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 the Claims:
Claims 1-26 and 31-34 are cancelled. Claims 27-30 and 35-44 are pending and are being examined. Claims 45-47 are withdrawn as being directed to unelected group.
Claim Interpretation
Optional embodiments are not required by the claim, and are not considered for patentability as they are not required elements. For example, section (c) of claim 1 requires an optional polynucleotide linker is not being considered for patentability.
WITHDRAWN REJECTIONS
Claim Rejections - 35 USC § 112
Claims 27-44 were rejected under 35 U.S.C. 112(b) or 35 U.S.C. 112 (pre-AIA ), second paragraph, as failing to set forth 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.
The rejection of the term “improved” in claim 27 is withdrawn following cancellation of the term.
The term “hyperactive piggybac” as used in claims 27, 31-38 were rejected as it was not a common, art recognized term.
The rejection is withdrawn following cancellation of the rejected term.
Claims 27, and 31-37 were rejected for containing the trademark/trade name, “PiggyBac.”
The rejection is withdrawn following cancellation of the term.
The term “higher” in claim 37 was rejected for being a relative term which rendered the claim indefinite.
The rejection is withdrawn following the cancellation of the term.
Claim 42 required the nucleic acid composition of claim 41 to be in the form of RNA, DNA or protein.
The rejection is withdrawn following clarification that the nucleic acid is in the form of RNA or DNA.
Claim Rejections - 35 USC § 103
Claim 27, 30, 38, 39, 40 and 44 were rejected under 35 U.S.C. 103 as being unpatentable over Shrock et al (WO2018175872A1; Hereinafter "Shrock;" Published Sep. 27, 2018; See PTO-892).
Claim 29 was rejected under 35 U.S.C. 103 as being unpatentable over Shrock et al (WO2018175872A1; Hereinafter "Shrock;" Published Sep. 27, 2018; See PTO-892) in view of Chen et al (Adv Drug Deliv Rev. 2013 Oct; hereinafter “Chen”; See PTO-892).
Claim 31-34 were rejected under 35 U.S.C. 103 as being unpatentable over Shrock et al (WO2018175872A1; Hereinafter "Shrock;" Published Sep. 27, 2018; See PTO-892) in view of Li et al (Proc Natl Acad Sci U S A. 2013 Jun 18; Hereinafter “Li;” See PTO-892)
Claim 36-37 were rejected under 35 U.S.C. 103 as being unpatentable over Shrock et al (WO2018175872A1; Hereinafter "Shrock;" Published Sep. 27, 2018; See PTO-892) in view of Wu et al (US20180320196A1; Published Nov 8, 2018; Hereinafter “Wu;” See PTO-892).
The rejections are withdrawn following claim amendments. New rejections are set forth below.
MAINTAINED REJECTIONS
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.
Claim 37 is 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 applications subject to pre-AIA 35 U.S.C. 112, the inventor(s), at the time the application was filed, had possession of the claimed invention.
The specification does not enable any person skilled in the art to which it pertains, or with which it is most nearly connected, to use the invention commensurate in scope with these claims.
Claim 37 recites: “The nucleic acid construct of claim 27, wherein the modified hyperactive PiggyBac transposase comprises an amino acid sequence having at least 95% identical to a sequence selected from the group consisting of SEQ ID NO: 119, 120, 121, 122, 123, 124, 125, 126, 127, 128 and 129, wherein the modified hyperactive PiggyBac shows higher specificity of DNA integration into a genome compared to hyperactive PiggyBac.”
Claim 37 is directed to all amino acid sequences having at least 95% identities to SEQ ID NOs: 119-129 which have higher specificity of DNA integration into a genome compared to hyperactive PiggyBac. It is also pointed out the current wording of the claim encompasses substitutions, deletions, and insertion mutations or combinations thereof.
