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 .
DETAILED ACTION
Acknowledgement is hereby made of receipt and entry of the communication filed on Jan. 28, 2026. Claims 29-30, 32-36 and 38-42, and 44-46 are pending and currently examined.
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.
(New Rejection-necessitated by amendment) Claims 29-30, 32-36 and 38-42 and 45-46 are rejected under 35 U.S.C. 103 as being unpatentable over Jin et al. (US 11698377 B2, patented on Jul. 11, 2023, PCT filed on Aug. 14, 2017, hereinafter, “Jin”) in view of Xiao et al. (J Virol. 1999 May;73(5):3994-4003, hereinafter. “Xiao”) as evidenced by Krokhin et al. (Anal Chem. 2006 Sep 15;78(18):6645-50, hereinafter, “Krokhin”), Martinez-Navio et al. (Mol Ther. 2016 Feb;24(1):76-86., hereinafter, “Martinez-Navio” ), and Cancer Research UK (https://www.cancerresearchuk.org/about-cancer/treatment/targeted-cancer-drugs/types/anti-angiogenics#:~:text=Types%20of%20anti%20angiogenesis%20treatment&text=Some%20drugs%20block%20vascular%20endothelial,ramucirumab).
The amended base claim 29 is directed to a composition comprising a mixed population of recombinant adeno- associated virus (rAAV), each of said rAAV comprising:
(a) an AAV1 capsid comprising a heterogeneous population of AAV1 vp1 proteins, a heterogeneous population of AAV 1 vp2 proteins, and a heterogeneous population of AAV1 vp3 proteins which contain amino acid modifications comprising 65% to 100% asparagines (N) deamidated at position N57 and 75% to 100% asparagines (N) deamidated at each of positions: N383, N512, and N718, based on the numbering of SEQ ID NO: 1, as determined using mass spectrometry, wherein vp1 comprises positions N57, N383, N512 and N718, vp2 comprises positions N383, N512 and N718 and vp3 comprises positions N383, N512 and N718,
wherein the deamidated asparagines are deamidated to an aspartic acid, an isoaspartic acid, an interconverting aspartic acid/isoaspartic acid pair, or combinations thereof; and
(b) a vector genome in the AAV capsid, wherein the vector genome comprises an AAV 5' ITR, an expression cassette comprising the non-AAV nucleic acid operably linked to the sequences which direct expression of the encoded product, and an AAV 3' ITR, wherein the product encoded by the non-AAV nucleic acid molecule encodes a therapeutic product.
Jin teaches a method for serotyping and/or determining the heterogeneity of a viral particle (e.g., an adeno-associated virus (AAV) particle) using mass determination, e.g., by employing liquid chromatography/mass spectrometry (LC/MS) or liquid chromatography/mass spectrometry-mass spectrometry (LC/MS/MS) (See column 1, lines 21-30). Jin teaches that the AAV heterogeneity in the composition is due to post-translational modifications such as deamidation. Substitution mutations may be introduced into vp1 and the amino acid substitution results in less deamidation of the AAV capsid (See e.g., column 8, lines 27-42). Jin indicates that the amino acids considered for high rate of deamidation are A35, N57, G58, N382, G383, N511, G512, N715, or G716 of VP1 (numbering in AAV2) and the one or more amino acid substitutions such as N57K or a N57Q substitution can result in a lower frequency of deamidation as compared to deamidation of VP1 and/or VP3 of the parent AAV particle including AAV1 particles (See e.g., column 10, lines 19-60), which can improve the stability, assembly and/or transduction efficiency (See e.g., column 11, lines 14-65). The percentage of the deamidation in AAV1 and AAV2 particles are also taught in Jin’s invention. Fig.6A & 6B show the results of LC/MS/MS analysis comparing the percentage of deamidation in AAV1 and AAV2 particles produced by the TTx and PCL methods. The T9 peptide YLGPFNGLDK (SEQ ID NO: 9) was used to monitor potential deamidation site N57 in both AAV1 and AAV2. FIGS. 8A & 8B show the results of LC/MS/MS analysis comparing the percentage of deamidation in AAV1 and AAV2 particles produced by the TTx and PCL methods. The T67 peptides SANVDFTVDNNGLYTEPR (SEQ ID NO: 13) and SVNVDFTVDTNGVYSEPR (SEQ ID NO: 14) were used to monitor potential deamidation site N715 in AAV1 and AAV2, respectively ((See e.g., Column 13). Here the description above indicates the NG pairs as the deamidation sites. Jin et al. also discloses that the "deamidation" refers to a chemical reaction in which an amide functional group in the side chain of asparagine or glutamine is removed or converted