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 .
Continued Examination Under 37 CFR 1.114
A request for continued examination under 37 CFR 1.114, including the fee set forth in 37 CFR 1.17(e), was filed in this application after final rejection. Since this application is eligible for continued examination under 37 CFR 1.114, and the fee set forth in 37 CFR 1.17(e) has been timely paid, the finality of the previous Office action has been withdrawn pursuant to 37 CFR 1.114. Applicant's submission filed on Dec. 23, 2025 has been entered.
DETAILED ACTION
Acknowledgement is hereby made of receipt and entry of the communication filed on Dec. 23, 2025. Claims 2, 5, 8-13, 15, 17-19 and 21-23 are pending and currently examined.
Claim Objection
(New) The base claim 5 is objected to because of the following informalities: The term “…does not comprises…” should be “…does not comprise…”
Appropriate correction is required.
Claim Rejections - 35 USC § 112
The following is a quotation of 35 U.S.C. 112(b):
(b) CONCLUSION. —The specification shall conclude with one or more claims particularly pointing out and distinctly claiming the subject matter which the inventor or a joint inventor regards as the invention.
The following is a quotation of 35 U.S.C. 112 (pre-AIA ), second paragraph:
The specification shall conclude with one or more claims particularly pointing out and distinctly claiming the subject matter which the applicant regards as his invention.
(Previous rejection- withdrawn) Claims 2, 5, 8-13, 15, 17-19 and 21-23 are rejected under 35 U.S.C. 112(b) or 35 U.S.C. 112 (pre-AIA ), second paragraph, as being indefinite for failing to particularly point out and distinctly claim the subject matter which the inventor or a joint inventor (or for applications subject to pre-AIA 35 U.S.C. 112, the applicant), regards as the invention.
This rejection is withdrawn in view of the amendment filed on Dec. 23, 2025.
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.
(Previous rejection- withdrawn) Claims 2, 5, 8, 10 and 21-23 are rejected under 35 U.S.C. 103 as being unpatentable over Pardoll et al. ( US 2004/0142468 A1, published on Jul. 22, 2024) as evidenced by Masternak et al. ( US 2009/0023152 A1, published on Jan. 22, 2009) and Julien et al. (Sci Rep. 2018 Jan 9;8(1):210), and in view of Ling et al. (J Mol Genet Med. 2015 Aug;9(3):175).
This rejection is withdrawn in view of the amendment filed on Dec. 23, 2025.
(Previous rejection- withdrawn) Claim 9 is rejected under 35 U.S.C. 103 as being unpatentable over Pardoll et al. ( US 2004/0142468 A1, published on Jul. 22, 2024) as evidenced by Masternak et al. ( US 2009/0023152 A1, published on Jan. 22, 2009) and Julien et al. (Sci Rep. 2018 Jan 9;8(1):210), and in view of Ling et al. (J Mol Genet Med. 2015 Aug;9(3):175) as applied to the claims 2, 5, 8, 10 and 21-23, and further in view of McCarty (Mol Ther. 2008 Oct;16(10):1648-56).
This rejection is withdrawn in view of the amendment filed on Dec. 23, 2025.
(Previous rejection- withdrawn) Claims 11-13 and 15 are rejected under 35 U.S.C. 103 as being unpatentable over Pardoll et al. ( US 2004/0142468 A1, published on Jul. 22, 2024) as evidenced by Masternak et al. ( US 2009/0023152 A1, published on Jan. 22, 2009) and Julien et al. (Sci Rep. 2018 Jan 9;8(1):210), and in view of Ling et al. (J Mol Genet Med. 2015 Aug;9(3):175) as applied to the claims 2, 5, 8, 10 and 21-23, and further in view of Buning et al. ( Mol Ther Methods Clin Dev. 2019 Jan 26;12:248-265), Cheng et al. (Gene Ther. 2012 Apr;19(4):375-84), Sayroo et al. (Gene Ther. 2016 Jan;23(1):18-25) and Lieshout et al. (Mol Ther Methods Clin Dev. 2018 Apr 14;9:323-329).
This rejection is withdrawn in view of the amendment filed on Dec. 23, 2025.
