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
This application is in response to the papers filed on February 10, 2026. Claims 1-14, and 16 are currently pending. Claims 1, 3, 4, 6-9, 11-14, have been amended, claim 15 had been cancelled, and claim 16 had been newly filed by in Applicant’s amendment filed June 9, 2023. No claims have been amended, added or cancelled in in Applicant’s amendment filed on February 10, 2026.
Applicant’s election with traverse of the invention of Group I, e.g., claims 1-13, drawn to a host cell comprising: a nucleic acid encoding Adeno-associated virus (AAV) capsid protein, wherein a protein kinase R (PKR) activating sequence surrounding a start codon of the AAV capsid protein VP1 is inactivated, while maintaining functional expression of the AAV capsid proteins VP1, VP2, and VP3; to a method of producing stem/progenitor cells, in the reply filed on February 10, 2026 in response to the restriction requirement filed on December 16, 2026 is acknowledged.
The applicant argues:
“Applicant's traversal is based on its belief that a search relating to the claimed invention of one group will identify any references that are material to the claimed invention of the other group. Therefore, it is respectfully submitted that a search for both claim groups would not pose an undue burden on the Patent Office.”:
The examiner argues the restriction is valid based on the Li reference anticipating group I, and therefore the remaining claims lack the same or corresponding special technical feature and as such, lack unity. The expression “special technical features” means those technical features that define a contribution which each of the claimed inventions, considered as a whole, makes over the prior art. Furthermore, there is no certainty that examination for the host cell drawn to Group I would lead to findings for the method of production of AAV drawn to Group II.
Claims 14 and 16 are withdrawn from further consideration by the Examiner, pursuant to 37 CFR 1.142(b), as being drawn to non-elected inventions, there being no allowable generic or linking claim. Reinstatement of claims drawn to non-elected inventions will be withdrawn during prosecution. The requirement for restriction between Groups I-II is maintained for reasons of record, and hereby made FINAL. Applicant timely responded to the restriction (election) requirement in the Paper filed on February 10, 2026. It is noted that when a final requirement for restriction is made by the examiner, applicant may file a petition under 37 CFR 1.144 for review of the restriction requirement. The propriety of a requirement to restrict, if traversed, is reviewable by petition under 37 CFR 1.144 . In re Hengehold, 440 F.2d 1395, 169 USPQ 473 (CCPA 1971).
Therefore, claims 1-13 are currently under examination to which the following grounds of rejection are applicable.
Priority
The instant application claims foreign priority 35 U.S.C. 119(a)-(d) to European Patent Application No. 20215905.9 filed on December 21, 2020 and PCT Application No. PCT/EP2021/086768 filed on December 20, 2021. Receipt is acknowledged of certified copies of papers required by 37 CFR 1.55.
Thus, the earliest possible priority for the instant application is December 21, 2020.
Information Disclosure Statement
The information disclosure statements (IDS) submitted on June 9, 2023, June 26, 2025, and January 13, 2026 were filed. The submissions are in compliance with the provisions of 37 CFR 1.97. Accordingly, the information disclosure statements are being considered by the examiner.
Drawings
The drawings are objected to under 37 CFR 1.83(a) because they fail to show:
Figures 5-8 fail to show to the y-axis labels and the chart titles, while only showing units.
Figures 11-12, and 14 fails to show the y-axis labels while only displaying the units. The charts/graphs should also include titles when the information depicted is not clear based on the axes labels and data labels. The Figures should be clear and concise in the information that is being represented, and as such this includes proper labeling.
Any structural detail that is essential for a proper understanding of the disclosed invention should be shown in the drawing. MPEP § 608.02(d). Corrected drawing sheets in compliance with 37 CFR 1.121(d) are required in reply to the Office action to avoid abandonment of the application. Any amended replacement drawing sheet should include all of the figures appearing on the immediate prior version of the sheet, even if only one figure is being amended. The figure or figure number of an amended drawing should not be labeled as “amended.” If a drawing figure is to be canceled, the appropriate figure must be removed from the replacement sheet, and where necessary, the remaining figures must be renumbered and appropriate changes made to the brief description of the several views of the drawings for consistency. Additional replacement sheets may be necessary to show the renumbering of the remaining figures. Each drawing sheet submitted after the filing date of an application must be labeled in the top margin as either “Replacement Sheet” or “New Sheet” pursuant to 37 CFR 1.121(d). If the changes are not accepted by the examiner, the applicant will be notified and informed of any required corrective action in the next Office action. The objection to the drawings will not be held in abeyance.