to another functional group. For example, asparagine may be converted to aspartic acid or isoaspartic acid (See column 27, lines 54-60). Jin et al. also discloses that the AAV particle is deamidated to a higher extent compared to a parental AAV particle. In some embodiments, the AAV particle is more than about any of 45 5%, 10%, 15%, 20%, 25%, 30%, 35%, 40%, 45%, 50%, 55%, 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, or 100% more deamidated compared to a parent AAV particle. In some embodiments, the AAV particle is deamidated between about any of 5%-10%, 10%-15%, 15%-20%, 20%-25%, 25%-30%, 30%-35%, 35%-40%, 40%-55%, 45%-50%, 50%-55%, 55%-60%, 60%-65%, 65%-70%, 70%-75%, 75%-80%, 80%-85%, 85%-90%, 90%-95%, 95%-100%, 5-25%, 25-50%, 50-75%, 75%-100%, 5-50% or 50%-100% more than a parent AAV particle (See e.g., column 28, lines 42-54), which teaches a 50% to 100% deamidation amino acid is present in the heterogeneous population of AAV particles.heterogeneous, Jin discloses that the "Heterogeneity" when used in reference to an AAV capsid refers to an AAV capsid characterized by one or more capsid polypeptides observed to deviate from a reference mass of a VP1, VP2, and/or VP3 polypeptide, or fragment thereof. A reference mass may include, without limitation, a theoretical, predicted, or expected mass of a VP1, VP2, and/or VP3 polypeptide, e.g., of a known AAV serotype. For example, an AAV capsid may be said to display heterogeneity if it demonstrates one or more of the following properties (without limitation): a mixed serotype, a variant capsid, a capsid amino acid substitution, a truncated capsid, or a modified capsid (See column 19, lines 41-60), where the substitution comprises a substitution with Asp at N57 of VP1, N382 of VP3, N511 ofVP3, or N715 of VP3, and results in a higher frequency of deamidation as compared to deamidation of VP1 and/or VP3 of the parent AAV particle (See e.g., column 10, lines 32-36). As for the vector genome in the AAV capsid, Jin teaches that the viral particle comprises an AAV1 ITR, an AAV2 ITR, an AAV3 ITR, an AAV4 ITR, an AAV5 ITR, an AAV6 ITR… an AAV11 ITR, or an AAV12 ITR. In some embodiments, the AAV particle comprises an AAV vector encoding a heterologous transgene (See Column 6, lines 57-64). Jin also discloses that a "recombinant viral vector" refers to a recombinant polynucleotide vector comprising one or more heterologous sequences (i.e., nucleic acid sequence not of viral origin). In the case of recombinant AAV vectors, the recombinant nucleic acid is flanked by at least one, e.g., two, inverted terminal repeat sequences (ITRs) (See Column 16, lines 36-41). Jin also discloses that in some embodiments, the heterologous nucleic acid is operably linked to a promoter [See column 33, lines 26-50). Jin also teaches that different AAV serotypes are used to optimize transduction of particular target cells or to target specific cell types within a particular target tissue (See column 43, lines 11-13). Jin also teaches that in some embodiments, the heterogeneity comprises one or more of mixed serotypes, variant capsids, capsid amino acid substitutions, truncated capsids, or modified capsids (See e.g., column 4, lines 8-11).
Accordingly, Jin teaches a composition comprising a mixed population of recombinant adeno- associated virus (rAAV) comprising AAV1 VP1, VP2 and VP3 that the heterogeneous population is caused by the high ratio of the deamidation, where can be determined by mass spectrometry. At the same time, Jin also teaches a vector genome in the AAV capsid comprising ITRs and a transgene encoded by a non-AAV nucleic acid sequence.
As for the new amended limitation “where the vector genome comprises an AAV 5' ITR, an expression cassette comprising the non-AAV nucleic acid operably linked to the sequences which direct expression of the encoded product, and an AAV 3' ITR, wherein the product encoded by the non-AAV nucleic acid molecule encodes a therapeutic product”, Jin teaches that an expression cassette may be flanked on the 5' and 3' end by at least one functional AAV ITR sequence (See column 35, lines 42-45) and the “transgene” refers to a nucleic acid for a desired therapeutic or diagnostic product (See column 17, lines 43-49), and also discloses that an AAV ITR, a term well-understood in the art, is an approximately 145-nucleotide sequence that is present at both termini of the native single-stranded AAV genome (See column 18, lines 10-14).
