DETAILED ACTION
Claims 3-8, 11-13, 16, 19, 21, 24-26, 28-29, 31 and 34-35 were/stand cancelled. Claims 2, 9-10, 14, 17, 20, 22-23, 27, 30 and 32-33 were amended. Claims 36-40 were added. Claims 1-2, 9-10, 14-15, 17-18, 20, 22-23, 27, 30, 32-33 and 36-40 are pending.
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 .
Priority
This application is a 371 of PCT/US22/79294 (11/04/2022) which claims benefit of 63/408,184 (09/20/2022) and claims benefit of 63/275,785 (11/04/2021) as reflected in the filing receipt issued July 7 2025.
Information Disclosure Statement
The information disclosure statement (IDS) submitted on April 30 2024 and August 21 2024 are in compliance with the provisions of 37 CFR 1.97. Accordingly, the information disclosure statement is being considered by the examiner.
Nucleotide and/or Amino Acid Sequence Disclosures
REQUIREMENTS FOR PATENT APPLICATIONS CONTAINING NUCLEOTIDE AND/OR AMINO ACID SEQUENCE DISCLOSURES
Items 1) and 2) provide general guidance related to requirements for sequence disclosures.
37 CFR 1.821(c) requires that patent applications which contain disclosures of nucleotide and/or amino acid sequences that fall within the definitions of 37 CFR 1.821(a) must contain a "Sequence Listing," as a separate part of the disclosure, which presents the nucleotide and/or amino acid sequences and associated information using the symbols and format in accordance with the requirements of 37 CFR 1.821 - 1.825. This "Sequence Listing" part of the disclosure may be submitted:
In accordance with 37 CFR 1.821(c)(1) via the USPTO patent electronic filing system (see Section I.1 of the Legal Framework for Patent Electronic System (https://www.uspto.gov/PatentLegalFramework), hereinafter "Legal Framework") as an ASCII text file, together with an incorporation-by-reference of the material in the ASCII text file in a separate paragraph of the specification as required by 37 CFR 1.823(b)(1) identifying:
the name of the ASCII text file;
ii) the date of creation; and
iii) the size of the ASCII text file in bytes;
In accordance with 37 CFR 1.821(c)(1) on read-only optical disc(s) as permitted by 37 CFR 1.52(e)(1)(ii), labeled according to 37 CFR 1.52(e)(5), with an incorporation-by-reference of the material in the ASCII text file according to 37 CFR 1.52(e)(8) and 37 CFR 1.823(b)(1) in a separate paragraph of the specification identifying:
the name of the ASCII text file;
the date of creation; and
the size of the ASCII text file in bytes;
In accordance with 37 CFR 1.821(c)(2) via the USPTO patent electronic filing system as a PDF file (not recommended); or
In accordance with 37 CFR 1.821(c)(3) on physical sheets of paper (not recommended).
When a “Sequence Listing” has been submitted as a PDF file as in 1(c) above (37 CFR 1.821(c)(2)) or on physical sheets of paper as in 1(d) above (37 CFR 1.821(c)(3)), 37 CFR 1.821(e)(1) requires a computer readable form (CRF) of the “Sequence Listing” in accordance with the requirements of 37 CFR 1.824.
If the "Sequence Listing" required by 37 CFR 1.821(c) is filed via the USPTO patent electronic filing system as a PDF, then 37 CFR 1.821(e)(1)(ii) or 1.821(e)(2)(ii) requires submission of a statement that the "Sequence Listing" content of the PDF copy and the CRF copy (the ASCII text file copy) are identical.
If the "Sequence Listing" required by 37 CFR 1.821(c) is filed on paper or read-only optical disc, then 37 CFR 1.821(e)(1)(ii) or 1.821(e)(2)(ii) requires submission of a statement that the "Sequence Listing" content of the paper or read-only optical disc copy and the CRF are identical.
Specific deficiencies and the required response to this Office Action are as follows:
Specific deficiency – Nucleotide and/or amino acid sequences appearing in the drawings are not identified by sequence identifiers in accordance with 37 CFR 1.821(d). Sequence identifiers for nucleotide and/or amino acid sequences must appear either in the drawings or in the Brief Description of the Drawings. Specifically, Fig. 6 contains sequences not identified by SEQ ID NO: in the drawing or in the specification.
