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 .
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and the fee set forth in 37 CFR 1.17(e) has been timely paid, the finality of the previous Office action has been withdrawn pursuant to 37 CFR 1.114.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 06/23/2025 has been entered.
Applicant’s amendments to the claims and arguments filed on June 23, 2025 have been received and entered. Claims 1-17 have been canceled. Claims 18-20, 23, 29-31, 33-35 have been amended. Claims 18-39 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 cont8inuation of US application no 17/590,613 filed on 02/01/2022, now USP 11365407, which is a continuation of 17/366,290 filed on 07/02/2021 now USP 11254930, which is a continuation of 16/800,444 filed on 02/25/2020 now USP 11091756, 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.
It is noted that
Information Disclosure Statement
The information disclosure statements (IDS) submitted 06/23/2025 is in compliance with the provisions of 37 CFR 1.97. Accordingly, the information disclosure statement has been considered by the examiner.
Claims 18-39 are under consideration.
New-Double Patenting
A rejection based on double patenting of the “same invention” type finds its support in the language of 35 U.S.C. 101 which states that “whoever invents or discovers any new and useful process... may obtain a patent therefor...” (Emphasis added). Thus, the term “same invention,” in this context, means an invention drawn to identical subject matter. See Miller v. Eagle Mfg. Co., 151 U.S. 186 (1894); In re Vogel, 422 F.2d 438, 164 USPQ 619 (CCPA 1970); In re Ockert, 245 F.2d 467, 114 USPQ 330 (CCPA 1957).
A statutory type (35 U.S.C. 101) double patenting rejection can be overcome by canceling or amending the claims that are directed to the same invention so they are no longer coextensive in scope. The filing of a terminal disclaimer cannot overcome a double patenting rejection based upon 35 U.S.C. 101.
Claim 29 is rejected under 35 U.S.C. 101 as claiming the same invention as that of claim 12 of prior U.S. Patent No. 11365407. In the instant case, claim 29 of the instant application is directed to an adeno-associated viral vector comprising:(i) a transgene comprising from 5' to 3' orientation a first splice acceptor, a first coding sequence, a first terminator, a second terminator reverse complement, a second coding sequence reverse complement, and a second splice acceptor reverse complement, wherein the first coding sequence is operably linked to the first splice acceptor and first terminator, and the second coding sequence is operably linked to the second splice acceptor and second terminator, wherein the first and second coding sequences differ in nucleic acid sequence but encode the same amino acids, wherein said amino acids encoded by the first and second coding sequences that are homologous to amino acids encoded by an endogenous gene present in a cell, and wherein the transgene is equal to or less than 4.7 kb; and(ii) adeno-associated virus inverted terminal repeats flanking the transgene. In contrast, claim 12 of the ‘407 is directed to an adeno-associated viral vector comprising: (i) a transgene comprising from 5′ to 3′ orientation a first splice acceptor, a first coding sequence, a first terminator, a second terminator reverse complement, a second coding sequence reverse complement, and a second splice acceptor reverse complement, wherein the first coding sequence is operably linked to the first splice acceptor and first terminator, and the second coding sequence is operably linked to the second splice acceptor and second terminator, wherein the first and second coding sequences differ in nucleic acid sequence but encode the same amino acids, wherein said amino acids encoded by the first and second coding sequences correspond to amino acids encoded by an endogenous gene, and wherein the transgene is equal to or less than 4.7 kb; and (ii) adeno-associated virus inverted terminal repeats flanking the transgene. In view of foregoing, it is apparent that claim 29 of instant application is claiming the same invention as that of prior US Patent ‘407. This is a statutory double patenting rejection.
Claim 29 is provisionally rejected under 35 U.S.C. 101 as claiming the same invention as that of claim 29 of copending Application No. 18526772. In the instant case, claim 29 of the instant application is directed to an adeno-associated viral vector comprising:(i) a transgene comprising from 5' to 3' orientation a first splice acceptor, a first coding sequence, a first terminator, a second terminator reverse complement, a second coding sequence reverse complement, and a second splice acceptor reverse complement, wherein the first coding sequence is operably linked to the first splice acceptor and first terminator, and the second coding sequence is operably linked to the second splice acceptor and second terminator, wherein the first and second coding sequences differ in nucleic acid sequence but encode the same amino acids, wherein said amino acids encoded by the first and second coding sequences that are homologous to amino acids encoded by an endogenous gene present in a cell, and wherein the transgene is equal to or less than 4.7 kb; and(ii) adeno-associated virus inverted terminal repeats flanking the transgene. In contrast, claim 29 of the ‘772 is directed to an adeno-associated viral vector comprising:(i) a transgene comprising from 5' to 3' orientation a first splice acceptor, a first coding sequence, a first terminator, a second terminator reverse complement, a second coding sequence reverse complement, and a second splice acceptor reverse complement, wherein the first coding sequence is operably linked to the first splice acceptor and first terminator, and the second coding sequence is operably linked to the second splice acceptor and second terminator, wherein the first and second coding sequences differ in nucleic acid sequence but encode the same amino acids, wherein said amino acids encoded by the first and second coding sequences are homologous to amino acids encoded by an endogenous gene present in a cell, and wherein the transgene is equal to or less than 4.7 kb; and(ii) adeno-associated virus inverted terminal repeats flanking the transgene.
