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 .
Status of Application/Amendments/Claims
Applicant’s response filed on 11/17/2025 has been considered. Claim 60 has been canceled. Claims 59 and 61 have been amended. Claims 59, 61-75 and 81-87 are pending. Claims 65-80 and 88-93 are currently withdrawn from further consideration pursuant to 37 CFR 1.142 (b) as being drawn to a nonelected invention, there being no allowable generic or linking claim. Applicant argues that claims 65-75 and 78-80 encompass the elected species as the second vector can comprise a sequence encoding factor VIII. It is emphasized that the restriction requirement on 10/26/2020 was directed to an election of “a single specific gene product encoded by the first AND second heterologous nucleic acid sequences” in which the applicant selected factor VIII as the first and/or second heterologous nucleic acid sequence. Since a gene product comprising a viral vector encoding factor VIII was not elected, applicants’ arguments are not found convincing. Thus, claims 59, 61-64 and 81-87 are the subject of the present Official Action. The text of those sections of Title 35, U.S. Code not included in this action can be found in a prior Office action.
Priority
Applicant’s claim for the benefit of a prior-filed application PRO 62/315,480 and PCT/US17/24951 filed on 3/30/2016 and 3/30/2017, respectively, under 35 U.S.C 119(e) or under 35 U.S.C 120, 121 or 365(c) is acknowledged.
Accordingly, the effective priority date of the instant application is granted as 3/30/2016.
Withdrawn Rejections
The 112d rejection of claim 60 has been withdrawn in light of applicant canceling claim 60.
The previous 103 rejections have been withdrawn in light of applicants claim amendments describing that the HEK cell lines produce rAAV vector particles.
Claim Rejections - 35 USC § 112a, Written Description
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 59, 61-64 and 82-87 are rejected under 35 U.S.C. 112(a) or 35 U.S.C. 112 (pre-AIA ), first paragraph, as failing to comply with the written description requirement. This rejection is supported by Jantz et al. US 2014/0179005, published 6/26/2014 (hereinafter Jantz, reference of record). This rejection is maintained for the same reasons as outlined in the office action mailed on 5/16/2025. A response to applicant’s traversal is found below.
Claim 59 describes a HEK cell line which does not express a functional DHFR and GS enzyme that is stably or transiently transfected with an AAV vector genome comprising a first heterologous nucleic acid sequence encoding a “therapeutic protein or inhibitory nucleic acid sequence” and a first selectable marker. The claims state that the therapeutic protein is a peptide or protein that itself corrects a genetic defect or gene deficiency thereby alleviating or reducing symptoms in a subject. The genus of “therapeutic protein or inhibitory nucleic acid sequence” refers to a genus that is considered extraordinarily broad. It is thought to encompass any known therapeutic protein both known and yet to be discovered including hormones, enzymes, antibodies, growth factors and cytokines. It encompasses any type of inhibitory nucleic acid sequence including antisense oligonucleotides, siRNAs and miRNAs at any length both known and yet to be discovered. Although applicant has described the therapeutic protein as one that reduces symptoms from an insufficient amount of a protein in a subject, this functional definition tells one of ordinary skill nothing about the structure of the therapeutic protein encoded by the first heterologous nucleic acid sequence. Claims 81 has been excluded from the instant rejection since it recites specific first and/or second heterologous nucleic acid sequences.
For each claim drawn to a genus, the written description requirement may be satisfied through sufficient description of a representative number of species by actual reduction to practice, reduction to drawings, or by disclosure of relevant identifying characteristics, i.e. structure or other physical and/or chemical properties, by functional characteristics coupled with a known or disclosed correlation between function and structure, or by a combination of such identifying characteristics, sufficient to show the applicant was in procession of the claimed genius. If a representative number of adequately descried species are not disclosed for a genus, the claim to that genus must be rejected as lacking adequate written description under 35 U.S.C. 112, para. 1.
