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 .
Continued Examination Under 37 CFR 1.114
A request for continued examination under 37 CFR 1.114, including
the fee set forth in 37 CFR 1.17(e), was filed in this application after final
rejection. Since this application is eligible for continued examination under
37 CFR 1.114, and the fee set forth in 37 CFR 1.17(e) has been timely
paid, the finality of the previous Office action has been withdrawn pursuant
to 37 CFR 1.114. Applicant's submission filed on 05/28/2026 has been
entered.
Election/Restrictions
Applicant's election with traverse of Group I and the species of (A) an artificial CRE recognizing histone tails with specific methylated sites; (B) a single chain antibody; (C) a hyperactive PiggyBac transposase; and (D) a polynucleotide encoding a polypeptide antibody; (C) a hyperactive PiggyBac transposase; and (D) a polynucleotide encoding a polypeptide.in the reply filed on 08/27/2025 is acknowledged. The traversal is on the ground(s) that claim 1 is drawn to a polypeptide comprising a transposase and at least one heterologous histone reader domain. Applicant contends that this polypeptide is the inventive technical feature commonly shared among all pending claims. This is not found persuasive because:
Jelinek exemplifies conjugation of an antibody to a Tn5 transposase (e.g., paragraphs [0088]-[0091]; Example 2). Jelinek teaches that the invention isn’t limited to antibody-transposon targeting and also includes a transposon that is conjugated to a protein that binds a chromosome (e.g., paragraph [0099]). Jelinek teaches a complex of a transposase and a PHD-finger, such as ADD from ATRX (e.g., paragraphs [0022], [0023] and [0099). Jelinek teaches that the two proteins are conjugated to each other via chemical conjugations (e.g., paragraphs [0118] and [0119]). Jelinek teaches that Tn5 transposase fusion proteins have been described and are functional (e.g., paragraph [0119]). Jelinek teaches that any suitable approach can be adapted for use in the context of the invention. It would have been obvious to one of ordinary skill in the art before the effective filing date of the claimed invention to modify the conjugate of the Tn5 transposase and ADD of ATRX of Jelinek to provide the two heterologous proteins as a fusion protein.
Upon further consideration, the restriction between Groups I and II has been withdrawn, and the restriction between Groups III and IV has been withdrawn. The restriction between Groups I/II and III/IV is maintained.
Once a restriction requirement is withdrawn, the provisions of 35 U.S.C. 121 are no longer applicable. See In re Ziegler, 443 F.2d 1211, 1215, 170 USPQ 129, 131-32 (CCPA 1971). See also MPEP § 804.01.
The requirement is still deemed proper and is therefore made FINAL.
Claims 22, 26, 28-29, 33, 36, 55-56 are withdrawn from further consideration pursuant to 37 CFR 1.142(b) as being drawn to a nonelected species, there being no allowable generic or linking claim. Election was made with traverse in the reply filed on 08/27/2025.
Claims 1, 9, 20, 22, 26, 39, 51, 55-61 are amended. Claims 63 and 64 are new.
Claims 1, 8-9, 20-21, 39, 51, 57-61, 63 and 64 are examined on the merits.
Priority
The application is a continuation of a 371 of application PCT/EP2019/053571 filed February 13 2019 is acknowledged.
Specification
The substitute specification filed 05/28/2026 has been entered.
Withdrawn Rejections
The objection of claims 8, 39, 51 has been withdrawn in view of Applicant’s amendments to the claims in the reply of 05/28/2026.
The rejection of claim 1, under 35 U.S 112(b) or 35 U.S.C. 112 (pre-AIA ), second paragraph, is withdrawn in view of Applicant’s amendment of the claims in the reply in the reply filed 05/28/2026.
The rejection of claim 59, under 35 U.S 112(a) or 35 U.S.C. 112 (pre-AIA ), first paragraph, is withdrawn in view of Applicant’s amendment of the claim in the reply in the reply filed 05/28/2026.
