DETAILED ACTION
The present application, filed on or after March 16, 2013, is being examined under the first inventor to file provisions of the AIA .
Applicant’s amendments to the claims and arguments filed on April 22, 2026 have been received and entered. Claims 1-17, 28-39 have been canceled. Claims 18 and 20 have been amended. Claims 18-27 are pending in the instant application.
Priority
This application is a continuation of US application no 17830011 filed on June 1, 2022 which is a continuation of US application no 17/590,613 filed on 02/01/2022, which is a continuation of 17/366,290 filed on 07/02/2021, which is a continuation of 16/800,444 filed on 02/25/2020, which is a continuation of 16/601,144 filed on 10/14/2019, which claims priority from US provisional 62/864,432 filed on 06/20/2019, US provisional 62/830,654 filed on 04/08/2019, US provisional of 62/746,497 filed on 10/16/2018.
Information Disclosure Statement
The information disclosure statements (IDS) submitted 02/28/2026 is in compliance with the provisions of 37 CFR 1.97. Accordingly, the information disclosure statement has been considered by the examiner.
Claims 18-27 are under consideration.
Withdrawn-Double Patenting
Claim 29 was rejected under 35 U.S.C. 101 as claiming the same invention as that of claim 12 of prior U.S. Patent No. 11365407. Applicants’ cancellation of claim 29 renders its rejections moot.
Claim 29 was provisionally rejected under 35 U.S.C. 101 as claiming the same invention as that of claim 29 of copending Application No. 18526794. Applicants’ cancellation of claim 29 renders its rejections moot.
Withdrawn -Claim Rejections - 35 USC § 112
Claims 28, 38 were rejected under 35 U.S.C. 112(a) or 35 U.S.C. 112 (pre-AIA ), first paragraph, as failing to comply with the written description requirement. Applicants’ cancellation of claims 28, 38 render their rejections moot.
Maintained -Claim Rejections - 35 USC § 112-in modified form
The following is a quotation of the first paragraph of 35 U.S.C. 112(a):
(a) IN GENERAL.—The specification shall contain a written description of the invention, and of the manner and process of making and using it, in such full, clear, concise, and exact terms as to enable any person skilled in the art to which it pertains, or with which it is most nearly connected, to make and use the same, and shall set forth the best mode contemplated by the inventor or joint inventor of carrying out the invention.
The following is a quotation of the first paragraph of pre-AIA 35 U.S.C. 112:
The specification shall contain a written description of the invention, and of the manner and process of making and using it, in such full, clear, concise, and exact terms as to enable any person skilled in the art to which it pertains, or with which it is most nearly connected, to make and use the same, and shall set forth the best mode contemplated by the inventor of carrying out his invention.
Claims 18-27 remain rejected under 35 U.S.C. 112(a) or 35 U.S.C. 112 (pre-AIA ), first paragraph, as failing to comply with the written description requirement. The claim(s) contains subject matter which was not described in the specification in such a way as to reasonably convey to one skilled in the relevant art that the inventor or a joint inventor, or for applications subject to pre-AIA 35 U.S.C. 112, the inventor(s), at the time the application was filed, had possession of the claimed invention.
Claims 18 require a specific combination of amino acids encoded by the first and second coding sequences are amino acids that are at least 85 percent identical to amino acids encoded by an endogenous gene for alpha- 1 antitrypsin present within a cell (wild type or cell having mutation in SERPINA1 gene), any two [splice acceptor - coding sequence - terminator] cassettes arranged in tail-to-tail orientation. The instant specification does not describe any splice acceptor of the endogenous gene for alpha-1 antitrypsin and terminator sequence.
The specification at best describes constructs of present application comprise the following elements in the following 5’ to 3’ order (cf. Examples 1-5 and Fig. 1-7) SA 1-CDS1 -T1 -T2-CDS2-SA2 or SA 1-CDS1 -BT-CDS2-SA2. It is relevant to note that at the 5’ end of SA 1 and the 3' end of SA2 there are always target sites (TS), i.e. a nucleic acid to which a rare-cutting endonuclease or CRISPR-associated transposase will bind (page 15, line 9-11), or homology arms (HA) (page 18, lines. 6-13) to be found (cf. Fig. 1-7).
