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 .
Claims Status
Applicant’s amendment submitted on 7/1/2026 is acknowledged. Claims 26, 32, 34, 37-39, 42, 44, and 62-70 are pending. Claims 28-31, 48-49, 52, and 56-61 are canceled. New claims 63-70 are added. Claims 37, 44, and 62 are withdrawn as being directed to non-elected subject matter. Claims 26, 32, 34, 38-39, 42, and 63-70 are under examination.
Election/Restrictions
Applicant's election without traverse of Invention I, claims 26, 28-32, 34, 37-39, & 42, and the
required species, in the reply filed on 12/26/2025 is acknowledged.
Claims 44 and 62 are withdrawn from further consideration pursuant to 37
CFR 1.142(b) as being drawn to a nonelected invention, Claim 37 is withdrawn from further
consideration pursuant to 37 CFR 1.142(b) as being drawn to a nonelected species, there being no
allowable generic or linking claim. Election was made without traverse in the reply filed on 12/26/2025.
Applicant elected the following species:
Group A) A specific peptide encoded by the isolated nucleic acid molecule: SEQ ID NO: 8.
Group B) A specific nucleic acid molecule sequence that corresponds to the elected peptide sequence: SEQ ID NO: 23.
Withdrawn Objections
The following objections are hereby withdrawn due to Applicant’s amendment submitted on 7/1/2026:
Claim objections: claims 29 and 32 for minor informalities.
Specification.
Withdrawn Rejections
The following rejections are hereby withdrawn due to Applicant’s amendment submitted on 7/1/2026:
35 U.S.C. §112(a)—Written Description: claims 26, 28-32,39, and 42.
35 U.S.C. §112(a)—Scope of Enablement: claims 26, 28-32, 34, 38-39, and 42.
35 U.S.C. §102: claims 26, 28-32, 34, 38, 39, and 42 under 35 U.S.C. 102(a)(1) as being anticipated by Ogden, et al. (Science. 2019 Nov 29;366(6469):1139-1143) as evidenced by Elmore, et al. (Nat Commun. 2021 Oct 29;12(1):6239); and claims 26, 28-30, 34, 38, 39, and 42 under 35 U.S.C. 102(a)(1) as being anticipated by Samulski, et al. (PGPub US 20090191597 A1, published 7/30/2009) as evidenced by Elmore, et al. (supra). The previous rejections under 35 U.S.C. §102 rejections are withdrawn in favor of new rejections, necessitated by amendment, presented below.
Maintained Rejections
Claim Rejections - 35 USC § 101
35 U.S.C. 101 reads as follows:
Whoever invents or discovers any new and useful process, machine, manufacture, or composition of matter, or any new and useful improvement thereof, may obtain a patent therefor, subject to the conditions and requirements of this title.
(Previous Rejection Maintained and Claims 63, 64, 65, and 68 Added) Claims 26, 34, 38, 63, and 68 are rejected under 35 U.S.C. 101 because:
the claimed invention is directed to a natural phenomenon without significantly more.
Applicant’s arguments have been carefully considered but are found unpersuasive:
Applicant presents the following arguments:
Applicant has cancelled Claims 28-31 herein, thereby rendering moot the rejection of these claims. Applicant has amended independent Claim 26 and dependent Claims 34 and 38 herein. Applicant submits that currently amended independent claim 26 and dependent claims 34 and 38 satisfy the requirements of 35 U.S.C. §101 as each is directed to a non-natural phenomenon.
Applicant’s arguments are unpersuasive because:
Applicant’s amendment changed claims 26, 34, and 38 to encompass cells rather than isolated nucleic acid molecules. New claims 63 and 64 are also drawn to cells, whereas new claim 68 is drawn to a nucleic acid molecule.
Notably, a naturally-occurring cell infected with AAV would still comprise the claimed limitations of a first nucleic acid molecule comprising a nucleic acid sequence encoding a membrane-associated accessory protein (MAAP) for promoting the formation of extracellular vesicles in the cell and/or increasing the rate or efficiency of secretion of extracellular vesicles from the cells; and a second nucleic acid molecule comprising a nucleic acid sequence encoding (i) one or more of: a polypeptide, a glycopeptide, a polysaccharide, a glycolipid, a lipid, or a nucleic acid polymer, or a combination thereof, or (ii) at least one therapeutic agent. The specification indicates that MAAPs have the capacity of promoting the formation of extracellular vesicles in the cell and/or increasing the rate or efficiency of secretion of extracellular vesicles from the cells.
Because an AAV-infected cell would comprise the AAV genome (a first nucleic acid molecule comprising a nucleic acid sequence encoding a MAAP), and would naturally comprise many other nucleic acid molecules encoding one or more polypeptides, for example, claim 26 is properly rejected herein as directed to a natural product or phenomenon.
