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 .
Applicant’s amendment filed on 02/27/2026 has been entered.
Claims 19-46 are pending in the present application.
Applicant elected previously without traverse of Group I.
Applicant also elected previously the following species: (i) SEQ ID NOs. 15-16 as species for the first intronic element and the second intronic element, respectively; (ii) an RNA silencing molecule as a species of a nucleotide sequence of interest; (iii) Human poliovirus 1 as a species of a source of IRES; (iv) one IRES; (v) AAV2 serotype for each of the first and second ITRs; and (vi) AAV9 serotype for AAV capsid protein or particle. The species of a nucleotide sequence of interest encoding a translatable mRNA was rejoined and examined together with the elected species of an RNA silencing molecule.
Claims 44-46 were withdrawn previously from further considerations because they are directed to a non-elected invention. Claims 28-29 were also withdrawn previously from further consideration because they are drawn to non-elected species.
Accordingly, claims 19-27 and 30-43 are examined on the merits herein with the above elected and rejoined species.
Terminal Disclaimer
The terminal disclaimer filed on 02/27/2026 disclaiming the terminal portion of any patent granted on this application which would extend beyond the expiration date of US Patent No. 11718862 and any patent granted on Application No. 16761876 has been reviewed and is accepted. The terminal disclaimer has been recorded.
Response to Amendment
1. The rejection on the ground of nonstatutory double patenting as being unpatentable over claims 1-25 of U.S. Patent No. 11,718,862 was withdrawn in light of the Terminal Disclaimer filed on 02/27/2026.
2. All provisional rejections on the ground of nonstatutory double patenting as being unpatentable over claims 1-4, 6-8 and 19-22 of copending Application No. 16/761,876 (reference application) were withdrawn in light of the Terminal Disclaimer filed on 02/27/2026.
Claim Rejections - 35 USC § 103
The following is a quotation of 35 U.S.C. 103 which forms the basis for all obviousness rejections set forth in this Office action:
A patent for a claimed invention may not be obtained, notwithstanding that the claimed invention is not identically disclosed as set forth in section 102, if the differences between the claimed invention and the prior art are such that the claimed invention as a whole would have been obvious before the effective filing date of the claimed invention to a person having ordinary skill in the art to which the claimed invention pertains. Patentability shall not be negated by the manner in which the invention was made.
Claims 19-27, 30-32 and 34-42 are rejected under 35 U.S.C. 103 as being unpatentable over Chang et al (US 2019/0345503 with an effective filing date of 06/20/2016; IDS) in view of Liang et al (Genes & Development 28:2233-2247, 2014; IDS), Sena-Esteves et al (WO 2016/172155; IDS) and Kruse (WO 2014/186334; IDS).
The instant claims are directed to an AAV genome encoding a circular RNA (circRNA), wherein the AAV genome comprises, from 5’ to 3’ the elements a)-e) as recited in independent claim 19; an AAV capsid or particle comprising the same AAV genome. It is noted that the term “rAAV genome” in this specification refers to an AAV genome (e.g., vDNA) that comprises one or more heterologous nucleic acid sequences; and rAAV vectors generally require only the terminal repeat(s) in cis to generate virus and all other viral sequences are dispensible and may be supplied in trans (page 12, line 33 continues to line 3 at page 13). Additionally, the specification explicitly teaches that the term “vector” may be used to refer to the vector genome/vDNA alone (page 12, lines 28-29).
Chang et al already taught a recombinant nucleic acid encoding an immunogenic circular target RNA encoding an immunogenic polypeptide derived from a bacterium, a virus or a parasite, wherein the recombinant nucleic acid comprises in a 5’ to 3’ order: (i) a 3’ portion of an exogenous intron comprising a 3’ splice site (an acceptor site), (ii) a nucleic acid sequence encoding the target RNA, and (iii) a 5’ portion of an exogenous intron comprising a 5’ splice site (a donor site), wherein the produced target RNA transcript is circularized by backsplicing or splicing of the exogenous introns, the recombinant nucleic acid comprises a viral vector such as an adenovirus, a retrovirus, and adeno-associated virus and others, and the recombinant nucleic acid further comprises a nucleic acid sequence encoding an IRES (e.g., IRES derived from encephalomyocarditis virus (EMCV) UTR) operably linked to the nucleic acid encoding the immunogenic polypeptide (Abstract; Summary; particularly paragraphs [005]-[0008], [0018], [0021]-[0022], [0050], [0096], [0099]-[0101], [0106], [0116]; and Example 1). Chang et al also taught a recombinant nucleic acid encoding a non-immunogenic circular target RNA encoding a therapeutic polypeptide (e.g., an enzyme, hormone, neurotransmitter, cytokine and others), wherein the recombinant nucleic acid comprises in a 5’ to 3’ order: (i) a 3’ portion of an endogenous intron comprising a 3’ splice site (an acceptor site), (ii) a nucleic acid sequence encoding the target RNA, and (iii) a 5’ portion of an endogenous intron comprising a 5’ splice site (a donor site), wherein the produced target RNA transcript is circularized by backsplicing or splicing of the endogenous introns, the recombinant nucleic acid comprises a viral vector such as an adenovirus, a retrovirus, and adeno-associated virus and others, and the recombinant nucleic acid further comprises a nucleic acid sequence encoding an IRES (e.g., IRES derived from encephalomyocarditis virus (EMCV) UTR) operably linked to the nucleic acid encoding the therapeutic polypeptide (paragraphs [0026]-[0027], [0051], [0104]-[0105], [0106], [0116]; and Example 1). Chang et al also taught that the circular RNA is produced by transcription in vivo or in vitro under transcriptional control of a promoter (e.g., SV40 early promoter or a CMV promoter for mammalian cell expression) in the recombinant nucleic acid (paragraphs [0110]-[0112]). Fig. 1A below depicts a schematic of circRNA synthesis by in vitro transcription from a permuted intron-exon template (5’ half placed at the 3’ position and vice versa) via self-splicing of Group I intron of phage T4 thymidylate synthase (td) gene, and circularization brings the IRES upstream of GFP sequence that allows protein translation.
