAATCCCAGTGAGCATCCACGTCAAT 581
Qy 101 ValIleLeuPheSerAlaIleLeuIleValLeuThrMetValGlyThrAlaPhePheMet 120
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 582 GTCATTCTCTTCTCTGCCATCCTTATTGTGTTAACCATGGTGGGGACAGCCTTCTTCATG 641
Qy 121 TyrAsnAlaPheGlyLysProPheGluThrLeuHisGlyProLeuGlyLeuTyrLeuLeu 140
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 642 TACAATGCTTTTGGAAAACCTTTTGAAACTCTGCATGGTCCCCTAGGGCTGTACCTTTTG 701
Qy 141 SerPheIleSerGlySerCysGlyCysLeuValMetIleLeuPheAlaSerGluValLys 160
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 702 AGCTTCATTTCAGGCTCCTGTGGCTGTCTTGTCATGATATTGTTTGCCTCTGAAGTGAAA 761
Qy 161 IleHisHisLeuSerGluLysIleAlaAsnTyrLysGluGlyThrTyrValTyrLysThr 180
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 762 ATCCATCACCTCTCAGAAAAAATTGCAAATTATAAAGAAGGGACTTATGTCTACAAAACG 821
Qy 181 GlnSerGluLysTyrThrThrSerPheTrpValIlePhePheCysPhePheValHisPhe 200
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 822 CAAAGTGAAAAATATACCACCTCATTCTGGGTCATTTTCTTTTGCTTTTTTGTTCATTTT 881
Qy 201 LeuAsnGlyLeuLeuIleArgLeuAlaGlyPheGlnPheProPheAlaLysSerLysAsp 220
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 882 CTGAATGGGCTCCTAATACGACTTGCTGGATTTCAGTTCCCTTTTGCAAAATCTAAAGAC 941
Qy 221 AlaGluThrThrAsnValAlaAlaAspLeuMetTyr 232
||||||||||||||||||||||||||||||||||||
Db 942 GCAGAAACAACTAATGTAGCTGCAGATCTAATGTAC 977
That alignment shows that the composition of WO900 comprises SEQ ID NO 3 itself, a 5’UTR, and a 3’UTR. Those are elements (v), (vi), and (vii) of the instant claims.
Powell teaches (§Polyadenylation Signal Sequences and Upstream Enhancer) one study, in human epithelial-like cells, found that a transgene had a 2.5-fold increase in expression with … bovine growth hormone polyA (bGHpA) signal sequences compared to a minimal synthetic polyA (SPA) signal.
It would have been obvious to an artisan before the effective filing date of the claimed invention to modify the invention of the App662 claims with the sequence encoding CLRN1 of WO900 and teachings of Powell for the benefits of using the App662 vectors to treat Usher syndrome and to increase transgene expression. One would have been motivated to do so with a reasonable expectation of success because WO900 teaches (¶3-4) expressing CLRN1 had known usage in treating Usher syndrome, including (¶11) for both hearing and vision losses, and it would have been a simple matter to swap the sequence encoding CLRN1 of WO900 for the sequence encoding otoferlin of App662. An artisan would know that they need only use one AAV vector to encode CLRN1 because WO900 teaches (¶99, 108-111) the entire mCLRN1 cDNA was placed on a single AAV vector, indicating the entire CLRN1 cDNA could fit on a single AAV vector. They would have been motivated to use a single vector because it is simpler to administer a single vector gene therapy than a dual vector gene therapy. Using the bovine growth hormone polyA signal of App178 would have been of benefit based on the teachings of Powell.
US952 teaches (Col 11 L3-15) a kit that comprises nucleic acid compounds within a container of solution and that the kit can comprise a pre-loaded syringe comprising the compounds. An artisan would have put their compounds into a kit comprising a pre-loaded syringe for the benefit of ensuring that the recipient has the exact dosage ready to administer and because doing so would have prevented any complications that arise from mixing a solution and then getting the mixed solution into a syringe.
Therefore the instant claims would have been obvious in view of the App662 claims, WO900, Powell, and US952.
This is a provisional nonstatutory double patenting rejection.
Claims 229-232, 247-254, and 256-270 are provisionally rejected on the ground of nonstatutory double patenting as being unpatentable over claims 1-2, 4-6, 8-9, and 11-13 of copending Application No. 19095986 (reference application; “App986”) in view of WO900 and US952. This rejection is new. All supporting references are of record.
Although the claims at issue are not identical, they are not patentably distinct from each other because both claim sets are directed to methods and compositions of gene therapies for expressing a gene of interest in the inner ear to treat hearing loss. The instant claims recite a composition comprising an AAV nucleic acid vector wherein the vector comprises a 5’ ITR, a CMV enhancer, a CBA promoter, a chimeric intron, a 5’UTR, a coding sequence (CDS) encoding a CLRN1 protein according to SEQ ID NO 3, a 3’UTR, a polyA signal, and a 3’ITR, wherein the CDS comprises a nt sequence spanning 2 consecutive exons of CLRN1 genomic DNA and lacks an intron sequence between them; wherein the composition can comprise other components such as SEQ ID NOs 16-17 or 20; to the composition comprising an excipient; to an AAV2 capsid comprising the composition, to an Anc80 capsid comprising the composition; to a kit comprising the composition; and to methods of introducing it to a cochlea of a mammal that can be a human who can have been previously identified as having a defective endogenous CLRN1 gene; to methods of increasing CLRN1 expression in the ear or eye; and to methods of treating hearing or vision loss.
The App986 claims recite an AAV particle comprising a nucleic acid construct comprising a 5’ITR and a 3’ITR or according to SEQ ID NO 91 or 92 (Claims 80-81) and an AAV capsid that is an Anc80 capsid; a composition comprising the particle, and methods of delivering the AAV particle to the inner ear. An artisan would not know what are SEQ ID NO 91 or 92 but they would consult the Spec. (¶29-30, ¶522-523, Fig. 6) and SEQ listing and find that those SEQ ID NOs comprise a 5’ITR, a CMV enhancer comprising claimed SEQ ID NO 17, a CBA promoter, a chimeric intron according claimed SEQ ID NO 16, a coding sequence for an anti-VEGF antibody, and a 3’ITR.