The examiner is interpreting CpG, which are naturally present in AAV genomes, such as 266 CpGs present in the wild-type AAV2 genome (see Toth, et al. Viruses. 2019 Jan 9;11(1):38. doi: 10.3390/v11010038. PMID: 30634383; Abstract), to be “therapeutic agents” as required by the claims, because unmethylated CpG dinucleotide-based motifs (CpGs) are known PAMPs that bind and dimerize TLR9, causing activation of the TLR9-MyD88 signaling pathway, thereby promoting CTL responses, and polynucleotides containing unmethylated CpGs are adjuvants used in vaccine development to stimulate strong cellular immune responses (Wright. Mol Ther. 2020 Mar 4;28(3):701-703. Epub 2020 Feb 8. PMID: 32035026; p. 701, col. 1). Accordingly, claim 68 is also rejected herein, because the AAV genome comprises a MAAP-encoding sequence and CpGs, which are interpreted as therapeutic agents.
Regarding claims 34 and 38, Samulski discloses an AAV8 VP1 encoding sequence, SEQ ID NO: 7, which is 100% identical to the instant SEQ ID NO: 23 (Samulski, PGPub US 20090191597 A1, published 7/30/2009; Samulski, SEQ ID NO: 7; para. [0013]), and the +1 frameshift of Samulski's SEQ ID NO: 7 translated contains a polypeptide that is 100% identical to SEQ ID NO: 8. Additionally, SEQ ID NO: 23 contains numerous CpGs.
Regarding claim 63, a mammalian cell or subject naturally infected with the AAV meets each limitation of the claim.
Therefore, Applicant’s arguments are not persuasive.
Claim Rejections - Improper Markush Grouping
(Previous Rejection Maintained) Claims 34 and 38 are rejected on the judicially-created basis that they contain an improper Markush grouping of alternatives.
Applicant’s arguments have been carefully considered but are found unpersuasive:
Applicant presents the following arguments:
First, each of SEQ ID NO: 01-SEQ ID NO: 15 is directed to a specific amino acid sequence while each of SEQ ID NO: 16-SEQ ID NO: 30 is directed to a specific nucleotide sequence. As the claims no longer recite “a fragment thereof”, each MAAP recited in the claims is now identified by a specific amino acid or a specific nucleotide sequence for a membrane-associated accessory protein or MAAP.
Second, Applicant directs the Office’s attention to FIG. 1B, which shows a sequence alignment for SEQ ID NO:1-15. The specification notes that “FIG. 1B shows a sequence alignment of the MAAPs from AAV serotypes 1 to 13 along with AAVrh.8 and AAVrh.10. An annotated multiple-sequence alignment of the AAP sequences of 15 AAV serotypes is shown.” The specification also explains, “Amino acid sequence alignment of MAAPs derived from different AAV serotypes revealed conserved N- and C-terminal regions containing hydrophobic and basic amino acid residues interconnected by a threonine/serine (T/S) rich region (FIG. 1B).” Similarly, the Specification notes, “Importantly, the secondary structure of MAAP is highlighted by an N-terminal hydrophobic domain linked to a cationic, amphipathic C-terminal domain (the putative membrane binding domain—residues 96-114), which strongly associates with the cell surface and subcellular membrane. Thus, these data show that MAAP is a unique virally encoded protein with an amphipathic, cationic membrane anchoring domain.” As each recited sequence is for a specific MAAP and only a MAAP (as compared to some other protein) and because MAAPs share structural commonalities, Applicant submits that the Markush grouping is proper.
Applicant’s arguments are unpersuasive because:
The examiner acknowledges that Applicant has removed fragment language from the rejected claims.
A proper Markush group requires a substantial structural feature essential for each member of the group. For the feature to be substantial, that means that each member’s of the group can be substituted for one another. See MPEP §2117(ii) "where a markush grouping describes part of a combination or process, the members following "selected from the group consisting of" (or a similarly introductory phrase) must be substitutable, one or the other, with the expectation that the same intended result would be achieved. Multilayer Stretch Cling Film Holdings, Inc. v. Berry Plastics Corp., 831 F.3d 1350, 1357. MPEP §2117(ii)(A) also indicates that each member could be substituted one for the other, with the expectation that the same intended result would be achieved. Regarding Fig. 1B’s sequence alignments, Applicant submits that each sequence has a hydrophobic region, but it is not apparent that any hydrophobic region can be substituted, and indeed the claimed sequences have different residues at particular positions (i.e., AAV9 has a glutamate, wherein most of the other species have glycine at position 17), so they cannot be part of the overall function of this group, because those residues are totally different chemically. Similarly, there are leucines and arginines at residue 22, and 1 cysteine among phenylalanines at residue 21. For the basic region, within the sequences provided in FIG. 1B, not all of the residues are basic within the Markush group. Residues 96-114 contain hydrophobic region 2 that has the problems discussed above. Regarding the T/S/-rich region, residue 88S is not needed for the function apparently, as some AAV have another amino acid at that position. What we end up with is a threonine at position 87 and a serine at position 92 shared, however, that is not a substantial structural feature that would confer function (e.g., directing things to the membrane). In summary, it appears that there is no consensus sequence that determines the shared function of these proteins.
The Examiner wishes to inform applicants of the following guidelines pertaining to arguments that mirror supported claims or facts but are not founded on a factual basis.
In the MPEP:
MPEP §2145 Consideration of Applicant's Rebuttal Arguments:
(I) ARGUMENT DOES NOT REPLACE EVIDENCE WHERE EVIDENCE IS NECESSARY
Attorney argument is not evidence unless it is an admission, in which case, an examiner may use the admission in making a rejection. See MPEP § 2129 and§ 2144.03 for a discussion of admissions as prior art.
