DETAILED ACTION
Status of the Application
Claims 135, 225-234 are pending.
The present application, filed on or after March 16, 2013, is being examined under the first inventor to file provisions of the AIA .
A preliminary amendment of claim 135, cancellation of claims 1-2, 24, 27, 47, 50, 73, 76, 78, 86, 93, 96, 98-100, 103, 115, 126, 129-130, 133-135, 165, 195, and addition of claims 225-234 as submitted in a communication filed on 6/29/2026 is acknowledged.
Applicant’s election of Group 430, claims 135, 165, 195, drawn in part to a method for genetically modifying a cell that comprises a modified dystrophin gene, wherein said method requires a polynucleotide that encodes a fusion protein that comprises the meganuclease of SEQ ID NO: 43 and the meganuclease of SEQ ID NO: 51, as submitted in a communication filed on 6/29/2026 is acknowledged. Because applicant did not distinctly and specifically point out the supposed errors in the restriction requirement, the election has been treated as an election without traverse (MPEP § 818.03(a)).
New claims 225-234 are directed to the elected invention. Claims directed to the non-elected invention have been cancelled. Claims 135, 225-234 are at issue and are being examined herein.
Specification
The first paragraph of the specification is objected to because it does not provide the current status of related applications (e.g., now US Patent No. X). Appropriate correction is required.
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. The claims are directed to a method and not to a polynucleotide. Appropriate correction is required.
Priority
Acknowledgment is made of a claim for domestic priority under 35 U.S.C. 119(e) to provisional application No. 63/113,131 filed on 11/12/2020, and 63/233,664 filed on 08/16/2021.
Acknowledgment is made of a claim for domestic priority under 35 U.S.C. 120 or 121 to 18/360,517 filed on 07/27/2023, 17/931,896 filed on 09/13/2022, and PCT/US2021/059146 filed on 11/12/2021.
Information Disclosure Statement
The information disclosure statement (IDS) submitted on 4/26/2024 is acknowledged. The submission is in compliance with the provisions of 37 CFR 1.97. Accordingly, the information disclosure statement is being considered by the examiner.
Drawings
The drawings submitted on 4/26/2026 have been reviewed and are accepted by the Examiner for examination purposes.
Claim Objections
Claim 228 is objected to due to the recitation of “IRES”. Abbreviations unless otherwise obvious and/or commonly used in the art, should not be recited in the claims without at least once reciting the entire phrase for which the abbreviation is used. Appropriate correction is required.
Claim Rejections - 35 USC § 112(b) or Second Paragraph (pre-AIA )
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 135, 225-234 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.
Claim 135 (claims 225-234 dependent thereon) are indefinite in the recitation of “wherein said modified dystrophin gene encodes a modified dystrophin polypeptide lacking the amino acids encoded by exons 45-55 of a wild type dystrophin gene” for the following reasons. A wild type dystrophin gene encompasses a genus of dystrophin genes from different organisms as well as alleles of said genes. The term “lacking the amino acids encoded by exons 45-55 of a wild type dystrophin gene” is unclear in the absence of the specific wild type dystrophin gene that has the recited exons because it is unknown if any wild-type dystrophin gene from any organism has exons 45-55. It is noted that alleles of a gene are also naturally occurring (wild type) and may not have all the exons of the gene from which the alleles derive. If the intended limitation is a modified dystrophin polypeptide lacking amino acids X-Y of SEQ ID NO: Z, the claim should be amended accordingly. For examination purposes, no patentable weight will be given to the term “wherein said modified dystrophin gene encodes a modified dystrophin polypeptide lacking the amino acids encoded by exons 45-55 of a wild type dystrophin gene”. Correction is required.
Claim 225 (claims 226-232 dependent thereon) is indefinite in the recitation of “introducing into said eukaryotic cell a polynucleotide comprising a first nucleic acid sequence….and a second nucleic acid sequence encoding said….meganuclease” for the following reasons. Claim 135, from which claim 225 depends, already requires the introduction of a polynucleotide that comprises a first nucleic acid sequence that encodes a first meganuclease, and a second nucleic acid sequence that encodes a second meganuclease. Therefore, it is unclear as to how claim 225 further limits claim 135. For examination purposes, it will be assumed that claim 225 is a duplicate of claim 135. Correction is required.