The guidance provided in the specification requires each of said elements and the order of said elements in specific configuration that are essential for integration of gene. The specification contemplates a method that can be used to alter the 3' end of the endogenous ATXN3 gene or CACNAIA gene. In specific embodiments, the target for integration of the transgenes described herein can be intron 9 of the ATXN3 gene or intron 46 of the CACNAIA gene (see para. 9). Applicant example disclose designing transgene to be inserted within intron 9 or the junction of intron 9 and exon 10 of the ATXN3 gene and all transgenes were designed to insert at least one splice acceptor and at least one functional coding sequence for exons 10 and 11 of the ATXN3 gene. The first plasmid, designated pBA1135, comprised a left and right homology arm with sequence homologous to the 3' end of intron 9 and 5' end of intron 10 (i.e., successful gene targeting would result in removal of exon 10 and replacement with the cargo sequence within pBA1135). Between the homology arms, from 5’ to 3', was a splice acceptor (splice acceptor from ATXN3 intron 9), coding sequence for exons 10 and 11 of ATXN3, SV40 terminator, reverse BGH terminator, reverse coding sequence for exons 10 and 11 (codon adjusted), and reverse splice acceptor. The results show that the described transgenes comprising bidirectional partial coding sequences can be integrated into genomic DNA through multiple different repair pathways (see example 1). It is noted that example 2 describes transfecting HEK293 cells with each of the plasmid constructs and combinations thereof using lipofectamine. Two days post transfection, DNA is extracted and assessed for mutations and targeted insertions within the CACNAIA gene. Nuclease activity is analyzed using the Cel-I assay or by deep sequencing of amplicons comprising the CRISPR/Cas 12a target sequence. Successful integration of the transgene is analyzed using PCR (FIG. 5) (example 2). Example 3 shows targeted integration of DNA in the ATXN3 gene in HEK293 cells (see fig. 7). Example 4 discloses targeted integration of DNA in the ATXN3 gene using Cas12k transposases in an HEK293 cells.
.The claims encompass amino acids encoded by the first and second coding sequences are amino acids that is at least 85% identical to the amino acids encoded by an endogenous gene for alpha-1 antitrypsin enzyme present within a cell. The art teaches a total of 14 rare alleles including 3 defined by novel mutations (p.Glu162Gly, p.Arg281Lysfs*17 and p.Met374Leufs*19) and 11 characterized by previously described variants (c.- 5þ2dupT, p.Arg39Cys, p.Phe52del, p.Thr68Ile, p.Asp256Val, p.Leu263Pro, p.Glu264Val, p.Leu353- Phefs*24, p.Pro369Ser and p.Pro369Leu) but in several instances differing in their molecular backgrounds (Silva et al Respiratory Medicine (2016), 116 8-18). The art further taches alpha-1 antitrypsin deficiency is caused by mutations in the SERPINA1 gene, which encodes the alpha-1 antitrypsin (AAT) protein. Currently, over 200 SERPINA1 variants have been identified, many of which cause the quantitative and/or qualitative changes in AAT responsible for AATD-associated lung and liver disease. The types of these pathogenic mutations are varied, often resulting in misfolding, or truncating of the AAT amino acid sequence, and improvements in sequencing technology are helping to identify known and novel genetic variants. However, due to the diversity and novelty of rare variants, the clinical significance of many is largely unknown. There is, therefore, a lack of guidance on how patients should be monitored and treated when the clinical significance of their variant combination is unclear or variable (see abstract in Foil et al Ther Adv Chronic Dis, 2021, 33-48).