Although Jin does not teach the specific positions of the amino acids of deamidation of SEQ ID NO: 1, it is a reference sequence so one of ordinary skill in the art can locate the specific amino acid positions in different capsid proteins. Nevertheless, Xiao teaches the SEQ ID NO: 1.
Xiao studies the Gene Therapy Vectors Based on Adeno-Associated Virus Type 1. It teaches a complete sequence of adeno-associated virus type 1 (AAV-1) and discloses the AAV-1 sequence with the GenBank accession # AF063497, where the CDS of” capsid protein” is identical to the claimed SEQ ID NO: 1 with an initial amino acid M (See below the aligned sequences in grey shadow). The aligned sequences are the amino acids sequences compared between the AAV1 VP1 amino acids sequences and the claimed SEQ ID NO: 1. It shows as: Query-SEQ ID NO: 1; Sbjct- 1“capsid protein”; N57-green, N383-blue, N512-pink and N-718-yellow), where the NG pairs (Asn-Gly) have been highlighted and considered as a “hot spot” associated with deamidation. This can be evidenced by Krokhin’s study. Krokhin describes the deamidation of -Asn-Gly- Sequences during Sample Preparation for Proteomics: Consequences for MALDI and HPLC-MALDI Analysis. It teaches that the peptides containing -Asn-Gly- sequences typically show ~70-80% degree of deamidation after standard overnight (~12 h) tryptic digestion at 37 °C (See Abstract), and the deamidation of Asn and Gln residues is one of the best known and studied posttranslational modifications in proteins. Since the degree of deamidation often controls the biological activity and functions of proteins, the reaction is particularly important in large-molecule therapeutics (See page 6645, left column, paragraph 2) and the highest deamidation rate was found where -Asn- is followed by -Gly- (See page 6647, left column, paragraph 1).
Query 1 MAADGYLPDWLEDNLSEGIREWWDLKPGAPKPKANQQKQDDGRGLVLPGYKYLGPFNGLD 60
MAADGYLPDWLEDNLSEGIREWWDLKPGAPKPKANQQKQDDGRGLVLPGYKYLGPFNGLD
Sbjct 1 MAADGYLPDWLEDNLSEGIREWWDLKPGAPKPKANQQKQDDGRGLVLPGYKYLGPFNGLD 60
Query 61 KGEPVNAADAAALEHDKAYDQQLKAGDNPYLRYNHADAEFQERLQEDTSFGGNLGRAVFQ 120
KGEPVNAADAAALEHDKAYDQQLKAGDNPYLRYNHADAEFQERLQEDTSFGGNLGRAVFQ
Sbjct 61 KGEPVNAADAAALEHDKAYDQQLKAGDNPYLRYNHADAEFQERLQEDTSFGGNLGRAVFQ 120
Query 121 AKKRVLEPLGLVEEGAKTAPGKKRPVEQSPQEPDSSSGIGKTGQQPAKKRLNFGQTGDSE 180
AKKRVLEPLGLVEEGAKTAPGKKRPVEQSPQEPDSSSGIGKTGQQPAKKRLNFGQTGDSE