This claimed composition encompasses all amino acid sequences having at least 95% identities and have higher specificity of DNA integration into a genome compared to hyperactive PiggyBac. However, Applicant’s specification only described polypeptides comprising SEQ ID NOs: 119-129. Applicant’s claim encompasses a large number of amino acid sequences. For example, there can be up to
594
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30
=
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different polypeptide sequences, if only substitutions were considered. It is reiterated that claim encompasses substitutions, deletions, and insertion mutations or combinations thereof, which results in a much greater number of polypeptides than
6.68
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. Applicant’s disclosure does not provide support for all polypeptides having amino acid combinations that can result in 98% identity to SEQ ID NOs: 119-129 with higher specificity of DNA integration into a genome compared to hyperactive PiggyBac to support the instant claims. Table 3 of Applicant’s disclosure at most only showed mutations of 38 amino acids and substituted to only specific amino acids, not any amino acid as currently encompassed by the claim (such as Alanine at position 245 or Asn at position 346 etc.). It is inconceivable that applicants had support for all the claimed polypeptides, even with the indicated support. Thus, Applicants were not in possession of the full scope of the claimed invention at the time of filing of the instant invention.
The specification as filed does not provide sufficient evidence that Applicants were in possession of the full scope of the claimed invention at the time of filing of the instant invention. In order to practice the claimed invention, the skilled artisan would have to define how every single amino acid is altered and determine its effect on the protein as a whole.
Response to Arguments: Applicant’s arguments that the specification discloses a “representative” species of 30 polypeptides to claim a genus of more than
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polypeptides is not persuasive. It is maintained that showing a limited number of examples or a library screen does not demonstrate possession of all sequences covered by the claim. Structural features and functional regions do not provide guidance for the combinatorial space of substitutions. Additionally, speculative statements regarding “neutral” substitutions outside the functional regions are not sufficient to establish possession.
Claim 37 is rejected under 35 USC 112(a) as failing to comply with the enablement requirement.
The claim contains subject matter which was not described in the specification in such a way as to enable one skilled in the art to which it pertains, or with which it is most nearly connected, to make and/or use the invention.
Applicant's specification is found enabling for a nucleic acid encoding a Cas9-hyperactive transposase fusion protein, wherein the hyperactive transposase comprises SEQ ID NO: 119-129.
Applicant's specification is not found to be enabling for a nucleic acid encoding a Cas9-hyperactive transposase fusion protein, wherein the hyperactive transposase comprises 95% identity to SEQ ID NO: 119-129, wherein the modified hyperactive PiggyBac shows higher specificity of DNA integration into a genome compared to hyperactive PiggyBac. The specification does not enable any person skilled in the art to which it pertains, or with which it is most nearly connected, to carry out the method of the invention commensurate in scope with the current claims.
Analysis of whether a particular claim is supported by the disclosure in an application requires a determination of whether that disclosure, when filed, contained sufficient information regarding the subject matter of the claims as to enable one skilled in the pertinent art to make and use the claimed invention without undue or unreasonable experimentation. See Mineral Separation v. Hyde, 242 U.S. 261, 270 (1916). The key word is 'undue,' not experimentation.' " (Wands, 8 USPQ2d 1404). The factors to be considered in determining whether undue experimentation is required are summarized In re Wands 858 F.2d 731, 8 USPQ2nd 1400 (Fed. Cir, 1988). The factors to be considered in determining whether undue experimentation is required include: (1) the quantity of experimentation necessary, (2) the amount or direction or guidance presented, (3) the presence or absence of working examples, (4) the nature of the invention, (5) the state of the 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. While all these factors are considered, a sufficient number are discussed below so as to create a prima facie case.
Applicants' claims are directed to any and all transposases that are 87% identical to the claimed sequences and have higher specificity of DNA integration into a genome compared to hyperactive PiggyBac. The breadth of the claims includes variants (including substitution, deletion, insertions or combinations thereof) other than the ones described in the specification and variants that are not yet discovered.
The specification provides examples of some Cas9-transposase (such as piggybac transposases or SB transposases) (5 in total) in cloning vectors. Next targeted insertion was probed in HEK293T cells. Several regions in the PBase were probes (~ 41, with specific amino acids) and were fused to ZFP. Applicants also described generation of library of hyperactive Piggybac transposases and validation by probing genomic integration.