Required response – Applicant must provide:
Replacement and annotated drawings in accordance with 37 CFR 1.121(d) inserting the required sequence identifiers;
AND/OR
A substitute specification in compliance with 37 CFR 1.52, 1.121(b)(3) and 1.125 inserting the required sequence identifiers into the Brief Description of the Drawings, consisting of:
A copy of the previously-submitted specification, with deletions shown with strikethrough or brackets and insertions shown with underlining (marked-up version);
A copy of the amended specification without markings (clean version); and
A statement that the substitute specification contains no new matter.
Claim Objections
Claim 17 is objected to because of the following informalities: the “I” in I378 looks like a 1. Appropriate correction is required.
Claim Rejections - 35 USC § 112
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 1-2, 10, 18, 23 and 26 are rejected under 35 U.S.C. 112(b) or 35 U.S.C. 112 (pre-AIA ), second paragraph, as being indefinite for failing to particularly point out and distinctly claim the subject matter which the inventor or a joint inventor (or for applications subject to pre-AIA 35 U.S.C. 112, the applicant), regards as the invention.
Claims 1-2, 10, 18, 23 and 26 contain the trademark/trade name piggyBac. Where a trademark or trade name is used in a claim as a limitation to identify or describe a particular material or product, the claim does not comply with the requirements of 35 U.S.C. 112(b) or 35 U.S.C. 112 (pre-AIA ), second paragraph. See Ex parte Simpson, 218 USPQ 1020 (Bd. App. 1982). The claim scope is uncertain since the trademark or trade name cannot be used properly to identify any particular material or product. A trademark or trade name is used to identify a source of goods, and not the goods themselves. Thus, a trademark or trade name does not identify or describe the goods associated with the trademark or trade name. In the present case, the trademark/trade name is used to identify/describe DNA transposon derived from the cabbage looper moth and, accordingly, the identification/description is indefinite. The examiner notes that TESS serial number for this trademark include 87939850 and 87939838.
Claim Rejections - 35 USC § 102
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.
Claim(s) 1-2, 9, 14-15, 18, 22, 27, 33, 36-37 and 40 is/are rejected under 35 U.S.C. 102(a)(1) and/or 102(a)(2) as being anticipated by Sanchez-Mejias et al. (WO2020250181).
The instant application claims a composition comprising an enzyme and a targeting element which directs the enzyme to a target site, optionally a genomic safe harbor site (GSHS), wherein the enzyme is a piggyBac transposase which comprises one or more mutations which cause decreased or ablated integration activity relative to an enzyme comprising an amino acid sequence of SEQ ID NO:11 or functional equivalent thereof.
The recitation “optionally” is interpreted as not requiring the limitations following the recitation. Therefore, the BRI of the claims is that any limitation following the word optionally is not required to be taught or present in the prior art.
Sanchez-Meijas et al. is directed to targeted gene editing constructs and methods of using the same. Claimed is a nucleic acid construct comprising a first polynucleotide sequence encoding a first DNA binding protein which is either a zinc finger protein or a Cas9 protein and a second polynucleotide sequence encoding a second DNA binding protein which is a hyperactive PiggyBac transposase and c) an optional polynucleotide sequence comprising a nucleic acid encoding a linker wherein the nucleic acid construct encodes a fusion protein comprising the first and second DNA binding protein and optional linker (claim 1). Cas9 protein is expressly claimed (claim 2). A specific modified hyperactive PiggyBac transposase comprises an amino acid sequence which includes SEQ ID NO: 122 (claim 13).
Thus, Sanchez-Meijas et al. expressly discloses a composition (i.e. construct) comprising a piggyBac transposase and a Cas (targeting element).
Regarding the claimed sequence of the piggyBac transposases. Sanchez-Meijas et al. expressly teaches SEQ ID No: 122. As shown in the alignment below, SEQ ID No: 122 contains a substitution at position 30 (V in place of I); position 347 (A in place of N).
PNG
media_image1.png
338
669
media_image1.png
Greyscale
PNG
media_image2.png
732
724
media_image2.png
Greyscale
Therefore, in order to arrive at the instantly claimed invention, one merely has to select SEQ ID NO: 122 out of a list of 10 different sequences. Thus, anticipating, claims 1-2, 9, 27, 36,
Where selection of one named species from a list of alternatives is all that isrequired to arrive at the instantly claimed subject matter, that species is anticipated. Ex Parte A., 17 USPQ2d 1716 (Bd. Pat. App. & Inter. 1990). See also In re Sivaramakrishnan, 213 USPQ 441 (CCPA 1982). MPEP 2131.02
Regarding the claimed decreased or ablated integration activity, firstly, Sanchez-Meijas et al. teaches the same mutation (i.e. substitution at position 30 (V in place of I); position 347 (A in place of N)).