Specification
Title of the Invention
The title of the invention is not descriptive. A new title is required that is clearly indicative of the invention to which the claims are directed. In particular, the claims are not currently directed to a “PRODUCER CELL HAVING LOW LEVELS OF VA-RNA” since claim 1 is directed to a host cell with an inactivated PKR activating sequence, which is not related to a producer cell with low levels of VA-RNA. The examiner acknowledges that CAP cells were used as seen in Example 1 for which there is low VA-RNA, but the current claims are not limited to such cells.
Claim Objections
Claims 3, 5, 13 are objected to because of the following informalities:
Claim 3 is objected to for punctuation, the claim should have a comma after the phrase “The host cell according to claim 1”.
Claim 5 is objected to for “SV 40”, as the proper recitation is “SV40” as listed on page 8, line 10 of the Specification.
Claim 13 is objected to because it appears the claim intended to recite “which is derived from a cell line” when describing the derivation of the host cell. This is supported by Table 1 on page 23 of the Specification. Appropriate corrections are required.
Claim Rejections - 35 USC § 112
The following is a quotation of the first paragraph of 35 U.S.C. 112(a):
(a) IN GENERAL.—The specification shall contain a written description of the invention, and of the manner and process of making and using it, in such full, clear, concise, and exact terms as to enable any person skilled in the art to which it pertains, or with which it is most nearly connected, to make and use the same, and shall set forth the best mode contemplated by the inventor or joint inventor of carrying out the invention.
The following is a quotation of the first paragraph of pre-AIA 35 U.S.C. 112:
The specification shall contain a written description of the invention, and of the manner and process of making and using it, in such full, clear, concise, and exact terms as to enable any person skilled in the art to which it pertains, or with which it is most nearly connected, to make and use the same, and shall set forth the best mode contemplated by the inventor of carrying out his invention.
Claims 1-13 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 (1) producer cell lines, i.e. CAP cells and HEK293 cells, that have integrated helper functions; (2) the PKR activation sequence is inactivated by replacing the endogenous promoter, p40, with either an inducible or constitutive promoter, and furthermore replacing part of the p40 intron containing the splice donor and splice acceptor site 1 outside of the coding capsid sequence by an intron of different origin, i.e. SV40 (contains an appropriate replacement splice donor and acceptor site), it does not reasonably provide enablement for the currently recited host cells in the claims.
In reference to claim 9, the limitation of “wherein the respective nucleotide sequence from the promoter to the start codon of the coding sequence of the AAV capsid protein has the structure Promoter – N1 - Intron - N2 -ATG” wherein the N1 or N2 are a sequence of nucleotides from 1-4000, is not fully enabled as there are no examples or general support for the entire range set forth. Particularly, there is no support for the whole length or any select number that is comprised for location, and moreover for any sequence to be comprised therein. For example, select sequences could potentially shift the reading frame of the translated protein and/or induce a conformational change in the structure of the mRNA wherein translation is affected, such as the splicing which is necessary for the production of the VP proteins. Based on the working examples, SEQ ID No:4 as listed on page 19, was the most successful for viral production as it entails: TRE3G-SV 40intron-ATG of capsid. Across SEQ ID NOs: 4-7, it can be seen that the N1 and N2 sequences are rather short and often zero in length for N2 for which this claim does not comprise.
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 and use the invention commensurate in scope with these claims. The claims when given the broadest possible interpretation encompass a host cell comprising a nucleic acid encoding Adeno-associated virus (AAV) capsid protein, wherein a protein kinase R (PKR) activating sequence surrounding a start codon of the AAV capsid protein VP1 is inactivated, while maintaining functional expression of the AAV capsid proteins VP1, VP2, and VP3.
In determining whether Applicant’s claims are enabled, it must be found that one of skill in the art at the time of invention by applicant would not have had to perform “undue experimentation” to make and/or use the invention claimed. Such a determination is not a simple factual consideration, but is a conclusion reached by weighing at least eight factors as set forth in In re Wands, 858 F.2d at 737, 8 USPQ 1400, 2d at 1404. Such factors are:
(1) The breadth of the claims; (2) The nature of the invention; (3) The state of the art; (4) The level of one of ordinary skill in the art; (5) The level of predictability in the art; (6) The amount of direction and guidance provided by Applicant; (7) The existence of working examples; and (8) The quantity of experimentation needed to make and/or use the invention.