At the time the invention was made it was known that piggybac transposase could be modified to generate excision positive and integration negative variants and can be fused to Cas9 or ZFP for efficient, targeted genomic integration of genes of interest (See Li Fig. 7; See Shrock Example I.) However, the prior art acknowledged that not all known PBase variants have been discovered. (See for example, evidence in Hew et al p. 10, col. 1, para 4). Therefore, there was a recognized level of unpredictability with regards to PBase mutations.
Due to the lack of teachings in the art regarding all the mutants and variants of PBases that 95% identical or higher to SEQ ID NOs: 119-129, when fused to Cas9 will result in, higher specificity of DNA integration into a genome compared to hyperactive PiggyBac and the recognized unpredictability in the area of genome engineering, a large amount of guidance and teachings would be necessary in order to be enabling for methods of such.
Guidance and teachings provided by Applicants in the instant specification is limited to disclosure that some generated variants resulted in higher integration efficiency (mutant combinations tested (“R245A/G325A/D450N/S573P) had a great increase of the targeted insertion being up to 30% of total integrative events instead of a 3% percent in the hyPB fusion” in Example 20). The Examiner acknowledges that the Office does not require the presence of working examples to be present in the disclosure of the invention (see MPEP §2164.02). However, in light of the state of the art, discussed above, which recognizes a high level of unpredictability in the field of genetic engineering using Cas9-transposase aided genetic engineering, and limited teachings with regards to various variants of hyperactive PBases, the Office would require appropriate disclosure to support the contention that Applicant’s disclosure adequately described the claimed composition. The amount of guidance or direction needed to enable the invention is inversely related to the amount of knowledge in the state of the art as well as the predictability in the art. In re Fisher, 427 F.2d 833, 839, 166 USPQ 18, 24 (CCPA 1970). Thus, due to the high level of unpredictability in the art, the current specification would have to provide greater amounts of teachings and guidance directed to methods of carrying out the claimed invention.
Therefore, due to the sum of all the aforementioned factors, one of ordinary skill in the art, at the time the invention was made, would not expect success arriving at the claimed compositions of 95% identical sequences of all SEQ ID NOs: 119-129. Given that the art fails to recognize and Applicant has failed to demonstrate any guidance of any and all mutations of PBases , the skilled artisan would be faced with the impermissible burden of undue experimentation in order to practice the claimed invention using any species of the claimed PBases. Accordingly, claims 37 is deemed properly rejected.
Response to Arguments: Applicants argued that fusion proteins comprising Cas9 and modified transposase were shown to experimentally perform targeted gene editing with improved insertion specificity. The Applicants indicated that a skilled artisan could easily make and use the claimed variants without undue experimentation, relying on the library screens and structure-function discussions and argued that the substitutions throughout the sequence are predictable in effect. It is noted that the claim covers 30 amino acids across 594 residues, actually representing
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polypeptides. It is submitted that functional consequences of most substitutions of a protein are not predictable. The specification only provides a small number of tested sequences. There is no experimental evidence that all substitutions across non-critical regions retain integration or specificity. The specification does not provide a person of ordinary skill in the art to make and use the full scope of sequences without undue experimentation. Under 35 U.S.C 112(a), the specification must demonstrate possession and enablement of the claimed subject matter across the full scope; speculation or expectation alone is not sufficient.
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.
Claim 27-28, 31-35 and 44 are provisionally rejected on the ground of nonstatutory double patenting as being unpatentable over claims 1-18, and 20-21 of copending Application No. 18/258,039 (reference application).
Although the claims at issue are not identical, they are not patentably distinct from each other for the following reasons.
This is a provisional nonstatutory double patenting rejection because the patentably indistinct claims have not in fact been patented.
Regarding claims 27-28: Claim 20 of ‘039 application disclosed a nucleic acid encoding a first DNA binding protein capable of binding and cleaving a nucleic acid construct and a second nucleic acid construct comprising a transposase is a modified hyperactive PiggyBac, comprising one or more amino acid mutations as compared to hyperactive PiggyBac of SEQ ID NO: 9. As such the disclosure of claim 1 of ‘039 application reads on the subject matter of claim 27.