The instant specification fails to describe any splice acceptor or amino acids encoded by the first and second coding sequences are amino acids that are at least 85% identical to amino acids encoded by an endogenous gene for alpha- 1 antitrypsin present within a cell (wild type or cell having mutation in SERPINA1 gene) and terminator sequence present in the cell. The specification fails to disclose or identify any known and novel genetic variants of SERPINA1 variants other than CACNAIA gene or ATXN3 gene. The reference of homologous sequence disclosed in the specification is limited to (i) homology arms can include sequence that is homologous to a genomic sequence at or near the desired site of integration (see page 23 of the specification) or (ii) partial coding sequence can be homologous to coding sequence within a wild type [CACNA1A or ATXN3] gene (see page 27 of the specification). Therefore, "amino acid encoded by an endogenous gene" specifies that the cell’s native DNA holds the design for the protein. The claim as written recite naturally occurring, original native SERPINA1 gene, However, the specification supports to a transgene have a sequence for modifying the sequence encoding a polypeptide that is lacking or non-functional or having a gain-of-function mutation in the subject having a genetic disease such as alpha-1 antitrypsin deficiency (mutation in SERPINA1 gene). There is no implicit or explicit support for amino acids encoded by the first and second coding sequences are amino acids are at least 85 percent identical to amino acids encoded by an endogenous gene for alpha- 1 antitrypsin present within a cell (native). Therefore, "encoded by an endogenous gene" requires that the cell’s native DNA holds the design for the protein. It does not describe a polypeptide modified directly by a transgene or a process where an entirely foreign gene produces the protein. It may be obvious from various parts of the specification to make the instantly claimed combination. However, what makes “obvious” or what “might” be possible does not comply with the written description requirement to reasonably convey that the inventors had possession of the claims as now claimed.
In the instant case, art teaches that the function of a splice site depends profoundly on its surrounding sequence and not just the canonical AG or GT dinucleotide at the boundaries. Anna et al (Journal of Applied Genetics (2018) 59:253–268) states that “the splicing process is also dependent from the presence of specific sequences: branch site and the polypyrimidine tract sequences that bind specific proteins involved in the formation of splicing complexes. The branch point motif, localized between − 9 and − 400 bp downstream from the acceptor site with the consensus sequence YUNAY in humans, is essential for early spliceosome complex formation. As the sequences of the branch point are highly degenerated, their exact localization is difficult to determine. Furthermore, mutations localized in the branch point sequence might lead to an exon skipping due to improper binding of the SF1 and U2 snRNP splicing proteins and disruption of the natural acceptor splicing site. Mutations in branch point sequence can also cause intron retention (whole or its fragment) if they create new 3′ splice site” (see page 261, col. 2, para. 3). The specification fails to provide any guidance with respect to using any splice acceptor of the endogenous gene for alpha-1 antitrypsin and terminator sequence. Lara ((Respiratory Research, 15,125, 1-13, 2014)) teaches impact of variants on splicing process . The art teaches PI*QOMadrid allele consist of a duplication of the thymine (T) in position +2 of the donor splice site of exon 1C (+2dupT) (abstract). The study shows that splicing mutations could yield multiple transcript species resulting in the production of variable amounts of aberrant splicing isoforms and thereby resulting in reduced correctly spliced mRNA (see figure 4). In view of foregoing , it is apparent that use of the amino acids that is at least 85 percent identical homologous to amino acids encoded by an endogenous gene for alpha- 1 antitrypsin present within a cell (wild type cell or cell having mutation in SERPINA1 gene) gene's splice acceptor site is unpredictable because multiple genetic factors and regulatory elements control the complex splicing process. This can lead to variable and unintended splicing outcomes.
In the instant case, there is no guidance and/or details on any of the first and second coding sequence encoding for the amino acids that is at least 85 percent identical to amino acids encoded by an endogenous gene for alpha- 1 antitrypsin present within any type of cell and corresponding splice acceptor exon junction of the endogenous gene for alpha-1 antitrypsin and terminator sequence used in the transgene as claimed. Additionally instant claim as written recite naturally occurring, original native SERPINA1 gene, However, the specification supports to a transgene have a sequence for modifying the sequence encoding a polypeptide that is lacking or non-functional or having a gain-of-function mutation in the subject having a genetic disease such as alpha-1 antitrypsin deficiency (mutation in SERPINA1 gene). There is no implicit or explicit support for amino acids encoded by the first and second coding sequences are amino acids are at least 85 percent identical to amino acids encoded by an endogenous gene for alpha- 1 antitrypsin present within a cell (native or cell having mutation in SERPINA1 gene).
It is emphasized that the description must be sufficiently clear that persons of skill in the art will recognize that the applicant made the invention having those limitations. In re Wertheim, 541 F.2d 257, 262, 191 USPQ 90, 96 (CCPA 1976). Note that the written description requirement inquiry is “not a question of whether one skilled in the art might be able to construct the patentee’s device [invention] from the teachings of the disclosure....Rather, it is a question whether the application necessarily discloses that particular device.” (original emphasis). Martin v. Mayer, 823 F.2d 500, 504, 3 USPQ2d 1333, 1337 (Fed. Cir. 1987).