The office has analyzed the specification in direct accordance to the factors outlines in In re Wands. MPEP 2164.04 states: “[W]hile the analysis and conclusion of a lack of enablement are based on factors discussed in MPEP 2164.01(a) and the evidence as whole, it is not necessary to discuss each factor in written enablement rejection.” These factors will be analyzed, in turn, to demonstrate that one of ordinary skill in the art would have had to perform “undue experimentation” to make and/or use the invention and therefore, applicant’s claims are not enabled.
(1) Breadth of the Claims: Claim 1 currently recites no limitation restricting the cell line of the host cell despite the working examples using only CAP cells and HEK293 cells, both of which contain viral helper genes, and wherein VA-RNA expression is low (at least for CAP cells). It worth noting that the Application Title is directed to host cells with low VA-RNA, of which is impacted by the host cell used rather than the inactivation of the PKR activation sequence itself. Furthermore, the claim does not recite how and where the PKR sequence is inactivated in which the capsid proteins are not affected. The examples only support a promoter and intron replacing the region depicted in Fig 1 that comprises the splice donor and acceptor sites of intron 1, and furthermore the replacement with the SV40 intron.
(2) Nature of the Invention: The invention encompasses a host cell which is directed to a composition. Such composition comprises a nucleic acid sequence encoding an AAV capsid protein, and furthermore wherein such sequence has an inactivated PKR sequence that does not impact the functional expression of these capsid proteins, VP1, VP2, and VP3. The invention is largely directed to a host cell line that does not require helper plasmids, and/or transient infections as all the genes for viral assembly are encoded by the cell. The summary of the invention described cells in the art being known to provide all helper functions, i.e. CAP cells, however, VA-RNA expression is low in such cells which then negatively impacts capsid expression and overall viral production. These cells would then require another vector to provide VA-RNA expression.
The inventive concept of the invention is the inactivation of the PKR activation sequence, of which VA-RNA acts upon to therefore prevent inhibition of capsid expression (as seen in the PKR and eIF2alpha pathway described therein), wherein VA-RNA no longer needs to be supplemented to these packaging cells to maintain capsid expression, and subsequent viral production. The general finding was that substitution of a particular region encompassing the PKR activation sequences with a promoter (inducible (Tet3G) or constitutive (CMV)), and a different intron that replaces the splice donor and acceptor site 1 of the first intron as seen with SV40, could maintain proper stoichiometric expression of the VP proteins (1:1:10) without the need of transient expression of VA-RNA.
(3) The state of the art: The state of the prior art is discussed in the Specification starting on page 2. The current AAV systems employ typically multiple plasmids to provide viral proteins into a host cell; however, there are many drawbacks. Another approach is using producer cell lines that express the gene of interest, that is then transfected with a helper virus, yet there are also issues with this approach in relation to downstream processes. There are challenges with the production of fully stable AAV producer cell lines, particularly with the expression of helper viral functions in which E2A and E4orf6 are toxic. However, this issue has been managed with inducible promoters, yet this remains a challenge for VA-RNA due to its respective promoter being located within the coding sequence; and therefore there are currently no stable cell lines with high expression of VA-RNA which is necessary for high-titer viral production.
The Specification further describes how Nayak et al. 2007 (of record IDS filed on June 9, 2023) “describe how VA RNA during the AAV infection cycle is important for capsid expression, i.e., how capsid pre-mRNA is activating PKR, which in turn phosphorylates eIF2a, which in turn leads to low expression of capsid proteins. Further, said document tries to identify PKR activating sequences by deletion experiments and narrows the same down to about 200 nucleotides around the AUG sequence of VP1. In summary, current AAV-based production systems are limited with respect to their reproducibility, scalability and robustness. Further, the requirement for helper viruses necessitates extensive purification and the costly proof of absence of helper virus.” (p 3, lines 23-29).”
Altogether, the state of the prior art is one wherein there is a lack of stable producer cell lines for high titer AAV production.
(4) The level of one of ordinary skill in the art: The level of skill in the art is high.
(5) The level of predictability in the art: There remains a high level of unpredictability of determining if cell lines that have no viral helper genes would allow for viral production, and furthermore if such cells are provided with a helper virus are capable of producing viruses. There is real uncertainty due to challenges that may arise with transfection, and in turn expression of the encoded viral proteins.
Secondly, there is uncertainty regarding the specific intron that is to replace the region comprising the PKR activation sequence as this intron would require another splice acceptor and donor site that sits at proper locations in relation to the VP1, 2, and 3 proteins, wherein the spliced mRNA would subsequently lead to the proper stoichiometric ratio of these proteins in order to successfully produce AAV particles. This is a major concern as the Applicant investigates these ratios in several of the Example and depicted in Figs. 3, 4, 9 and 13, and wherein all these examples show that the SV40 intron was the only successful intron.