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In example 1 (paragraphs [0202]-[0205] and Fig. 5), Chang et al also disclosed the GFP-IRES circRNA exon and endogenous human ZKSCAN1 introns described in Liang et al (Genes Dev. 28:2233-2247, 2014) which do not have autocatalytic-splicing properties, but complementary Alu repeats that are present in these flanking introns enable human ZKSCAN1 to splice GFP-IRES into a circRNA without innate immune gene induction in human HeLa cells unlike the DNA construct that expresses the phage self-splicing IRES-GFP circRNA containing exogenous td introns as depicted in Fig. 5A below. Chang et al further taught a pharmaceutical composition comprising circular RNAs or recombinant nucleic acids encoding circular RNAs and a pharmaceutically acceptable carrier (paragraph [0151]).
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Chang et al did not teach explicitly at least an AAV genome encoding a circRNA, wherein the AAV genome comprises the elements (a)-(e) in 5’ to 3’ order as recited in independent claim 19, and particularly the first intronic element comprises SEQ ID NO:15 and the second intronic element comprises SEQ ID NO:16 (elected pair of first and second intronic elements); the nucleotide sequence of interest encodes a non-coding RNA such as an RNA silencing molecule (elected species); selecting IRES from human poliovirus 1 (elected species) to drive translation of the translatable mRNA transcribed from the nucleotide sequence of interest; a promoter located between the first inverted terminal repeat and the first intronic element, with first and second intronic elements flank the gene of interest, a 5’ UTR located 3’ to the first inverted terminal repeat and/or a 3’ UTR located 5’ to the second inverted terminal repeat; and an AAV capsid or virus comprising the same AAV genome.
Before the effective filing date of the present application (11/07/2017), Liang et al already demonstrated at least that miniature introns containing the splice sites along with short (about 30- to 40- nucleotide) inverted repeats, such as Alu elements, derived from human ZKSCAN1 and HIPK3 genes are sufficient to allow the intervening exons to circularize in cells; and the intronic repeats must base-pair to one another, thereby bringing the splice sites into close proximity to each other (Abstract; sections titled “Short repeat sequences are sufficient for ZKSCAN1 circular RNA production” on pages 2236-2238 and “Short repeats are sufficient for production of the HIPK3 circular RNA” on pages 2238 and 2240-2241; Figs. 2 and 4). Liang et al selected and cloned a 2803-nt region of the HIPK3 premRNA into pcDNA3.1 as depicted in reproduced Fig. 4A, 4D and 4E below and confirmed that this expression vector efficiently generates a circular RNA when transfected into HeLa cells, then demonstrated that a 32-nt region of the upstream AluSz element (nucleotides 300-331) and a 32-nt region of the downstream AluSq2 element (nucleotides 2607-2638) are sufficient to support HIPK3 circularization.
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The pcDNA3.1(+) HIPK3 300-2703∆2450-2609 (used in Figure 4E showing formation of a circular RNA) in Supplemental Methods comprises the first 391-nucleotide sequence that is 100% identical to the first intronic element of SEQ ID NO: 15 of the present application and the last 754-nucleotide sequence that is 100% identical to SEQ ID NO: 16 of the present application (see attached sequence below on page 34 of this office action; it is a typo error that the first G appears in front of the phrase “Used in Figure 4E” on the line above the main body of the listed sequence). Additionally, each of the pcDNA3.1(+) HIPK3 300-2703, pcDNA3.1(+) HIPK3 300-2703∆2450-2574, pcDNA3.1(+) HIPK3 300-2703∆2450-2599 and pcDNA3.1(+) HIPK3 300-2703∆2450-2609 constructs contain truncated flanking introns (relative to the wild-type 2803-nucleotide region) and are capable of generating circular RNA as shown in Figs. 4D-E above.
Additionally, Sena-Esteves et al already disclosed recombinant adeno-associated viruses/virions (rAAVs) comprising artificial genetic regulatory elements that modulate transgene expression to provide therapeutic amounts of transgene levels without the induction of adverse events for the treatment of lysosomal storage disorders, and that AAV vectors have emerged as an effective platform for in vivo gene therapy (Abstract; Summary of Invention; page 22, lines 22-25; page 23, lines 11-26). Sena-Esteves et al taught that the rAAV comprising a capsid (e.g., AAV9, AAV10 and others) containing a nucleic acid comprising a hybrid promoter operably linked to a transgene encoding a lysosomal storage disorder-associated protein, and the rAAV comprises two ITRs wherein the hybrid promoter and transgene are located between two ITRs, AAV-ITR sequences may be from any known AAV (e.g., AAV1 ITR, AAV2 ITR, AAV3 ITR, AAV4 ITR, AAV5 ITR, or AAV6 ITR) and the rAAV has the serotype AAV9 (page 3, second paragraph; page 29, lines 8-9). Fig. 1 depicts schematically an exemplary rAAV vector comprising two inverted terminal repeats (ITRs) flank an expression vector on each end as shown below. Sena-Esteves et al also taught the use of a polyadenylation sequence (e.g., SV40 polyA and BGH polyA) being inserted following the transgene sequences and immediately before the 3’ AAV-TR sequence (page 27, lines 4-5; and Fig. 1). Sena-Esteves et al also taught that a transgene may encode an interfering RNA such as dsRNA, siRNA, shRNA, miRNA or amiRNA (page 5, lines 3-8).