Regarding claims 14-15, 18, 22 Sanchez-Meijas et al. expressly claims fusion of the Cas9 and PiggyBac. As expressly claimed the 3’ end of the first polynucleotide (i.e. Cas9) is connected to the 5’ end of the second polynucleotide (PiggyBac)
Regarding claim 33, 37, 40, Sanchez-Meijas et al. claims a method for controlled, site-specific integration of a single copy or multiple copies of an exogenous nucleic acid sequence into a cell. The method comprises delivery the nucleic acid construct to the cell (i.e. contacting a cell with the fusion protein of Cas9-PiggyBac), delivering the exogenous nucleic acid to cell wherein binding of the fusion protein to the specific genomic DNA sequence in the genome of the cell, results in cleavage of the genome and integration of one or more copies of the exogenous nucleic acid into the genome of the cell (claim 23).
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 of this title, if the differences between the claimed invention and the prior art are such that the claimed invention as a whole would have been obvious before the effective filing date of the claimed invention to a person having ordinary skill in the art to which the claimed invention pertains. Patentability shall not be negated by the manner in which the invention was made.
The factual inquiries set forth in Graham v. John Deere Co., 383 U.S. 1, 148 USPQ 459 (1966), that are applied for establishing a background for determining obviousness under 35 U.S.C. 103 are summarized as follows:
1. Determining the scope and contents of the prior art.
2. Ascertaining the differences between the prior art and the claims at issue.
3. Resolving the level of ordinary skill in the pertinent art.
4. Considering objective evidence present in the application indicating obviousness or nonobviousness.
This application currently names joint inventors. In considering patentability of the claims the examiner presumes that the subject matter of the various claims was commonly owned as of the effective filing date of the claimed invention(s) absent any evidence to the contrary. Applicant is advised of the obligation under 37 CFR 1.56 to point out the inventor and effective filing dates of each claim that was not commonly owned as of the effective filing date of the later invention in order for the examiner to consider the applicability of 35 U.S.C. 102(b)(2)(C) for any potential 35 U.S.C. 102(a)(2) prior art against the later invention.
Claims 30, 32 and 38-39 are rejected under 35 U.S.C. 103 as being unpatentable over Sanchez-Mejias et al. (WO2020250181) as applied to claims 1-2, 9, 14-15, 18, 22, 27, 33, 36-37 and 40 above.
Applicant Claims
The instant application claims the enzyme comprises an insertion at a position corresponding to V371-I378, Y312-V322, K407-M413, S385-T392, A424-K432, and/or R275-K290 or position E71, K93, T105, V390, R315, G321, R376, S387, K409, and/or E428 with reference to SEQ ID NO:11.
The instant application claims the composition is in the form of lipid nanoparticle.
Determination of the Scope and Content of the Prior Art
(MPEP §2141.01)
The teachings of Sanchez-Mejias et al. et al. are set forth above. A host cell comprising the nucleic acid construct or the vector is claimed (claim 18). It is taught that in some embodiments, the composition is viral-free and the packaging vector is a nanoparticle e.g. a polymeric or lipid nanoparticle (paragraph 0235). The term mutation refers to a substitution of a residue within a sequence with another residue, or a deletion or insertion of one or more residues within a sequence (paragraph 0077).
Ascertainment of the Difference Between Scope the Prior Art and the Claims
(MPEP §2141.02)
While Sanchez-Mejias et al. suggest lipid nanoparticles, Sanchez-Mejias et al. does not expressly exemplify lipid nanoparticles with the nucleic acid construct.
Finding of Prima Facie Obviousness Rationale and Motivation
(MPEP §2142-2143)
It would have been obvious to one of ordinary skill in the art before the effective filing date of the claimed invention to utilize lipid nanoparticles. One skilled in the art would have been motivated to utilize lipid nanoparticles as the packaging vector for the nucleic acid construct as Sanchez-Mejias et al. teaches that this is one option to package the construct. Therefore, all of the claimed elements were known in the prior art and one skilled in the art could have combined the elements as claimed by known methods with no change in their respective functions and the combination would have yielded predictable results to one of ordinary skill in the art at the time of the invention. Note: MPEP 2143 KSR International Co. v. Teleflex Inc., 550 US 398, 82 USPQ 2d 1385 (2007).
Regarding claim 32, Sanchez-Meijas et al. teaches a host cell. Therefore, use of the lipid nanoparticles as the packaging vector in combination with the expressly taught host cell renders claim 32 obvious.