Sbjct 121 AKKRVLEPLGLVEEGAKTAPGKKRPVEQSPQEPDSSSGIGKTGQQPAKKRLNFGQTGDSE 180
Query 181 SVPDPQPLGEPPATPAAVGPTTMASGGGAPMADNNEGADGVGNASGNWHCDSTWLGDRVI 240
SVPDPQPLGEPPATPAAVGPTTMASGGGAPMADNNEGADGVGNASGNWHCDSTWLGDRVI
Sbjct 181 SVPDPQPLGEPPATPAAVGPTTMASGGGAPMADNNEGADGVGNASGNWHCDSTWLGDRVI 240
Query 241 TTSTRTWALPTYNNHLYKQISSASTGASNDNHYFGYSTPWGYFDFNRFHCHFSPRDWQRL 300
TTSTRTWALPTYNNHLYKQISSASTGASNDNHYFGYSTPWGYFDFNRFHCHFSPRDWQRL
Sbjct 241 TTSTRTWALPTYNNHLYKQISSASTGASNDNHYFGYSTPWGYFDFNRFHCHFSPRDWQRL 300
Query 301 INNNWGFRPKRLNFKLFNIQVKEVTTNDGVTTIANNLTSTVQVFSDSEYQLPYVLGSAHQ 360
INNNWGFRPKRLNFKLFNIQVKEVTTNDGVTTIANNLTSTVQVFSDSEYQLPYVLGSAHQ
Sbjct 301 INNNWGFRPKRLNFKLFNIQVKEVTTNDGVTTIANNLTSTVQVFSDSEYQLPYVLGSAHQ 360
Query 361 GCLPPFPADVFMIPQYGYLTLNNGSQAVGRSSFYCLEYFPSQMLRTGNNFTFSYTFEEVP 420
GCLPPFPADVFMIPQYGYLTLNNGSQAVGRSSFYCLEYFPSQMLRTGNNFTFSYTFEEVP
Sbjct 361 GCLPPFPADVFMIPQYGYLTLNNGSQAVGRSSFYCLEYFPSQMLRTGNNFTFSYTFEEVP 420
Query 421 FHSSYAHSQSLDRLMNPLIDQYLYYLNRTQNQSGSAQNKDLLFSRGSPAGMSVQPKNWLP 480
FHSSYAHSQSLDRLMNPLIDQYLYYLNRTQNQSGSAQNKDLLFSRGSPAGMSVQPKNWLP
Sbjct 421 FHSSYAHSQSLDRLMNPLIDQYLYYLNRTQNQSGSAQNKDLLFSRGSPAGMSVQPKNWLP 480
Query 481 GPCYRQQRVSKTKTDNNNSNFTWTGASKYNLNGRESIINPGTAMASHKDDEDKFFPMSGV 540
GPCYRQQRVSKTKTDNNNSNFTWTGASKYNLNGRESIINPGTAMASHKDDEDKFFPMSGV
Sbjct 481 GPCYRQQRVSKTKTDNNNSNFTWTGASKYNLNGRESIINPGTAMASHKDDEDKFFPMSGV 540
Query 541 MIFGKESAGASNTALDNVMITDEEEIKATNPVATERFGTVAVNFQSSSTDPATGDVHAMG 600
MIFGKESAGASNTALDNVMITDEEEIKATNPVATERFGTVAVNFQSSSTDPATGDVHAMG
Sbjct 541 MIFGKESAGASNTALDNVMITDEEEIKATNPVATERFGTVAVNFQSSSTDPATGDVHAMG 600
Query 601 ALPGMVWQDRDVYLQGPIWAKIPHTDGHFHPSPLMGGFGLKNPPPQILIKNTPVPANPPA 660
ALPGMVWQDRDVYLQGPIWAKIPHTDGHFHPSPLMGGFGLKNPPPQILIKNTPVPANPPA
Sbjct 601 ALPGMVWQDRDVYLQGPIWAKIPHTDGHFHPSPLMGGFGLKNPPPQILIKNTPVPANPPA 660
Query 661 EFSATKFASFITQYSTGQVSVEIEWELQKENSKRWNPEVQYTSNYAKSANVDFTVDNNGL 720
EFSATKFASFITQYSTGQVSVEIEWELQKENSKRWNPEVQYTSNYAKSANVDFTVDNNGL
Sbjct 661 EFSATKFASFITQYSTGQVSVEIEWELQKENSKRWNPEVQYTSNYAKSANVDFTVDNNGL 720
Query 721 YTEPRPIGTRYLTRPL 736
YTEPRPIGTRYLTRPL
Sbjct 721 YTEPRPIGTRYLTRPL 736
Accordingly, Xiao teaches a AAV1 gene delivery vector with a GenBank accession number of AF063497 that is identical to the claimed SEQ ID NO. 1. Based on the released sequence of capsid protein and the teaching of Jin and Krokhin, the four high deamidation NG sites in SEQ ID NO: 1, which is identical to the AAV1 VP1 sequences, are at N57, N383, N512, and N718 as claimed.