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Moreover, Kruse also disclosed a DNA vector (e.g., a plasmid or a viral vector) comprising a sequence encoding a circular mRNA molecule for production of a desired polypeptide inside eukaryotic cells (e.g., mammalian cells), and an exemplary vector comprises the following elements operably connected to each other and arranged in the 5’ to 3’ order as depicted schematically in Fig. 1 below: i) an RNA polymerase promoter (e.g., a T7 polymerase), ii) a first Group I intron sequence, iii) an IRES (e.g., Human poliovirus 1 IRES, Encephalomyocarditis virus IRES and others), iv) a 5’-UTR (e.g., human beta globin 5’-UTR), v) a gene of interest, vi) a 3’-UTR (e.g., human beta globin 3’-UTR), vii) a polyA tract at least 30 nucleotides long, viii) a second Group I intron sequence, and ix) an RNA polymerase terminator (e.g., a T7 terminator), wherein at least Group I self-splicing by permutated intron-exon sequences derived from T4 bacteriophage gene td is used to produce circular mRNA (Abstract; Summary of the Disclosure; particular paragraphs [0029]-[0036], [0056], [0058], [0098]-[0099]; and Fig. 1).
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Accordingly, it would have been obvious for an ordinary skilled artisan before the effective filing date of the present application to modify the teachings of Chang et al by also preparing at least a recombinant AAV vector/virion/genome comprising the following elements in the 5’ to 3’ order: (i) a first AAV ITR, (ii) a first endogenous truncated human HIPK3 intron containing a 3’ splice site such as SEQ ID NO: 15, (iii) a nucleotide sequence encoding a non-immunogenic circular target RNA encoding a therapeutic polypeptide or a non-coding RNA (e.g., a dsRNA, siRNA, shRNA, or miRNA), (iv) a second endogenous truncated human HIPK3 intron containing a 5’ splice site such as SEQ ID NO: 16, and (v) a second AAV ITR, wherein the produced target RNA transcript is circularized by backsplicing of the endogenous truncated/miniature human introns; the same recombinant AAV vector/virion/genome further comprising a promoter located between the first AAV ITR and the first endogenous truncated/miniature human HIPK3 intron containing a 3’ splice site, and a 3’-UTR including a polyadenylation sequence that is located immediately 5’ of the second AAV ITR; in light of the teachings of Liang et al, Sena-Esteves et al and Kruse as presented above.
An ordinary skilled artisan would have been motivated to carry out the above modifications because: (i) Liang et al already demonstrated successfully that miniature introns containing the splice sites along with short (about 30- to 40- nucleotide) inverted repeats, such as Alu elements, derived from human ZKSCAN1 and HIPK3 genes are sufficient to allow the intervening exons to circularize in cells; and at least the exemplary pCDNA3.1(+) HIPK3 300-2703∆2450-2609 (used in Figure 4E showing formation of a circular RNA) in Supplemental Methods comprises the first 391-nucleotide sequence that is 100% identical to the first intronic element of SEQ ID NO: 15 of the present application and the last 754-nucleotide sequence that is 100% identical to the second intronic element of SEQ ID NO: 16 of the present application; (ii) Sena-Esteves et al already taught at least a rAAV comprising an AAV9 capsid containing a nucleic acid comprising a hybrid promoter operably linked to a transgene (e.g. a transgene encoding a therapeutic lysosomal storage disorder-associated protein or an interfering RNA such as dsRNA, siRNA, shRNA, miRNA or amiRNA), the rAAV comprises two ITRs wherein the hybrid promoter and transgene are located between two ITRs, AAV ITR sequences may be from any known AAV such as AAV2 ITRs, as well as the use of a polyadenylation sequence such as SV40 polyA signal being inserted following the transgene sequences and before the 3’ AAV-TR sequence; and (iii) Kruse also disclosed a vector comprising a sequence encoding a circular mRNA molecule for production of a desired polypeptide inside mammalian cells, which vector comprises an RNA polymerase promoter located 5’ of a first intronic element, a gene of interest that is immediately flanked by 5’ UTR and 3’ UTR, and the use of the human poliovirus 1 IRES for translating the produced circular mRNA molecule. Please also noting that the primary Chang reference already taught the circular RNA is produced by transcription in vivo or in vitro under transcriptional control of a promoter and the recombinant nucleic acid comprises a viral vector such an adeno-associated virus, as well as the use of a 3’ portion of an endogenous or exogenous intron comprising a 3’ splice site (a truncated intron) together with a 5’ portion of an endogenous or exogenous intron comprising a 5’ splice site (a truncated intron) for back-splicing.
An ordinary skilled artisan would have a reasonable expectation of success in light of the teachings of Chang et al, Liang et al, Sena-Esteves et al and Kruse; coupled with a high level of skill for an ordinary skilled artisan in the relevant art.
The modified rAAV vector/virion/genome resulting from the combined teachings of Chang et al, Liang et al, Sena-Esteves et al and Kruse as set forth above is indistinguishable and encompassed by the presently claimed invention.
Therefore, the claimed invention as a whole was prima facie obvious in the absence of evidence to the contrary.
Response to Arguments
Applicant’s arguments related to the above 103 rejection in the Amendment filed on 02/27/2026 (pages 9-11) have been fully considered, but they are respectfully not found persuasive for the reasons discussed below.