Claim 226 (claims 227-232 dependent thereon) is indefinite in the recitation of “wherein said polypeptide is introduced into said eukaryotic cell by a recombinant virus” because there is no antecedent basis for said polypeptide. If the intended limitation is “wherein said polynucleotide is introduced into said eukaryotic cell by a recombinant virus”, the claim should be amended accordingly. Correction is required.
When amending the claims, applicant is advised to carefully review all examined claims and make the necessary changes to ensure proper antecedent basis and dependency.
Claim Rejections - 35 USC § 112(a) or First Paragraph (pre-AIA )
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 135, 225-234 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. The claim(s) contains subject matter which was not described in the specification in such a way as to reasonably convey to one skilled in the relevant art that the inventor or a joint inventor, or for pre-AIA the inventor(s), at the time the application was filed, had possession of the claimed invention.
As stated in MPEP 2111.01, during examination, the claims must be interpreted as broadly as their terms reasonably allow. Claims 135, 225-234 are directed in part to an in vivo method for modifying a dystrophin gene in a eukaryotic cell in a multicellular organism, wherein said method comprises delivering to the eukaryotic cell in the multicellular organism a polynucleotide that encodes the meganuclase of SEQ ID NO: 43 and the meganuclease of SEQ ID NO: 51, and expression of said meganucleases to cleave a dystrophin gene in said cell and remove a region of said dystrophin gene, thus obtaining a modified dystrophin gene in said cell of said multicellular organism. Please note that the eukaryotic cell is not required to be an isolated cell. Therefore, the eukaryotic cell can be part of a multicellular organism, like a human.
In University of California v. Eli Lilly & Co., 43 USPQ2d 1938, the Court of Appeals for the Federal Circuit has held that “A written description of an invention involving a chemical genus, like a description of a chemical species, ‘requires a precise definition, such as by structure, formula, [or] chemical name,’ of the claimed subject matter sufficient to distinguish it from other materials”. As indicated in MPEP § 2163, the written description requirement for a claimed genus 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 that Applicant was in possession of the claimed genus. In addition, MPEP § 2163 states that a representative number of species means that the species which are adequately described are representative of the entire genus. Thus, when there is substantial variation within the genus, one must describe a sufficient variety of species to reflect the variation within the genus.
The claims as written encompass an in vivo method for cleaving a target dystrophin gene by introducing into a multicellular organism, such as a human being, a nucleic acid that encodes meganucleases that can be expressed in said multicellular organism to produce the meganucleases to cleave the desired target dystrophin gene and remove a region of said dystrophin gene. While the specification discloses examples of cleavage of a target human dystrophin gene in vitro in isolated cultured cells, there is no disclosure in the specification or the art at the time of the invention regarding a method to cleave and modify a target dystrophin gene in a multicellular organism, including in a human being, with a meganuclease, wherein the meganuclease is expressed by a polynucleotide which is delivered to the multicellular organism so that expression of said meganuclease can occur, and obtained a dystrophin gene having a deletion. The specification provides no information as to a method to successfully cleave a specific gene in vivo and delete a particular section of said gene. The specification is silent as to how to deliver a nucleic acid that encodes a meganuclease to a multicellular organism and successfully express the required meganuclease so that the desired target nucleic acid is cleaved without non-specific cleavage. The art at the time of the invention indicates that there was high unpredictability with regard to the successful delivery and expression of a particular nucleic acid in humans. See discussion below with regard to enablement. Therefore, in view of the fact that the specification only discloses a method to cleave and remove a section of a dystrophin gene in an isolated/cultured eukaryotic cell acid in vitro and the lack of description regarding the successful delivery of a nucleic acid that encodes a meganuclease to a multicellular organism, the expression of said meganuclease in a multicellular organism, cleavage of the desired target gene in a multicellular organism without unspecific non-intended cleavage, and the actual removal of a section of a target gene in vivo, one of skill in the art would not recognize from the disclosure that Applicant was in possession of the claimed invention.