The instant specification lists therapeutic proteins as those that may be used to treat a disease with nonlimiting examples to blood clotting disorders (Spec, para 79). The instant specification provides two examples, which are prophetic in nature, that demonstrate how to generate HEK cells with DHFR and GS knockouts. Importantly, these examples lack any examples of a DHFR/ GS knockout HEK cell line that expresses any first and/or second therapeutic protein. Given the breadth of the genus of all imagined therapeutic proteins in contrast to the exemplified and prophetic proportions of the specification, which are largely drawn only DHFR/ GS knockout HEK cell lines, the instant specification does not adequately disclose a sufficient number of adequately described species of the genus of all therapeutic proteins or inhibitory nucleic acid sequences.
Furthermore, the prior art does not support the breadth of applicants claim to all therapeutic proteins or inhibitory nucleic acid sequences. In particular, the prior art reveals that transgenic cell lines may be programmed to express a protein of interest, however, each protein requires different biomanufacturing processes which are highly specific to the protein being expressed. This is supported by Jantz who shows that there is a great amount of unpredictability and a high level of adaptation of biomanufacturing processes depending on the particular therapeutic protein being expressed (Jantz, para 131-133).
Thus, although the specification prophetically considers and discloses therapeutic proteins related towards treating blood clotting disorders like factor VIII, the instant specification does not disclose a sufficient number of adequately described species to support the claim to all therapeutic proteins or inhibitory nucleic acid sequences.
Response to Traversal
Applicant traverses the instant rejection by arguing that the claims are directed to cell lines that produce rAAV vector particles and not methods for manufacturing the particular therapeutic proteins encoded by such AAV vectors. Applicant argues that the appropriate analysis is whether the specification provides sufficient evidence that one of skill would understand that the Applicant possessed the strategies for producing such cell lines, which is wholly unrelated to the teachings of Jantz who is focused on biomanufacturing antibodies and recombinant proteins.
These arguments have been fully considered, but are not found persuasive. Although it is acknowledged that the claims are directed to a composition comprising a HEK cell line which produces rAAV vector particles, the claims recite that the rAAV particles nonetheless contain the first heterologous nucleic acid sequence which encodes the therapeutic protein or inhibitory nucleic acid. Claims must be read in context and in their entirety. With respect to Jantz, the prior art shows that there is a great amount of unpredictability and a high level of adaptation of biomanufacturing processes depending on the particular therapeutic protein being expressed (Jantz, para 131-133). Thus, although the specification prophetically considers and discloses therapeutic proteins related towards treating blood clotting disorders like factor VIII, the instant specification does not disclose a sufficient number of adequately described species to support the claim to all therapeutic proteins or inhibitory nucleic acid sequences.
Claim Rejections - 35 USC § 112b
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 59, 61-64 and 81-87 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 pre-AIA the applicant regards as the invention. This rejection is newly applied to address applicants claim amendments on 11/17/2025.
Claim 59 describes transfecting a HEK cell link with an AAV vector genome comprising a first heterologous nucleic acid sequence encoding a therapeutic protein or an inhibitory nucleic acid sequence and a first selectable marker…wherein the HEK cell line produces rAAV vector particles “having packaged therein” the first heterologous nucleic acid sequence. It is unclear what is exactly being produced by the transfected HEK cell line; rAAV vector particles (which encode for factor VIII) or a therapeutic protein itself (factor VIII). The newly added limitations to claim 59 indicate that the HEK cell lines exclusively produce rAAV particles which encode for the first heterologous nucleic acid. However, the preamble only describes an AAV vector genome comprising a first heterologous nucleic acid sequence encoding a therapeutic protein or an inhibitory nucleic acid sequence and a first selectable marker that corrects a gene deficiency. It is unclear if the first heterologous nucleic acid sequence encoding a therapeutic protein is ever expressed or how this may result in reducing symptoms that result from an insufficient protein in a cell. Please note that the language of a claim must make it clear what subject matter the claim encompasses to adequately delineate its "metes and bounds", see MPEP 2173.
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 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.
Claims 59, 61-64 and 82-87 are rejected under 35 U.S.C. 103 as being unpatentable over Liu et al. US 2010/0129869A1, published 5/27/2010 (hereinafter Liu, reference of record) in view of XL Liu et al. "Production of recombinant adeno-associated virus vectors using a packaging cell line and a hybrid recombinant adenovirus." Gene therapy 6.2 (1999): 293-299 (hereinafter XL Liu) and Collingwood et al. US 2008/0015164, published 1/17/2008 (hereinafter Collingwood, reference of record). This rejection is newly applied to address applicants claim amendments filed on 11/17/2025.