The arguments of counsel cannot take the place of evidence in the record. In re Schulze, 346 F.2d 600, 602,145 USPQ 716, 718 (CCPA 1965); In re Geisler, 116F.3d 1465, 43 USPQ2d 1362 (Fed. Cir. 1997) (“An assertion of what seems to follow from common experience is just attorney argument and not the kind of factual evidence that is required to rebut a prima facie case of obviousness.”). See MPEP § 716.01(c) for examples of attorney statements which are not evidence and which must be supported by an appropriate affidavit or declaration.
MPEP §716.01 (c) Probative Value of Objective Evidence
I. TO BE OF PROBATIVE VALUE, ANY OBJECTIVE EVIDENCE SHOULD BE SUPPORTED BY ACTUAL PROOF
Objective evidence which must be factually supported by an appropriate affidavit or declaration to be of probative value includes evidence of unexpected results, commercial success, solution of a long-felt need, inoperability of the prior art, invention before the date of the reference, and allegations that the author(s) of the prior art derived the disclosed subject matter from the applicant. See, for example, In re De Blauwe, 736 F.2d 699, 705, 222 USPQ191, 196 (Fed. Cir. 1984) (“It is well settled that unexpected results must be established by factual evidence.” “[A]ppellants have not presented any experimental data showing that prior heat-shrinkable articles split. Due to the absence of tests comparing appellant’s heat shrinkable articles with those of the closest prior art, we conclude that appellant’s assertions of unexpected results constitute mere argument.”). See also In re Lindner, 457 F.2d 506, 508, 173 USPQ 356,358 (CCPA 1972); Ex parte George, 21 USPQ2d 1058(Bd. Pat. App. & Inter. 1991).
II. ATTORNEY ARGUMENTS CANNOT TAKE THE PLACE OF EVIDENCE
The arguments of counsel cannot take the place of evidence in the record. In re Schulze, 346 F.2d 600, 602,145 USPQ 716, 718 (CCPA 1965). Examples of attorney statements which are not evidence and which must be supported by an appropriate affidavit or declaration include statements regarding unexpected results, commercial success, solution of a long-felt need, inoperability of the prior art, invention before the date of the reference, and allegations that the author(s) of the prior art derived the disclosed subject matter from the applicant.
See MPEP § 2145 generally for case law pertinent to the consideration of applicant’s rebuttal arguments.
III. OPINION EVIDENCE
Although factual evidence is preferable to opinion testimony, such testimony is entitled to consideration and some weight so long as the opinion is not on the ultimate legal conclusion at issue. While an opinion as to a legal conclusion is not entitled to any weight, the underlying basis for the opinion may be persuasive. In re Chilowsky,306 F.2d 908, 134 USPQ 515 (CCPA 1962) (expert opinion that an application meets the requirements of 35U.S.C. 112 is not entitled to any weight; however, facts supporting a basis for deciding that the specification complies with 35 U.S.C. 112 are entitled to some weight); In re Lindell, 385 F.2d 453, 155 USPQ 521 (CCPA 1967)(Although an affiant’s or declarant’s opinion on the ultimate legal issue is not evidence in the case, “some weight ought to be given to a persuasively supported statement of one skilled in the art on what was not obvious to him.” 385 F.2d at 456, 155 USPQ at 524 (emphasis in original)).
Presently and in view of the guidance from MPEP §2145 and §716 above, Applicants statements regarding that the members of the Markush groups are proper and share a substantial structural feature has not been found convincing.
New Objections
Claim Objections
Claim 26 is objected to because of the following informalities: on line 10, claim 26 recites “or to a combination thereof”, but should instead recite” or “a combination thereof”. Appropriate correction is required.
Claims 26, 32, 39, and 68 are objected to because of the following informalities: the claims state that a nucleic acid encodes a polypeptide, a glycopeptide, a polysaccharide, a glycolipid, a lipid, a nucleic acid polymer, or a combination thereof. Because nucleic acids encode proteins, and not polysaccharides, glycolipids, lipids, etc., the examiner suspects that Applicant did not intend to include them in the claims as being encoded by a nucleic acid. Appropriate correction is required.
Claim 67 is objected to because of the following informalities: claim 67 states that the oligonucleotide therapeutic agent comprises a CRISPR-based endonuclease, but an endonuclease is a protein, not an oligonucleotide, and so the examiner suspects that Applicant did not intend to include the language as presented. Appropriate correction is required.
New Rejections
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.
Claims 32 and 42 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.
Claim 32 states “wherein the encoded MAAP is fused to the encoded polypeptide [..]”. However, claim 26, upon which claim 32 depends, indicates that the MAAP is encoded by a first nucleic acid molecule, and the polypeptide is encoded by a second nucleic acid molecule. Because fusion of a protein sequence (MAAP to the encoded polypeptide) would require the MAAP and encoded polypeptide to be expressed from the same ORF, it is unclear how such a fusion of MAAP and the encoded polypeptide is possible.