Both claim sets are directed to AAV constructs for gene expression, wherein the constructs comprise the same elements including a chimeric intron comprising SEQ ID NO 16 and a CVM enhancer comprising SEQ ID NO 17 and a polyA sequence comprising SEQ ID NO 20. US726 SEQ ID NOs 91 and 92 comprise regions identical to claimed SEQ ID NOs 17, 16, and 20:
RESULT 1
US-19-095-986-91
Query Match 100.0%; Score 380; DB 1; Length 3847;
Best Local Similarity 100.0%;
Matches 380; Conservative 0; Mismatches 0; Indels 0; Gaps 0;
Qy 1 GACATTGATTATTGACTAGTTATTAATAGTAATCAATTACGGGGTCATTAGTTCATAGCC 60 SEQ ID NO 17
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 168 GACATTGATTATTGACTAGTTATTAATAGTAATCAATTACGGGGTCATTAGTTCATAGCC 227 US726 SEQ 91
Qy 61 CATATATGGAGTTCCGCGTTACATAACTTACGGTAAATGGCCCGCCTGGCTGACCGCCCA 120
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 228 CATATATGGAGTTCCGCGTTACATAACTTACGGTAAATGGCCCGCCTGGCTGACCGCCCA 287
Qy 121 ACGACCCCCGCCCATTGACGTCAATAATGACGTATGTTCCCATAGTAACGCCAATAGGGA 180
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 288 ACGACCCCCGCCCATTGACGTCAATAATGACGTATGTTCCCATAGTAACGCCAATAGGGA 347
Qy 181 CTTTCCATTGACGTCAATGGGTGGACTATTTACGGTAAACTGCCCACTTGGCAGTACATC 240
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 348 CTTTCCATTGACGTCAATGGGTGGACTATTTACGGTAAACTGCCCACTTGGCAGTACATC 407
Qy 241 AAGTGTATCATATGCCAAGTACGCCCCCTATTGACGTCAATGACGGTAAATGGCCCGCCT 300
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 408 AAGTGTATCATATGCCAAGTACGCCCCCTATTGACGTCAATGACGGTAAATGGCCCGCCT 467
Qy 301 GGCATTATGCCCAGTACATGACCTTATGGGACTTTCCTACTTGGCAGTACATCTACGTAT 360
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 468 GGCATTATGCCCAGTACATGACCTTATGGGACTTTCCTACTTGGCAGTACATCTACGTAT 527
Qy 361 TAGTCATCGCTATTACCATG 380
||||||||||||||||||||
Db 528 TAGTCATCGCTATTACCATG 547
SEQ ID NO 16:
RESULT 1
US-19-095-986-91
Query Match 100.0%; Score 1013; DB 1; Length 3847;
Best Local Similarity 100.0%;
Matches 1013; Conservative 0; Mismatches 0; Indels 0; Gaps 0;
Qy 1 GGAGTCGCTGCGTTGCCTTCGCCCCGTGCCCCGCTCCGCGCCGCCTCGCGCCGCCCGCCC 60 SEQ ID NO 16
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 828 GGAGTCGCTGCGTTGCCTTCGCCCCGTGCCCCGCTCCGCGCCGCCTCGCGCCGCCCGCCC 887 US726 SEQ 91
Qy 61 CGGCTCTGACTGACCGCGTTACTCCCACAGGTGAGCGGGCGGGACGGCCCTTCTCCTCCG 120
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 888 CGGCTCTGACTGACCGCGTTACTCCCACAGGTGAGCGGGCGGGACGGCCCTTCTCCTCCG 947
Qy 121 GGCTGTAATTAGCGCTTGGTTTAATGACGGCTCGTTTCTTTTCTGTGGCTGCGTGAAAGC 180
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 948 GGCTGTAATTAGCGCTTGGTTTAATGACGGCTCGTTTCTTTTCTGTGGCTGCGTGAAAGC 1007
Qy 181 CTTAAAGGGCTCCGGGAGGGCCCTTTGTGCGGGGGGGAGCGGCTCGGGGGGTGCGTGCGT 240
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 1008 CTTAAAGGGCTCCGGGAGGGCCCTTTGTGCGGGGGGGAGCGGCTCGGGGGGTGCGTGCGT 1067
Qy 241 GTGTGTGTGCGTGGGGAGCGCCGCGTGCGGCCCGCGCTGCCCGGCGGCTGTGAGCGCTGC 300
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 1068 GTGTGTGTGCGTGGGGAGCGCCGCGTGCGGCCCGCGCTGCCCGGCGGCTGTGAGCGCTGC 1127
Qy 301 GGGCGCGGCGCGGGGCTTTGTGCGCTCCGCGTGTGCGCGAGGGGAGCGCGGCCGGGGGCG 360
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 1128 GGGCGCGGCGCGGGGCTTTGTGCGCTCCGCGTGTGCGCGAGGGGAGCGCGGCCGGGGGCG 1187
Qy 361 GTGCCCCGCGGTGCGGGGGGGCTGCGAGGGGAACAAAGGCTGCGTGCGGGGTGTGTGCGT 420
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 1188 GTGCCCCGCGGTGCGGGGGGGCTGCGAGGGGAACAAAGGCTGCGTGCGGGGTGTGTGCGT 1247
Qy 421 GGGGGGGTGAGCAGGGGGTGTGGGCGCGGCGGTCGGGCTGTAACCCCCCCCTGCACCCCC 480
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 1248 GGGGGGGTGAGCAGGGGGTGTGGGCGCGGCGGTCGGGCTGTAACCCCCCCCTGCACCCCC 1307
Qy 481 CTCCCCGAGTTGCTGAGCACGGCCCGGCTTCGGGTGCGGGGCTCCGTGCGGGGCGTGGCG 540
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 1308 CTCCCCGAGTTGCTGAGCACGGCCCGGCTTCGGGTGCGGGGCTCCGTGCGGGGCGTGGCG 1367
Qy 541 CGGGGCTCGCCGTGCCGGGCGGGGGGTGGCGGCAGGTGGGGGTGCCGGGCGGGGCGGGGC 600
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 1368 CGGGGCTCGCCGTGCCGGGCGGGGGGTGGCGGCAGGTGGGGGTGCCGGGCGGGGCGGGGC 1427
Qy 601 CGCCTCGGGCCGGGGAGGGCTCGGGGGAGGGGCGCGGCGGCCCCCGGAGCGCCGGCGGCT 660
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 1428 CGCCTCGGGCCGGGGAGGGCTCGGGGGAGGGGCGCGGCGGCCCCCGGAGCGCCGGCGGCT 1487
Qy 661 GTCGAGGCGCGGCGAGCCGCAGCCATTGCCTTTTATGGTAATCGTGCGAGAGGGCGCAGG 720
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 1488 GTCGAGGCGCGGCGAGCCGCAGCCATTGCCTTTTATGGTAATCGTGCGAGAGGGCGCAGG 1547
Qy 721 GACTTCCTTTGTCCCAAATCTGTGCGGAGCCGAAATCTGGGAGGCGCCGCCGCACCCCCT 780
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 1548 GACTTCCTTTGTCCCAAATCTGTGCGGAGCCGAAATCTGGGAGGCGCCGCCGCACCCCCT 1607
Qy 781 CTAGCGGGCGCGGGGCGAAGCGGTGCGGCGCCGGCAGGAAGGAAATGGGCGGGGAGGGCC 840
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 1608 CTAGCGGGCGCGGGGCGAAGCGGTGCGGCGCCGGCAGGAAGGAAATGGGCGGGGAGGGCC 1667
Qy 841 TTCGTGCGTCGCCGCGCCGCCGTCCCCTTCTCCCTCTCCAGCCTCGGGGCTGTCCGCGGG 900