(6) The amount of direction and guidance provided by Applicant & (7) The existence of working examples: The Specification provides 6 examples that are depicted across 15 Figures. The used cell lines are further recited in Table 1 on page 23, and Table 2 on page 24 in which they are comprise: “Tet3G, inducible Rep, inducible Helper”. In respect to the cell types employed, Examples 1-13 use either CAP cells or HEK293T cells. CAP cells are described as human amniocyte-derived suspension cells, that have been immortalized by stable transfection with a construct encoding E1A/E1B (p 26). Furthermore, the human embryonic kidney cell line, HEK293T, another immortalized cell line for the production of viruses (p 2).
Secondly, in relation to the inactivation of the PKR activation sequence the Examples primarily employed, as listed in Table 2, the stable integrated components were an inducible promoter (e.g. TRE3G) followed by SV40 intron. Furthermore, a complementary sequence was investigated rather than stable integration into the host cell, wherein the promoter was either constitutive (e.g. CMV) or inducible followed by SV40 or p40 (which is the same endogenous intron). Altogether, the findings were that the inducible promoter in combination with SV40 intron was successful in viral production despite low levels of VA RNA. This is supported by Example 3 that describes “when transfecting the p40 intron constructs with the capsid under the control of the same TRE3G promoter were significantly lower (more than 10-fold) for pre-packaging clones based on both cell lines… The differences in capsid expression between the intron configurations resulted also in differences in the viral genome titer as shown by qPCR.” (p 30).
(8) The quantity of experimentation needed to make and/or use the invention: There is considerable experimentation to determine which introns are suitable for the replacement on intron 1 to inactivate the PKR activation sequence because no particular nucleotides are recited for this site, and therefore it not clear which nucleotides need to be altered. Moreover, it would be challenging to determine which intron have the suitable splice donor and acceptor sites that would provide this outcome while maintaining the expression of the capsid proteins at the required levels for successful viral assembly. Secondly, it would be extensive experimentation to determine which cell lines are capable of transfection, and furthermore subsequent viral production and isolation via purification methods. The only cell lines used were immortalized cell lines that contained viral helper functions in order for viral production to be feasible without an accessory helper plasmid. Therefore, the host cell should be limited to only HEK293 or CAP cell lines in addition to the SV40 intron for the replacement of the PKR activation sequence.
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 1-5, 8, 9, and 12 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 1 recites the limitation “the AAV capsid proteins VP1, VP2, and VP3” in line 5. There is insufficient antecedent basis for this limitation in the claim. In particular, there is no previous introduction of all three of the capsid proteins. It is acknowledged there is introduction of “ a nucleic acid encoding Adeno-associated virus (AAV) capsid protein”, yet is unclear if all three of VP1, VP2, and VP3 proteins are encoded by this nucleic acid.
Claim 1 is indefinite in not providing a specific SEQ ID for the region that is being inactivated, as it remains unclear based on the current recitation of the claim where the PKR activation sequence is located. It states surrounding a start codon of the AAV capsid protein VP1, yet this remains broad and vague as this would potentially include the promoter and/or downstream elements from the start codon.
Claim 2 recites the limitation “the splice donor and splice acceptor site 1 of the intron of the sequence encoding the capsid pre-mRNA” in the claim. There is insufficient antecedent basis for this limitation in the claim. In particular, there is no previous introduction of the “splice donor”, “splice acceptor site 1”, “intron”, “sequence” and “capsid pre-mRNA”.
Claim 3 recites the limitation “the native AAV capsid protein promoter p40”. There is insufficient antecedent basis for this limitation in the claim.
Claim 4 recites the limitations “the native AAV capsid protein promoter p40”, “the native AAV capsid protein promoter p40 intron”, “the capsid coding sequence”, and “the splice donor and splice acceptor site 1”. There are insufficient antecedent basis for these limitations in the claim.
Claim 5 recites the limitation “the replacement intron”. There is insufficient antecedent basis for this limitations in the claim.
Claim 8 recites the limitation “the inducible promoter” in lines 1-2. There is insufficient antecedent basis for this limitations in the claim.
Claim 9 recites the limitations “the native AAV capsid protein promoter p40”, “the p40 intron”, “the splice donor and splice acceptor site 1”, “the coding capsid sequence”, “the promoter”, “the start codon of the coding sequence”, “the structure”, “the minimal consensus sequences GT/ AG”, and “the start codon of the AAV capsid protein coding sequence”. There are insufficient antecedent basis for these limitations in the claim.