Claim 42 recites the limitation "the recombinant AAV vector of Claim 38" in line 1. There is insufficient antecedent basis for this limitation in the claim, because claim 38 is drawn to a cell.
Claim Rejections - 35 USC § 112
Claims 26, 32, 34, 38, 39, 42, and 63-70 are rejected under 35 U.S.C. 112(a) or 35 U.S.C. 112 (pre-AIA ), first paragraph, because the specification, while being enabling for isolated cells, isolated recombinant AAV vectors, or isolated nucleic acid molecules comprising a nucleic acid sequence encoding a MAAP and a second nucleic acid sequence encoding (i) one or more of a polypeptide, a glycopeptide, a polysaccharide, a glycolipid, a lipid, or a nucleic acid polymer, or combination thereof, or (ii) at least one therapeutic agent, does not reasonably provide enablement for similar cells, recombinant AAV vectors, or nucleic acid molecules that are not isolated. The specification does not enable any person skilled in the art to which it pertains, or with which it is most nearly connected, to make or use the invention commensurate in scope with these claims.
Applicant broadly claims cells, recombinant AAV vectors, or nucleic acid molecules comprising a nucleic acid sequence encoding a MAAP and a second nucleic acid sequence encoding (i) one or more of a polypeptide, a glycopeptide, a polysaccharide, a glycolipid, a lipid, or a nucleic acid polymer, or combination thereof, or (ii) at least one therapeutic agent (claims 26, 39, 68, and respective dependents). The claims reads on a cell within a transgenic animal or a transgene therein given that the term "isolated" is not denoted in describing the host cell, nucleic acid, or vector.
With respect to the unisolated host cells and transgenes as “cells” or “vectors“ or “nucleic acid molecules” of the instant claims discussed above, the state of the art at the time of filing was such that one of skill could not predict the phenotype of transgenics. The art of transgenic animals has for many years stated that the unpredictability lies, in part, with the site or sites of transgene integration into the target genome and that "the position effect" as well as unidentified control elements are recognized to cause aberrant expression of a transgene (Wall et al., Theriogenology, Vol. 45, Pg. 57-68, 1996).
The elements of the particular construct used to make transgenic animals are also held to be critical, and they must be designed case by case without general rules to obtain good expression of a transgene; e.g., specific promoters, presence or absence of introns, etc. (Houdebine et al., Journal of Biotechnology, Vol. 34, Pg. 269- 287, 1994). Furthermore, transgenic animals are regarded to have within their cells, cellular mechanisms that prevent expression of the transgene, such as methylation or deletion from the genome (Kappell et al., Current Opinions in Biotechnology, Vol. 3, Pg. 548-553, 1992). Houdebine (Comparative Immunology, Microbiology, and Infectious Diseases, Vol. 32, Pg. 107-121, 2009) teaches progress has been made in the field of transgenic animals for production of foreign proteins (Abstract); however, constructing an efficient expression vector to produce a therapeutic protein is not a standard operation (Pg. 116, Paragraph, second). Therefore, undue experimentation is required to make and use a transgene and transgenic animal to produce the cells and components thereof of the instant claims.
Examples in the literature aptly demonstrate that even closely related species carrying the same transgene construct can exhibit widely varying phenotypes. Mullins (1993, Hypertension, Vol. 22, No. 4, pp. 630-633) states that not all animals express a transgene sufficiently to provide a model for a disease as the integration of a transgene into different species of animal has been reported to give divergent phenotypes. For example, several animal models of human diseases have relied on transgenic rats when the development of mouse models was not feasible. Mullins (1990, Nature, Vol. 344, 541-544) produced outbred Sprague-Dawley x WKY rats with hypertension caused by expression of a mouse Ren-2 renin transgene. Hammer (1990, Cell, Vol. 63, 1099- 1112) describes spontaneous inflammatory disease in inbred Fischer and Lewis rats expressing human class I major histocompatibility allele HLA-B27 and human 02- microglobulin transgenes. Both investigations were preceded by the failure to develop human disease-like symptoms in transgenic mice expressing the same transgenes that successfully caused the desired symptoms in transgenic rats (Mullins, 1989, EMBO J., Vol. 8, pages 4065-4072). Thus, the use of nonmurine species for transgenesis will continue to reflect the suitability of a particular species for the specific questions being addressed, bearing in mind that a given construct may react very differently from one species to another.
At the time of filing, the phenotype of a transgene and transgenic cell contained within any animal was unpredictable. The claims as written, encompassing a transgene and cell in a transgenic animal, is not adequately described in the specification as to prevent excessive experimentation by the public to generate and use the invention. Applicants can obviate the instant rejection by amending the claims to specify they are not in a transgenic animal. Applicant may consider using purified in such claims if description is appropriate for such a term and it is not redefined away from standard meaning. Method claims using these products should also carry the appropriate adjectives above. As discussed in the earlier action, the specification’s definition of “isolated” is a relative term, and so inclusion of it in the claim before the claimed compositions would necessitate a rejection for indefiniteness under 35 U.S.C. §112(b).