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 1668 TTCGTGCGTCGCCGCGCCGCCGTCCCCTTCTCCCTCTCCAGCCTCGGGGCTGTCCGCGGG 1727
Qy 901 GGGACGGCTGCCTTCGGGGGGGACGGGGCAGGGCGGGGTTCGGCTTCTGGCGTGTGACCG 960
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 1728 GGGACGGCTGCCTTCGGGGGGGACGGGGCAGGGCGGGGTTCGGCTTCTGGCGTGTGACCG 1787
Qy 961 GCGGCTCTAGAGCCTCTGCTAACCATGTTCATGCCTTCTTCTTTTTCCTACAG 1013
|||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 1788 GCGGCTCTAGAGCCTCTGCTAACCATGTTCATGCCTTCTTCTTTTTCCTACAG 1840
SEQ ID NO 20:
RESULT 1
US-19-095-986-92
Query Match 100.0%; Score 225; DB 1; Length 3845;
Best Local Similarity 100.0%;
Matches 225; Conservative 0; Mismatches 0; Indels 0; Gaps 0;
Qy 1 CTGTGCCTTCTAGTTGCCAGCCATCTGTTGTTTGCCCCTCCCCCGTGCCTTCCTTGACCC 60 SEQ ID NO 20
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 3438 CTGTGCCTTCTAGTTGCCAGCCATCTGTTGTTTGCCCCTCCCCCGTGCCTTCCTTGACCC 3497 US726 SEQ 92
Qy 61 TGGAAGGTGCCACTCCCACTGTCCTTTCCTAATAAAATGAGGAAATTGCATCGCATTGTC 120
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 3498 TGGAAGGTGCCACTCCCACTGTCCTTTCCTAATAAAATGAGGAAATTGCATCGCATTGTC 3557
Qy 121 TGAGTAGGTGTCATTCTATTCTGGGGGGTGGGGTGGGGCAGGACAGCAAGGGGGAGGATT 180
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 3558 TGAGTAGGTGTCATTCTATTCTGGGGGGTGGGGTGGGGCAGGACAGCAAGGGGGAGGATT 3617
Qy 181 GGGAAGACAATAGCAGGCATGCTGGGGATGCGGTGGGCTCTATGG 225
|||||||||||||||||||||||||||||||||||||||||||||
Db 3618 GGGAAGACAATAGCAGGCATGCTGGGGATGCGGTGGGCTCTATGG 3662
Therefore the App986 claims recite elements (i), (ii), (iii), (iv), (viii), and (ix) of the claimed invention. Then the other prior art teaches the other claim elements that the App986 claims do not recite, including a sequence encoding CLRN1 and administration to retinal cells:
WO900 teaches (¶99) an rAAV vector comprising the CLRN1 cDNA including the 5’ and 3’UTRs, and teaches driving it with the chicken β-actin promoter. WO900 teaches (¶9-10) the polynucleotide (polynt) can include a sequence having SEQ ID NO 2 (which it specifies comprises a 5’UTR and 3’UTR) and can be included on a vector that can be an adeno-associated viral vector (AAV) that can be used for transfecting ocular cells or cells of the inner ear. WO900 teaches using (¶72) AAV2 vectors to administer the composition. WO900 teaches (¶21) that the heterologous polynucleotide comprised in the AAV vector is flanked by at least one, and generally by two AAV inverted terminal repeat sequence (ITRs); an artisan would realize that being flanked by two ITRs refers to one ITR on either side, which is a 5’ITR and a 3’ITR.
WO900 SEQ ID NO 2 comprises a polynt comprising a sequence encoding the amino acid sequence of claimed SEQ ID NO 3 (which has been back-translated from AA[Wingdings font/0xE0]nucleotides). This is shown by the following sequence alignment:
RESULT 7
BDA01054
ID BDA01054 standard; cDNA; 2352 BP.
XX
AC BDA01054;
XX
DT 16-JUN-2016 (first entry)
XX
DE Human derived clarin-1 (CLRN1) polynucleotide SEQ ID NO:2.
XX
KW CLRN1 gene; auditory; clarin-1; gene therapy; hearing loss;
KW ophthalmological; ss; therapeutic; usher syndrome iii; vision disorder.
XX
OS Homo sapiens.
XX
CC PN WO2016073900-A1.
XX
CC PD 12-MAY-2016.
XX
CC PF 06-NOV-2015; 2015WO-US059546.
XX
PR 06-NOV-2014; 2014US-0076114P.
PR 08-MAY-2015; 2015US-0158846P.
XX
CC PA (UCWR ) UNIV CASE WESTERN RESERVE.
XX
CC PI Alagramam KN;
XX
DR WPI; 2016-282935/37.
XX
CC PT New polynucleotide comprising a nucleic acid sequence that includes a
CC PT cDNA coding sequence of a clarin-1 gene, useful for treating vision
CC PT and/or hearing loss associated with Usher syndrome III.
XX
CC PS Claim 9; SEQ ID NO 2; 43pp; English.
XX
CC The invention relates to a novel polynucleotide, used for treating vision
CC and/or hearing loss associated with Usher syndrome III. This
CC polynucleotide comprises a nucleic acid sequence that includes a cDNA
CC coding sequence of a clarin-1 (CLRN1) gene and a 3' untranslated region
CC (UTR) nucleic acid that is derived from the 3' UTR of the clarin-1 gene,
CC where the 3' UTR nucleic acid enhances expression of clarin-1 in a cell
CC transfected with the polynucleotide compared to a cell transfected with a
CC similar polynucleotide devoid of the 3' UTR nucleic acid. The invention
CC further claims: a nucleic acid construct comprising a polynucleotide
CC defined above; a vector for transfecting a cell, comprising a
CC polynucleotide defined above, where the transfected cell expresses clarin
CC -1; and a method of treating vision and/or hearing loss associated with
CC Usher syndrome III in a subject by administering to the ocular cells
CC and/or cells of the inner ear of the subject, a vector that promotes
CC expression of clarin-1 in the cells. The present sequence is a clarin-1
CC polynucleotide, used for treating vision and/or hearing loss associated
CC with Usher syndrome III in a subject.
