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 .
Information Disclosure Statement
The information disclosure statements (IDS) submitted on 01/30/2026 are in compliance with the provisions of 37 CFR 1.97. Accordingly, the information disclosure statements are being considered by the examiner.
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and the fee set forth in 37 CFR 1.17(e) has been timely paid, the finality of the previous Office action has been withdrawn pursuant to 37 CFR 1.114.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 01/30/2026 has been entered.
Status of Claims
Claims 38-43, 45-52, and 58-66 are pending and under examination. Claims 58-66 are new. Claims 1-37, 44, and 53-57 are cancelled.
MAINTAINED REJECTIONS
Claim Rejections - 35 USC § 103
In the event the determination of the status of the application as subject to AIA 35 U.S.C. 102 and 103 (or as subject to pre-AIA 35 U.S.C. 102 and 103) is incorrect, any correction of the statutory basis (i.e., changing from AIA to pre-AIA ) for the rejection will not be considered a new ground of rejection if the prior art relied upon, and the rationale supporting the rejection, would be the same under either status.
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.
The factual inquiries for establishing a background for determining obviousness under 35 U.S.C. 103 are summarized as follows:
1. Determining the scope and contents of the prior art.
2. Ascertaining the differences between the prior art and the claims at issue.
3. Resolving the level of ordinary skill in the pertinent art.
4. Considering objective evidence present in the application indicating obviousness or nonobviousness.
This application currently names joint inventors. In considering patentability of the claims the examiner presumes that the subject matter of the various claims was commonly owned as of the effective filing date of the claimed invention(s) absent any evidence to the contrary. Applicant is advised of the obligation under 37 CFR 1.56 to point out the inventor and effective filing dates of each claim that was not commonly owned as of the effective filing date of the later invention in order for the examiner to consider the applicability of 35 U.S.C. 102(b)(2)(C) for any potential 35 U.S.C. 102(a)(2) prior art against the later invention.
Claims 38-39, 42-43, 45-52, and 58-66 are rejected under 35 U.S.C. 103 as being unpatentable over Hanlon et al (Mol Ther Methods Clin Dev. 2019 Oct 23; previously cited, IDS filed 4/20/2023, hereinafter "Hanlon"), in view of Ye et al (J Virol. 2006 Jul; previously cited on PTO-892; hereinafter "Ye") further as evidenced by Xu et al (Mol Ther Methods Clin Dev. 2022 May 29; previously cited on PTO-892; hereinafter "Xu").
Regarding claim 38, 39, 56, 59-60 and 66: Hanlon taught generation of adeno-associated virus (AAV) capsid libraries. (See Hanlon Abstract). The methodology of Hanlon called iTRANSDUCE involved use of a two-component system of the library construct. (1) Cre recombinase is driven by a minimal chicken b-actin (CBA) promoter and (2) p41 promoter-driven AAV9 capsid with random heptamer peptide is inserted between amino acids 588 and 589, cloned downstream of the Cre cassette. (See Hanlon Figure 1A, reproduced below).
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Hanlon described that variant capsids are obtained by packaging the capsid library and transducing into transgenic mice (Ai9) carrying a floxed-STOP tdTomato cassette. Hanlon described that the variant capsid sequences containing the 21-mer insert were amplified, and identified by next-gen sequencing and re-cloned it back into
the AAV plasmid backbone and repackaged capsids (“brain-enriched
capsid library”) for a second round of selection. (See Hanlon, p. 322, col. 2, para 1). It is noted that p41 drives cap expression in AAV5 serotypes, while p40 drives cap expression in AAV2, as taught by Ye (See Ye FIG. 1). As such, Hanlon described achieving a construct comprising a 5’ ITR, a second promoter (CBA), a first promoter (equivalent of p40 promoter), nucleic acid encoding variant AAV capsid, poly A and 3’ ITR.
It is also submitted that Hanlon did not teach use of a tissue-specific promoter as the claimed second promoter. However, Hanlon indicated that they demonstrated an “iTransduce system using an agnostic approach to cell type (whole brain), it is not surprising that AAV-F was highly tropic to astrocytes and neurons, cells that are transduced by AAV9. In future studies we will combine cell-specific promoters to drive Cre expression from the AAV library vector to isolate capsids that can transduce cells that are refractory to conventional AAV vector transduction.” (See Hanlon p. 327, col. 2, 2nd para). As such Hanlon indicated use of a cell-specific promoter as the natural next step. It would have been obvious for a person of ordinary skill in the art to use a tissue specific promoter in place of the CBA promoter. It is also noted that Hanlon used a helper plasmid and not a helper virus. It is also noted that there is no evidence of unexpected results that the claimed limitation has any greater or unexpected results than that exemplified by Hanlon.