Claim 59: Liu describes methods and compositions for inactivating glutamine synthetase (GS) and dihydrofolate reductase (DHFR) in human embryonic kidney (HEK) cells) using fusion proteins comprising a zinc finger protein (ZFN) and a cleavage domain (Liu, abstract). Liu explains that DHFR deficient cells have long been used for the production of recombinant proteins since they will only grow in media supplemented by certain factors involved in folate metabolisms or if DHFR is provided to the cell as a transgene (Liu, para 6). Similarly, GS can also be used in conjunction with DHFR as a selection marker gene in HEK cell based recombinant protein expression systems (Liu, para 4-9). Liu describes the use of viral vectors to deliver the transgene to GS-DHFR deficient HEK cell lines including AAV vectors with two ITRs that flank the 5’ and/or 3’ ends of the heterologous nucleic acid sequence as well as AAV rep sequences (Liu, para 113-120 and 125-127). Liu describes the use of inhibitors such as methotrexate (MTX) to amplify the DHFR gene copy number (Liu, para 6). Liu describes the integration of the therapeutic gene into the target cell to provide permanent transgene expression with a therapeutic effect (Liu, para 18 and 113). Liu does not specifically describe the transfection of HEK cells with a heterologous nucleic acid sequence and a separate selection marker or expression of rAAV particles as described in newly amended claim 59.
Claims 61: Liu describes stable transgene delivery due to efficient gene transfer via rAAV delivery (Liu, para 117).
Claim 82: Liu does not describe selection markers that provide resistance to antibiotics.
Claims 83-85: Liu explains that DHFR deficient cells have long been used for the production of recombinant proteins since they will only grow in media supplemented by certain factors involved in folate metabolisms or if DHFR is provided to the cell as a transgene (Liu, para 6). Similarly, GS can also be used in conjunction with DHFR as a selection marker gene in HEK cell based recombinant protein expression systems (Liu, para 4-9).
Claims 86: Liu provides preferred embodiments to HEK293 cell lines (Liu, para 19).
Claim 87: Liu describes the use of various culturing medium formulations for cell growth and long-term storage (Liu, examples 2-4).
Claims 59: XL Liu describes methods for producing rAAV vectors from HEK 293 cells (XL Liu, abstract). XL Liu provides background into vector design and how to insert a heterologous nucleic acid sequence into the resulting rAAV vector (XL Liu, Fig 1).
It would have been prima facie obvious to one of ordinary skill in the art to generate HEK cell lines that produce rAAV vectors encoding a heterologous nucleic acid as described by XL Liu and apply it in the method of transforming HEK knockout cell lines as described by Liu. It would have been a matter of combining prior art elements according to known methods to yield predictable results since XL Liu uses the same HEK cell line and shows this to be a predictable means to produce rAAV vector particles. One of ordinary skill would be motivated to make this combination in order to selectively produce large numbers of rAAV particles. One would have a reasonable expectation of successes given that HEK cell lines have high transfection efficiencies and abilities to grow in suspension.
However, Neither Liu nor XL Liu describe the transfection of HEK cells with a heterologous nucleic acid sequence and a separate selection marker.
Claim 59: Collingwood describes the insertion of two nucleic acid sequences into DHFR knockout cells and the use of one as a selection marker (Collingwood, para 18). Collingwood describes selecting cells in which the transgene is stably integrated into and expressed by the host cell, thereby producing the recombinant protein. Collingwood states that the copy number of the integrated DHFR marker gene, along with the associated expression cassette of the target recombinant protein can be amplified by applying a selective pressure, such as the use of a DHFR inhibitor like methotrexate (Collingwood, para 18 and 35).
Claim 62-64: Collingwood describes the use of a second heterologous nucleic acid sequence and selectable marker encoded by a second viral vector (Collingwood, para 17).