Claims 17 and 20 are rejected under 35 U.S.C. 103 as being unpatentable over Sanchez-Mejias et al. (WO2020250181) as applied to claims 1-2, 9, 14-15, 18, 22, 27, 30, 32-33 and 36-40 above in view of Ostertag et al. (US Patent No. 10131885).
Applicant Claims
The instant application claims the enzyme comprises an insertion at a position corresponding to V371-I378, Y312-V322, K407-M413, S385-T392, A424-K432, and/or R275-K290 or position E71, K93, T105, V390, R315, G321, R376, S387, K409, and/or E428 with reference to SEQ ID NO:11.
Determination of the Scope and Content of the Prior Art
(MPEP §2141.01)
The teachings of Sanchez-Mejias et al. are set forth above. A host cell comprising the nucleic acid construct or the vector is claimed (claim 18). It is taught that in some embodiments, the composition is viral-free and the packaging vector is a nanoparticle e.g. a polymeric or lipid nanoparticle (paragraph 0235). The term mutation refers to a substitution of a residue within a sequence with another residue, or a deletion or insertion of one or more residues within a sequence (paragraph 0077). Mutation at amino acids such as 315 is taught (claim 8).
Ascertainment of the Difference Between Scope the Prior Art and the Claims
(MPEP §2141.02)
While Sanchez-Mejias et al. teaches mutations includes insertions, Sanchez-Mejias et al. does not expressly teach an insertion. However, this deficiency is cured by Ostertag et al.
Ostertag et al. is directed to a hyperactive piggyBac transposases. These hyperactive PiggyBac transposases are intended to include polypeptides bearing one or more insertions, deletions or substitutions of amino acid residues (column 8, lines 44-50). Positions in which mutations can occur include 315, 319, 282, etc. (table 2).
Finding of Prima Facie Obviousness Rationale and Motivation
(MPEP §2142-2143)
It would have been obvious to one of ordinary skill in the art before the effective filing date of the claimed invention to combine the teachings of Sanchez-Mejias et al. and Ostertag et al. and form a PiggyBac transposase with an insertion at position 315 (i.e. falling within Y312-V322 or R315). One skilled in the art would have been motivated to utilize an insertion as both Sanchez-Mejias et al. and Ostertag et al. teaches that mutations of the PiggyBac include insertions and both teach that this position is a position which can be mutated. Thus, absent a demonstration of the criticality, one skilled in the art would have been motivated to insert any amino acid at any of the specifically taught mutation positions with a reasonable expectation of success.
Claims 10 and 23 are rejected under 35 U.S.C. 103 as being unpatentable over Sanchez-Mejias et al. (WO2020250181) as applied to claims 1-2, 9, 14-15, 18, 22, 27, 30, 32-33 and 36-40 above and in further view of Craig (US Patent No. 10415022).
Applicant Claims
The instant application claims the piggyBac transposase further comprises a deletion of about 5 to about 190 amino acids from the N-terminus and/or C-terminus of the polypeptide having an amino acid sequence of SEQ ID NO: 11.
Determination of the Scope and Content of the Prior Art
(MPEP §2141.01)
The teachings of Sanchez-Mejias et al. are set forth above. A host cell comprising the nucleic acid construct or the vector is claimed (claim 18). It is taught that in some embodiments, the composition is viral-free and the packaging vector is a nanoparticle e.g. a polymeric or lipid nanoparticle (paragraph 0235). The term mutation refers to a substitution of a residue within a sequence with another residue, or a deletion or insertion of one or more residues within a sequence (paragraph 0077).
Ascertainment of the Difference Between Scope the Prior Art and the Claims
(MPEP §2141.02)
While Sanchez-Mejias et al. teaches that the mutation includes a deletion, Sanchez-Mejias et al. does not expressly teach a deletion of amino acids from the N-terminus. However, this deficiency is cured by Craig.
Craig is directed to trichoplusia ni piggyBac transposases with reduced integration activity. Claimed is an improved Trichoplusia ni piggyBac transposase comprising a substitution at one or more of amino acid positions 245, 275, 277, 341, 372, 375, and 388 of SEQ ID NO: 52, wherein SEQ ID NO: 52 consists of amino acid residues 181-540 of the wild type Trichoplusia ni piggyBac transposase, and wherein the improved transposase exhibits enhanced piggyBac transposon excision activity and no or significantly diminished piggyBac transposon integration as compared to a wild type Trichoplusia ni piggyBac transposase (claim 1). The piggyBac transposases are taught as hyperactive (abstract).