(Previous rejection- withdrawn) Claims 17-19 are rejected under 35 U.S.C. 103 as being unpatentable over Pardoll et al. ( US 2004/0142468 A1, published on Jul. 22, 2024) as evidenced by Masternak et al. ( US 2009/0023152 A1, published on Jan. 22, 2009) and Julien et al. (Sci Rep. 2018 Jan 9;8(1):210), and in view of Ling et al. (J Mol Genet Med. 2015 Aug;9(3):175) as applied to the claims 2, 5, 8, 10 and 21-23,and further in view of Ono et al. (WO 96/12823, published on May 2, 1996), Lambert et al. (GenBank Accession: S72810, published on Jan. 26, 1995) and Achatz et al. (WO9627005, published on Sep. 6, 1996).
This rejection is withdrawn in view of the amendment filed on Dec. 23, 2025.
(New Rejection-necessitated by amendment) Claims 2, 5, 8-10, 21 and 23 are rejected under 35 U.S.C. 103 as being unpatentable over Ling et al. (J Virol. 2015 Jan 15;89(2):952-61) in view of Julien et al. (Sci Rep. 2018 Jan 9;8(1):210) and Masternak et al. (US 2009/0023152 A1, published on Jan. 22, 2009).
The amended base claim 2 is directed to a recombinant adeno-associated virus (rAAV) particle, comprising: an rAAV nucleic acid comprising a 5' inverted terminal repeat (ITR), an insert nucleic acid comprising a transgene, and a 3' ITR, wherein the 5' ITR and/or the 3' ITR comprise(s) one or more X-box sequences and does not comprise a D-sequence.
The amended base claim 5 is directed to a recombinant adeno-associated virus (rAAV) particle, comprising: an rAAV nucleic acid comprising a 5' inverted terminal repeat (ITR), an insert nucleic acid comprising a transgene, and a 3' ITR, wherein the 5' ITR and/or the 3' ITR comprise(s) one or more X2 box and/or Y box sequences and does not comprise a D-sequence.
Ling discloses that a rAAV is flanked by inverted terminal repeats (ITRs) of 145 nucleotides (nts), 5’ ITR and 3’ ITR, and a transgene such as hrGFP is insert between the 5’-ITR and 3’-ITR (See page 954, bridging columns left and right). Ling further teaches that the D-sequence is a 20-nucleotide sequence from both ends of the inverted terminal repeats (ITRs) in the adeno-associated virus. They identified a transcription suppressor sequence in one of the D-sequences, which shares homology with the binding site for the cellular NF-κB-repressing factor (NRF). The removal of this D-sequence from, and replacement with a sequence containing putative binding sites for transcription factors in, single-stranded AAV (ssAAV) vectors significantly augments transgene expression both in human cell lines in vitro and in murine hepatocytes in vivo. The development of these genome-modified ssAAV vectors has implications not only for the basic biology of AAV but also for the optimal use of these vectors in human gene therapy (See Abstract). Fig. 1 of Ling shows the effect of one D-sequence substitution on viral genome rescue and replication (See page 955 and below). For the substitution sequence “S”, Ling teaches that they performed computational analyses of both the D sequence and the S sequence using the databases available at chip-mapper.org and http://www.cbrc.jp/research/db/TFSEARCH.html, which allow the identification of putative transcription factor binding-sites in DNA genomes (See page 959, left column). Based on the description, replacing D-sequence in one of the ITRs by a putative transcription factor binding other than the AAV genome DNA (substitution sequence) is beneficial for increasing the rAAV transduction.
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Accordingly, Ling teaches a rAAV, wherein the D-sequence from 5' ITR or the 3' ITR is replaced by a substitution sequence (S), such as a putative binding sites for transcription factors, can be successfully packaged into rAAV vectors and that the transduction efficiency of these vectors was significantly higher than that of conventional AAV vectors (See page 953, left column, paragraph 2). However, Ling is silent on the X-box sequence, X2 box sequence and/or Y box sequence in the 5’ ITR and/or 3’ ITR.
Julien et al. teaches that the D2-sequence of AAV ITRs contain the consensus sequence of the MHC class II X-box site in the HLA-DRA (X-box), and RFX proteins which interact with transcriptional enhancers of several mammalian DNA viruses, can act as regulators of AAV mediated transgene expression (See Figure 3, page 4 and below; page 1, paragraph 1). Julien et al. discloses the homologies between the D2 sequence, the consensus binding motif for the RFX family of transcription factors and the X-DRA sequence (X-box). The X-box found in the promoter of HLA class II genes is efficiently recognized by all members of the RFX transcription factors family including RFX1, RFX2, RFX3 and RFX5 (See page 3, paragraph 1), and the RFX/CREB complex in the context of MHC II promoter, transcription factors binding the ITR can protect AAV promoters against DNA methylation (See page 8, paragraph 1).