In view of the lack of the predictability of the art to which the invention pertains as evidenced by the art above, the lack of guidance and direction provided by Applicant, and the absence of working examples, undue experimentation would be required to make and use functional transgenes and transgenic animals encompassed by the instant claims, with a reasonable expectation of success, absent a specific and detailed description in Applicant’s specification of how to effectively practice this and absent working examples providing evidence which is reasonably predictive that the claimed components are functional, commensurate in scope with the claimed invention. Thus, the claims are rejected here.
Claim Rejections - 35 USC § 102
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 the appropriate paragraphs of 35 U.S.C. 102 that form the basis for the rejections under this section made in this Office action:
A person shall be entitled to a patent unless –
(a)(1) the claimed invention was patented, described in a printed publication, or in public use, on sale, or otherwise available to the public before the effective filing date of the claimed invention.
(New Rejection Necessitated by Amendment) Claims 26, 32, 39, 42, 63, and 68-70 are rejected under 35 U.S.C. 102(a)(1) as being anticipated by Ogden, et al. (Science. 2019 Nov 29;366(6469):1139-1143; hereinafter referred to as "Ogden") as evidenced by Toth, et al. (Viruses. 2019 Jan 9;11(1):38. PMID: 30634383) and Wright (Mol Ther. 2020 Mar 4;28(3):701-703. Epub 2020 Feb 8. PMID: 32035026).
The Prior Art
Ogden teaches that AAV encodes a +1 frameshifted ORF in the VP1 region, which is 119 amino acids in length (Fig. 2A; p. 1139, col. 3, para. 3), which they named membrane-associated accessory protein (MAAP; p. 1140, cols 2-3). Ogden further discloses that to validate the ORF's translation, they added a FLAG tag at the C-terminus and transfected the plasmid into HEK293T cells (p. 1139, col. 3, para. 4). Ogden also created a C-terminal GFP fusion of the ORF, from sequences derived from AAV5, AAV8, and AAV9, in addition to the AAV2 ORF (p. 1140, col. 2, para. 1). Notably, MAAP localized to the cell membrane (Figs. 2C, S6, and S8). Ogden also generated recombinant MAAP-null viruses, including 27AStart, where the VP-P27-CCT codon was mutated to CCC, and 32AStop, in which the VP-P32-CCT codon was mutated to ATA (V), making an early stop codon in MAAP (Fig. 2D-2E; p. 1140, col. 3; Supplemental materials, pp. 4-5). Additionally, Ogden generated single-codon mutants of the AAV2 cap gene, and the full library (along with WT AAV2 sequences and stop substitution controls) was made through mutant synthesis and plasmid assembly, wherein the final constructs contained ITRs flanking the full-length capsid gene with an upstream promoter and a downstream barcode, enabling pooled measurements of mutant frequencies by sequencing (p. 1139, cols. 1-2). Ogden then transfected the plasmid library into human embryonic kidney (HEK) 293T cells to produce recombinant AAV and purified the resulting virus (p. 1139, col. 2, para. 2). Additionally, Ogden teaches that for head-to-head comparison of MAAP mutants vs wild type AAV2, viral production was performed by introducing MAAP mutations into plasmids carrying full length Rep and Cap genes, and then cloned into ITR plasmids and transfected with helper plasmid to produce the virus (supplemental, p. 6, paras. 2 and 3).
The instant specification indicates that MAAP overexpression promotes secretion of a specific type of extracellular vesicle, and MAAP overexpression was associated with a notable increase in vesicles (Example 10). Therefore, the examiner is interpreting promoting the formation and/or secretion of extracellular vesicles to be an inherent function of MAAP.
Regarding claims 26 and 32, the examiner is interpreting applicant to intend that the sequences encoding MAAP and encoded polypeptide are present on the same molecule. Accordingly, the cells transfected with MAAP-HA or MAAP-GFP are anticipatory of claims 26 and 32. Ogden’s mutant library experiment reads on a cell comprising: a first nucleic acid molecule comprising a nucleic acid sequence encoding a membrane-associated accessory protein (MAAP) for promoting the formation and/or rate or efficiency of secretion of extracellular vesicles in the cell. The cells that produce the recombinant AAV also will naturally comprise additional nucleic acid molecules encoding proteins, such as cellular DNA and transcripts, in addition to genes necessary for AAV helper function, therefore, claim 26 is anticipated. Additionally, the HEK293T cells are mammalian cells, so claim 63 is anticipated.
Regarding claims 39 and 42, Ogden’s wild type AAV2 vector used for head-to-head comparison with MAAP mutant anticipates the claims because it further contains a full length Rep gene and must contain a promoter in order to function.
Regarding claims 68-70, the examiner is interpreting CpG, which is naturally present in AAV genomes, such as 266 CpGs present in the wild-type AAV2 genome (see Toth; Abstract), to be “therapeutic agents” as required by the claims, because unmethylated CpG dinucleotide-based motifs (CpGs) are known PAMPs that bind and dimerize TLR9, causing activation of the TLR9-MyD88 signaling pathway, thereby promoting CTL responses, and polynucleotides containing unmethylated CpGs are adjuvants used in vaccine development to stimulate strong cellular immune responses (Wright. Mol Ther. 2020 Mar 4;28(3):701-703. Epub 2020 Feb 8. PMID: 32035026; p. 701, col. 1). Additionally, instant SEQ ID NO: 23, which is the AAV8 cap-encoding gene, contains numerous CpGs. The instant specification indicates that MAAP overexpression promotes secretion of a specific type of extracellular vesicle, and MAAP overexpression was associated with a notable increase in vesicles (Example 10). Therefore, the examiner is interpreting promoting the formation and/or secretion of extracellular vesicles to be an inherent function of MAAP. Accordingly, the WT and mutant AAVs disclosed by Ogden each anticipate a nucleic acid molecule or recombinant AAV vector comprising a nucleic acid sequence encoding a MAAP and (ii) at least one therapeutic agent, and they would naturally further comprise a promoter operably linked to the nucleic acid sequence.