Finding of Prima Facie Obviousness Rationale and Motivation
(MPEP §2142-2143)
It would have been obvious to one of ordinary skill in the art before the effective filing date of the claimed invention to combine the teachings of Sanchez-Mejias et al. and Craig and utilize the piggyBac transposase of Craig in the nucleic acid construct of Sanchez-Mejias et al. Sanchez-Mejias et al. teaches the use of a hyperactive piggyBac transposases and Craig teaches an improved transposase. Thus, to arrive at the claimed invention all that is required is simple substitution of one piggyBac transposase for another. Note: MPEP 2143.
Regarding the claimed sequence. As shown below, SEQ ID NO: 52 of Craig has a deletion of amino acids 1-180 whereas the rest of the sequence corresponds to instantly claimed SEQ ID NO: 11:
PNG
media_image3.png
804
863
media_image3.png
Greyscale
As recited in claim 1 of Craig, the amino acid at position 245 of SEQ ID NO: 52 can be substituted. This corresponds to a substitution at amino acid 425 of instantly claimed SEQ ID No: 11. Thus, use of the transposase of Craig not only include a N-terminal deletion but also a substitution as a position claimed.
Double Patenting
The nonstatutory double patenting rejection is based on a judicially created doctrine grounded in public policy (a policy reflected in the statute) so as to prevent the unjustified or improper timewise extension of the “right to exclude” granted by a patent and to prevent possible harassment by multiple assignees. A nonstatutory double patenting rejection is appropriate where the conflicting claims are not identical, but at least one examined application claim is not patentably distinct from the reference claim(s) because the examined application claim is either anticipated by, or would have been obvious over, the reference claim(s). See, e.g., In re Berg, 140 F.3d 1428, 46 USPQ2d 1226 (Fed. Cir. 1998); In re Goodman, 11 F.3d 1046, 29 USPQ2d 2010 (Fed. Cir. 1993); In re Longi, 759 F.2d 887, 225 USPQ 645 (Fed. Cir. 1985); In re Van Ornum, 686 F.2d 937, 214 USPQ 761 (CCPA 1982); In re Vogel, 422 F.2d 438, 164 USPQ 619 (CCPA 1970); In re Thorington, 418 F.2d 528, 163 USPQ 644 (CCPA 1969).
A timely filed terminal disclaimer in compliance with 37 CFR 1.321(c) or 1.321(d) may be used to overcome an actual or provisional rejection based on nonstatutory double patenting provided the reference application or patent either is shown to be commonly owned with the examined application, or claims an invention made as a result of activities undertaken within the scope of a joint research agreement. See MPEP § 717.02 for applications subject to examination under the first inventor to file provisions of the AIA as explained in MPEP § 2159. See MPEP § 2146 et seq. for applications not subject to examination under the first inventor to file provisions of the AIA . A terminal disclaimer must be signed in compliance with 37 CFR 1.321(b).
The filing of a terminal disclaimer by itself is not a complete reply to a nonstatutory double patenting (NSDP) rejection. A complete reply requires that the terminal disclaimer be accompanied by a reply requesting reconsideration of the prior Office action. Even where the NSDP rejection is provisional the reply must be complete. See MPEP § 804, subsection I.B.1. For a reply to a non-final Office action, see 37 CFR 1.111(a). For a reply to final Office action, see 37 CFR 1.113(c). A request for reconsideration while not provided for in 37 CFR 1.113(c) may be filed after final for consideration. See MPEP §§ 706.07(e) and 714.13.
The USPTO Internet website contains terminal disclaimer forms which may be used. Please visit www.uspto.gov/patent/patents-forms. The actual filing date of the application in which the form is filed determines what form (e.g., PTO/SB/25, PTO/SB/26, PTO/AIA /25, or PTO/AIA /26) should be used. A web-based eTerminal Disclaimer may be filled out completely online using web-screens. An eTerminal Disclaimer that meets all requirements is auto-processed and approved immediately upon submission. For more information about eTerminal Disclaimers, refer to www.uspto.gov/patents/apply/applying-online/eterminal-disclaimer.
Claims 1-2, 9-10, 14-15, 17-18, 20, 22-23, 27, 30, 32-33 and 36-40 are rejected on the ground of nonstatutory double patenting as being unpatentable over claims 1-12 of U.S. Patent No. 9783790 in view of Sanchez-Meijas et al. Although the conflicting claims are not identical, they are not patentably distinct from each other because both sets of claims overlap in scope.
The instant application claims a composition comprising an enzyme and a targeting element which directs the enzyme to a target site, optionally a genomic safe harbor site (GSHS), wherein the enzyme is a piggyBac transposase which comprises one or more mutations which cause decreased or ablated integration activity relative to an enzyme comprising an amino acid sequence of SEQ ID NO:11 or functional equivalent thereof.