Actually, besides the deamidation of N57 of AAV1 taught by Jin, Jin also teaches a NG-sites deamidation at N382, N511 and N713 (See Table 7, column 63 and below). After comparing Jin’s SEQ ID NOs: 10, 11 and 13 with Xiao’s AF063497 (AAV1) and the instant SEQ ID NO: 1, it discloses that the AAV1 deamidation sites of Jin matches with the claimed N57, N383, N512 and N718 (See the tables 4-6 below prepared by the
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Examiner).
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Accordingly, Jin also teaches the four sites deamidation of AAV1 as claimed.
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 use known AAV1 capsid sequences, such as the AAV1 sequence of Xiao, in Jin’s invention and use the mass spectrometry method of Jin to determine the deamidation percentages in Xiao’s AAV1 VP1 sequence in the heterogeneous AAV1 composition. Based on the teachings of Krokhin regarding the NG pair sites for being a high frequency of deamidation, one of skill in the art would have been motivated to use the method of Jin to identify and modify the deamidations of the known AAV1 sequence of Xiao at GenBank accession # AF063497. See MPEP 2144.06: Substituting equivalents known for the same purpose. There would be a reasonable expectation of success to identify and determine a AAV1 composition comprising the mixed populations of VP1, VP2 and VP3 with deamidation as claimed.
As for the “…comprising 65% to 100% asparagines (N) deamidated at position N57, and 75% to 100% asparagines (N) deamidated at each of positions: N383, N512, and N718, based on the numbering of SEQ ID NO: 1…’ as claimed in the amended base claim 29, Jin teaches that in some embodiments, the AAV particle is deamidated at about 50%-100% ranges (See e.g., column 28, lines 42-53), which include the deamidation percentage range as claimed. Because Xiao teaches an identical sequence to the claimed SEQ ID NO: 1 that contains only four “NG” pairs sites as claimed, based on the teaching of Jin, it is reasonably considered that the asparagine (N) deamidated at each of positions of N57, N383, N512, and N718 in SEQ ID NO: 1 is at 50%-100% ranges. At the same time, Jin also discloses that “the extracted ion chromatograms (XIC) of peptides containing NG sites (T9, T49, and T67 in AA1 and AAV2 VP) and their corresponding deamidated species were used for calculation of deamidation levels” (See column 62, lines 64-67), where the T9 is SEQ ID NO: 9 (AAV1, see Table 7 above and Fig. 6A), T49 is SEQ ID NO: 11 (AAV1, see Table 7 above and column 13, lines 21-26) and T67 is SEQ ID NO: 13 (AAV1, see Table 7 above and column 13, lines 27-33). Here this description further discloses that the deamidation percentage Jin taught is based on the AAV1 NG pairs at positions: N57, N383, N512, and N718 (See Tables 4-6 above). Also, Krokhin et al. teaches the peptides containing -Asn-Gly- sequences (NG pair) typically show ~70-80% degree of deamidation (See Abstract).
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 30, it requires that the AAV1 Vp1, VP2 and VP3 are produced from a nucleic acid sequence encoding a selected AAV vp 1 amino acid sequence. Jin et al. teaches that the rAAV particle is produced by an AAV
producer cell comprising nucleic acid encoding the rAAV vector and nucleic acid encoding AAV rep and cap functions, and providing nucleic acid encoding AAV helper functions (See e.g., column 8, lines 1-19). It discloses an amino acid sequence of “major coat protein VP1” containing the VP1, VP2 and VP3 of AAV2. The table 3 of Jin shows the theoretical masses of predicted sequences of 13 AAV serotypes based on sequence alignment and the intact protein analysis of several AAV serotypes (See below Table 3). Nevertheless, Xiao et al. discloses the AAV1 major coat protein VP1 nucleic acid sequence that encoding the VP1-3 (See Fig. 2 and the below).
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Regarding claim 32, they require the capsid comprises 80% to 100% deamidated asparagine at each of position N383, N512, and/or N718 relative to the numbering of AAV1, as determined using mass spectrometry.
Jin teaches that in some embodiments, the AAV particle is deamidated to a higher extent compared to a parental AAV particle. In some embodiments, the AAV particle is more than about any of 5%, 10%, 15%, 20%, 25%, 30%, 35%, 40%, 45%, 50%, 55%, 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, or 100% more deamidated compared to a parent AAV particle (See e.g., Column 28, lines 42-47), where one of the deamidation can be N57, N382, N511 and or N715 (See e.g., column 26, lines 58-67). Because the amino acids numbers in Jin is based on AAV2 (See e.g., column 10, lines 52-56), the deamidated amino acids of N57, N382, N511 and or N715 in AAV2 is equal to the amino acid’s numbers N57, N383, N512 (See Table 1 below).