Applicant argued that one of ordinary skill in the art would have no reason or motivation to modify the alleged teachings of Chang because Chang teaches producing circular RNAs in vitro and delivering those circular RNAs to target cells using liposomes (e.g., working examples, particular paragraphs [0209], [0215] and [0212]). Applicant also argued that Chang merely provides a generic list of viral vectors without including any further description, guidance, or working examples involving any type of viral vector, let alone AAV; and such undeveloped disclosures are not particularized teachings that would have provided one of ordinary skill in the art to arrive at the claimed subject matter. Applicant also argued that similar to Chang, Liang generally discloses non-viral plasmids encoding circular RNA that are delivered to cells in vitro using liposome-mediated transfection techniques; and Liang provides no evidence that these truncated elements would retain backsplicing activity in the context of AAV with non-viral plasmids delivered by lipofection persist as large, supercoiled episomes transcribed without the physical and structural constraints imposed by an AAV genome. Thus, in the absence of any data or guidance addressing these substantial differences a person of ordinary skill in the art would not have had a reasonable expectation of success in substituting the nonviral plasmids of Liang with AAV. Applicant further argued that Sena-Esteves does not disclose an AAV genome encoding a circular RNA, and one of ordinary skill in the art would have no reason or motivation to combine the generic AAV vectors in Sena-Esteves with the circular RNAs taught in Chang and Liang, let alone the specific combination of elements recited in claim 19. Applicant further argued that the vectors in Kruse rely on Group I intron sequences, which generate circular RNA through self-splicing rather than backsplicing, and because Kruse uses an entirely different mechanism for circRNA formation its teachings provide no guidance, motivation or reasonable expectation of success for creating the presently claimed AAV genome. Finally, Applicant cited In re Kubin, and argued that the Office cannot pick and choose isolated elements of Chang, Liang, Sena-Esteves, and Kruse and piece them together using the Applicant’s specification as a template, and such approach is impermissible because it relies on hindsight rather than considering the art from the viewpoint of the skilled artisan at the time the present application was filed.
First, since the rejection was made under 35 U.S.C. 103 none of the cited references have to teach every limitation of the instant claims. For example, none of Liang and Sena-Esteves have to teach an AAV genome encoding a circular RNA; or none of Chang and Kruse have to teach the first intronic element comprising SEQ ID NO: 15 and the second intronic element comprising SEQ ID NO: 16. It is also apparent that Applicant considered each of the cited references in total isolation one from the others, without taking into consideration of the specific combination of Chang, Liang, Sena-Esteves and Kruse.
Second, the teachings of Chang are not necessarily limited only to working examples. Chang stated explicitly at least “In certain embodiments, the recombinant nucleic acid comprises a bacterial plasmid vector or a viral vector” (last sentence of paragraph [0018]); “In certain embodiments, the recombinant nucleic acid comprises a bacterial plasmid vector or a viral vector (e.g., measles virus, vesicular stomatitis virus, adenovirus, retrovirus (e.g., γ-retrovirus and lentivirus), pox-virus, adeno-associated virus, baculovirus, or herpes simplex virus vectors)” (paragraph [0027]); “In certain embodiments, a virus or engineered construct derived from a viral genome is used for delivery of a circular RNA to a cell. A number of viral based systems have been developed for transfer of nucleic acids into mammalian cells. These include adeno-viruses, retroviruses (γ-retroviruses and lentiviruses), poxviruses, adeno-associated viruses, baculoviruses, and herpes simplex viruses” (paragraph [0114]); and “AAV vectors can be readily constructed using techniques well known in the art” (paragraph [0116]). Thus, Chang does not have to provide any further description, guidance or working example on the construction of a recombinant AAV vector comprising a nucleotide sequence encoding a circular RNA for delivery to a cell, particularly AAV vectors can be readily constructed using techniques well known in the art.
Third, there is no evidence of record indicating or remotely suggesting that the disclosed truncated intronic elements of Liang would not retain back-splicing activity upon expression from a rAAV vector instead of a non-viral plasmid. Especially, Liang taught specifically that miniature introns containing the splice sites along with short (about 30- to 40- nucleotide) inverted repeats, such as Alu elements, derived from human ZKSCAN1 and HIPK3 genes are sufficient to allow the intervening exons to circularize in cells. The back-splicing activity is clearly not dependent on a vector comprising a nucleotide sequence encoding the miniature introns. Additionally, Chang already taught clearly that an engineered AAV vector can be used for delivery of a circular RNA to a cell.
Fourth, Sena-Esteves was cited to demonstrate the arrangement of various elements (e.g., ITRs, promoter, transgene, and polyA sequence) in a typical recombinant AAV vector known in the art, and to supplement the combined teachings of Chang, Liang and Kruse for numerous additional limitations recited in various dependent claims. Similarly, Kruse was also cited to demonstrate the arrangement of various elements in an exemplary DNA vector (e.g., a plasmid or a viral vector) comprising a sequence encoding a circular mRNA molecule for production of a desired polypeptide inside eukaryotic cells, and to supplement the combined teachings of Chang, Liang and Sena-Esteves for an additional limitation recited in a dependent claim (e.g., human poliovirus 1 IRES). Moreover, please note that Chang already taught generation of circular RNAs through both self-splicing (Fig. 1A) and back-splicing (Example 1; paragraphs [0202]-[0205]; Fig. 5).
Fifth, with respect to Applicant’s argument on impermissible hindsight reconstruction Examiner would like to recite a paragraph from in re Oetiker, 977, F.2d 1443, 1448 (Fed. Cir. 1992).
"[T]here must be some teaching, reason, suggestion, or motivation found "in the prior art" or "in the prior art references" to make a combination to render an invention obvious within the meaning of 35 U.S.C. 103 (1998). Similar language appears in a number of opinions and if taken literally would mean that an invention cannot be held to have been obvious unless something specific in a prior art reference would lead an inventor to combine the teachings therein with another piece of prior art. This restrictive understanding of the concept of obviousness is clearly wrong…. While there must be some teaching, reason, suggestion, or motivation to combine existing elements to produce the claimed device, it is not necessary that the cited references or prior art specifically suggest making the combination…. In sum, it is off the mark for litigants to argue, as many do, that an invention cannot be held to have been obvious unless a suggestion to combine the prior art teachings is found in a specific reference."
Although the cited artisans do not specifically point out a motivation to in their disclosure, an ordinarily skilled artisan would have been able to identify the need for the combination of the teachings without the disclosure of the instant application. It must be recognized that any judgment on obviousness is in a sense necessarily a reconstruction based upon hindsight reasoning. But so long as it takes into account only knowledge which was within the level of ordinary skill at the time the claimed invention was made, and does not include knowledge gleaned only from the applicant's disclosure, such a reconstruction is proper. See In re McLaughlin, 443 F.2d 1392, 170 USPQ 209 (CCPA 1971). Please refer to the above 103 rejections for details along with the motivations for combining the cited references.