New Rejections are necessitated by claim Amendments
Claim Objections
Claim 9 is objected to as being dependent upon a rejected base claim, but would be allowable if rewritten in independent form including all of the limitations of the base claim and any intervening claims.
The prior art does not teach or suggest the linkage of the following elements present in SEQ ID NO: 20 (136 amino acids).
Alignment of instant SEQ ID NO: 20 with NP_114129.1:
PNG
media_image1.png
250
624
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Greyscale
Alignment of instant SEQ ID NO: 20 with linker 1 of the disclosure (SEQ ID NO: 22):
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media_image2.png
197
624
media_image2.png
Greyscale
Alignment of instant SEQ ID NO: 20 with instant SEQ ID NO: 6 (PiggyBac wt transposase):
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media_image3.png
200
624
media_image3.png
Greyscale
Claim 59 is objected to because of the following informalities:
1. The phrase “at least one heterologous histone reader domain and a polypeptide comprising a transposase” is recited twice.
2. The phrase in line 11 ending in "wherein." is not proper English.
Each claim begins with a capital letter and ends with a period. Periods may not be used elsewhere in the claims except for abbreviations." See Fressola v. Manbeck, 36 USPQ2d 1211 (D.D.C. 1995).
It would be remedial to delete all text that follows the first period.
Appropriate correction is required.
Claim Rejections - 35 USC § 112
The following is a quotation of the first paragraph of 35 U.S.C. 112(a):
(a) IN GENERAL.—The specification shall contain a written description of the invention, and of the manner and process of making and using it, in such full, clear, concise, and exact terms as to enable any person skilled in the art to which it pertains, or with which it is most nearly connected, to make and use the same, and shall set forth the best mode contemplated by the inventor or joint inventor of carrying out the invention.
The following is a quotation of the first paragraph of pre-AIA 35 U.S.C. 112:
The specification shall contain a written description of the invention, and of the manner and process of making and using it, in such full, clear, concise, and exact terms as to enable any person skilled in the art to which it pertains, or with which it is most nearly connected, to make and use the same, and shall set forth the best mode contemplated by the inventor of carrying out his invention.
Claim 64 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. This is a new matter rejection.
Claim 1, recites a polypeptide comprising a transposase and at least one heterologous histone reader domain, wherein the domain is a plant homeodomain (PHD) type zinc finger.
The dependent claim 64, further narrows the transposase to “a DNA transposase that integrates a transposon flanked by inverted terminal repeat sequences into TTAA genomic target sites”.
The reply filed 5/28/2026 asserts that support for the amendment can be found at page 1, lines 23-33 by reciting the phrase “a DNA transposase that integrates a transposon flanked by inverted terminal repeat sequences into TTAA genomic target sites.”
Page 1, lines 29-34 state the following:
For instance, the PiggyBac (PB) DNA transposon (previously described as IFP2) is used technologically and commercially in genetic engineering by virtue of its property to efficiently transpose between vectors and chromosomes [US 6218185 B1]. For these applications the DNA to be integrated is flanked by two PB ITRs in a PB vector. By co-delivery of PB transposase the flanked DNA is excised precisely form the PB vector and integrated into the target genome at TTAA specific sites.
The claim is drawn to a genus of transposases from any type of transposon that integrates into TTAA genomic target sites, yet the disclosure is specifically limited to the description of the piggyBac or (IFP2) transposon and its transposase. The named species does not provide support for the unnamed subgenus as claimed in claim 64.
The prior art provides evidence that claim 64 is drawn to a genus that includes other transposases beyond piggyBac. Penton et al. (J. of Mol. Evol., 2002) teaches that Pokey is similar to piggyBac and, as such, is a member of the TTAA specific family of elements. Wu et al. (J. of Bioscience Bioeng., 2014) teaches that PLE-wu another member of the piggyBac transposon family that recognizes TTAA sites.
The original specification, drawings and claims were thoroughly reviewed and no support could be found for the amendment. Accordingly, the amendment is a departure from the specification and claims as originally filed, and the passages that Applicant has provided do not provide support.