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Regarding claims 33 and 34, it requires all or a subpopulation of the AAV vp 1 proteins and/or vp3 proteins have a truncation of about 1 to about 5 amino acids at its N-terminus or -C-terminus respectively. Jin et al. teaches that in some embodiments, the heterogeneity comprises one or more of mixed serotypes, variant capsids, capsid amino acid substitutions, truncated capsids, or modified capsids (See column 2, lines 51-54). It teaches that the N-terminus of an AAV capsid protein (e.g., VP1 or VP3) may refer to the first amino acid after the initiating methionine, which in some cases may be removed by, e.g., a Met-aminopeptidase (See Column 26, lines 4-17). In Fig. 3, Jin et al. also teaches that the complete N-terminal and C-terminal peptides were covered by Lys-C digests as underlined in FIG. 3 (See Fig. 3; Column 55, lines 20-31), which indicates the truncated subpopulation of the AAV VP1 or VP3 proteins. Jin et al. discloses that in particular, a potential deamidation site is found at N57/G58 in the phospholipase A2 domain (Ca++ binding site), which is conserved among AAV 1, 2, 8 and others. The following experiments were aimed at exploring whether deamidation at N57 can lead to reduced potency and/or truncation of AAV2 (See Column 62, lines 26-41). 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 set up an experimental to determine the truncation peptides and study the relations between the N57 deamidation and the truncation through N-terminus and C-terminus with a serial amino acids truction in order to improve/identify the stability, assembly and transduction of rAAAV particles.
Regarding claims 35, 36 and 38, they require that the AAV1 capsid comprises AAV1 vp l proteins, AAV1 vp2 proteins and/or AAV1 vp2 proteins and AAV1 vp3 proteins which are 70% to 100% N deamidated at each of positions: N57, N383, N512, N718, based on the numbering of SEQ ID NO: 1, where the amino acid sites are numbered in AAV1.
Based on the description above, Jin et al. teaches a composition comprising AAV particles wherein the AAV particles comprise one or more amino acid substitutions at amino acid residue A35, N57, G58, N382, G383, N511, G512, N715, or G716 of VP1 or VP3, residue numbering based on VP1 of AAV2, wherein the amino acid substitution alters deamidation as compared to deamidation of VP1 and/or VP3 of the parent AAV particle (See column 10, lines 52-67). Among the predicted/potential deamidation sites, the N57G58 is a highly conserved deamidation site among the AAV serotypes (See Fig. 13 and below). Therefore, the AAV1 numbers the N57. Since the SEQ ID NO: 1 is identical to AAV 1 capsid protein VP1 (See table 1 above), the aligned sequences teaches the potential NG deamidation sites as: the N382 in AAV2 is the N383 of AAV1 and the N511in AAV2 is N512 of AAV1 (See Table 1 above, where they are all in a N-G pairs. Jin et al. teaches that the AAV particle is more than about any of 5%, 10%, 15%, 20%, 25%, 30%, 35%, 40%, 45%, 50%,55%, 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, or 100% more deamidated compared to a parent AAV particle (See column 28, lines 42-63), where the percentage ranges of the deamidated asparagine claimed in the instant application is taught in Jin’s deamidation ranges.
Regarding claims 39-41, Jin et al. teaches that in some embodiments, the viral particle comprises an AAV ITR sequence. For example, an expression cassette may be flanked on the 5' and 3' end by at least one functional AAV ITR sequence to contain the heterologous transgene encoding a heterologous polypeptide (See e.g., column 35, lines 42-45; column 17, lines 33-41), where the heterologous transgene (i.e., nucleic acid sequence not of viral origin) that is flanked by at least one, e.g., two, inverted terminal repeat sequences (ITRs) (See e.g., column 16, lines 36-41). Also, Jin et al. teaches that an "AAV inverted terminal repeat (ITR)" sequence is an approximately 145-nucleotide sequence that is present at both termini of the native single-stranded AAV genome (See e.g., column 18, lines 10-13), and the viral particles comprising a recombinant self-complementing genome (See e.g., column 42, lines 41-45).