Claim 33 is rejected under 35 U.S.C. 103 as being unpatentable over Chang et al (US 2019/0345503 with an effective filing date of 06/20/2016; IDS) in view of Liang et al (Genes & Development 28:2233-2247, 2014; IDS), Sena-Esteves et al (WO 2016/172155; IDS) and Kruse (WO 2014/186334; IDS) as applied to claims 19-27, 30-32 and 34-42 above, and further in view of Kay et al (US 2016/0053282).
The combined teachings of Chang et al, Liang et al, Sena-Esteves et al and Kruse were presented above. However, none of the cited references teach specifically that the first AAV2 ITR and/or the second AAV2 ITR sequences comprise one or more insertions, deletions, truncations and/or missense mutations.
Before the effective filing date of the present application (11/07/2017), Kay et al already taught a method of enhancing the genetic stability of parvovirus vectors, wherein the nucleotide sequence of either the 5’ ITR or 3’ ITR is a heterologous ITR having a sequence that is less than 90% complementary to the other ITR sequence to prevent ITR repair or conversion and create a stabilized parvovirus vector (Abstract; and Summary of the Invention; particularly paragraph [0016]-[0017]). Kay et al stated “In some embodiments, the parvovirus is an adeno-associated virus such as, for example, AAV-2. In some embodiments, the heterologous ITR is an AAV-4 ITR. In some embodiments, the heterologous ITR is a synthetic ITR containing a rep protein binding site and having a hairpin secondary structure. In some embodiments, the foreign DNA domain comprises one or more expression cassettes, each independently ranging in size from about 0.2 kb to about 5 kb, and adding up to a total size of no more than about 5kb” (paragraph [0021]); and “The 3’ ITR and 5’ ITR domains can include any naturally occurring parvoviral ITR (or functional synthetic variant thereof). The ITRs can also be a synthetic construct having a hairpin secondary structure. In some embodiments, the ITR is an AAV ITR from any one of the AAV serotypes 1, 2, 3, 4, 5 and 6….In some embodiments, the ITRs do not have a wild-type ITR sequence and may be altered by insertion, deletion, truncation or mutations, as long as the ITR mediates the desired functions, such as virus packaging, integration, provirus rescue, and the like” (paragraph [0073]). Kay et al noted that both ss and dsAAV vectors in the prior art carrying identical (or nearly identical, when considering the 6bp deletion in one ITR in dsAAV) ITRs making them extremely prone to homologous recombination; and a frequent result is either deletion of large parts of one ITR or gene conversion between the two ITRs; and the genetic instability of ss or dsAAV vectors with two (nearly) identical ITRs increases inversely with the insert size, making it impossible to clone inserts smaller than 2.5 kb into a conventional ssAAV vector, or smaller than 1kb into dsAAV (paragraphs [0012] and [0014]). Kay et al also taught that the foreign DNA encodes a protein, and in some other embodiments the foreign DNA encodes an RNAi product such as shRNA or micro-RNA (paragraph [0018]).
Accordingly, it would have been obvious for an ordinary skilled artisan before the effective filing date of the present application to further modify the combined teachings of Chang et al, Liang et al, Sena-Esteves et al and Kruse by also using a recombinant AAV2 vector with AAV2 ITRs that are altered by insertion, deletion, truncation or mutations, in light of the teachings of Kay et al as presented above.
An ordinary skilled artisan would have been motivated to further carry out the above modification because Kay et al already taught a method of enhancing the genetic stability of parvovirus vectors, wherein the nucleotide sequence of either the 5’ ITR or 3’ ITR is a heterologous ITR having a sequence that is less than 90% complementary to the other ITR sequence to prevent ITR repair or conversion and create a stabilized parvovirus vector; particularly and particularly the genetic instability of ss or dsAAV vectors with two (nearly) identical ITRs increases inversely with the insert size, making it impossible to clone inserts smaller than 2.5 kb into a conventional ssAAV vector, or smaller than 1kb into dsAAV.
The modified recombinant AAV vector/virion resulting from the combined teachings of Chang et al, Liang et al, Sena-Esteves et al, Kruse and Kay et al is indistinguishable from and encompassed by the presently claimed invention.
An ordinary skilled artisan would have a reasonable expectation of success in light of the teachings of Chang et al, Liang et al, Sena-Esteves et al, Kruse and Kay et al; coupled with a high level of skill for an ordinary skilled artisan in the relevant art.
Therefore, the claimed invention as a whole was prima facie obvious in the absence of evidence to the contrary.
Response to Arguments
Applicant’s arguments related to the above 103 rejection in the Amendment filed on 02/27/2026 (last paragraph at page 11) have been fully considered, but they are respectfully not found persuasive for the reasons discussed below.
Applicant argued basically that Kay fails to cure the deficiencies of Chang, Liang, Sena-Esteves, and Kruse as discussed above.
Please refer to the Examiner’s responses regarding to the alleged deficiencies of Chang, Liang, Sena-Esteves, and Kruse above. Kay was cited to supplement the combined teachings of Chang, Liang, Sena-Esteves, and Kruse for the limitation recited in dependent claim 33.
Claim 43 is rejected under 35 U.S.C. 103 as being unpatentable over Chang et al (US 2019/0345503 with an effective filing date of 06/20/2016; IDS) in view of Liang et al (Genes & Development 28:2233-2247, 2014; IDS), Sena-Esteves et al (WO 2016/172155; IDS) and Kruse (WO 2014/186334; IDS) as applied to claims 19-27, 30-32 and 34-42 above, and further in view of Srivastava et al (US 2013/0310443; IDS).