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Masternak teaches that MHC-II promoters contain the X-X2-Y box region (See e.g. [0083]), and discloses that Major Histocompatibility Complex class II (MHC-II) molecules are transmembrane glycoproteins playing a central role in the development and control of the adaptive immune response. They are encoded by a family of genes that are co-regulated at the level of transcription by a 150 bp regulatory module conserved in their promoter proximal regions. This module contains four sequences, the W, X, X2 and Y boxes, that contribute synergistically to optimal promoter activity. Three ubiquitously expressed factors, RFX, X2BP and NF-Y bind co-operatively to the X, X2 and Y boxes to form a remarkably stable higher order nucleoprotein complex (enhanceosome) (See [0030]).
Based on the teachings of Julien and Masternak, the D sequence is homologues with the MHC-II promoter regions that contains the X-box sequences, X2 box and/or Y box sequences, where these motifs can interact with RFX proteins to regulate AAV mediated transgene expression, where the RFX is a transcription factor. Thus, Julien and Masternak indicates that the D-sequences of ITRs are transcription factor binding sites that share a partial sequence homology with the X-box in the HLA-DR promoter of MHC II, where the HLA-DR promoter contains the X, X2 and Y boxes sequences.
It would have been prima facie obvious for one having ordinary skill in the art before the effective filing date of the claimed invention to combine the teachings of Ling, Julien and Masternak to arrive at an invention as claimed. Ling teaches that the removal of the D sequence and replacement with a sequence containing putative binding sites for transcription factors in either 5’ ITR or 3’ ITR can significantly augment transgene expression both in human cell lines in vitro and in murine hepatocytes in vivo. Julien teaches that the D-sequences of AAV ITR share the homologous sequence with X-box sequence of HLA-DR promoter of MHC II and the RFX protein (transcription factor) interacts with the D-sequence, where the RFX/CREB complex in the context of MHCII promoter can protect AAV promoters against DNA methylation (See page 8, paragraph 2). At the same time, Masternak teaches that the HLA promoter comprises the X, X2, and Y boxes. Thus, one of skill in the art would have been motivated to replace the S substitution with the HLA-DR promoter region including the X-box, X2-box, and Y boxes sequences as claimed to augment the transduction efficiency of the AAV vectors. There would be a reasonable expectation of success to develop a recombinant adeno-associated virus (rAAV) particle as claimed because D-sequence from 5' ITR or the 3' ITR replaced by a substitution sequence with transcription factors binding sites, such as the sequences of X, X2, and Y boxes, can enhance the AAV transgene expression.
Thus, the invention as a whole was clearly prima facie obvious to one of ordinary skill in the art before the effective filing date of the claimed invention.
Regarding claim 8, it requires the transgene is about 2- to 5-kb in length. Ling teaches that the capacity of AAV vectors is about 2.8 kb (See page 954, right column, paragraph 1).
Regarding claim 9, it requires that the nucleic acid vector is a self-complementary AAV (scAAV) vector. Ling teaches that recently, the development of self-complementary AAV (scAAV) vectors, which can bypass the requirement of viral second-strand DNA synthesis, has shown remarkable efficacy in the treatment of hemophilia B patients (See page 952, left column).
Regarding claim 10, it requires the rAAV particle has a serotype that is selected from AAV2, AAV3, and AAV6, AAV3PM, AAV3QM, AAV6TM, AAV6QM, or a variant thereof. Ling teaches the rAAV is AAV2 (See page 953, right column, paragraph 4).
Regarding claims 21-23, they require a pharmaceutical composition comprising:(a) the rAAV particle of claim2: and (b) a pharmaceutically acceptable excipient, and the composition is formulated for administering an effective amount of the rAAV particle of claim 2 to the cell. Ling teaches the recombinant AAV vector transduction in vivo and in vitro. Ling discloses that the recombinant AAV vectors are injected intravenously via the tail vein into C57BL/6J mice at 1 x10^10 vector genomes (vgs) per animal. Phosphate-buffered saline (PBS)-injected mice were used as an appropriate control (See page 954, left column, paragraph 5), which teaches claim 21 at rAAV particles and a pharmaceutically acceptable excipient such as PBS. For the in Vitro experiment, Ling teaches cells were seeded in 96-well plates at 10,000 cells per well in C-DMEM. AAV infections were performed in serum- and antibiotic-free DMEM for 2 h (See page 954, left column, paragraph 3) that teaches claim 23. As for the claim 22, it is interpreted as the same as claim 21 because claim 22 does not provide additional structure or elements to claim 21. Accordingly, the in vivo injection taught by Ling also teaches the claim 22.