Therefore, claims 26, 32, 39, 42, 63, and 68-70 are anticipated by Ogden as evidenced by Toth and Wright.
Applicant’s arguments have been carefully considered but are found unpersuasive as they relate to this rejection:
Applicant presents the following arguments:
Ogden does not teach cells or vectors that comprise nucleic acids that respectively encode a MAAP protein and a payload or cargo (i.e., one or more of a polypeptide, a glycopeptide, a polysaccharide, a glycolipid, a lipid, or a nucleic acid polymer, or a combination thereof, or at least one therapeutic agent) as currently claimed. Moreover, Elmore does not qualify as prior art. The Office Action identified the publication date of Elmore as 29 October 2021, but the present application (which was filed first as a PCT application on May 2021) claims priority to 2 provisional applications filed 10 December 2020, and 5 May 2020, respectively. Both the PCT application and the underlying provisional applications were all filed prior to the publication of Elmore. Therefore, the application of Elmore in this anticipation is untenable.
Accordingly, Applicant asserts that Ogden is not a teaching of the currently claimed subject matter and Elmore is not prior art.
Applicant’s arguments are unpersuasive because:
MPEP §2131.01 instructs that normally, only one reference should be used in making a rejection under 35 U.S.C. 102. However, a 35 U.S.C. 102 rejection over multiple references has been held to be proper when the extra references are cited to: (C) Show that a characteristic not disclosed in the reference is inherent. Also note that the critical date of extrinsic evidence showing a universal fact need not antedate the filing date. See also MPEP § 2124.
As discussed in the previous rejection, MAAP is inherent to AAV, and its functions are also inherent, as demonstrated by the instant specification. Ogden anticipates the claims, as described above.
(New Rejection Necessitated by Amendment) Claims 26, 34, and 38 are rejected under 35 U.S.C. 102(a)(1) as being anticipated by Samulski, et al. (PGPub US 20090191597 A1, published 7/30/2009) as evidenced by as evidenced by Toth, et al. (Viruses. 2019 Jan 9;11(1):38. PMID: 30634383) and Wright (Mol Ther. 2020 Mar 4;28(3):701-703. Epub 2020 Feb 8. PMID: 32035026).
The Prior Art
Samulski discloses methods of producing recombinant adeno-associated viruses (rAAV) in insect
cells and uses thereof (para. [0003]). Samulski discloses an AAV8 VP1 encoding sequence, SEQ ID NO: 7,
which is 100% identical to the instant SEQ ID NO: 23 (Samulski, SEQ ID NO: 7; para. [0013]). Further, the +1 frameshift of Samulski's SEQ ID NO: 7 translated contains a polypeptide that is 100% identical to SEQ ID NO: 8.
Regarding claims 26, 34, and 38, Samulski teaches methods of producing recombinant adeno-associated viruses in insect cells and uses thereof, as well as an AAV8 VP1 encoding sequence, SEQ ID NO: 7, which is 100% identical to the instant SEQ ID NO: 23 (Samulski, SEQ ID NO: 7; para. [0013]). Further, the +1 frameshift of Samulski’s SEQ ID NO: 7 translated contains a polypeptide that is 100% identical to SEQ ID NO: 8. The instant disclosure indicates that SEQ ID NO: 23 encodes a MAAP (SEQ ID NO: 8), which is identical to that sequence disclosed by Samulski; therefore, the instant disclosure demonstrates that Samulski’s SEQ ID NO: 7 inherently encodes a MAAP. Further, a cell producing the recombinant AAV vector would inherently possess a second nucleic acid molecule comprising a nucleic acid sequence encoding, at the very least (i) one or more of a polypeptide.
The examiner is interpreting CpG, which is naturally present in AAV genomes, such as 266 CpGs present in the wild-type AAV2 genome (see Toth; Abstract), to be “therapeutic agents” as required by the claims, because unmethylated CpG dinucleotide-based motifs (CpGs) are known PAMPs that bind and dimerize TLR9, causing activation of the TLR9-MyD88 signaling pathway, thereby promoting CTL responses, and polynucleotides containing unmethylated CpGs are adjuvants used in vaccine development to stimulate strong cellular immune responses (Wright. Mol Ther. 2020 Mar 4;28(3):701-703. Epub 2020 Feb 8. PMID: 32035026; p. 701, col. 1). Additionally, SEQ ID NO: 23 contains numerous CpGs. Therefore, the insect cells in Samulski’s methods would comprise the AAV VP1 gene disclosed by Samulski (SEQ ID NO: 7), which encodes a MAAP, and CpGs, which are therapeutic agents. The instant specification indicates that MAAP overexpression promotes secretion of a specific type of extracellular vesicle, and MAAP overexpression was associated with a notable increase in vesicles (Example 10). Therefore, the examiner is interpreting promoting the formation and/or secretion of extracellular vesicles to be an inherent function of MAAP.