The combined teachings of Chang et al, Liang et al, Sena-Esteves et al and Kruse were presented above. However, none of the cited references teach specifically that the recombinant capsid protein and/or virion comprising one or more insertions, deletions and/or substitutions in the capsid or particle sequence relative to a wild type AAV.
Before the effective filing date of the present application (11/07/2017), Srivastava et al already taught recombinant AAV virions comprising AAV capsid proteins comprising modification/substitution of one or a combination of the surface-exposed lysine, serine, threonine and/or tyrosine residues in the VP3 region, including the VP3 region of AAV9, wherein the recombinant AAV virions have improved efficiency in transduction of a variety of cells, tissues and organs of interest when compared to wild-type recombinant AAV virions; and the recombinant AAV virions are suitable for gene therapy (see at least Abstract; Brief Summary; particularly paragraphs [0007]-[0008], [0013], [0026], [0050]-[0052], [0057]-[0058]; and Figs. 1-2).
Accordingly, it would have been obvious for an ordinary skilled artisan before the effective filing date of the present application to further modify the combined teachings of Chang et al, Liang et al, Sena-Esteves et al and Kruse by also utilizing at least a recombinant AAV9 vector/virion comprising AAV9 capsid proteins with modification/substitution of one or a combination of the surface-exposed lysine, serine, threonine and/or tyrosine residues in the VP3 region for gene therapy, in light of the teachings of Srivastava et al as presented above.
An ordinary skilled artisan would have been motivated to further carry out the above modification because Srivastava et al already taught that recombinant AAV virions with modified surface-exposed lysine, serine, threonine and/or tyrosine residues in their capsid proteins have improved efficiency in transduction of a variety of cells, tissues and organs of interest.
The modified recombinant AAV vector/virion resulting from the combined teachings of Chang et al, Liang et al, Sena-Esteves et al, Kruse and Srivastava et al is indistinguishable from and encompassed by the presently claimed invention.
An ordinary skilled artisan would have a reasonable expectation of success in light of the teachings of Chang et al, Liang et al, Sena-Esteves et al, Kruse and Srivastava et al; coupled with a high level of skill for an ordinary skilled artisan in the relevant art.
Therefore, the claimed invention as a whole was prima facie obvious in the absence of evidence to the contrary.
Response to Arguments
Applicant’s arguments related to the above 103 rejection in the Amendment filed on 02/27/2026 (first two paragraphs at page 12) have been fully considered, but they are respectfully not found persuasive for the reasons discussed below.
Applicant argued basically that Srivastava fails to cure the deficiencies of Chang, Liang, Sena-Esteves, and Kruse as discussed above.
Please refer to the Examiner’s responses regarding to the alleged deficiencies of Chang, Liang, Sena-Esteves, and Kruse above. Srivastava was cited to supplement the combined teachings of Chang, Liang, Sena-Esteves, and Kruse for the limitation recited in dependent claim 43.
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 USPTO Internet website contains terminal disclaimer forms which may be used. Please visit www.uspto.gov/patent/patents-forms. The 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/process/file/efs/guidance/eTD-info-I.jsp.
Claims 19-27 and 30-43 are provisionally rejected on the ground of nonstatutory double patenting as being unpatentable over claims 20-33 of copending Application No. 17/796,874 (reference application) in view of Liang et al (Genes & Development 28:2233-2247, 2014; IDS), Sena-Esteves et al (WO 2016/172155; IDS), Kruse (WO 2014/186334; IDS), Kay et al (US 2016/0053282) and Srivastava et al (US 2013/0310443; IDS).
The claims of the present application differ from claims 20-33 of copending Application No. 17/796,874 in reciting specifically an AAV genome encoding a circRNA, wherein the AAV genome comprises the elements (a)-(e) in 5’ to 3’ order as recited in independent claim 19 of the present application, and particularly the first intronic element comprises SEQ ID NO:15 and the second intronic element comprises SEQ ID NO:16 (elected pair of first and second intronic elements); the nucleotide sequence of interest encodes a non-coding RNA such as an RNA silencing molecule (elected species); selecting IRES from human poliovirus 1 (elected species) to drive translation of the translatable mRNA transcribed from the nucleotide sequence of interest; a promoter located between the first inverted terminal repeat and the first intronic element, with first and second intronic elements flank the gene of interest, a 5’ UTR located 3’ to the first inverted terminal repeat and/or a 3’ UTR located 5’ to the second inverted terminal repeat; the first AAV2 ITR and/or the second AAV2 ITR sequences comprise one or more insertions, deletions, truncations and/or missense mutations; and the recombinant capsid protein and/or virion comprising one or more insertions, deletions and/or substitutions in the capsid or particle sequence relative to a wild type AAV.
Before the effective filing date of the present application (11/07/2017), Liang et al already demonstrated at least that miniature introns containing the splice sites along with short (about 30- to 40- nucleotide) inverted repeats, such as Alu elements, derived from human ZKSCAN1 and HIPK3 genes are sufficient to allow the intervening exons to circularize in cells; and the intronic repeats must base-pair to one another, thereby bringing the splice sites into close proximity to each other (Abstract; sections titled “Short repeat sequences are sufficient for ZKSCAN1 circular RNA production” on pages 2236-2238 and “Short repeats are sufficient for production of the HIPK3 circular RNA” on pages 2238 and 2240-2241; Figs. 2 and 4). Liang et al selected and cloned a 2803-nt region of the HIPK3 premRNA into pcDNA3.1 as depicted in reproduced Fig. 4A, 4D and 4E below and confirmed that this expression vector efficiently generates a circular RNA when transfected into HeLa cells, then demonstrated that a 32-nt region of the upstream AluSz element (nucleotides 300-331) and a 32-nt region of the downstream AluSq2 element (nucleotides 2607-2638) are sufficient to support HIPK3 circularization.