Patent ‘790 claims a mutagenized Trichoplusia ni piggyBac transposase mutagenized to exhibit enhanced piggyBac transposon excision activity and no or significantly diminished piggyBac transposon integration as compared to a wild type Trichoplusia ni piggyBac transposase comprising replacement in SEQ ID NO:52 of one or more arginines at amino acid positions 65, 95, 97, 135, 161, 192, and 208 with alanine or glutamate, and/or one or more lysines at amino acid positions 176 and 195 with alanine or glutamate, and wherein said SEQ ID NO:52 is amino acid residues 181-540 of said wild type Trichoplusia ni piggyBac transposase.
As shown in the alignment below, SEQ ID No: 52 has 100% identity with instantly claimed SEQ ID NO: 11 except amino acids 1-180 are removed. A substitution at position 208 which corresponds to position 388 of SEQ ID NO: 11 is taught.
Regarding claim 36, taught is replacement of aspartate at amino acid position 270 in SEQ ID NO: 52 with asparagine. This corresponds to position 450 in SEQ ID NO: 11 instantly claimed.
PNG
media_image4.png
764
889
media_image4.png
Greyscale
While Patent ‘790 claims a piggyBac transposase reading on the instant claimed, Patent ‘790 does not claim a targeting element. However, this deficiency is cured by Sanchez-Mejias et al.
Sanchez-Meijas et al. is directed to targeted gene editing constructs and methods of using the same. Claimed is a nucleic acid construct comprising a first polynucleotide sequence encoding a first DNA binding protein which is either a zinc finger protein or a Cas9 protein and a second polynucleotide sequence encoding a second DNA binding protein which is a hyperactive PiggyBac transposase and c) an optional polynucleotide sequence comprising a nucleic acid encoding a linker wherein the nucleic acid construct encodes a fusion protein comprising the first and second DNA binding protein and optional linker (claim 1). Cas9 protein is expressly claimed (claim 2). A specific modified hyperactive PiggyBac transposase comprises an amino acid sequence which includes SEQ ID NO: 122 (claim 13). A host cell comprising the nucleic acid construct or the vector is claimed (claim 18). It is taught that in some embodiments, the composition is viral-free and the packaging vector is a nanoparticle e.g. a polymeric or lipid nanoparticle (paragraph 0235). The term mutation refers to a substitution of a residue within a sequence with another residue, or a deletion or insertion of one or more residues within a sequence (paragraph 0077).
It would have been obvious to one of ordinary skill in the art before the effective filing date of the claimed invention to combine the teachings of Sanchez-Meijas et al. and Patent ‘790 and utilize the piggyBac transposase of Patent ‘790 with the nucleic acid construct of Sanchez-Meijas et al. Sanchez-Meijas et al. teaches the use of a hyperactive piggyBac transposases and Patent ‘790 claims an improved transposase. One skilled in the art would have been motivated to utilize the nucleic acid construct of Sanchez-Meijas et al. in order to deliver a fusion protein to a cell. Since Sanchez-Meijas et al. teaches the use of a piggyBac transposase there is a reasonable expectation of success.
Regarding claim 9, Sanchez-Meijas et al. teaches Cas9.
Regarding claims 14-15, 18, 22 Sanchez-Meijas et al. expressly claims fusion of the Cas9 and PiggyBac. As expressly claimed the 3’ end of the first polynucleotide (i.e. Cas9) is connected to the 5’ end of the second polynucleotide (PiggyBac).
Regarding claims 17 and 20, as claimed is replacing arginines at position 135 with alanine or glutamate (claim 1). This corresponds to R315 of SEQ ID NO: 11. Sanchez-Meijas et al. teaches that mutations include insertions. Therefore, absent a demonstration of critically, it would have been obvious to combine the teachings of Patent ‘790 and Sanchez-Meijas et al. and insert any amino acid at any of the specifically taught mutation positions with a reasonable expectation of success.
Regarding claim 33, 37, 40, Sanchez-Meijas et al. claims a method for controlled, site-specific integration of a single copy or multiple copies of an exogenous nucleic acid sequence into a cell. The method comprises delivery the nucleic acid construct to the cell (i.e. contacting a cell with the fusion protein of Cas9-PiggyBac), delivering the exogenous nucleic acid to cell wherein binding of the fusion protein to the specific genomic DNA sequence in the genome of the cell, results in cleavage of the genome and integration of one or more copies of the exogenous nucleic acid into the genome of the cell (claim 23).