Therefore, claims 26, 34, and 38 are anticipated by Samulski as evidenced by Toth and Wright.
Applicant’s arguments have been carefully considered but are found unpersuasive as they relate to this rejection:
Applicant presents the following arguments:
Elmore does not qualify as prior art. The Office Action identified the publication date of Elmore as 29 October 2021, but the present application claims priority to 2 provisional applications and was originally filed as a PCT application, the dates of which all were before the publication of Elmore. Therefore, the application of Elmore in this anticipation rejection is untenable.
Second, Samulski does not teach or disclose extracellular vesicles or MAAP, or how MAAP can be used to promote the formation of extracellular vesicles, or how MAAP can be used to increase the rate or efficiency of the secretion of extracellular vesicles encapsulating (i) one or more of a polypeptide, a glycopeptide, a polysaccharide, a glycolipid, or a nucleic acid polymer, or a combination thereof, or (ii) at least one therapeutic agent from cells as currently claimed. Accordingly, Samulski is not a teaching of the currently claimed subject matter and Elmore is not prior art.
Applicant’s arguments are unpersuasive because:
MPEP §2131.01 instructs that normally, only one reference should be used in making a rejection under 35 U.S.C. 102. However, a 35 U.S.C. 102 rejection over multiple references has been held to be proper when the extra references are cited to: (C) Show that a characteristic not disclosed in the reference is inherent. Also note that the critical date of extrinsic evidence showing a universal fact need not antedate the filing date. See also MPEP § 2124.
As discussed in the previous rejection, MAAP is inherent to AAV, and its functions are also inherent, as demonstrated by the exact same sequence taught by Samulski being associated with these functions in the current disclosure. Applicant’s argument is not commensurate in scope with the claims’ breadth. The claims do not explicitly require MAAP can be used to increase the rate or efficiency of the secretion of extracellular vesicles encapsulating (i) one or more of a polypeptide, a glycopeptide, a polysaccharide, a glycolipid, or a nucleic acid polymer, or a combination thereof, or (ii) at least one therapeutic agent.
(New Rejection Necessitated by Amendment) Claims 26 and 63-66 are rejected under 35 U.S.C. 102(a)(1) as being anticipated by Tomar, et al. (Oncogene 22.36 (2003): 5712-5715).
The Prior Art
Tomar, et al. teaches adaptation of AAV for siRNA delivery into mammalian cells, and that AAV-based vectors are efficient vectors for the delivery of siRNA into mammalian cells (Abstract). Tomar also teaches that AAVs require coinfection with a helper adenovirus or herpesvirus for productive infection, and to develop an AAV-2 based vector for siRNA delivery, they utilized the AAV Helper free system, in which the rep and cap genes are removed from the viral vector and are provided in trans on the plasmid pAAV-RC, while a second plasmid, pHelper, provides the adenovirus gene products required for the production of AAV particles in 293 cells (p. 5713, col. 1, paras. 2-3). The AAV vector expresses enhanced green fluorescent protein (EGFP) under the control of CMV immediate-early promoter and a hairpin siRNA against p53 under the control of H1 RNA promoter (p. 5713, col. 1, para. 3). Tomar also teaches that RNA interference (RNAi) is an evolutionary conserved mechanism of sequence-specific post-transcriptional gene silencing (p. 5712, col. 1), and siRNA effectively inhibit endogenous genes in a sequence-specific manner (p. 5712, col. 1).
Regarding claim 26, the 293 cells in which siRNA-delivering AAV-2 is produced read on a cell comprising: a first nucleic acid molecule comprising a nucleic acid sequence encoding a membrane-associated accessory protein (MAAP) for promoting the formation and/or rate or efficiency of secretion of extracellular vesicles in the cell. Additionally, the siRNA expression cassette reads on a second nucleic acid molecule comprising a nucleic acid sequence encoding (ii) at least one therapeutic agent (claim 26), an oligonucleotide therapeutic agent (claim 64), an siRNA (claim 65), and an interfering RNA (RNAi; claim 66). The cells that produce the recombinant AAV also will naturally comprise additional nucleic acid molecules encoding proteins, such as cellular DNA and transcripts, in addition to genes necessary for AAV helper function, therefore, claims 26 and 63-66 are anticipated. Additionally, the 293 cells are mammalian cells, so claim 63 is anticipated. The specification provides evidence that the AAV-2 cap gene, which is what is used in Tomar, encodes a MAAP and that MAAPs have the claimed functions of promoting the formation and/or rate or efficiency of secretion of extracellular vesicles in the cell.
Therefore, Tomar anticipates claims 26 and 63-66.
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 26, 64, and 67 are rejected under 35 U.S.C. 103 as being unpatentable over Senis, et al. (Biotechnol. J. 2014, 9, 1402–1412) in view of Tomar, et al. (Oncogene 22.36 (2003): 5712-5715).