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The pcDNA3.1(+) HIPK3 300-2703∆2450-2609 (used in Figure 4E showing formation of a circular RNA) in Supplemental Methods comprises the first 391-nucleotide sequence that is 100% identical to the first intronic element of SEQ ID NO: 15 of the present application and the last 754-nucleotide sequence that is 100% identical to SEQ ID NO: 16 of the present application (see attached sequence below on page 34 of this office action; it is a typo error that the first G appears in front of the phrase “Used in Figure 4E” on the line above the main body of the listed sequence). Additionally, each of the pcDNA3.1(+) HIPK3 300-2703, pcDNA3.1(+) HIPK3 300-2703∆2450-2574, pcDNA3.1(+) HIPK3 300-2703∆2450-2599 and pcDNA3.1(+) HIPK3 300-2703∆2450-2609 constructs contain truncated flanking introns (relative to the wild-type 2803-nucleotide region) and are capable of generating circular RNA as shown in Figs. 4D-E above.
Additionally, Sena-Esteves et al already disclosed recombinant adeno-associated viruses/virions (rAAVs) comprising artificial genetic regulatory elements that modulate transgene expression to provide therapeutic amounts of transgene levels without the induction of adverse events for the treatment of lysosomal storage disorders, and that AAV vectors have emerged as an effective platform for in vivo gene therapy (Abstract; Summary of Invention; page 22, lines 22-25; page 23, lines 11-26). Sena-Esteves et al taught that the rAAV comprising a capsid (e.g., AAV9, AAV10 and others) containing a nucleic acid comprising a hybrid promoter operably linked to a transgene encoding a lysosomal storage disorder-associated protein, and the rAAV comprises two ITRs wherein the hybrid promoter and transgene are located between two ITRs, AAV-ITR sequences may be from any known AAV (e.g., AAV1 ITR, AAV2 ITR, AAV3 ITR, AAV4 ITR, AAV5 ITR, or AAV6 ITR) and the rAAV has the serotype AAV9 (page 3, second paragraph; page 29, lines 8-9). Fig. 1 depicts schematically an exemplary rAAV vector comprising two inverted terminal repeats (ITRs) flank an expression vector on each end as shown below. Sena-Esteves et al also taught the use of a polyadenylation sequence (e.g., SV40 polyA and BGH polyA) being inserted following the transgene sequences and immediately before the 3’ AAV-TR sequence (page 27, lines 4-5; and Fig. 1). Sena-Esteves et al also taught that a transgene may encode an interfering RNA such as dsRNA, siRNA, shRNA, miRNA or amiRNA (page 5, lines 3-8).
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Moreover, Kruse also disclosed a DNA vector (e.g., a plasmid or a viral vector) comprising a sequence encoding a circular mRNA molecule for production of a desired polypeptide inside eukaryotic cells (e.g., mammalian cells), and an exemplary vector comprises the following elements operably connected to each other and arranged in the 5’ to 3’ order as depicted schematically in Fig. 1 below: i) an RNA polymerase promoter (e.g., a T7 polymerase), ii) a first Group I intron sequence, iii) an IRES (e.g., Human poliovirus 1 IRES, Encephalomyocarditis virus IRES and others), iv) a 5’-UTR (e.g., human beta globin 5’-UTR), v) a gene of interest, vi) a 3’-UTR (e.g., human beta globin 3’-UTR), vii) a polyA tract at least 30 nucleotides long, viii) a second Group I intron sequence, and ix) an RNA polymerase terminator (e.g., a T7 terminator), wherein at least Group I self-splicing by permutated intron-exon sequences derived from T4 bacteriophage gene td is used to produce circular mRNA (Abstract; Summary of the Disclosure; particular paragraphs [0029]-[0036], [0056], [0058], [0098]-[0099]; and Fig. 1).
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Additionally, Kay et al already taught a method of enhancing the genetic stability of parvovirus vectors, wherein the nucleotide sequence of either the 5’ ITR or 3’ ITR is a heterologous ITR having a sequence that is less than 90% complementary to the other ITR sequence to prevent ITR repair or conversion and create a stabilized parvovirus vector (Abstract; and Summary of the Invention; particularly paragraph [0016]-[0017]). Kay et al stated “In some embodiments, the parvovirus is an adeno-associated virus such as, for example, AAV-2. In some embodiments, the heterologous ITR is an AAV-4 ITR. In some embodiments, the heterologous ITR is a synthetic ITR containing a rep protein binding site and having a hairpin secondary structure. In some embodiments, the foreign DNA domain comprises one or more expression cassettes, each independently ranging in size from about 0.2 kb to about 5 kb, and adding up to a total size of no more than about 5kb” (paragraph [0021]); and “The 3’ ITR and 5’ ITR domains can include any naturally occurring parvoviral ITR (or functional synthetic variant thereof). The ITRs can also be a synthetic construct having a hairpin secondary structure. In some embodiments, the ITR is an AAV ITR from any one of the AAV serotypes 1, 2, 3, 4, 5 and 6….In some embodiments, the ITRs do not have a wild-type ITR sequence and may be altered by insertion, deletion, truncation or mutations, as long as the ITR mediates the desired functions, such as virus packaging, integration, provirus rescue, and the like” (paragraph [0073]). Kay et al noted that both ss and dsAAV vectors in the prior art carrying identical (or nearly identical, when considering the 6bp deletion in one ITR in dsAAV) ITRs making them extremely prone to homologous recombination; and a frequent result is either deletion of large parts of one ITR or gene conversion between the two ITRs; and the genetic instability of ss or dsAAV vectors with two (nearly) identical ITRs increases inversely with the insert size, making it impossible to clone inserts smaller than 2.5 kb into a conventional ssAAV vector, or smaller than 1kb into dsAAV (paragraphs [0012] and [0014]). Kay et al also taught that the foreign DNA encodes a protein, and in some other embodiments the foreign DNA encodes an RNAi product such as shRNA or micro-RNA (paragraph [0018]).