XX
SQ Sequence 2352 BP; 705 A; 475 C; 484 G; 688 T; 0 U; 0 Other;
Alignment Scores:
Length: 2352
Score: 1214.00 Matches: 232
Percent Similarity: 100.0% Conservative: 0
Best Local Similarity: 100.0% Mismatches: 0
Query Match: 100.0% Indels: 0
Gaps: 0
US-17-253-658-3 (1-232) x BDA01054 (1-2352)
Qy 1 MetProSerGlnGlnLysLysIleIlePheCysMetAlaGlyValPheSerPheAlaCys 20 SEQ ID NO 3 translated[Wingdings font/0xE0]NT
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 282 ATGCCAAGCCAACAGAAGAAAATCATTTTTTGCATGGCCGGAGTGTTCAGTTTTGCATGT 341 WO900 SEQ ID NO 2
Qy 21 AlaLeuGlyValValThrAlaLeuGlyThrProLeuTrpIleLysAlaThrValLeuCys 40
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 342 GCCCTCGGAGTTGTGACAGCCTTGGGGACACCGTTGTGGATCAAAGCCACTGTCCTCTGC 401
Qy 41 LysThrGlyAlaLeuLeuValAsnAlaSerGlyGlnGluLeuAspLysPheMetGlyGlu 60
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 402 AAAACGGGAGCTCTGCTCGTCAATGCCTCAGGGCAGGAGCTGGACAAGTTTATGGGTGAA 461
Qy 61 MetGlnTyrGlyLeuPheHisGlyGluGlyValArgGlnCysGlyLeuGlyAlaArgPro 80
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 462 ATGCAGTACGGGCTTTTCCACGGAGAGGGTGTGAGGCAGTGTGGGTTGGGAGCAAGGCCC 521
Qy 81 PheArgPheSerPhePheProAspLeuLeuLysAlaIleProValSerIleHisValAsn 100
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 522 TTTCGGTTCTCATTTTTTCCAGATTTGCTCAAAGCAATCCCAGTGAGCATCCACGTCAAT 581
Qy 101 ValIleLeuPheSerAlaIleLeuIleValLeuThrMetValGlyThrAlaPhePheMet 120
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 582 GTCATTCTCTTCTCTGCCATCCTTATTGTGTTAACCATGGTGGGGACAGCCTTCTTCATG 641
Qy 121 TyrAsnAlaPheGlyLysProPheGluThrLeuHisGlyProLeuGlyLeuTyrLeuLeu 140
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 642 TACAATGCTTTTGGAAAACCTTTTGAAACTCTGCATGGTCCCCTAGGGCTGTACCTTTTG 701
Qy 141 SerPheIleSerGlySerCysGlyCysLeuValMetIleLeuPheAlaSerGluValLys 160
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 702 AGCTTCATTTCAGGCTCCTGTGGCTGTCTTGTCATGATATTGTTTGCCTCTGAAGTGAAA 761
Qy 161 IleHisHisLeuSerGluLysIleAlaAsnTyrLysGluGlyThrTyrValTyrLysThr 180
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 762 ATCCATCACCTCTCAGAAAAAATTGCAAATTATAAAGAAGGGACTTATGTCTACAAAACG 821
Qy 181 GlnSerGluLysTyrThrThrSerPheTrpValIlePhePheCysPhePheValHisPhe 200
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 822 CAAAGTGAAAAATATACCACCTCATTCTGGGTCATTTTCTTTTGCTTTTTTGTTCATTTT 881
Qy 201 LeuAsnGlyLeuLeuIleArgLeuAlaGlyPheGlnPheProPheAlaLysSerLysAsp 220
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 882 CTGAATGGGCTCCTAATACGACTTGCTGGATTTCAGTTCCCTTTTGCAAAATCTAAAGAC 941
Qy 221 AlaGluThrThrAsnValAlaAlaAspLeuMetTyr 232
||||||||||||||||||||||||||||||||||||
Db 942 GCAGAAACAACTAATGTAGCTGCAGATCTAATGTAC 977
That alignment shows that the composition of WO900 comprises SEQ ID NO 3 itself, a 5’UTR, and a 3’UTR. Those are elements (v), (vi), and (vii) of the instant claims. WO900 teaches (¶10-11) treating retinal cells.
The App986 claims do not recite a kit that comprises a pre-loaded syringe. However, US952 teaches (Col 11 L3-15) a kit that comprises nucleic acid compounds within a container of solution and that the kit can comprise a pre-loaded syringe comprising the compounds. An artisan would have put their compounds into a kit comprising a pre-loaded syringe for the benefit of ensuring that the recipient has the exact dosage ready to administer and because doing so would have prevented any complications that arise from mixing a solution and then getting the mixed solution into a syringe.
Therefore it would have been obvious to use WO900’s SEQ ID NO 2 with the AAV particle of App986 in order to express CLRN1. An artisan would have known that using WO900’s sequence and teachings with the invention recited in the App986 claims and modified by the teachings of WO900 and US952 would have provided a benefit of treating hearing or vision loss because WO900 teaches that (¶11), and it would have been a simple matter to swap the sequence encoding CLRN1 of WO900 for the sequence encoding a VEGF antibody of the App986 claims. Packaging it into a pre-loaded syringe would also have been of benefit as taught by US952. Using WO900’s sequence and teachings with the invention recited in the App986 claims and modified by the teachings of US952 would have produced the instant invention.
Therefore the instant claims would have been obvious in view of the App986 claims, WO900, and US952.
This is a provisional nonstatutory double patenting rejection.
Potentially Allowable Subject Matter
SEQ ID NO 16 was searched and found to be nonobvious over the prior art of record within the context of the claims.
International Patent Application Publication No WO2011061937 (“WO937”) teaches SEQ ID NOs 10, 13, 18, and 20 which are promoters that comprise claimed SEQ ID NO 16. An alignment of SEQ ID NO 16 with WO937’s SEQ ID NO 20 is shown here:
RESULT 70
AZI43343
ID AZI43343 standard; DNA; 6871 BP.
XX
AC AZI43343;
XX
DT 07-JUL-2011 (first entry)
XX
DE Gallus gallus antibody variable light chain targeting vector 2, SEQ 20.
XX
KW antibody production; ds; recombinant dna; recombination.
XX
OS Unidentified.