This is a provisional statutory double patenting rejection since the claims directed to the same invention have not in fact been patented.
Maintained-Claim Rejections - 35 USC § 112-new matter
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 28, 38 are rejected under 35 U.S.C. 112(a) or 35 U.S.C. 112 (pre-AIA ), first paragraph, as failing to comply with the written description requirement. The claim(s) contains subject matter which was not described in the specification in such a way as to reasonably convey to one skilled in the relevant art that the inventor or a joint inventor, or for applications subject to pre-AIA 35 U.S.C. 112, the inventor(s), at the time the application was filed, had possession of the claimed invention. 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(s), at the time the application was filed, had possession of the claimed invention.
In the instant case, claims have been amended to introduce the limitation “wherein the first splice acceptor comprises a splice acceptor sequence from an intron of the endogenous gene for acid maltase
The specification at best provide guidance on that the transgene may include 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, including but not limited to acid maltase deficiency (see page 30, lines 17-20). There is no explicit or implicit support for the limitation wherein the first splice acceptor comprises a splice acceptor sequence from an intron of the endogenous gene for acid maltase enzyme. Thus, at the time the application was filed, an Artisan of skill would not recognize from the disclosure that Applicant was in possession of the essential subject matter, as claimed. In case if applicants have evidence to support otherwise, applicants are invited to indicate page and line number for the written support specifically for newly added limitation that is deemed essential subject matter. This is a new matter rejection.
Response to arguments
Applicant disagree with the rejection arguing “Acid maltase deficiency (Pompe disease)” “results from a defect in the gene for the acid maltase enzyme (also known as acid alpha glucosidase) that prevents the breakdown of glycogen (stored sugar).” There are two main forms of the disease, namely Infantile-onset Form and Late-onset. As explained in the attached page from UF Health, “[i]Jn people with the infantile form of the disease, alpha-glucosidase is either entirely missing or inactive.” This is consistent with the language from the specification of the priority application. Indeed, p. 14 of the priority application provides that “the transgene may include 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, including but not limited to. . . acid maltase deficiency.” p. 14, ll. 17-21. The language in the specification correlates precisely with the language in the UF Health page, namely “encoding a polypeptide that is lacking” [corresponds to “entirely missing’] or “non-functional” [corresponds to “inactive”]. Consequently, no new matter was introduced. Applicants’ arguments have been considered, but are not fully found persuasive.
As an initial matter, applicant’s argument pertaining to support for amino acids encoded by the first and second coding sequences are amino acids that are homologous to amino acids encoded by the corresponding endogenous gene for acid maltase enzyme present in a cell is found persuasive, therefore, previous rejection of claims 18-27, 30-37 and 39 are hereby withdrawn. Applicants’ arguments with respect to the withdrawn rejections are thereby rendered moot.
With respect to claims 28 and 38, it is noted that applicant fail to rebut the rejection of record by not providing the support for the limitation wherein the first splice acceptor comprises a splice acceptor sequence from an intron of the endogenous gene for acid maltase
Claim Rejections - 35 USC § 112-written description
The following is a quotation of the first paragraph of 35 U.S.C. 112(a):
(a) IN GENERAL.—The specification shall contain a written description of the invention, and of the manner and process of making and using it, in such full, clear, concise, and exact terms as to enable any person skilled in the art to which it pertains, or with which it is most nearly connected, to make and use the same, and shall set forth the best mode contemplated by the inventor or joint inventor of carrying out the invention.
The following is a quotation of the first paragraph of pre-AIA 35 U.S.C. 112:
The specification shall contain a written description of the invention, and of the manner and process of making and using it, in such full, clear, concise, and exact terms as to enable any person skilled in the art to which it pertains, or with which it is most nearly connected, to make and use the same, and shall set forth the best mode contemplated by the inventor of carrying out his invention.
Claims 18-39 are rejected under 35 U.S.C. 112(a) or 35 U.S.C. 112 (pre-AIA ), first paragraph, as failing to comply with the written description requirement. The claim(s) contains subject matter which was not described in the specification in such a way as to reasonably convey to one skilled in the relevant art that the inventor or a joint inventor, or for applications subject to pre-AIA 35 U.S.C. 112, the inventor(s), at the time the application was filed, had possession of the claimed invention.
Claims 18 and 29 require a specific combination of an endogenous gene for acid maltase comprising two [splice acceptor - coding sequence - terminator] cassettes arranged in tail-to-tail orientation. The instant specification does not describe any splice acceptor from intron or intron exon junction of the endogenous gene for acid maltase 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.