Regarding claim 42, Jin et al. teaches that in some embodiments, the heterologous nucleic acid encodes a therapeutic nucleic acid. In some embodiments, a therapeutic nucleic acid may include without limitation an siRNA, an shRNA, an RNAi, a miRNA, an antisense RNA, a ribozyme or a DNAzyme (See column 31, lines 12-16).
Regarding claims 44, 45 and 46, Jin et al. teaches in some embodiments, an AAV particle of the present disclosure (e.g., a rAAV particle) is in a pharmaceutical composition. The pharmaceutical compositions may be suitable for any mode of administration described herein or known in the art (See e.g., column 49, lines 47-63). As for the immunoglobulin product, Jin et al. teaches that the AAV vector may comprise as a transgene, a nucleic acid encoding a protein or functional RNA. Here one of the transgenes is the anti-angiogenic polypeptide (See e.g., claim 30, lines 31-50). The anti-angiogenic polypeptide can be an antibody such as bevacizumab (Avastin). Bevacizumab is a monoclonal antibody that targets vascular endothelial growth factor (VEGF), effectively blocking angiogenesis by preventing VEGF from binding to its receptors on endothelial cells (See Cancer Research UK, downloaded on 1-30-2025), which also teaches claim 45. Also, claim 45 does not provide any structural differences from the Ab of claim 44.
As for the claim 46, it is a common knowledge and technique that one of skilled in the art to select expressing an anti-viral immunoglobulin in claim 44 based on needs. Many researches can be evidenced for using AAV to deliver antiviral antibodies. For example, Martinez-Navio et al. teaches using AAV vector to deliver antibodies against HIV and SIV in Rhesus Monkeys (See Abstract).
Responses to Applicant’s Remarks
Applicant’s arguments filed on Jan. 28, 2026 has been received and fully considered.
Applicant’s arguments on the rejections under 35 U.S.C. 103 are not persuasive as follows:
1). Applicant argued that Jin et al. does not teach or suggest the deamidated AAV1 amino acid residues that are defined in the instant application, or the recited high level of
deamidation for each of these positions in an AAVI capsid, much less does Jin et al.
teach or suggest deamidation at each of the recited positions in any AAV capsid, i.e. 65%
to I00% in position N57 and 75% to I00% in each of positions N383, N5I2 and N7I8 (See Remarks, page 7).
Applicant’s argument is not persuasive.
Jin teaches the same “deamidation” as claimed for the deamidated asparagines being deamidated to an aspartic acid, an isoaspartic acid, or combination (See column 27, lines 54-60), and discloses that the AAV particle is deamidated to a higher extent compared to a parental AAV particle, and the AAV particle is more than about any of 45%... 65%, 70%, 75%...100% more deamidated compared to a parent AAV particle (See column 28, lines 42-50). Here the percentage of the deamidation is within the range as claimed at 65% to 100%. At the same time, Jin teaches a deamidation at N57, N382, N511, and N715 (See e.g., column 11, lines 25-45), where the N57, N382 and N511 are based on AAV2 sequence of SEQ ID NO: 3 and is corresponded to N57, N383 and N512 as claimed based on the instant SEQ ID NO: 1 (See Table 1 above). Although Jin does not refer a corresponding deamidation site of N718 (based on the Seq ID NO: 1), Jin teaches a SEQ ID NO: 13 with a deamidation site of NG that matches to the SEQ ID NO: 1 at position N718 (See Table 6 above and below). At the last, the instant SEQ ID NO: 1 is taught by Xiao’s AAV1 AF063497.
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Accordingly, Jin in view of Xiao teaches the deamidated AAV1 amino acid residues and the level of the high level of deamidation.
2). Applicant argued that Jin et al. focuses on diagnostics and not rAAV being delivered to a subject for therapeutic purposes. In contrast, the instant amended claims are focused on a vector genome comprising an expression cassette for a therapeutically useful molecule (See Remarks, page 7).
Applicant’s argument is not persuasive.
First, Jin teaches that in some embodiments, the heterologous nucleic acid encodes a therapeutic polypeptide (See e.g., column 30, lines 4-20).
Second, the “focus” on an invention or study does not limit in the instant claims.
3). Applicant argued that the addition of the secondary references does not supply the missing suggestion to provide a recombinant AAV having a deamidated AAV1 as recited. Nor do the additional secondary references teach or suggest such an rAAV that includes a vector genome comprising an expression cassette for a therapeutically useful molecule (See Remarks, page 7).