Regarding claim 31-35: Claim 8 of ‘039 application disclosed mutations at R275, R277, R347, R372, K375, R376, E377, and/or E380.
Regarding claim 44: Claim 21 of 039 Application recited “method for site specific integration of an exogenous nucleic acid sequence into the genome of a cell, the method comprising delivering to the cell the composition according to claim 1, a guide RNA, and the exogenous nucleic acid”. As such it would have been obvious for a person to arrive at the claimed method of site specific integration using the nucleic acid of claim 27 and an exogenous nucleic acid in view of the steps taught by ‘039 application.
Response to Arguments: Applicants argued that the present application has an effective filing date of June 11, 2020, which is earlier than the effective filing date of December 16, 2021, for the 18/258,039 Application. Consequently, pursuant to M.P.E.P. § 1490(VI)(D) this rejection should be withdrawn.
It is submitted that according to MPEP 804(I)(B)(1)(b)(i) and MPEP 1490(VI)(D)(2)(a), a provisional nonstatutory double patenting rejection is only withdrawn when it is the only rejection remaining in an application having the earliest effective U.S. filing date (taking into account any benefit under 35 U.S.C. 120, 121, 365(c), or 386(c) ) with respect to the conflicting claims); at which point the "provisional" nonstatutory double patenting rejection in the other (later filed) application(s) will be converted into a nonstatutory double patenting rejection when the application with the earliest U.S. effective filing date issues as a patent.
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NEW REJECTIONS
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 (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 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.
The factual inquiries 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.
Claim 27, 30, 38, 39, 40 and 44 are rejected under 35 U.S.C. 103 as being unpatentable over Shrock et al (WO2018175872A1; Hereinafter "Shrock;" Published Sep. 27, 2018; See PTO-892 of 10/07/2025) in view of Li et al (Proc Natl Acad Sci U S A. 2013 Jun 18; Hereinafter “Li;” See PTO-892 of 10/07/2025).
Regarding claims 27-28, 30, 38-40 and 44: Claim 32 of Shrock (WO2018175872A1) disclosed a method of altering a target nucleic acid sequence in a cell using Cas9 fused to a hyperactive piggybac transposase. Cas9 reads on the first polynucleotide sequence. Hyperactive piggybac transposase reads on the claimed (b)(i) element – a second polynucleotide comprising a nucleic acid encoding a second DNA binding protein which enables insertion of an exogenous nucleic acid into a genome, wherein the second DNA binding protein is a hyperactive piggybac transposase. While Shrock did not explicitly teach a nucleic acid encoding a hyperactive piggybac transposase Cas9 fusion protein, Example I of Shrock taught a hyperactive piggyBac transposase sequence downstream of Cas9 was cloned into a pcDNA3.3 backbone vector using Gateway recombination. (this orientation reads on Cas9-piggyback as required by claim 30 and vector of claim 38). A such, Shrock taught a method to arrive at a nucleic acid encoding the Cas9-hyperactive piggybac fusion protein. It is also pointed out that Shrock taught in Example I, [i]n certain embodiments, linkers are included between Cas9 and the hyperactive piggyBac transposase. Shrock also taught integration of GFP in ROSA26 locus of porcine fibroblast cells nucleofected with a Cas9-piggyBac transposase fusion construct, a 20 kb piggyBac transposon (harboring a GFP reporter sequence), and a gRNA targeting the ROSA26 locus of the porcine genome. The porcine fibroblasts nucleofected with a Cas9-piggyBac transposase fusion construct read on claim 39. Additionally successful integration of the GFP reporter requires expression of Cas9-transposase protein as required by claim 40. (Also see Claims 1 and 34 of Shrock). As such Shrock taught a method for controlled site-specific integration of an exogenous nucleic acid by delivering Cas9-transposase and exogenous nucleic acid and resulting in integration of one nucleic acid into the genome of cells.