(New Rejection-necessitated by amendment) Claims 11-13 and 15 are rejected under 35 U.S.C. 103 as being unpatentable over Ling et al. (J Virol. 2015 Jan 15;89(2):952-61) in view of Julien et al. (Sci Rep. 2018 Jan 9;8(1):210) and Masternak et al. (US 2009/0023152 A1, published on Jan. 22, 2009) as applied to claims 2, 5, 8-10, 21 and 23 above, and further in view of Buning et al. ( Mol Ther Methods Clin Dev. 2019 Jan 26;12:248-265), Cheng et al. (Gene Ther. 2012 Apr;19(4):375-84), Sayroo et al. (Gene Ther. 2016 Jan;23(1):18-25), Lieshout et al. (Mol Ther Methods Clin Dev. 2018 Apr 14;9:323-329), Russell et al. (US6156303A, patented on De. 5, 2000), Bartlett J. (US 20020192823 A1, published on Dec. 19, 2002 and Aslanidi et al. (US 20180030096 A1, published on Feb. 01, 2018).
Claims 11-13 and 15 are directed to a rAAV particles of AAV2, AAV3 and AAV6 that comprises modified capsid protein with specific positions and amino acids.
Based on the description above, Ling, Julien and Masternak teach the rAAV particles with ITR, transgene and X box sequences or X2-box and/or Y-box sequences as claimed, however, it is silent on the capsid protein modification especially with point mutation at specific amino acid sites based on SEQ ID NOs: 29, 30 and 9.
For the newly amended reference sequences, SEQ ID NO: 29 is identical to the SEQ ID NO: 5 of Russell’s invention (See Table A), SEQ ID NO: 30 is identical the SEQ ID NO: 13 of Barlett’s invention (See Table B) and SEQ ID NO: 9 is identical to the SEQ ID NO: 3 of Aslanidi’s invention (See Table C).
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The teachings of the specific mutation as follows:
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Buning et al. describes the capsid modifications for targeting and improving the efficacy of AAV vectors and teaches that since the WT AAV did not evolve for the purposes of delivery of therapeutic genes, there is ample basis for optimism that their capsid-modified AAV vectors and future improvements will further add to the safety, efficacy, and specificity of their potential use in gene therapy for a wide variety of human diseases in the foreseeable future (See page 260, right column, paragraph 3). Buning et al. teaches claims 11-13 in Figure 5 (See page 259 and below). Figure 5 shows that the capsid-Modified next Generation of Recombinant AAV Serotype AAV2, AAV3 and AAV6 has non-tyrosine (Y-), non- threonine (T-) and non-serine (S-) mutations.
Specifically, for the amended claim 11, Buning et al. teaches a AAV3 mutations at T492, S663, but it is silent on Y705 or Y731. However, Cheng et al. teaches that they document that AAV3 vectors are targeted for degradation by the host cell proteasome machinery, and that site-directed mutagenesis of surface exposed tyrosine (Y) to phenylalanine (F) residues on AAV3 capsids significantly improves the transduction efficiency of Y701F, Y705F and Y731F mutant AAV3 vectors (See page 2, paragraph 1).
For the amended claim 12, Buning et al. teaches a mutation of AAV2 at Y444F, T581 and S578 (See page 258, left column, paragraph 2; right column, paragraph 3). For the amended claim 13 and 15, Buning et al. teaches mutations of AAV6 at Y731F (claim 15), Y705 and T492 (claim 13) (See page 260, left column, paragraph 1). Although Bunning does not teach the S663 and a non-phenylalanine residue at position 129 in claim 13 and Y445F and F129L in claim 15, Sayroo et al. teaches that the capsid of AAV serotype 6 contains 17 serine (264, 268, 277, 385, 453, 455, 467, 472, 499, 547, 551, 587, 588, 663, 669, 703 708) residues that are surface exposed (See page 19, right column, paragraph 1), which include the serine position at S663. Also, Lieshout et al. describes a Novel Triple-Mutant AAV6 Capsid Induces Rapid and Potent Transgene Expression in the Muscle and Respiratory Tract of Mice and teaches that we describe a triple AAV6 mutant, termed AAV6.2FF, containing F129L, Y445F, and Y731F mutations. AAV6.2FF yielded 10-fold greater transgene expression in lung than AAV6 after 21 days. Additionally, this novel capsid demonstrated 101-fold and 49-fold increased transgene expression in the muscle and lungs, respectively, 24 hr post vector delivery when compared with the parental AAV6 (See Abstract), which teaches the F129L as claimed in claims 13 and 15.