Hanlon taught a method of producing adeno-associated virus (AAV) capsid variants by administering an AAV library to a mammalian subject in vivo and recovering progeny AAV particles exhibiting desired properties. Hanlon discloses intravenous administration of recombinant AAV particles comprising variant cap sequences and a functional reporter to mice, wherein AAV replication and selection occur in the absence of any helper-virus co-infection. The reference describes euthanizing the animals twenty-one days post-injection, isolating brain tissue, and recovering viral genomes for subsequent amplification and further rounds of selection.
Thus, Hanlon et al. teaches a method of making recombinant AAV capsid variants by administering AAV particles to a mammalian host (mouse) under helper-virus-free conditions, allowing in vivo replication and selection of new AAV particles, as required by claim 66.
Helper virus co-infection: It is noted that Hanlon taught producing AAV using 293T cells by plating “15-cm tissue culture dishes with
1.5
×
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293T cells/dish. The next day cells were transfected using the calcium phosphate method, with the adenovirus helper plasmid (pAdDF6, 26 mg per plate), rep/cap plasmid (AAV9, AAV-F, AAV-S, 12 mg per plate), and ITR-flanked transgene cassette plasmid (single-stranded AAV-CBA-GFP-WPRE, 10 mg per plate) to induce production of AAV.” (See Hanlon p. 329 col. 2, last para – p. 330 col. 1, first para). As such Hanlon did not teach use of Helper virus co-infection as required by the claims.
Regarding claim 42: Hanlon taught insertion of 21-mers (See Hanlon Figure 1A).
Regarding claim 43: Hanlon taught insertion of peptides between aa 588 and 589. As evidenced by Xu the region of AAV9 falls in the variable region VIII (See Xu Fig. 3).
Regarding claim 45: Hanlon taught the use of 293T cells for the production of AAV library production (See Hanlon p. 298, col. 2, last para); and incubating the cells in DMEM with FBS to purify AAV.
Regarding claim 46 and 61: Hanlon taught injection of the AAV construct into mice and isolation of liver, brain or other organs (See Hanlon p. 322, col. 1, 2nd para-col. 2, 1st para.). It is also noted that Hanlon taught intravenous administration. (See Hanlon p. 327, col. 2, last para) as required by claim 61.
Regarding claim 47 and 63: Hanlon taught isolation of brain, as indicated above; which comprises neuronal cells. It is also noted that Hanlon taught the transduction and imaging of cortex. (See p. 331, col. 1, para 1)
Regarding claim 48 and 64: Hanlon did not teach extraction of RNA and reverse transcription. However, Hanlon taught extraction of DNA from the brain (See Hanlon, p. 322, col. 2, para 1). and using the isolated capsid variants to screen more variants. It is noted that isolation of RNA and reverse transcription of the RNA to arrive at a DNA is well known to a person of ordinary skill in the art.
Regarding claim 49-50: Hanlon taught increased transgene expression in the target tissue (brain) compared to a wild-type AAV9. As such this translates to increased AAV capsid polypeptide in the target tissue as claimed. For example, Hanlon taught “AAV-F (Hanlon’s engineered capsid generated by directed evolution) demonstrated a 119-fold (p < 0.0001) and 68-fold (p = 0.0004) increased GFP fluorescence coverage compared to the parental AAV9 vector” (See Hanlon p. 32, col. 1, last para)
Regarding claim 51: Hanlon taught selection of variants at least 2 times (See Hanlon, p. 322, col. 2, para 1-2).
Regarding claim 52: Hanlon selected the variant capsid polypeptides that were highly enriched in the brain after selection (See Hanlon p. 324, col. 1, para 1). This indicates enrichment of variant AAV capsid in the target tissue.
Regarding claim 58: Hanlon used a p41 promoter as the claimed first promoter. It is noted that p41 drives cap expression in AAV5 serotypes, while p40 drives cap expression in AAV2, as taught by Ye (See Ye FIG. 1). It would have been obvious for a person of ordinary skill in the art to substitute one promoter that drives cap expression for another.
One of ordinary skill in the art would recognize this as simply substituting one type of promoter for another useful for the same purpose ((KSR Int’l Co. v. Teleflex, Inc., 550 U.S. 398 (2007) pg 14 and 12).
Regarding claim 62: Hanlon indicated that “1.27 x 1011 vector genomes (vg; 5 _ 1012 vg/kg) of the library were injected intravenously through the tail vein of one adult male and one female Ai9 mouse, and 3 weeks post-injection the mice were killed; sections of liver, brain, spleen, and kidney were cut and immunostaining of tdTomato was performed. As such Hanlon taught isolation of target tissue after 21 days.” (See Hanlon p. 322, col. 1, last para).