“One shows that one is “in possession’ of the invention by describing the invention, with all its claim limitations, not that which makes it obvious.” (original emphasis). Lockwood v. Am. Airlines, Inc., 107 F.3d 1565, 41 USPQ2d 1961 (Fed. Cir. 1997).
Accordingly, claims 18-27 introduce matter that is not adequately described by the instant specification. Applicant is advised to point out a specific disclosure in the specification for the transgene comprising specific combination of pair of splice acceptor, terminator and coding sequences recited in the claim. Accordingly, the instant specification fails to reasonably convey that the applicants completed and had possession of the transgene comprising the transgene of the invention before the effective filing date of instant application.
Response to arguments
Applicant disagree with the rejection arguing claim 18 has been amended to overcome the rejection of record. Applicant’s cancellation of claim 28 renders its rejections moot.
In response as stated above, claims require a specific combination of amino acids encoded by the first and second coding sequences are at least 85 percent identical to amino acids encoded by a genus of alpha- 1 antitrypsin present in a cell (wild type cell or cell having unknown or know mutation in alpha- 1 antitrypsin gene), genus of two [splice acceptor - coding sequence - terminator] arranged in tail-to-tail orientation. The guidance provided in the specification is limited to a transgene to be inserted within intron 9 or the junction of intron 9 and exon 10 of the ATXN3 gene and all transgenes were designed to insert at least one splice acceptor (splice acceptor from ATXN3 intron 9) and at least one functional coding sequence for exons 10 and 11 of the ATXN3 gene. The art teaches that the function of a splice site depends profoundly on its surrounding sequence and not just the canonical AG or GT dinucleotide at the boundaries. Anna et al (Journal of Applied Genetics (2018) 59:253–268) states that “the splicing process is also dependent from the presence of specific sequences: branch site and the polypyrimidine tract sequences that bind specific proteins involved in the formation of splicing complexes. The branch point motif, localized between − 9 and − 400 bp downstream from the acceptor site with the consensus sequence YUNAY in humans, is essential for early spliceosome complex formation. As the sequences of the branch point are highly degenerated, their exact localization is difficult to determine. Furthermore, mutations localized in the branch point sequence might lead to an exon skipping due to improper binding of the SF1 and U2 snRNP splicing proteins and disruption of the natural acceptor splicing site. Mutations in branch point sequence can also cause intron retention (whole or its fragment) if they create new 3′ splice site” (see page 261, col. 2, para. 3). The specification fails to provide any guidance with respect to using any splice acceptor of the endogenous gene for alpha- 1 antitrypsin. The specification at best describes that the partial coding sequence can be homologous to coding sequence within a wild type ATXN3 gene, or a functional variant of the wild type ATXN3 gene, or a mutant of the wild type ATXN3 gene (see page 32 of the specification). The specification describes the term homologous sequences can have at least 85%, sequence identity to one another. The reference of homologous sequence disclosed in the specification is limited to (i) homology arms can include sequence that is homologous to a genomic sequence at or near the desired site of integration (see page 23 of the specification) or (ii) partial coding sequence can be homologous to coding sequence within a wild type [CACNA1A or ATXN3] gene (see page 27 of the specification). There is no explicit or implicit support for the limitation using any splice acceptor site for a coding sequence encoding amino acids encoded by the first and second coding sequences are amino acids at least 85 percent identical to amino acids encoded by an endogenous gene for alpha- 1 antitrypsin present in a broadly recited cell of any origin.