Applicant’s argument is not persuasive.
Based on the description above, Jin teaches the claimed deamidation sites and percentage. Xiao’s study is used here to teach the claimed SEQ ID NO: 1 and to compare with the deamidation sites of Jin. It is applicable to use Jin in view of Xiao in the office actions.
4). Applicant argued the combination teachings of references of Xiao, Krokhin, Martinez-Navia et al., and Cancer Research UK (See Remarks, bridging pages 7-8).
Applicant’s argument is not persuasive.
The prior arts of Xiao, Krokhin, Martinez-Navia et al., and Cancer Research UK used here are for addressing a specific limitation as claimed. For example, Xiao teaches that the claimed SEQ ID NO: 1. As evidence, Krokhin teaches Deamidation of -Asn-Gly- Sequences during Sample Preparation for Proteomics and discloses the NG “hot spot” for deamidation. The Caner Research UK teaches the Bevacizumab. Martinez-Navio et al. teaches using AAV vector to deliver antibodies against HIV and SIV in Rhesus Monkeys. Therefore, it is applicable to use these references to combine with Jin’s invention for the current office action.
5). Applicant argued that Jin et al. suggests amino acid substitutions alter deamidation and deamidation decreases AAV potency, there would be no motivation to combine the teachings of Xiao et al., Krokhin et al., Martinez- Navia et al. and Cancer Research UK with Jin et al. to arrive at the instant invention (See Remarks, page 7).
Applicant’s argument is not persuasive.
The discussion of AAV potency in Jin is related to a specific experiment (See column 63). The teaching of Jin is “…the invention provides viral particles (e.g., rAAV particles) with improved stability and/or improved transduction efficiency by increasing the acetylation and/or deamidation of capsid proteins” (See Abstract).
6). Applicant argued that Neither Jin et al. nor any of the other cited prior art documents teach or suggest an rAAV being delivered to a subject for a therapeutic purpose
Applicant’s argument is not persuasive.
Jin teaches that a "vector," as used herein, refers to a recombinant plasmid or virus that comprises a nucleic acid to be delivered into a host cell, either in vitro or in vivo (See column 15, lines 59-61), and the term "transgene" refers to a nucleic acid that is introduced into a cell and is capable of being transcribed into RNA and optionally, translated and/or expressed under appropriate conditions for therapeutic or diagnostic application (See column 17, pages 42-49).
7). Applicant argued that is no motivation to combine any of the cited prior art references to arrive at an rAAV with a vector genome comprising an expression cassette for a therapeutically useful molecule. It is only through the use of impermissible hindsight that one may arrive at the instant invention through the combination of Jin et al., Xiao et al., Krokhin et al., Martinez- Navia et al. and Cancer Research UK (See Remarks, page 8).
Applicant’s argument is not persuasive.
As for the s hindsight argument, MPEP § 2145(X)(A) states that “[a]ny judgement on obviousness is in a sense necessarily a reconstruction based on hindsight reasoning, but so long as it takes into account only knowledge which was within the level of ordinary skill in the art at the time the claimed invention was made and does not include knowledge gleaned only from applicant' s disclosure, such a reconstruction is proper.” In re McLaughlin 443 F.2d 1392, 1395, 170 USPQ 209, 212 (CCPA 1971). Here, the obviousness rejections take into account only knowledge which was within the level of ordinary skill in the art at the time the claimed invention was made and does not include knowledge gleaned only from applicant' s disclosure.
Conclusion
No claims are allowed.
Accordingly, THIS ACTION IS MADE FINAL. See MPEP § 706.07(a). Applicant is reminded of the extension of time policy as set forth in 37 CFR 1.136(a).
A shortened statutory period for reply to this final action is set to expire THREE MONTHS from the mailing date of this action. In the event a first reply is filed within TWO MONTHS of the mailing date of this final action and the advisory action is not mailed until after the end of the THREE-MONTH shortened statutory period, then the shortened statutory period will expire on the date the advisory action is mailed, and any extension fee pursuant to 37 CFR 1.136(a) will be calculated from the mailing date of the advisory action. In no event, however, will the statutory period for reply expire later than SIX MONTHS from the date of this final action.
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/RUIXUE WANG/ Examiner, Art Unit 1672
/THOMAS J. VISONE/ Supervisory Patent Examiner, Art Unit 1672
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