Regarding claims 30, 32 and 38-39, it would have been obvious to one of ordinary skill in the art before the effective filing date of the claimed invention to utilize lipid nanoparticles. One skilled in the art would have been motivated to utilize lipid nanoparticles as the packaging vector for the nucleic acid construct as Sanchez-Mejias et al. teaches that this is one option to package the construct. Therefore, all of the claimed elements were known in the prior art and one skilled in the art could have combined the elements as claimed by known methods with no change in their respective functions and the combination would have yielded predictable results to one of ordinary skill in the art at the time of the invention. Note: MPEP 2143 KSR International Co. v. Teleflex Inc., 550 US 398, 82 USPQ 2d 1385 (2007).
Regarding claim 32, Sanchez-Meijas et al. teaches a host cell. Therefore, use of the lipid nanoparticles as the packaging vector in combination with the expressly taught host cell renders claim 32 obvious.
Claims 1-2, 9-10, 14-15, 18, 22-23, 27, 30, 32-33 and 37-40 are rejected on the ground of nonstatutory double patenting as being unpatentable over claims 1-7 of U.S. Patent No. 10415022 in view of Sanchez-Meijas et al. Although the conflicting claims are not identical, they are not patentably distinct from each other because both sets of claims overlap in scope.
The instant claims are set forth above.
Patent ‘022 claims a improved Trichoplusia ni piggyBac transposase comprising a substitution at one or more of amino acid positions 245, 275, 277, 341, 372, 375, and 388 of SEQ ID NO: 52, wherein SEQ ID NO: 52 consists of amino acid residues 181-540 of the wild type Trichoplusia ni piggyBac transposase, and wherein the improved transposase exhibits enhanced piggyBac transposon excision activity and no or significantly diminished piggyBac transposon integration as compared to a wild type Trichoplusia ni piggyBac transposase.
Regarding the claimed sequence. As shown below, SEQ ID NO: 52 of Patent ‘022 has a deletion of amino acids 1-180 whereas the rest of the sequence corresponds to instantly claimed SEQ ID NO: 11:
PNG
media_image3.png
804
863
media_image3.png
Greyscale
As recited in claim 1 of Patent ‘022, the amino acid at position 245 of SEQ ID NO: 52 can be substituted. This corresponds to a substitution at amino acid 425 of instantly claimed SEQ ID No: 11. Thus, use of the transposase of Patent ‘022 not only include a N-terminal deletion but also a substitution at a position claimed.
While Patent ‘022 claims a piggyBac transposase reading on the instant claimed, Patent ‘022 does not claim a targeting element. However, this deficiency is cured by Sanchez-Mejias et al.
The teachings of Sanchez-Meijas et al. are set forth above.
It would have been obvious to one of ordinary skill in the art before the effective filing date of the claimed invention to combine the teachings of Sanchez-Meijas et al. and Patent ‘022 and utilize the piggyBac transposase of Patent ‘022 with the nucleic acid construct of Sanchez-Meijas et al. Sanchez-Meijas et al. teaches the use of a hyperactive piggyBac transposases and Patent ‘022 claims an improved transposase. One skilled in the art would have been motivated to utilize the nucleic acid construct of Sanchez-Meijas et al. in order to deliver a fusion protein to a cell. Since Sanchez-Meijas et al. teaches the use of a piggyBac transposase there is a reasonable expectation of success.
Regarding claim 9, Sanchez-Meijas et al. teaches Cas9.
Regarding claims 14-15, 18, 22 Sanchez-Meijas et al. expressly claims fusion of the Cas9 and PiggyBac. As expressly claimed the 3’ end of the first polynucleotide (i.e. Cas9) is connected to the 5’ end of the second polynucleotide (PiggyBac).
Regarding claim 33, 37, 40, Sanchez-Meijas et al. claims a method for controlled, site-specific integration of a single copy or multiple copies of an exogenous nucleic acid sequence into a cell. The method comprises delivery the nucleic acid construct to the cell (i.e. contacting a cell with the fusion protein of Cas9-PiggyBac), delivering the exogenous nucleic acid to cell wherein binding of the fusion protein to the specific genomic DNA sequence in the genome of the cell, results in cleavage of the genome and integration of one or more copies of the exogenous nucleic acid into the genome of the cell (claim 23).