Claim 9 is indefinite in the recitation of “fitting splice donor and splice acceptor site” as it is currently unclear what constitutes as “fitting” based on the full disclosure provided or rather if “fitting” is based on the minimal consensus sequence of GT/ AG.
Regarding claims 9 and 12, the phrase "i.e." which translates to “that is” renders the claim indefinite because it is unclear whether the limitation(s) following the phrase are part of the claimed invention. See MPEP § 2173.05.
Claim 12 recites the limitations “the native AAV capsid protein promoter p40”, “the part of the p40 intron” “the splice donor and splice acceptor site 1”, “the capsid coding sequence”, “the respective nucleotide sequence from the promoter”, “start codon of the coding sequence of the AAV capsid protein”. There are insufficient antecedent basis for these limitations in the claim.
Claim 11 is indefinite in the recitation of the intron being a: “SV 40 intron, a synthetic CAG promoter intron, and a beta-globin intron” in view of dependency from claim 9 that states the intron as one “selected from the group consisting of introns supplying a fitting splice donor and splice acceptor site with the minimal consensus sequences GT/ AG,”. In particular, it is not clear if these introns are encompassed by the range set forth in claim 9, and therefore based on the scope being uncertain the claim is indefinite.
Claim 13 is rejected by dependency.
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.
(a)(2) the claimed invention was described in a patent issued under section 151, or in an application for patent published or deemed published under section 122(b), in which the patent or application, as the case may be, names another inventor and was effectively filed before the effective filing date of the claimed invention.
Claims 1-13 are rejected under 35 U.S.C. 102(a)(1)(2) as being anticipated by Li et al. (US 2005/0112765 A1).
Regarding claim 1, Li teaches the production of AAV vectors for gene therapy (Figure 1 ). In particular, Li teaches the adenovirus vector ADTRErep.CMVcap which expresses the AAV capsid proteins under the CMV promoter, which is characterized as a mutated (reading on “inactivated”) endogenous p40 promoter (par 0035-0038, 0139; Fig. 1B). In the presence of doxycycline the CAP proteins VP1, VP2 and VP3 are constitutively expressed (par 0040, 0140-0142; Fig. 2A). In reference to “wherein a protein kinase R (PKR) activating sequence surrounding a start codon of the AAV capsid protein VP1 is inactivated,” since the site is not explicitly defined with a particular sequence alignment recited in the claim, there is an expectation that the swapping of the endogenous p40 promoter region comprises the activating sequence since this region is outside the start codon of the VP1 codon. Therefore, there is an expectation that the splice donor and splice acceptor site 1 of the intron of the sequence encoding the capsid pre-mRNA as recited in claim 2 are included in this region.
Regarding claim 4, dependent on claim 1, Li teaches wherein the native AAV capsid protein promoter p40 is replaced by an inducible promoter as seen in paragraph 0012.
Regarding claim 6, dependent on claim 1, Li teaches a nucleic acid encoding AAV replicase (Rep) proteins under the control of an inducible promoter as seen in paragraph 0011.
Regarding claim 7, dependent on claim 1, Li teaches the host cell further comprising a nucleic acid encoding a transfer vector containing one or more gene(s) of interest (GOI) (paragraph 0019, 0020).
Regarding claim 8, dependent on claim 1, Li teaches wherein the inducible promoter controlling expression of AAV replicase proteins and, is selected from the group consisting of a tet-inducible promoter and heat shock promoter-driven (paragraph 0011-0012).
Regarding claim 13, dependent on claim 1, Li teaches the host cell is derived from the HEK293 cell line (paragraph 0023).
Allowable Subject Matter
It is acknowledged that SEQ ID NOs 4 & 5, as recited in claim 12, were not known prior to filing of the instant application. SEQ ID NO: 4 shows a maximum of ~70% sequence similarity to other known sequences, and SEQ ID No: 5 shows a maximum of ~95% sequence similarity to other known sequences (alignments provided in the office action).
Conclusion
Claims 1-13 are rejected. No claims are allowed.
Any inquiry concerning this communication or earlier communications from the examiner should be directed to MICHAEL A RIGA whose telephone number is (571)270-0984. The examiner can normally be reached Monday-Friday (8AM-6PM).
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If attempts to reach the examiner by telephone are unsuccessful, the examiner’s supervisor, Maria G Leavitt can be reached at (571) 272-1085. The fax phone number for the organization where this application or proceeding is assigned is 571-273-8300.
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/MICHAEL ANGELO RIGA/Examiner, Art Unit 1634
/TERESA E KNIGHT/Primary Examiner, Art Unit 1634
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