Regarding claim 65: Hanlon taught “For each production, we plated 15-cm tissue culture dishes (usually 10-15 dishes total) with 1.5 x 107 293T cells/dish. The next day cells were transfected using the calcium phosphate method, with the adenovirus helper plasmid (pAdDF6, 26 mg per plate), rep plasmid (pAR9-Cap9-stop/AAP/Rep, 12 mg per plate), and ITR-flanked AAV library (pAAV-CBA-Cre-mut/p41-Cap9-7-mer, 1 mg per plate) to induce production of AAV.” (See Hanlon 0. 328. Col. 2, last para). It is noted that Hanlon taught use of helper plasmid not virus. As such Hanlon taught the claimed method.
Claims 40-41 are rejected under 35 U.S.C. 103 as being unpatentable over Hanlon et al (Mol Ther Methods Clin Dev. 2019 Oct 23; See IDS filed 4/20/2023, hereinafter "Hanlon"), in view of Ye et al (J Virol. 2006 Jul; See PTO-892; hereinafter "Ye") further as evidenced by Xu et al (Mol Ther Methods Clin Dev. 2022 May 29; See PTO-892; hereinafter "Xu"), further in view of Manikandan et al (Cancer Gene Ther; 18 July 2019; See PTO-892; hereinafter "Manikandan").
Regarding claim 40-41: The teachings of Hanlon et al (Mol Ther Methods Clin Dev. 2019 Oct 23; See IDS filed 4/20/2023, hereinafter "Hanlon"), in view of Ye et al (J Virol. 2006 Jul; See PTO-892; hereinafter "Ye") further as evidenced by Xu et al (Mol Ther Methods Clin Dev. 2022 May 29; See PTO-892; hereinafter "Xu") are set forth above. Hanlon did not teach the use of a promoter other than CBA promoter, while suggesting a cell-type specific promoter as the natural next step as explained above. However, Manikandan taught the use of tissue-specific promoter such as GFAP for tissue specific screening of gene therapy products. (See Manikandan p. 276, col. 1, 4th para). As such it would have been obvious for a person of ordinary skill in the art to substitute a GFAP or SYN, as taught by Manikandan for use as cell-type specific promoters (See Manikandan p. 275, col. 1, 4th para), in place of CBA promoter of Hanlon, for the reasons stated in Hanlon. The person would have recognized this as simply substituting one type of promoter for another useful for the same purpose ((KSR Int’l Co. v. Teleflex, Inc., 550 U.S. 398 (2007) pg 14 and 12).
Response to Arguments and Claim Amendments: The claims have been amended to recite providing a first and second plurality of nucleic acid wherein the first plurality of nucleic acid comprises in 5’ to 3’ order,
(i) a 5' inverted terminal repeat (ITR):
(ii) the second promoter, which is a cell-type specific promoter
(iii) the first promoter
(iv) a nucleotide sequence encoding the variant AAV capsid polypeptide having the region of randomized sequence of at least 2, 3, 4, 5, 6, 7, 8, or 9 consecutive amino acids:
(v) a polyadenylation (polyA) sequence: and
(vi) a 3’ ITR;
wherein the first and second promoters are present upstream of the nucleotide sequence encoding the variant AAV capsid polypeptide having the region of randomized sequence of at least 2, 3, 4, 5, 6, 7, 8, or 9 consecutive amino acids and together drive capsid mRNA expression in the absence of helper virus co-infection.
Applicant’s extensive arguments regarding the TRACER platform and the presently claimed methods have been carefully reviewed. Applicant asserts that the claimed methods are distinct from Hanlon including the use of dual promoter system to drive capsid mRNA expression in the absence of helper virus as well as the avoidance of Cre/loxP-based selection and compatibility with non-transgenic animals. It is acknowledged that the TRACER platform described in the specification represents a functionally distinct and commercially valuable approach for generating AAV capsid variants.
However, as currently drafted, the claims are broader than the TRACER platform. In particular, the claims recite vectors comprising two promoters upstream of the capsid coding sequence in 5’ [Wingdings font/0xE0] 3’ order without requiring that both promoters functionally drive the capsid ORF, or that intervening elements (such as Cre) be absent. As such, the claims structurally encompass the vector architecture disclosed and expressly contemplated in Hanlon, including vectors with two promoters (one for Cre and one for capsid) and ITR-flanked capsid libraries. Accordingly, while the TRACER platform may be distinct, the claim language itself covers Hanlon, and a person of ordinary skill in the art would have found the claimed method obvious in view of the cited prior art and by routine modifications.
It is additionally pointed out that Hanlon supplied adenoviral helper functions via a plasmid rather than via infectious adenovirus co-infection. A plasmid encoding adenoviral “helper virus.” Therefore, Hanlon does not rely on helper virus co-infection and satisfies (or at least renders obvious) the claimed “absence of helper virus” limitation.
Conclusion
No claim is free of art.
No claim is allowed.
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/JAGAMYA NMN VIJAYARAGHAVAN/Examiner, Art Unit 1633
/EVELYN Y PYLA/Primary Examiner, Art Unit 1633