Regarding claims 30, 32 and 38-39,t would have been obvious to one of ordinary skill in the art before the effective filing date of the claimed invention to utilize lipid nanoparticles. One skilled in the art would have been motivated to utilize lipid nanoparticles as the packaging vector for the nucleic acid construct as Sanchez-Mejias et al. teaches that this is one option to package the construct. Therefore, all of the claimed elements were known in the prior art and one skilled in the art could have combined the elements as claimed by known methods with no change in their respective functions and the combination would have yielded predictable results to one of ordinary skill in the art at the time of the invention. Note: MPEP 2143 KSR International Co. v. Teleflex Inc., 550 US 398, 82 USPQ 2d 1385 (2007).
Regarding claim 32, Sanchez-Meijas et al. teaches a host cell. Therefore, use of the lipid nanoparticles as the packaging vector in combination with the expressly taught host cell renders claim 32 obvious.
Claims 1-2, 9-10, 14-15, 17-18, 20, 22-23, 27, 30, 32-33 and 36-40 are provisionally rejected on the ground of nonstatutory double patenting as being unpatentable over claims 99-118 of copending Application No. 19480506. Although the conflicting claims are not identical, they are not patentably distinct from each other because both sets of claims overlap in scope.
This is a provisional nonstatutory double patenting rejection because the patentably indistinct claims have not in fact been patented.
The instant claims are set forth above.
Copending ‘506 claims a composition comprising a transposase enzyme or a nucleic acid encoding the transposase enzyme, wherein the transposase enzyme comprises an amino acid sequence having at least about 80% sequence identity to SEQ ID NO:1, and wherein the transposase enzyme comprises an amino acid substitution at one or more of positions N374X, K375X, R315X, L324X, N347X, R372X, S373X, R376X, E377X, K409X, and/or K412X of SEQ ID NO:1, or an amino acid substitution at a position corresponding thereto, optionally wherein the amino acid substitution comprises N374A, N374S, N374K, N374H, N374E, N374Q, N374G, N374F, N374Y, N374L, N374W, K375A, K375S, K375Q, K375H, K375L, K375W, K375G, K375E, K375F, K375Y, R315A, R315K, R315S, R315E, R315Q, R315G, R315L, R315H, R315F, R315Y, L324A, N347A, N347D, R372A, R372K, R372H, R372S, R372Q, S373A, S373K, S373H, S373E, S373D, S373Q, S373G S373F, S373Y, S373L, S373R, R376A, R376K, R376E, R376S, R376Q, R376G, R376A, R376L, R376H, E377A, K409A, K409R, K409S, or K412R. As claimed the transposase enzyme further comprises a deletion of about 30 to about 100 amino acids from the N-terminus and/or C-terminus. As claimed the transposase enzyme further comprises a targeting element which can be a Cas enzyme. Claimed is a linker connecting the transposase and the targeting element. The linker can be inserted within the transposase enzyme selected from V390, R315, etc. A host cell and lipid nanoparticles are claimed. A method for inserting a gene into the genome of a cell is claimed.
As shown in the alignment below, SEQ ID NO: 1 has 100% identity with instantly claimed SEQ ID NO: 11:
PNG
media_image5.png
328
710
media_image5.png
Greyscale
PNG
media_image6.png
740
775
media_image6.png
Greyscale
Therefore, the scopes of the copending claims and the instant application overlap and thus they are obvious variants of one another as both claim overlapping substitutions and insertions of the piggyBac transposase.
Conclusion
Any inquiry concerning this communication or earlier communications from the examiner should be directed to ABIGAIL VANHORN whose telephone number is (571)270-3502. The examiner can normally be reached M-Th 6 am-4 pm EST.
Examiner interviews are available via telephone, in-person, and video conferencing using a USPTO supplied web-based collaboration tool. To schedule an interview, applicant is encouraged to use the USPTO Automated Interview Request (AIR) at http://www.uspto.gov/interviewpractice.
If attempts to reach the examiner by telephone are unsuccessful, the examiner’s supervisor, Neil Hammell can be reached on 571-270-5919. The fax phone number for the organization where this application or proceeding is assigned is 571-273-8300.
Information regarding the status of published or unpublished applications may be obtained from Patent Center. Unpublished application information in Patent Center is available to registered users. To file and manage patent submissions in Patent Center, visit: https://patentcenter.uspto.gov. Visit https://www.uspto.gov/patents/apply/patent-center for more information about Patent Center and https://www.uspto.gov/patents/docx for information about filing in DOCX format. For additional questions, contact the Electronic Business Center (EBC) at 866-217-9197 (toll-free). If you would like assistance from a USPTO Customer Service Representative, call 800-786-9199 (IN USA OR CANADA) or 571-272-1000.
/ABIGAIL VANHORN/Primary Examiner, Art Unit 1636
Prosecution Insights