XX
FH Key Location/Qualifiers
FT sig_peptide 1869..1914
FT /*tag= a
FT /product= "Antibody variable region signal peptide"
FT intron 1915..2039
FT /*tag= b
FT sig_peptide 2040..2056
FT /*tag= c
FT /product= "Antibody variable region signal peptide"
FT misc_feature 2076..2109
FT /*tag= d
FT /note= "LoxP_LE"
FT promoter 2137..3478
FT /*tag= e
FT /note= "Marker gene promoter"
FT misc_feature 3967..4953
FT /*tag= f
FT /note= "marker gene"
FT /note= "Poly A additon of marker gene"
FT misc_feature 4960..4993
FT /*tag= g
FT /note= "LoxP_RE"
FT misc_feature 5002..6861
FT /*tag= h
FT /note= "3' homologous DNA of antibody variable region"
XX
CC PN WO2011061937-A1.
XX
CC PD 26-MAY-2011.
XX
CC PF 18-NOV-2010; 2010WO-JP006759.
XX
PR 19-NOV-2009; 2009JP-00264398.
PR 20-NOV-2009; 2009US-0263285P.
XX
CC PA (IMMU-) IMMUNO TEC LAB CO LTD.
XX
CC PI Fujii S, Kanayama N, Ohmori H;
XX
DR WPI; 2011-F88240/36.
XX
CC PT Homologously recombining a DNA construct and a region comprising a DNA
CC PT encoding an antibody variable region of an antibody-producing cell by
CC PT introducing into the antibody-producing cell a targeting vector.
XX
CC PS Example; SEQ ID NO 20; 121pp; English.
XX
CC The present invention relates to a method for homologously recombining a
CC DNA construct and a region comprising a DNA encoding an antibody variable
CC region of an antibody-producing cell which comprises introducing into an
CC antibody-producing cell a targeting vector comprising a DNA construct
CC that comprises: (a) a promoter DNA that functions in the cell; (b) a DNA
CC that encodes a desired amino acid sequence; and (c) a DNA that inhibits
CC the production of a polypeptide comprising the desired amino acid
CC sequence, and can be removed from the DNA construct. The invention also
CC includes: (1) a method for selecting a cell; (2) a method for producing
CC an antibody-producing cell or polypeptide that produces a polypeptide
CC into which a mutation is introduced; (3) a method for producing a DNA
CC encoding a polypeptide or a polypeptide into which a mutation is
CC introduced; (4) an antibody-producing cell in which a region comprising a
CC DNA encoding an antibody variable region is homologously recombined with
CC a DNA construct; (5) a kit comprising the cell and targeting vector; and
CC (6) a gene targeting vector comprising the DNA construct. The methods of
CC the invention are useful for targeting vectors for introducing a DNA
CC encoding a desired amino acid sequence into the antibody variable region
CC gene locus of an antibody producing cells. The present sequence is a
CC Gallus gallus antibody variable light chain targeting vector 2 which is
CC used to allow insertion of a foreign antibody variable region gene
CC immediately after the signal peptide, the nucleotide sequence of the end
CC of the signal peptide is modified to have an SphI site.
XX
SQ Sequence 6871 BP; 1609 A; 1538 C; 1907 G; 1817 T; 0 U; 0 Other;
Query Match 100.0%; Score 1013; Length 6871;
Best Local Similarity 100.0%;
Matches 1013; Conservative 0; Mismatches 0; Indels 0; Gaps 0;
Qy 1 GGAGTCGCTGCGTTGCCTTCGCCCCGTGCCCCGCTCCGCGCCGCCTCGCGCCGCCCGCCC 60 SEQ ID NO 16
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 2408 GGAGTCGCTGCGTTGCCTTCGCCCCGTGCCCCGCTCCGCGCCGCCTCGCGCCGCCCGCCC 2467 prior art SEQ
Qy 61 CGGCTCTGACTGACCGCGTTACTCCCACAGGTGAGCGGGCGGGACGGCCCTTCTCCTCCG 120
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 2468 CGGCTCTGACTGACCGCGTTACTCCCACAGGTGAGCGGGCGGGACGGCCCTTCTCCTCCG 2527
Qy 121 GGCTGTAATTAGCGCTTGGTTTAATGACGGCTCGTTTCTTTTCTGTGGCTGCGTGAAAGC 180
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 2528 GGCTGTAATTAGCGCTTGGTTTAATGACGGCTCGTTTCTTTTCTGTGGCTGCGTGAAAGC 2587
Qy 181 CTTAAAGGGCTCCGGGAGGGCCCTTTGTGCGGGGGGGAGCGGCTCGGGGGGTGCGTGCGT 240
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 2588 CTTAAAGGGCTCCGGGAGGGCCCTTTGTGCGGGGGGGAGCGGCTCGGGGGGTGCGTGCGT 2647
Qy 241 GTGTGTGTGCGTGGGGAGCGCCGCGTGCGGCCCGCGCTGCCCGGCGGCTGTGAGCGCTGC 300
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 2648 GTGTGTGTGCGTGGGGAGCGCCGCGTGCGGCCCGCGCTGCCCGGCGGCTGTGAGCGCTGC 2707
Qy 301 GGGCGCGGCGCGGGGCTTTGTGCGCTCCGCGTGTGCGCGAGGGGAGCGCGGCCGGGGGCG 360
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 2708 GGGCGCGGCGCGGGGCTTTGTGCGCTCCGCGTGTGCGCGAGGGGAGCGCGGCCGGGGGCG 2767
Qy 361 GTGCCCCGCGGTGCGGGGGGGCTGCGAGGGGAACAAAGGCTGCGTGCGGGGTGTGTGCGT 420
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 2768 GTGCCCCGCGGTGCGGGGGGGCTGCGAGGGGAACAAAGGCTGCGTGCGGGGTGTGTGCGT 2827
Qy 421 GGGGGGGTGAGCAGGGGGTGTGGGCGCGGCGGTCGGGCTGTAACCCCCCCCTGCACCCCC 480
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 2828 GGGGGGGTGAGCAGGGGGTGTGGGCGCGGCGGTCGGGCTGTAACCCCCCCCTGCACCCCC 2887
Qy 481 CTCCCCGAGTTGCTGAGCACGGCCCGGCTTCGGGTGCGGGGCTCCGTGCGGGGCGTGGCG 540
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 2888 CTCCCCGAGTTGCTGAGCACGGCCCGGCTTCGGGTGCGGGGCTCCGTGCGGGGCGTGGCG 2947
Qy 541 CGGGGCTCGCCGTGCCGGGCGGGGGGTGGCGGCAGGTGGGGGTGCCGGGCGGGGCGGGGC 600
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 2948 CGGGGCTCGCCGTGCCGGGCGGGGGGTGGCGGCAGGTGGGGGTGCCGGGCGGGGCGGGGC 3007
Qy 601 CGCCTCGGGCCGGGGAGGGCTCGGGGGAGGGGCGCGGCGGCCCCCGGAGCGCCGGCGGCT 660
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 3008 CGCCTCGGGCCGGGGAGGGCTCGGGGGAGGGGCGCGGCGGCCCCCGGAGCGCCGGCGGCT 3067