It would have been prima facie obvious for one having ordinary skill in the art before the effective filing date of the claimed invention to develop the claimed rAAV particles by introducing the capsid protein modification of Buning, Cheng, Sayroo and Lieshout into Ling’s study to arrive at an invention as claimed. One would have been motivated to do so for the advantages of greater transgene expression safety and efficacy. Also, one of skill in the art would be motivated to substitute the wild-type reference sequences by using the AAV3 of Russell, AAV2 of Barlett and AAV6 of Aslanidi for the mutations (See MPEP 2144.06: Substituting equivalents known for the same purpose). Based on the reference sequences of Russell’s AAV3, Barlett’s AAV2 and Aslanidi’s AAV6, and the teachings from Ling, Buning, Cheng, Sayroo and Lieshout, there would have been a reasonable expectation of success to develop a rAAV as claimed.
(New Rejection-necessitated by amendment) Claims 17-19 are rejected under 35 U.S.C. 103 as being unpatentable over Ling et al. (J Virol. 2015 Jan 15;89(2):952-61) in view of Julien et al. (Sci Rep. 2018 Jan 9;8(1):210) and Masternak et al. (US 2009/0023152 A1, published on Jan. 22, 2009) as applied to claims 2, 5, 8-10, 21 and 23 above, and further in view of Ono et al. (WO 96/12823, published on May 2, 1996), Lambert et al. (GenBank Accession: S72810, published on Jan. 26, 1995) and Achatz et al. (WO9627005, published on Sep. 6, 1996).
Claims 17-19 require that one or more X-box sequences differ by zero, one or two nucleotides relative to SEQ ID NO: 2, one or more X2-box sequences differ by zero, one or two nucleotides relative to SEQ ID NO: 3, and one or more Y-box sequences differ by zero, one or two nucleotides relative to SEQ ID NO: 4., respectively.
Based on the description above, Ling, Masternak and Julien teach the rAAV particles with ITR, transgene and an MHC promoter (HLA-DR promoter), which contains X box, X2 box and Y-box sequences as claimed. However, they do not teach SEQ ID NOs: 2-4.
Ono et al. describes the cloned transcription factor regulating MHC expression and teaches that a novel DNA binding protein, NF-X1, which regulates expression of major histocompatibility complex (MHC) class II molecules. The NF-X1 contain sequences that is identical to the SEQ ID NO: 2 as claimed (See Page 42 and Table 1 below).
Lambert et al. studies the MHC class II transcription in two type III bare lymphocyte syndrome patients of a single family and the X_Y box released at Accession number S72810 contains sequence that is identical to SEQ ID NO: 3 as claimed (See the Table 2 below).
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Achatz et al. describes the recombinant DNA molecules that code for polypeptides with antigenic properties of allergens clah8 and clah12 and teach a Y-box motif that contains the SEQ ID NO: 4 as claimed (See Table 3 below).
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It would have been prima facie obvious for one having ordinary skill in the art before the effective filing date of the claimed invention to combine the teachings of Ling in view of Julien and Masternak and Ono, Lambert and Achatz to arrive at an invention as claimed. One would have been motivated to do so to use the known X box, X2 box and Y-box sequences in the construct of Ling and to substitute the X box, X2 box and Y-box sequences for another (See MPEP 2144.06: Substituting equivalents known for the same purpose). There would have been a reasonable expectation of success to develop a rAAV as claimed
Responses to Applicant’s Remarks
Applicant’s arguments filed on Dec. 23, 2025 has been received and fully considered.
Regarding the rejection under 35 U.S. C. § 112 (b), Applicant’s amendment and argument are considered, the 112 (b) rejection is withdrawn.
Applicant’s arguments on rejection under 35 U.S.C. § 103 is moot because a new reference is cited as the primary prior art based on applicant’s amendments to the claims. Accordingly, the 103 rejections are withdrawn.
Conclusion
No claims are allowed.
Any inquiry concerning this communication or earlier communications from the examiner should be directed to RUIXUE WANG whose telephone number is (571)272-7960. The examiner can normally be reached Monday-Friday 8:00 am to 4:30 pm, EST.
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/RUIXUE WANG/ Examiner, Art Unit 1672
/NICOLE KINSEY WHITE/Primary Examiner, Art Unit 1672