Furthermore, Srivastava et al already taught recombinant AAV virions comprising AAV capsid proteins comprising modification/substitution of one or a combination of the surface-exposed lysine, serine, threonine and/or tyrosine residues in the VP3 region, including the VP3 region of AAV9, wherein the recombinant AAV virions have improved efficiency in transduction of a variety of cells, tissues and organs of interest when compared to wild-type recombinant AAV virions; and the recombinant AAV virions are suitable for gene therapy (see at least Abstract; Brief Summary; particularly paragraphs [0007]-[0008], [0013], [0026], [0050]-[0052], [0057]-[0058]; and Figs. 1-2).
Accordingly, it would have been obvious for an ordinary skilled artisan before the effective filing date of the present application to modify the AAV vector/particle comprising a nucleic acid sequence encoding at least two circular RNAs comprising a first circRNA and a second circRNA in claims 20-33 of copending Application No. 17/796,874 by also having the “features” recited in the AAV genome encoding a circular RNA and an AAV capsid or particle comprising the same AAV genome of the present application, in light of the teachings of Sena-Esteves et al, Kruse, Kay et al and Srivastava et al as presented above.
An ordinary skilled artisan would have been motivated to carry out the above modifications because: (i) Liang et al already demonstrated successfully that miniature introns containing the splice sites along with short (about 30- to 40- nucleotide) inverted repeats, such as Alu elements, derived from human ZKSCAN1 and HIPK3 genes are sufficient to allow the intervening exons to circularize in cells; and at least the exemplary pCDNA3.1(+) HIPK3 300-2703∆2450-2609 (used in Figure 4E showing formation of a circular RNA) in Supplemental Methods comprises the first 391-nucleotide sequence that is 100% identical to the first intronic element of SEQ ID NO: 15 of the present application and the last 754-nucleotide sequence that is 100% identical to the second intronic element of SEQ ID NO: 16 of the present application; (ii) Sena-Esteves et al already taught at least a rAAV comprising an AAV9 capsid containing a nucleic acid comprising a hybrid promoter operably linked to a transgene (e.g. a transgene encoding a therapeutic lysosomal storage disorder-associated protein or an interfering RNA such as dsRNA, siRNA, shRNA, miRNA or amiRNA), the rAAV comprises two ITRs wherein the hybrid promoter and transgene are located between two ITRs, AAV ITR sequences may be from any known AAV such as AAV2 ITRs, as well as the use of a polyadenylation sequence such as SV40 polyA signal being inserted following the transgene sequences and before the 3’ AAV-TR sequence; (iii) Kruse also disclosed a vector comprising a sequence encoding a circular mRNA molecule for production of a desired polypeptide inside mammalian cells, which vector comprises an RNA polymerase promoter located 5’ of a first intronic element, and a gene of interest that is immediately flanked by 5’ UTR and 3’ UTR; (iv) Kay et al already taught a method of enhancing the genetic stability of parvovirus vectors, wherein the nucleotide sequence of either the 5’ ITR or 3’ ITR is a heterologous ITR having a sequence that is less than 90% complementary to the other ITR sequence to prevent ITR repair or conversion and create a stabilized parvovirus vector; particularly and particularly the genetic instability of ss or dsAAV vectors with two (nearly) identical ITRs increases inversely with the insert size, making it impossible to clone inserts smaller than 2.5 kb into a conventional ssAAV vector, or smaller than 1kb into dsAAV; and (v) Srivastava et al already taught that recombinant AAV virions with modified surface-exposed lysine, serine, threonine and/or tyrosine residues in their capsid proteins have improved efficiency in transduction of a variety of cells, tissues and organs of interest.
An ordinary skilled artisan would have a reasonable expectation of success in light of the AAV vector/particle comprising a nucleic acid sequence encoding at least two circular RNAs comprising a first circRNA and a second circRNA in claims 20-33 of copending Application No. 17/796,874 along with the teachings of Liang et al, Sena-Esteves et al, Kruse, Kay et al and Srivastava et al, coupled with a high level of skill for an ordinary skilled artisan in the relevant art.
The modified AAV vector/particle comprising a nucleic acid sequence encoding at least two circular RNAs resulting from claims 20-33 of copending Application No. 17/796,874 along with the teachings of Liang et al, Sena-Esteves et al, Kruse, Kay et al and Srivastava et al is indistinguishable and encompassed by the presently claimed invention.
This is a provisional nonstatutory double patenting rejection.
Response to Arguments
Applicant’s arguments related to the above provisional nonstatutory double patenting rejection in the Amendment filed on 02/27/2026 (page 13) have been fully considered, but they are respectfully not found persuasive for the reasons discussed below.
Applicant argued basically that the rejection over the ‘874 application is improper because the ‘874 application has an effective filing date of April 1, 2021 which is later than the effective filing date of the present application (November 7, 2028); and thus the ‘874 application cannot serve as a proper reference for an OTDP analysis.
It is noted that this provisional nonstatutory double patenting rejection is not the only remaining rejection in the present application.
Conclusions
No claim is allowed.
THIS ACTION IS MADE FINAL. 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.
Any inquiry concerning this communication or earlier communications from the examiner should be directed to Quang Nguyen, Ph.D., at (571) 272-0776.
If attempts to reach the examiner by telephone are unsuccessful, the examiner’s SPE, James Douglas (Doug) Schultz, Ph.D., may be reached at (571) 272-0763.
To aid in correlating any papers for this application, all further correspondence regarding this application should be directed to Group Art Unit 1631; Central Fax No. (571) 273-8300.
Any inquiry of a general nature or relating to the status of this application or proceeding should be directed to (571) 272-0547.
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/QUANG NGUYEN/Primary Examiner, Art Unit 1631
pcDNA3.1(+) HIPK3 300-2703 D2450-2609
g Used in Figure 4E
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