The Prior Art
Senis, et al. teaches a versatile set of plasmids and vectors derived from AAV that allow robust and specific delivery of the two essential CRISPR components, Cas9 and chimeric g(uide)RNA, either alone or in combination, which can packaged into potent synthetic AAV capsids, permitting CRISPR delivery even into hard-to-transfect targets (Abstract). To generate AAV, HEK293T cells were transfected with (i) the AAV vector plasmid (encoding gRNA and/or Cas9), (ii) an AAV helper plasmid carrying AAV rep and cap genes, and (iii) an adenoviral plasmid providing helper functions for AAV production (p. 1404, col. 1).
However, Senis does not teach a MAAP or AAV cap gene known to encode a MAAP.
Tomar, et al. teaches adaptation of AAV for siRNA delivery into mammalian cells, and that AAV-based vectors are efficient vectors for the delivery of siRNA into mammalian cells (Abstract). Tomar also teaches that AAVs require coinfection with a helper adenovirus or herpesvirus for productive infection, and to develop an AAV-2 based vector for siRNA delivery, they utilized the AAV Helper free system, in which the rep and cap genes are removed from the viral vector and are provided in trans on the plasmid pAAV-RC, while a second plasmid, pHelper, provides the adenovirus gene products required for the production of AAV particles in 293 cells (p. 5713, col. 1, paras. 2-3). The AAV vector expresses enhanced green fluorescent protein (EGFP) under the control of CMV immediate-early promoter and a hairpin siRNA against p53 under the control of H1 RNA promoter (p. 5713, col. 1, para. 3). Tomar also teaches that RNA interference (RNAi) is an evolutionary conserved mechanism of sequence-specific post-transcriptional gene silencing (p. 5712, col. 1), and siRNA effectively inhibit endogenous genes in a sequence-specific manner (p. 5712, col. 1).
It would have been obvious to one of ordinary skill in the art to modify the Cas9 and/or gRNA-encoding AAVs and methods of production taught by Senis to utilize the pHelper system, including vectors and pAAV-RC AAV2 cap encoding plasmid disclosed by Tomar in place of Senis’s packaging system and AAV helper plasmid carrying AAV rep and cap genes.
The MPEP (§2143(I)) states that (B) simple substitution of one known element for another to obtain predictable results is an example of rationale that may support a conclusion of obviousness. In the instant case, Tomar’s AAV packaging system (pHelper) is different than that taught by Selis, however, it would have been obvious to one of ordinary skill in the art to utilize Tomar’s pHelper system as a means of generating AAV. The results would have been predictable because each method is known to package AAV, and thus they have the same purpose. Regarding claim 26, the HEK293T cells in which Senis’s Cas9 and/or gRNA encoding AAVs are produced read on a cell comprising: a first nucleic acid molecule comprising a nucleic acid sequence encoding a membrane-associated accessory protein (MAAP) for promoting the formation and/or rate or efficiency of secretion of extracellular vesicles in the cell. Additionally, the Cas9 and/or gRNA expression encoding sequence reads on a second nucleic acid molecule comprising a nucleic acid sequence encoding (ii) at least one therapeutic agent (claim 26), an oligonucleotide therapeutic agent (claim 64), and a CRISPR-based endonuclease (Cas9; claim 67). The cells that produce the recombinant AAV also will naturally comprise additional nucleic acid molecules encoding proteins, such as cellular DNA and transcripts, in addition to genes necessary for AAV helper function, therefore, claims 26, 64, and 67 are rendered obvious. The specification provides evidence that the AAV-2 cap gene, which is what is used in Tomar, encodes a MAAP and that MAAPs have the claimed functions of promoting the formation and/or rate or efficiency of secretion of extracellular vesicles in the cell.
One of ordinary skill in the art would have been motivated to generate AAV for delivery of Cas9 and/or gRNA. There would be a reasonable expectation of success because Senis demonstrates packaging of Cas9 and gRNA into AAV and Tomar demonstrates use of the pHelper system for packaging AAV with transgenes. Therefore, claims 26, 64, and 67 were prima facie obvious before the priority date of the instant invention.
Conclusion
Applicant's amendment necessitated the new ground(s) of rejection presented in this Office action. Accordingly, THIS ACTION IS MADE FINAL. See MPEP § 706.07(a). Applicant is reminded of the extension of time policy as set forth in 37 CFR 1.136(a).
A shortened statutory period for reply to this final action is set to expire THREE MONTHS from the mailing date of this action. In the event a first reply is filed within TWO MONTHS of the mailing date of this final action and the advisory action is not mailed until after the end of the THREE-MONTH shortened statutory period, then the shortened statutory period will expire on the date the advisory action is mailed, and any nonprovisional extension fee (37 CFR 1.17(a)) pursuant to 37 CFR 1.136(a) will be calculated from the mailing date of the advisory action. In no event, however, will the statutory period for reply expire later than SIX MONTHS from the mailing date of this final action.
No claim is allowed.
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/JEFFREY MARK SIFFORD/Examiner, Art Unit 1671 /Michael Allen/Supervisory Patent Examiner, Art Unit 1671
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