Claims 135, 225-234 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 an in vitro method for producing a genetically modified eukaryotic cell having a modified dystrophin gene, wherein said method requires introducing into an isolated eukaryotic cell a polynucleotide encoding the meganuclease of SEQ ID NO: 43 and the meganuclease of SEQ ID NO: 51, wherein the meganuclease of SEQ ID NO: 43 cleaves a dystrophin gene at a site that comprises a recognition sequence consisting of SEQ ID NO: 6 to produce a first cleavage site, and wherein the meganuclease of SEQ ID NO: 51 cleaves said dystrophin gene at a site that comprises a recognition sequence consisting of SEQ ID NO: 10 to produce a second cleavage site, wherein the intervening DNA between the first and second cleavage sites in said dystrophin gene is removed, does not reasonably provide enablement for an in vivo method for producing a genetically modified eukaryotic cell having a modified dystrophin gene, wherein said eukaryotic cell is in a multicellular organism. 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/or use the invention commensurate in scope with these claims.
Factors to be considered in determining whether undue experimentation is required are summarized in In re Wands (858 F.2d 731, 737, 8 USPQ2nd 1400 (Fed. Cir. 1988)) as follows: 1) quantity of experimentation necessary, 2) the amount of direction or guidance presented, 3) the presence and absence of working examples, 4) the nature of the invention, 5) the state of prior art, 6) the relative skill of those in the art, 7) the predictability or unpredictability of the art, and 8) the breadth of the claims. The factors which have led the Examiner to conclude that the specification fails to teach how to make and/or use the claimed invention without undue experimentation, are addressed in detail below.
The breadth of the claims. Claims 135, 225-234 broadly encompass an in vivo method for modifying a dystrophin gene in a eukaryotic cell in a multicellular organism, wherein said method comprises delivering to the eukaryotic cell in the multicellular organism a polynucleotide that encodes the meganuclase of SEQ ID NO: 43 and the meganuclease of SEQ ID NO: 51, and expression of said meganucleases to cleave a dystrophin gene in said cell and remove a region of said dystrophin gene, thus obtaining a modified dystrophin gene in said cell of said multicellular organism. As indicated above, the eukaryotic cell is not required to be an isolated cell. Therefore, the eukaryotic cell can be part of a multicellular organism, like a human being. Therefore, in its broadest reasonable interpretation, the claims encompass methods to generate transgenic multicellular organisms and gene therapy. The enablement provided is not commensurate in scope with the claim due to the extremely large number of transgenic multicellular organisms, including humans, comprising the cells encompassed by the claims which the specification fails to teach how to generate or how to use, as well as the lack of information as to how to practice the claimed method in humans to obtain the desired gene modification.
In the instant case, the specification enables an in vitro method for producing a genetically modified eukaryotic cell having a modified dystrophin gene, wherein said method requires introducing into an isolated eukaryotic cell a polynucleotide encoding the meganuclease of SEQ ID NO: 43 and the meganuclease of SEQ ID NO: 51, wherein the meganuclease of SEQ ID NO: 43 cleaves a dystrophin gene at a site that comprises a recognition sequence consisting of SEQ ID NO: 6 to produce a first cleavage site, and wherein the meganuclease of SEQ ID NO: 51 cleaves said dystrophin gene at a site that comprises a recognition sequence consisting of SEQ ID NO: 10 to produce a second cleavage site, wherein the intervening DNA between the first and second cleavage sites in said dystrophin gene is removed.
The amount of direction or guidance presented and the existence of working examples. While the specification discloses how to practice the claimed invention in vitro using isolated/cultured cells, the specification fails to disclose how to deliver a polynucleotide that encodes the desired meganuclease to a multicellular organism, such as a human being, so that the desired meganuclease would be expressed and cleave the desired target nucleic acid without unintended cleavage of other nucleic acids in said multicellular organism. There are no working examples or specific methods disclosed showing a transgenic animal capable of expressing a polynucleotide encoding a meganuclease, or the successful cleavage of a target nucleic acid after delivery of such polynucleotide to a subject without unspecific cleavage. Also, there are no working examples or specific methods disclosed showing how to deliver a polynucleotide encoding a meganuclease as recited in the claims to human tissues so that the meganuclease can be used for therapeutic purposes. There is no disclosure of the deletion of a fragment of a gene by introducing a polynucleotide encoding a meganuclease in a multicellular organism, let alone in a human being, as encompassed by the claims.