However, Li taught R372A and D450N mutations in iPB7, a piggyback transposase with I30V, S103P, G165S, M282V, S509G, N570S, N538K (See Li, Fig. 7). Li explicitly taught that engineered ZFPs fused to the iPB7R372A/D450N
can restore the DNA target-binding function and demonstrated preservation of iPB7 integration activity. (See Li E2283, col. 1, para 2, Fig. 7). It is submitted that as both Li and Shrock taught the claimed Cas9 (or ZFN)-transposase construct, and the Li taught the use of claimed mutations, the claimed mutants represent a predictable combination of known elements and rendering the claims prima facie obvious. It would have been obvious for a person of ordinary skill in the art to incorporate one or more of the known piggybac fusion construct of Shrock. Li taught that R372A/D450N retain integration activity, and thus a skilled artisan would have a reasonable expectation of success that a Cas9-piggybac transposase fusion containing integration competent substitution would still achieve the site specific insertion.
Regarding claim 28: Shrock taught that “mechanism of integration involves simultaneous cleavage of the ROSA26 locus by Cas9 and the transposon by the piggyBac transposase, followed by non-homologous end joining of the transposon at the site of Cas9 cleavage.” (See Shrock, Example I). It is also submitted that in Example I, Shrock used a gRNA targeting the ROSA26 locus of the porcine genome. As such it is submitted that the Cas9 protein used in Shrock comprises an active DNA cleavage domain and gRNA binding domain as required by the claim.
Claim 29 is rejected under 35 U.S.C. 103 as being unpatentable over Shrock et al (WO2018175872A1; Hereinafter "Shrock;" Published Sep. 27, 2018; See PTO-892 of 10/07/2025) in view of Li et al (Proc Natl Acad Sci U S A. 2013 Jun 18; Hereinafter “Li;” See PTO-892 of 10/07/2025) and further in view of Chen et al (Adv Drug Deliv Rev. 2013 Oct; hereinafter “Chen”; See PTO-892 of 10/07/2025).
Regarding claim 29: Example I of Shrock taught that there is a 6-amino acid linker (GSGSGS (glycine-serine-glycine-serine-glycine-serine)) downstream of the gateway attachment site and upstream of the hyperactive piggyBac transposase. While Shrock and Li did not explicitly teach a GGS or XTEN linker, Chen taught that linkers have shown increasing importance in the construction of stable, bioactive fusion proteins. (See Chen Abstract). Chen exemplified several linkers for design of fusion proteins including GGS linkers (See Table 1). Chen taught that “[t]he rational choice of linkers should be based on the properties of the linkers and the desired fusion proteins.“ (See Chen p. 7, para 3). it would have been obvious for a person of ordinary skill in the art to substitute the GSGSGS linker in the fusion protein of Shrock with the GGS linker as taught by Chen because the choice of linker is a matter of routine experimentation depending on the desired properties of the fusion protein. Chen taught that GGS linker is known flexible linker and a POSITA would have had a reasonable expectation of success in achieving a functional fusion protein by such substitutions.
Claim 36-37 are rejected under 35 U.S.C. 103 as being unpatentable over Shrock et al (WO2018175872A1; Hereinafter "Shrock;" Published Sep. 27, 2018; See PTO-892 of 10/07/2025) in view of Li et al (Proc Natl Acad Sci U S A. 2013 Jun 18; Hereinafter “Li;” See PTO-892 of 10/07/2025) and further in view of Wu et al (US20180320196A1; Published Nov 8, 2018; Hereinafter “Wu;” See PTO-892 of 10/07/2025).
Regarding claims 36-37: Shrock and Li did not specifically teach a transposase comprising SEQ ID NO: 120 as claimed. However, US20180320196A1 (Published Nov 8, 2018; Hereinafter “Wu”) taught a transposase that is 100% identical to the claimed and elected SEQ ID NO: 120. Wu taught that an exogenous sequence can be integrated into the genome of an organism using the transposase comprising instant SEQ ID NO: 120.