Claim 82: Collingwood does not describe selection markers that provide resistance to antibiotics.
It would have been prima facie obvious to one of ordinary skill in the art to incorporate a separate first and second selectable marker along with the first and second heterologous nucleic acid sequence as described by Collingwood into the method of transforming HEK knockout cell lines as described by Liu. It would have been a matter of combining prior art elements according to known methods to yield predictable results since Collingwood shows this to be a predictable means to allow the selection of transformed HEK cells. One of ordinary skill would be motivated to make this combination in order to select HEK cells successful transformed with proteins of interest that are not themselves suitable as selection markers. One would have a reasonable expectation of successes given that Collingwood demonstrates this selection technique on HEK cell lines with a high degree of predictable success. Accordingly, in the absence of evidence to the contrary, one of ordinary skill in the art would have considered claims 59-64 and 82-87 to have been prima facie obvious to at the time the invention was made.
Claims 59, 61-64 and 81-87 are rejected under 35 U.S.C. 103 as being unpatentable over Liu (supra), XL Liu (supra) and Collingwood (supra) as applied to claims 59, 61-64 and 82-87 above in further view of Jantz et al. US 2014/0179005, published 6/26/2014 (hereinafter Jantz, reference of record). This rejection is newly applied to address applicants claim amendments filed on 11/17/2025.
A description of Liu and Collingwood can be found above. Neither Liu nor Collingwood describes a first and/or second heterologous nucleic acid sequence encoding for a protein useful for correction of in born errors including factor VIII as recited in claim 81. It is noted that factor VIII is the elected heterologous nucleic acid sequence.
Claim 81: However, predictable methods exist for inserting an exogenous transgene proximal to an endogenous selectable gene in an amplifiable locus which does not inhibit amplification of the endogenous selectable gene and can be co-amplified (Jantz, para 12). For example, Jantz describes such methods for mammalian cell lines including HEK cell lines (Jantz, para 5, 127). Jantz describes techniques using both GS and DHFR as selectable markers (Jantz, para 129, 130, 135 and example 2). Jantz also describes the use of selectable genes in combination with selection agents like MTX and MSX (Jantz, para 17). Furthermore, Jantz provides embodiments for transgenes encoding therapeutic proteins like factor VIII (Jantz, para 131).
It would have been prima facie obvious to one of ordinary skill in the art to select factor VIII as the therapeutic transgene as disclosed by Jantz in the GS-DHFR double knockout HEK cell line described by Liu and XL Liu. Both Jantz and Liu have a clear appreciation for the use of GS and DHFR as selectable markers for amplifying HEK cells expressing therapeutic transgenes. Although Liu does not list factor VIII as a therapeutic transgene of interest, Jantz provides preferred embodiments towards the use of factor VIII, which is a well-known blood clotting agent useful in treating disorders like hemophilia A. Thus, it would have been a matter of simple substitution for one therapeutic transgene for another to obtain predictable results. One would have been motivated to make this substitution given the clinical importance of factor VIII as a therapeutic in treating diseases like hemophilia A. Thus, one of ordinary skill would naturally look to use cell lines like the GS-DHFR double knockout HEK cell line described by Liu to produce large quantities of factor VIII given the efficiency of this amplification strategy. One would have a reasonable expectation of successes given that predictable methods exist for inserting exogenous transgenes proximal to endogenous selectable genes. Furthermore, both authors show that HEK cell lines are readily attainable and can be modified using gene editing techniques like ZFN. Accordingly, in the absence of evidence to the contrary, one of ordinary skill in the art would have considered the claimed invention to have been prima facie obvious to at the time the invention was made.
Conclusion
No claims allowed.
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 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 mailing date of this final action.
Any inquiry concerning this communication or earlier communications from the examiner should be directed to ALEXANDER NICOL whose telephone number is (571)272-6383. The examiner can normally be reached on M-F 8-5 EST.
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If attempts to reach the examiner by telephone are unsuccessful, the examiner’s supervisor, Maria Leavitt can be reached on (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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Alexander Nicol
Patent Examiner
Art Unit 1634
/ALEXANDER W NICOL/Examiner, Art Unit 1634