The state of prior art, the relative skill of those in the art, and the predictability or unpredictability of the art. The prior art teaches that making genetically modified animals is still unpredictable. Houdebine (Journal of Biotechnology 98:145-160, 2002) admits that many transgenes work poorly and that their expression often is very low or not does not correlate to the promoter added in the gene construct (page 150, left column, fourth paragraph). According to Houdebine, transgenesis is and will always remain limited by theoretical and technical problems and that one limitation comes from the fact that the gene transfer into an animal is the comeback of an isolated gene to the complexity of a whole living organism. Houdebine teaches that genes contain multiple signals in the regulatory regions as well as in the coding regions whose structures and functions are still unknown and that situations such as alternative splicing, mRNA instability, etc. are artifacts that cannot be prevented as long as all the mechanisms of gene expression are not better understood (pages 154-155). In regard to DNA delivery and expression in human tissues, the art teaches the high unpredictability of delivering DNA to human tissues and achieving the desired expression. For example, Phillips (J. Pharm. Pharmacology 53:1169-1174, 2001) teaches that the major challenges in gene therapy have been delivery of DNA to target cells and duration of expression (Abstract). According to Phillips, the problem regarding gene therapy is twofold in that (a) a system must be design to deliver DNA to a specific target while preventing degradation within the body, and (b) an expression system must be built into the DNA construct to allow the target cell to express the protein at therapeutic levels for a determined amount of time (page 1170, left column, lines 7-15). Gardlik et al. (Med. Sci. Monit. 11(4):RA110-121, 2005) teach that (a) while there are a number of methods known for delivery of DNA, there is no clear ideal delivery system (RA119, last paragraph), and (b) the main problem in gene therapy lies in the secure and efficient delivery of genes into target cells and tissues (RA110, Summary). Silva et al. (Current Gene Therapy 11:11-27, 2011) teach that X-SCID patients treated with gene therapy have experienced severe adverse events (SAEs) associated with the integration of the transgene next to a proto-oncogene, thus resulting in proto-oncogene activation by insertional mutagenesis (page 11, left column, first paragraph). Silva et al. teach that while the use of meganucleases in gene therapy has been considered as a potential approach for targeted genome engineering, there are some challenges associated with it. Silva et al. teach that one of the issues with regard to the potential use of meganucleases in gene therapy is the % of targeted integration and how there is a need for more data regarding targeted recombination in stem cells (page 21, left column, lines 1-11; page 21, right column, first paragraph). Silva et al. teach that a true benchmark for specificity remains elusive as the very nature of monitored events can vary by assay (page 21, right column, Specificity). Silva et al. teach that for endonuclease-base approaches, proper expression of the nuclease within the target cell is one of the most important aspects for efficacy and specificity. Silva et al. teach that while in some instances off-site cleavage can be reduced, there is a low-level off-site cleavage activity that over an extended period of time could have significant consequences (page 22, right column, last paragraph).
The quantity of experimentation required to practice the claimed invention based on the teachings of the specification. Given the teachings of the art regarding the limitations associated with the integration and expression of a transgene, the unpredictability of delivering and expressing a nucleic acid in human tissues, and the unpredictability of using meganucleases in gene therapy, and in view of the lack of guidance provided by the specification, it would have required undue experimentation to practice the full scope of the claimed methods.
Conclusion
No claim is in condition for allowance.
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Any inquiry concerning this communication or earlier communications from the examiner should be directed to DELIA M RAMIREZ, Ph.D., whose telephone number is (571) 272-0938. The examiner can normally be reached on Monday-Friday from 8:30 AM to 5:00 PM. If attempts to reach the examiner by telephone are unsuccessful, the examiner’s supervisor, Robert B. Mondesi, can be reached at (408) 918-7584. The fax phone number for the organization where this application or proceeding is assigned is 571-273-8300.
/DELIA M RAMIREZ/Primary Examiner, Art Unit 1652
DR
July 10, 2026
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