Qy 661 GTCGAGGCGCGGCGAGCCGCAGCCATTGCCTTTTATGGTAATCGTGCGAGAGGGCGCAGG 720
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 3068 GTCGAGGCGCGGCGAGCCGCAGCCATTGCCTTTTATGGTAATCGTGCGAGAGGGCGCAGG 3127
Qy 721 GACTTCCTTTGTCCCAAATCTGTGCGGAGCCGAAATCTGGGAGGCGCCGCCGCACCCCCT 780
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 3128 GACTTCCTTTGTCCCAAATCTGTGCGGAGCCGAAATCTGGGAGGCGCCGCCGCACCCCCT 3187
Qy 781 CTAGCGGGCGCGGGGCGAAGCGGTGCGGCGCCGGCAGGAAGGAAATGGGCGGGGAGGGCC 840
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 3188 CTAGCGGGCGCGGGGCGAAGCGGTGCGGCGCCGGCAGGAAGGAAATGGGCGGGGAGGGCC 3247
Qy 841 TTCGTGCGTCGCCGCGCCGCCGTCCCCTTCTCCCTCTCCAGCCTCGGGGCTGTCCGCGGG 900
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 3248 TTCGTGCGTCGCCGCGCCGCCGTCCCCTTCTCCCTCTCCAGCCTCGGGGCTGTCCGCGGG 3307
Qy 901 GGGACGGCTGCCTTCGGGGGGGACGGGGCAGGGCGGGGTTCGGCTTCTGGCGTGTGACCG 960
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 3308 GGGACGGCTGCCTTCGGGGGGGACGGGGCAGGGCGGGGTTCGGCTTCTGGCGTGTGACCG 3367
Qy 961 GCGGCTCTAGAGCCTCTGCTAACCATGTTCATGCCTTCTTCTTTTTCCTACAG 1013
|||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 3368 GCGGCTCTAGAGCCTCTGCTAACCATGTTCATGCCTTCTTCTTTTTCCTACAG 3420
However, WO937 provides no reason for an artisan to choose specifically bp 2408-3420 from SEQ ID NO 20, bp 2417-3429 from SEQ ID NO 18, bp 3233-4245 from SEQ ID NO 13, 3244-4256 from SEQ ID NO 10 and use them in the claimed invention.
Response to Arguments
Applicant's arguments filed 27 March 2026 have been fully considered but they are not persuasive. Each rejection is addressed below. Arguments that are no longer relevant are not addressed.
Claim objection
Claim 267 is objected to for minor informalities as discussed above.
112b rejections
Claims 264-270 are rejected because they are ambiguous as to whether the claims are directed to compositions or method of using the compositions. The metes and bounds of the claims are unclear. Applicant’s remarks dated 27 March 2026 discuss (p. 11 §Claim interpretation of Claims 269-270) the interpretation of Claims 269-270 wherein Applicant states that they respectfully disagree[e] with the interpretation. However, they have provided no reasons why they disagree and have not explained how the claims are not ambiguous. Although they have re-written Claim 248 in independent form, that doesn’t render the claim interpretation moot because the claims are still ambiguous as to what they encompass.
Claims 264-270 recite both a composition (i.e., a kit comprising a composition, wherein the composition comprises…) and an instruction sheet for performing method steps. The claim(s) are considered indefinite because there is a question or doubt as to what are the metes and bounds of the claims. Method claims that depend from composition claims are not permitted.
II. PRODUCT AND PROCESS IN THE SAME CLAIM
A single claim which claims both an apparatus and the method steps of using the apparatus is indefinite under 35 U.S.C. 112(b) or pre-AIA 35 U.S.C. 112, second paragraph. See In re Katz Interactive Call Processing Patent Litigation, 639 F.3d 1303, 1318, 97 USPQ2d 1737, 1748-49 (Fed. Cir. 2011). In Katz, a claim directed to "[a] system with an interface means for providing automated voice messages…to certain of said individual callers, wherein said certain of said individual callers digitally enter data" was determined to be indefinite because the italicized claim limitation is not directed to the system, but rather to actions of the individual callers, which creates confusion as to when direct infringement occurs. Katz, 639 F.3d at 1318, 97 USPQ2d at 1749 (citing IPXL Holdings v. Amazon.com, Inc., 430 F.3d 1377, 1384, 77 USPQ2d 1140, 1145 (Fed. Cir. 2005), in which a system claim that recited "an input means" and required a user to use the input means was found to be indefinite because it was unclear "whether infringement … occurs when one creates a system that allows the user [to use the input means], or whether infringement occurs when the user actually uses the input means."); Ex parte Lyell, 17 USPQ2d 1548 (Bd. Pat. App. & Inter. 1990) (claim directed to an automatic transmission workstand and the method of using it held ambiguous and properly rejected under 35 U.S.C. 112, second paragraph).
MPEP §2173.05(p)
Similar to the case described above, these claims are indefinite because the method limitations are not directed to the kit, but rather to instructions that describe actions or potential actions of an individual in possession of the kit, which creates confusion as to when direct infringement occurs. In this case it is ambiguous whether or not the method steps on the instructions must be carried out to meet the terms of the claims.
112d rejections
Claims 264-270 are rejected because they fail to limit the subject matter of Claim 248 (from which they depend) as discussed above. Claims 264-270 merely recite intended use for the composition/kit claim of Claim 248.
NSDP rejections
Regarding the NSDP rejections, Applicant has disagreed with them and (p. 14) refers to their previous remarks. In the previous remarks, they argued (Remarks Oct. 2025 pp. 10-14) the instantly claimed invention is filed earlier than any of the reference applications. That is not found persuasive because making NSDP rejections over other applications and issued patents is proper.