This transgene or adeno-associated viral vector comprising transgene that is actually made and exemplified by the applicant is not the claimed transgene or an adeno-associated viral vector. The claims encompass amino acids encoded by the first and second coding sequences are amino acids homologous to amino acids encoded by an endogenous gene for acid maltase enzyme present within a cell. The art teaches that the mutational spectrum of GAA is very heterogeneous, and genetic variants are often private, only found in a single-family or in a small population. For this reason, until now, more than 600 disease-causing variants have been described in the acid maltase gene (GAA) on Chromosome 17 (Balendran-Braun et al Human Mutation Volume 2024, Article ID 6248437, 1-11). The instant specification fails to describe any splice acceptor from intron or intron exon junction of the endogenous gene for acid maltase and terminator sequence present in the cell. 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 from any intron or intron exon junction of the endogenous gene for acid maltase and terminator sequence. Post filing art summarized by the Peruzzo (Molecular Medicine (2025) 31:45, 1-14) teaches acid alpha glucosidase (GAA) c.-32-13T>G variant is defined as a leaky splicing mutation that interferes with the correct processing of GAA pre-mRNA resulting in the production of variable amounts of aberrant splicing isoforms, which are characterized by the complete or partial exclusion of exon 2 from the mature GAA mRNA (see page 2, col. 2, para. 1). In view of foregoing , it is apparent that use of the endogenous acid alpha-glucosidase (GAA) 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.
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 18-39 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 combination of an endogenous gene for acid maltase comprising two [splice acceptor - coding sequence - terminator] cassettes arranged in tail-to-tail orientation as arranged in the claims. Accordingly, the instant specification fails to reasonably convey that the applicants completed and had possession of the transgene or an adeno-associated viral vector comprising the transgene of the invention before the effective filing date of instant application.
Claim Rejections - 35 USC § 101
35 U.S.C. 101 reads as follows:
Whoever invents or discovers any new and useful process, machine, manufacture, or composition of matter, or any new and useful improvement thereof, may obtain a patent therefor, subject to the conditions and requirements of this title.
Claims 20-2, 31-33 are rejected under 35 U.S.C. 101 because the claimed invention is directed to patent eligible subject matter. Based upon an analysis with respect to the claim as a whole, claims do not recite something significantly different than a judicial exception. The rationale for this determination is explained below.
The claims 20 and 31 recite, the transgene, wherein the amino acids encoded by the first and second coding sequences have at least 80% sequence identity to the amino acids encoded by the endogenous gene for acid maltase enzyme, wherein the percent sequence identity that is calculated by matching amino acids encoded by the first and second coding sequence with amino acids encoded by the endogenous gene for acid maltase enzyme and dividing the number of matches by the length of the amino acids encoded by the first and second coding sequence, followed by multiplying the resulting value by 100.
Step 1: This part of the eligibility analysis evaluates whether the claim falls within any statutory category. MPEP 2106.03. The claim encompasses transgene, wherein the percent sequence identity t is calculated by matching amino acids encoded by the first and second coding sequence with amino acids encoded by the endogenous gene for acid maltase enzyme and dividing the number of matches by the length of the amino acids encoded by the first and second coding sequence, followed by multiplying the resulting value by 100. Thus, the claim is directed to a product, which is one of the statutory categories of invention (Step 1: YES).
Step 2A Prong One: This part of the eligibility analysis evaluates whether the claim recites a judicial exception. In the instant case, claims recite wherein clause that only relates to mental step of calculating percentage identity. In the instant case, the BRI requires performing an arithmetic calculation (division) in order to obtain the percentage identity. This limitation therefore recites a mathematical calculation. In addition, this type of simple arithmetic calculation (division) can be practically performed in the human mind, and is in fact performed in the human mind on a daily basis. Further, use of a calculator to help them complete the recited calculation, the use of such physical aid does not negate the mental nature of this limitation. Thus, limitation (a) also falls into the "mental process" groupings of abstract ideas. Accordingly, limitation (a) recites a judicial exception (an abstract idea that falls within the mathematical concept and mental process groupings), and the analysis must therefore proceed to step 2A prong two.
Step 2A: Besides the abstract idea, the claims do not recite any other additional element. The limitation is at best the equivalent of merely adding the words "how to perform mathematical calculation to determine percentage identity” to the judicial exception. Accordingly, limitation does not integrate the recited judicial exception into a practical application and the claim is therefore directed to the judicial exception (Step 2A: YES).
Step 2B: This part of the eligibility analysis evaluates whether the claim as a whole amount to significantly more than the recited exception, i.e., whether any additional element, or combination of additional elements, adds an inventive concept to the claim. MPEP 2106.05. In the instant case, there are no other additional elements recited in the claims that would amount to significantly more than the judicial exceptions, the claim does not require any particular application of the recited calculation and is at best the equivalent of merely adding the words "calculation" to the judicial exception. Mere instructions to mentally apply an exception cannot provide an inventive concept (Step 2B: NO). The claims are not eligible.
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.
Conclusion
No claims allowed.
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 extension fee 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 date of this final action.
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/ANOOP K SINGH/ Primary Examiner, Art Unit 1632