Lara ((Respiratory Research, 15,125, 1-13, 2014)) teaches impact of variants on splicing process . The art teaches PI*QOMadrid allele consist of a duplication of the thymine (T) in position +2 of the donor splice site of exon 1C (+2dupT) (abstract). The study shows that splicing mutations could yield multiple transcript species resulting in the production of variable amounts of aberrant splicing isoforms and thereby resulting in reduced correctly spliced mRNA (see figure 4). In view of foregoing , it is apparent that use of the amino acids that is at least 85 percent identical to amino acids encoded by an endogenous gene for alpha- 1 antitrypsin present within a cell (wild type cell or cell having mutation in SERPINA1 gene) gene's splice acceptor site is unpredictable because multiple genetic factors and regulatory elements control the complex splicing process. This can lead to variable and unintended splicing outcomes. In view of foregoing, it is apparent that claims 18-27 introduce matter that is not adequately described by the instant specification nor pointed out by applicant in the specification for the transgene that would be functional into a chosen intron or intron-exon junction so the cell’s normal splicing machinery stitching the new coding pieces into the final RNA. . Applicant is advised to point out the specific disclosure in the specification for the transgene as recited in the claims.
Withdrawn-Claim Rejections - 35 USC § 101
Claims 20-2, 31-33 were rejected under 35 U.S.C. 101 because the claimed invention is directed to patent eligible subject matter. Applicant’s argument is found persuasive, therefore, previous rejection of claims 20-21 are hereby withdrawn.
Conclusion
No claims allowed.
The prior art made of record and not relied upon is considered pertinent to applicant's disclosure.
Finn (US 20200270617, EFD 10/18/2018) teaches a nucleic acid construct is a bidirectional nucleic acid construct. In some embodiments, the construct comprises: i. a first segment comprising a coding sequence for a heterologous polypeptide; and ii. a second segment comprising a reverse complement of a coding sequence of the heterologous polypeptide. In some embodiments, the construct comprises a polyadenylation signal sequence. In some embodiments, the construct comprises a splice acceptor site. In some embodiments, the construct does not comprise a homology arm (see para. 12, Fig. 1-5).
Finn is not applied as prior art as effective filing date of Finn is 2 days after the EFD of instant application.
The closest prior art of Ranga (WO/2018/009534, dated 01/11/2018, EFD07/5/2016, IDS) teaches a transgene comprising two coding sequences, a bidirectional promoter and an endonuclease (Claims 1, 15, page 3 line 25-31, page 4 , line 15-26, page 5 line. 7, page 27 lines 8-20, page 40 line. 32-pahe 41 line. 8, example 6). It is further disclosed that the construct may comprises at least one that includes 2 terminator sequences (see claim 55-56). Jaskula-Ranga teaches that nuclease is a CRISPR and wherein the genome-targeted nuclease is Cas9 protein (see claim 66, page 8 line 22, and page 41 line 26-27). With respect to claim 3, Jaskula-Ranga shows potential configurations for HDR delivery and targeting within an intronic region (see figure 24).
Carlo et al (US20200040362) teaches use of one or more including two splicing site comprising a natural or enhanced 3’ splice site for insertion of donor transgene (see claim 2 and 18 and 27). Carlo et al teach donor polynucleotide comprises a coding sequence, wherein the first strand comprises a first coding sequence, wherein the second strand comprises a second coding sequence, wherein the first nucleotide sequence that corrects the mutation in the gDNA comprises the first coding sequence, wherein the second nucleotide sequence that corrects the mutation in the gDNA comprises the second coding sequence, wherein the first coding sequence is located downstream of the first 3' splice site (3 end of intron), and wherein the second coding sequence is located downstream of the second 3' splice site (3 end of intron) (see para. 46).
Prior art fails to teach or suggest recombinant nucleic acid comprising a transgene comprising two [splice acceptor - coding sequence - terminator] cassettes arranged in tail-to-tail orientation.
Applicant's amendment necessitated the new ground(s) of rejection presented in this Office action. Accordingly, THIS ACTION IS MADE FINAL. See MPEP § 706.07(a). Applicant is reminded of the extension of time policy as set forth in 37 CFR 1.136(a).
A shortened statutory period for reply to this final action is set to expire THREE MONTHS from the mailing date of this action. In the event a first reply is filed within TWO MONTHS of the mailing date of this final action and the advisory action is not mailed until after the end of the THREE-MONTH shortened statutory period, then the shortened statutory period will expire on the date the advisory action is mailed, and any nonprovisional extension fee (37 CFR 1.17(a)) pursuant to 37 CFR 1.136(a) will be calculated from the mailing date of the advisory action. In no event, however, will the statutory period for reply expire later than SIX MONTHS from the mailing date of this final action.
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/ANOOP K SINGH/Primary Examiner, Art Unit 1632
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