The claims of issued US Patents US867, US773, and US191 and copending application App662disclose vector sequences that comprise claimed SEQ ID NO 16, and all of the other claim elements would have been obvious in view of the cited prior art. Furthermore, it would have been obvious to an artisan to use a single vector to express CLRN1 because the prior art (i.e., WO900) discloses single AAV vectors for expressing CLRN1 and because it is simpler to administer a single vector gene therapy rather than a dual vector gene therapy. WO900 teaches (¶85) vectors can be associated with immunogenic response and although AAV presents low risk for pathogenic reactions, (¶82) therapeutic effects must be balanced with toxic or detrimental effects from a vector; that would have motivated an artisan to minimize the number of vectors administered. Since the art teaches that expressing CLRN1 requires only a single AAV vector, an artisan would have found it obvious and beneficial to do so.
The other prior art teaches the other elements of the claimed invention: WO900 teaches a nt sequence encoding 5’- and 3’-UTRs and claimed SEQ ID NO 3. WO900 teaches administration to retinal cells. Landegger teaches administering an Anc80 serotype. Powell teaches benefits of using a polyA signal and App178 teaches the polyA sequence that is claimed SEQ ID NO 20. US952 teaches a kit that comprises a pre-loaded syringe.
Regarding US726, those claims are broadly directed to an AAV particle wherein the nucleic acid construct comprises SEQ ID NOs 91 or 92. As discussed in the NSDP rejection, those SEQ ID NOs comprise claimed SEQ ID NOs 16, 17, and 20. Like the other NSDP rejections, the other cited prior art teaches the remaining claim limitations that the reference application claims do not teach. It would have been obvious to swap the CLRN1 sequence of WO900 for the coding sequences within SEQ ID NOs 91 or 92.
Regarding the copending applications, MPEP §804(I)(B)(1)(b)(i) does not yet apply because those NSDP rejections are not the sole rejections remaining; there are NSDP rejections over issued patents.
Regarding App266, those claims are broadly directed to a construct for expressing a coding sequence of an NDP protein . The App266 claims recite a chimeric intron sequence that is the same as claimed SEQ ID NO 16 and a CMV enhancer that is the same as claimed SEQ ID NO 17. There is no reason why an artisan could not use the construct of App266 claims to express another protein besides for NDP protein, including the CLRN1 protein of WO900.
Regarding App131, those claims are very directed to a construct or AAV particle comprising SEQ ID NO 333 which, as discussed, comprises many of the instantly claimed elements, including SEQ ID NOs 16 and 17. Like the other NSDP rejections, the other cited prior art teaches the remaining claim limitations that the reference application claims do not teach and it would have been obvious to swap the CLRN1 sequence of WO900 for the coding sequences within SEQ ID NO 333.
Regarding App307, the NSDP rejection explains that those claims recite all the elements of the claimed invention besides for the kit and preloaded syringe. App307 also recites SEQ ID NOs 64 and 68 which are at least 90% and at least 95% identical to claimed SEQ ID NO 42.
Regarding App986, the NSDP rejection explains that those claims recite a composition comprising AAV particles that comprise a nucleic acid sequence that comprises the same chimeric intron sequence as claimed SEQ ID NO 16, the same CVM enhancer sequence of claimed SEQ ID NO 17, and the same polyA sequence as claimed SEQ ID NO 20.
In each case it would have been obvious to use the sequence encoding a CLRN1 protein of WO900 with the patented/copending inventions because WO900 teaches (¶3-4) expressing CLRN1 had known usage in treating Usher syndrome, including (¶11) for both hearing and vision losses, and it would have been a simple matter to swap the sequence encoding CLRN1 of WO900 for the sequences of the patented/copending claims.
Applicant argues (Oct. 2025 Remarks pp. 10-11) the rejections over the issued patents should be removed because double patenting is to avoid an unjustified extension or improper timewise extension of the right to exclude granted by a patent. Applicant argues that the granted patents have a later expiration date than the instant claims would have if they were granted.
Those arguments are not found persuasive. The following chart from MPEP 804 indicates that NSDP rejections should be made over the issued patents:
PNG
media_image1.png
2200
1700
media_image1.png
Greyscale
Note that withdrawal of an NSDP rejection when the application under examination has the earlier patent term filing date applies to provisional NSDP rejections, not rejections over issued patents:
If a provisional nonstatutory double patenting rejection is the only rejection remaining in an application having the earlier patent term filing date, the examiner should withdraw the rejection in the application having the earlier patent term filing date and permit that application to issue as a patent, thereby converting the provisional nonstatutory double patenting rejection in the other application into a nonstatutory double patenting rejection upon issuance of the patent. [emphasis added.] MPEP 804(I)(B)(1)(b)(i)
Furthermore, Applicant should note that the instant claims, if allowed, would improperly extend the "right to exclude" already granted in the issued patents. The subject matter claimed in the instant application would have been obvious in view of the issued patents and the prior art, as discussed in each NSDP rejection. Furthermore, there is no apparent reason why applicant was prevented from presenting claims corresponding to those of the instant application during prosecution of the applications which each matured into a patent. See In re Schneller, 397 F.2d 350, 158 USPQ 210 (CCPA 1968). See also MPEP § 804.
Information in the § about Terminal Disclaimers touches on the right to exclude (MPEP 804.02[IV]):
Each one of the commonly owned conflicting nonstatutory double patenting references must be included in the terminal disclaimer to avoid the problem of dual ownership of patents to patentably indistinct inventions in the event that the patent issuing from the application being examined ceases to be commonly owned with any one of the double patenting references that have issued or may issue as a patent. Note that 37 CFR 1.321(c)(3) requires that a terminal disclaimer for commonly owned conflicting claims "[i]nclude a provision that any patent granted on that application or any patent subject to the reexamination proceeding shall be enforceable only for and during such period that said patent is commonly owned with the application or patent which formed the basis for the judicially created double patenting."
Filing a terminal disclaimer including each one of the conflicting nonstatutory double patenting references is also necessary to avoid the problem of separate enforcement of patents to patentably indistinct inventions by parties to a joint research agreement.
MPEP 804.02(IV)
That § makes clear that “unjustified extension of exclusivity” refers not only to patent term, but also to ownership/licensing of the technology.
In response to Applicant’s arguments (Oct. 2025 Remarks pp. 10-11) that the Patent Trial Appeal Board (PTAB) concluded that the later patent generally is determined by looking at the expiration date and that double patenting only invalidates the later patent, those arguments are not found persuasive because Examiners follow the MPEP, not the PTAB. There is nothing in MPEP concerning not making NSDP over later-expiring patent. Rather, MPEP 804.I.B.1.(b).(i) makes clear that a provisional double patenting rejection should be made and maintained by the examiner until the rejection has been overcome by amendment or the rejection is the only rejection remaining in an application having the earlier patent term filing date. Regarding the copending applications, the claims are still rejected under §112(b) and §112(d), so the rejection(s) for nonstatutory double patenting is/are maintained. Regarding the issued patents, this case was discussed with a Quality Assurance Specialist who agreed the rejections should be maintained.