Therefore, it would have been prima facie obvious to one having ordinary skill in the art at the time of filing the invention to substitute transposase taught by Wu for the transposase domain taught by Shrock since both polypeptides are known to have transposase capability. Therefore, one of ordinary skill in the art would recognize this as simply substituting one type of transposase for another useful for the same purpose ((KSR Int’l Co. v. Teleflex, Inc., 550 U.S. 398 (2007) pg 14 and 12). It would have been obvious to a person of ordinary skill in the art to use the sequence comprising SEQ ID NO: 120 in the nucleic acid composition as recited in claim 27.
Query Match 100.0%; Score 3132; Length 899;
Best Local Similarity 100.0%;
Matches 594; Conservative 0; Mismatches 0; Indels 0; Gaps 0;
Qy 1 MGSSLDDEHILSALLQSDDELVGEDSDSEVSDHVSEDDVQSDTEEAFIDEVHEVQPTSSG 60
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 19 MGSSLDDEHILSALLQSDDELVGEDSDSEVSDHVSEDDVQSDTEEAFIDEVHEVQPTSSG 78
Qy 61 SEILDEQNVIEQPGSSLASNRILTLPQRTIRGKNKHCWSTSKPTRRSRVSALNIVRSQRG 120
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 79 SEILDEQNVIEQPGSSLASNRILTLPQRTIRGKNKHCWSTSKPTRRSRVSALNIVRSQRG 138
Qy 121 PTRMCRNIYDPLLCFKLFFTDEIISEIVKWTNAEISLKRRESMTSATFRDTNEDEIYAFF 180
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 139 PTRMCRNIYDPLLCFKLFFTDEIISEIVKWTNAEISLKRRESMTSATFRDTNEDEIYAFF 198
Qy 181 GILVMTAVRKDNHMSTDDLFDRSLSMVYVSVMSRDRFDFLIRCLRMDDKSIRPTLRENDV 240
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 199 GILVMTAVRKDNHMSTDDLFDRSLSMVYVSVMSRDRFDFLIRCLRMDDKSIRPTLRENDV 258
Qy 241 FTPVRKIWDLFIHQCIQNYTPGAHLTIDEQLLGFRGRCPFRVYIPNKPSKYGIKILMMCD 300
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 259 FTPVRKIWDLFIHQCIQNYTPGAHLTIDEQLLGFRGRCPFRVYIPNKPSKYGIKILMMCD 318
Qy 301 SGTKYMINGMPYLGRGTQTNGVPLGEYYVKELSKPVHGSCRNITCDNWFTSIPLAKNLLQ 360
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 319 SGTKYMINGMPYLGRGTQTNGVPLGEYYVKELSKPVHGSCRNITCDNWFTSIPLAKNLLQ 378
Qy 361 EPYKLTIVGTVRSNKREIPEVLKNSRSRPVGTSMFCFDGPLTLVSYKPKPAKMVYLLSSC 420
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 379 EPYKLTIVGTVRSNKREIPEVLKNSRSRPVGTSMFCFDGPLTLVSYKPKPAKMVYLLSSC 438
Qy 421 DEDASINESTGKPQMVMYYNQTKGGVDTLDQMCSVMTCSRKTNRWPMALLYGMINIACIN 480
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 439 DEDASINESTGKPQMVMYYNQTKGGVDTLDQMCSVMTCSRKTNRWPMALLYGMINIACIN 498
Qy 481 SFIIYSHNVSSKGEKVQSRKKFMRNLYMGLTSSFMRKRLEAPTLKRYLRDNISNILPKEV 540
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 499 SFIIYSHNVSSKGEKVQSRKKFMRNLYMGLTSSFMRKRLEAPTLKRYLRDNISNILPKEV 558
Qy 541 PGTSDDSTEEPVMKKRTYCTYCPSKIRRKASASCKKCKKVICREHNIDMCQSCF 594
||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 559 PGTSDDSTEEPVMKKRTYCTYCPSKIRRKASASCKKCKKVICREHNIDMCQSCF 612
Alignment of SEQ ID NO: 126 with SEQ ID NO: 4 of USPN 11345926
Claims 41-43 are rejected under 35 U.S.C. 103 as being unpatentable over Shrock et al (WO2018175872A1; Hereinafter "Shrock;" Published Sep. 27, 2018; See PTO-892 of 10/07/2025) in view of Li et al (Proc Natl Acad Sci U S A. 2013 Jun 18; Hereinafter “Li;” See PTO-892 of 10/07/2025) and further in view of Hart et al (G3 (Bethesda). 2017 Aug 7; Hereinafter "Hart;" See PTO-892 of 10/07/2025).