Regarding Applicant’s arguments (Oct. 2025 Remarks pp. 11-12) about In re Cellect (IN RE: CELLECT, LLC. US Court of Appeals for the Federal Circuit. 23 August 2023, “Decision”), the MPEP has makes only three references to that case and none of them is in the context discussed in Applicant’s arguments. A screen shot of those search results is presented here:
PNG
media_image2.png
574
1064
media_image2.png
Greyscale
Furthermore, Cellect is about effects of PTA and PTE on NSDP. The Decision indicates the Cellect case is about (§I) PTA, (§II) a promise to avoid multiple ownership, and (§III) the fact that it isn’t possible to determine during re-exam whether an Examiner considered NSDP rejections during initial examination. Conversely, examination of the instant application doesn’t take into account PTA. Altogether, Cellect doesn’t apply to the instant case because PTA is not of issue here.
While Applicant’s Remarks apply parts of Cellect to the instant claims, there are other parts of the Board’s decision (with which the Federal Court agreed) they haven’t applied, including parts about (p. 8 full ¶1; pp. 21-23, §II) a risk of divided ownership and subsequent harassment by multiple assignees. That is a risk that pertains to the claimed invention and the claims of the issued patents. Notably, Applicant’s Remarks have not addressed any of those points (or explained why the claimed invention isn’t obvious). The Cellect decision discusses (p. 15 ¶4-5):
First, we note that an ODP determination depends on an assessment of obviousness, i.e., whether the claims of a later-expiring patent would have been obvious over the claims of an earlier-expiring patent owned by the same party. If so, absent a terminal disclaimer, the later-expiring claims are invalid. Application of that determination requires determining which is the later-expiring patent, which is why the date when PTA or PTE is applied matters.
We conclude that… the expiration date used for an ODP analysis where a patent has received PTA is the expiration date after the PTA has been added. [emphasis added.]
That indicates a calculation of PTA is required before Applicant can factually assert that the instant claims would, if issued, expire before the patented or copending claims.
The fact pattern of Cellect simply isn’t the same as (or similar to) that in the instant situation because Cellect is directed to the effect of PTA on NSDP. Nothing in the current rejections discusses PTA.
Similarly, Powers (2025. 2024 Federal Circuit IP Appeals – Allergan USA, Inc. v. MSN Labs. Private LTD, 111 F.4th 1358 [Fed. Cir. 2024] [Lourie, Dyk, Reyna], “Powers”) discusses (¶2-3) the Allergan case (which Applicant describes on Remarks pp. 11-12 ¶4) is about patents in the same family and:
The court held that a “first-filed, first-issued, later-expiring claim cannot be invalidated by a later-filed, later-issued, earlier-expiring reference claim having a common priority date.” The Federal Circuit distinguished its holding in Cellect by stating that “Cellect does not address, let alone resolve, any variation of the question presented here—namely, under what circumstances can a claim properly serve as an ODP reference—and therefore has little to say on the precise issue before us.”
Once again, the fact pattern of Allergan is not the same as or even similar to that of the claimed invention. The claimed invention and the patented and copending inventions are not in the same family. Furthermore, “a first-filed, first-issued, later-expiring claim” is not being compared with “a later-filed, later-issued, earlier-expiring reference claim” because the later-filed claims (i.e., in this case, the issued patents) are first-issued and later-expiring. Powers’ summary of the case indicates that Allergan applies strictly to parent–child situations: (Powers, second-to-last ¶) the court held, in such circumstances there is no unjust extension of patent term of the invention claimed in the child patent when the claims in the child patent did not even exist until after the parent patent issued. That doesn’t apply to the instant case for obvious reasons: this isn’t a parent–child situation, and the claims in the later-filed patents/applications clearly existed (and issued) before this case issued.
On Remarks (Oct. 2025, p. 12, ¶1) Applicant discusses that ODP is to prevent a second patent that extends the life of the first patent. But as discussed, that is only one purpose of NSDP rejections. The other is to prevent splitting ownership of related patents and subsequent potential harassment by multiple owners or assignees.
Regarding Applicant’s arguments (Oct. 2025 Remarks pp. 11-12) about Ex parte Baurin, Applicants assert that the NSDP rejections should be withdrawn because the patent term of the instant application, if issued as a patent, would not extend the patent term of any of the cited patents or applications. However, Ex parte Baurin is a non-precedential decision, and thus is not applicable to the instant application. In addition, an appeal has been filed in Ex parte Baurin. As such, Ex parte Baurin has not reached a final decision, and for this reason as well, is not applicable to the NSDP rejections in the instant application.
Thus, each of these NSDP rejections are proper and are maintained.
Note that the only way to overcome the NSDP rejections over the issued US patents is with persuasive arguments or a terminal disclaimer (TD).
Therefore all the NSDP rejections must be maintained until all the claims are ready to allow. The NSDP rejections over the issued patents must be maintained until they are either persuasively argued or a TD is filed.
Conclusion
No claim is allowed.
Any inquiry concerning this communication or earlier communications from the examiner should be directed to RUTHIE S ARIETI whose telephone number is (571)272-1293. The examiner can normally be reached M-Th 8:30AM-4PM, alternate Fridays 8:30AM-4PM (ET).
Examiner interviews are available via telephone, in-person, and video conferencing using a USPTO supplied web-based collaboration tool. To schedule an interview, applicant is encouraged to use the USPTO Automated Interview Request (AIR) at http://www.uspto.gov/interviewpractice.
If attempts to reach the examiner by telephone are unsuccessful, the examiner’s supervisor, Ram R Shukla can be reached on (571)272-0735. The fax phone number for the organization where this application or proceeding is assigned is 571-273-8300.
Information regarding the status of published or unpublished applications may be obtained from Patent Center. Unpublished application information in Patent Center is available to registered users. To file and manage patent submissions in Patent Center, visit: https://patentcenter.uspto.gov. Visit https://www.uspto.gov/patents/apply/patent-center for more information about Patent Center and https://www.uspto.gov/patents/docx for information about filing in DOCX format. For additional questions, contact the Electronic Business Center (EBC) at 866-217-9197 (toll-free). If you would like assistance from a USPTO Customer Service Representative, call 800-786-9199 (IN USA OR CANADA) or 571-272-1000.
RUTHIE S ARIETI
Examiner
Art Unit 1635
/RUTH SOPHIA ARIETI/Examiner, Art Unit 1635
/NANCY J LEITH/Primary Examiner, Art Unit 1636
Prosecution Insights