Regarding claims 41-43: The teachings of Shrock and Li are set forth above. Shrock and Li however, did not teach a packaging vector bound to a piggybac-cas9 fusion construct. It is noted that co-transfection of lentiviral vectors with packaging vectors, envelope vectors and the vectors encoding CRISPR enzymes and the inserts are well known in the art of gene editing with lentivirus. For example, Hart taught “TKOv3 library lentivirus was produced by co-transfection of lentiviral vectors psPAX2 (packaging vector) and pMDG.2 (envelope vector) with TKOv3 lentiCRISPR plasmid library, using X-tremeGene 9 transfection reagent (Roche).” Hart taught that the packaging vector is a lentivirus particle as required by claim 43. Hart taught the gRNAs were cloned into the lentiCRISPR plasmid library, which contains cas9. Hart taught a composition comprising a nucleic acid insert and the Crispr enzyme comprising vector bound to a packaging vector as required by claim 41. Hart taught that the nucleic acid inserts are amplified into a DNA and cloned into the vector comprising Cas9 nuclease as required by claim 42. As such it would have been obvious for a person of ordinary skill in the art to use the nucleic acid construct taught by Shrock and gRNA inserts bound to the packaging vector as taught by Hart to generate lentivirus to transduce mammalian cells.
It would have been obvious for a person of ordinary skill in the art to arrive at the claimed invention by combining the teachings of Shrock and Hart. Shrock taught a composition of Cas9-hyperactive piggybac transposase as enumerated above. Hart taught a method of delivering vectors by packaging into a viral vector. It would have been obvious to combine the teachings to the person of skill in the art to arrive at the claimed composition with a reasonable expectation of success.
Response to Arguments:
Applicant argues that the SEQ ID NO: 120 is significantly smaller than the sequence taught in the Wu reference and is therefore not fully disclosed. Further Applicants argues that Wu does not disclose a fusion protein comprising the transposase or a construct capable of targeted integration. Applicant’s arguments are not persuasive. The fact that Wu’s sequence includes additional residues does not negate disclosure of the included region. It is also noted that obviousness cannot be argued by attacking the references individually. It is pointed out that the rejection did not rely on Wu to teach the fusion protein. The rejection only relies on Wu for substitution of the transposase sequence. It is maintained that it would have been obvious for a skilled artisan to substitute Wu’s transposase region for Shrock’s transposase as both sequences are known to possess transposase activity.
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.
Claim 35 is 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 applications subject to pre-AIA 35 U.S.C. 112, the inventor(s), at the time the application was filed, had possession of the claimed invention.
The claim recites a modified hyperactive piggybac transposase comprising a set of specific amino acid substitutions, including R245A, S315E/A/P and K375A, among others and required that the fusion protein enables insertion of an exogenous nucleic acid into the genome.
It is noted that the specification disclosed a SEQ ID NO: 10, which can comprise various substitutions. However, the specification did not provide any experimental data or examples demonstrating that this specific combination is capable of performing genome integration as required by the claim. The disclosure of a sequence alone does not demonstrate possession of the claimed functional invention, as 112(a) requires.
It is also noted that the prior art (for example Li et al) indicated that certain substitutions including S351 can substantially reduce or abolish integration activity, making the functional outcome of the claimed combination unpredictable. The specification fails to provide guidance or representative data showing the full combination of substitutions retains integration activity.
Thus, Applicants were not in possession of the full scope of the claimed invention at the time of filing of the instant invention.
Conclusion
No claim is allowed.
Claim 35 appears free of art but lacks written description.
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/JAGAMYA NMN VIJAYARAGHAVAN/Examiner, Art Unit 1633
/EVELYN Y PYLA/Primary Examiner, Art Unit 1633