Claim Rejections - 35 USC § 102
In the event the determination of the status of the application as subject to AIA 35 U.S.C. 102 and 103 (or as subject to pre-AIA 35 U.S.C. 102 and 103) is incorrect, any correction of the statutory basis (i.e., changing from AIA to pre-AIA ) for the rejection will not be considered a new ground of rejection if the prior art relied upon, and the rationale supporting the rejection, would be the same under either status.
The following is a quotation of the appropriate paragraphs of 35 U.S.C. 102 that form the basis for the rejections under this section made in this Office action:
A person shall be entitled to a patent unless –
(a)(1) the claimed invention was patented, described in a printed publication, or in public use, on sale, or otherwise available to the public before the effective filing date of the claimed invention.
Claim 59 is rejected under 35 U.S.C. 102(a)(1) as being anticipated by Wang. F. et al. (“Wang”, PhD thesis, 2016).
Under the broad reasonable interpretation, the claim is interpreted as a kit comprising the components: 1) transposable element comprising a cloning site for inserting at least one polynucleotide of interest; 2) a heterologous histone reader, where the histone reader includes a PHD domain; and 3) a transposase.
Regarding claim 59, Fang teaches 1) an inducible PiggyBac vector, PBQM530A-1, comprising a multiple cloning site (MCS) for inserting a polynucleotide of interest (e.g., page 42, 1st full paragraph); 2) a heterologous ING5 protein, which contains a PHD motif, expressed in BT 189 cells (e.g., paragraph bridging pages 42-43; page 43, 1st full paragraph); and 3) a PiggyBac transposase expressed in BT 189 cells (e.g., paragraph bridging pages 42-43).
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.
Claims 1 , 20-21 are rejected under 35 U.S.C. 103 as being unpatentable over Jelinek (US Patent Application Publication No. 2016/0115474 A1), as evidenced by Dhayalan (Human Molecular Genetics, 2011).
Regarding claim 1, Jelinek exemplifies conjugation of an antibody to a Tn5 transposase (e.g., paragraphs [0088]-[0091]; Example 2). The antibody directs the transposome to chromatin in a specific manner by binding to trimethyl lysine at residue 4 of histone H3 (H3K4me3) (e.g., paragraph [0097]). Jelinek teaches that the invention isn’t limited to antibody-transposon targeting and also includes a transposon that is conjugated to a protein that binds a chromosome (e.g., paragraph [0099]). Jelinek teaches a complex of a transposase and a PHD-finger, such as ADD from ATRX, which is a protein capable of binding methylated histone (e.g., paragraphs [0022], [0023] and [0099). Dhayalan, (Human Molecular Genetics, 2011) is cited only to show that the ADD from ATRX is a PHD type zinc finger domain. Jelinek teaches that the two proteins are conjugated to each other via chemical conjugations (e.g., paragraphs [0118] and [0119]). Jelinek teaches that Tn5 transposase fusion proteins have been described and are functional (e.g., paragraph [0119]). Jelinek teaches that any suitable approach can be adapted for use in the context of the invention.
Jelinek does not explicitly teach fusion of the Tn5 to a PHD-finger, such as ADD from ATRX.
It would have been obvious to one of ordinary skill in the art before the effective filing date of the claimed invention to modify the conjugate of the Tn5 transposase and ADD of ATRX of Jelinek to provide the two proteins as a fusion protein, because Jelinek teachings it is within the skill of the art to make Tn5 fusion proteins that are functional. Jelinek suggests that any suitable approach can be adapted in the context of the invention. Thus, one would have substituted the chemical conjugation disclosed by Jelinek for the fusion of the two proteins in order to receive the predictable result of linking the two functional proteins together using linkage type known in the art to be functional.
Furthermore, It would have been obvious to one of ordinary skill in the art before the effective filing date of the claimed invention, once the fusion protein is rendered obvious, providing a polynucleotide encoding that polypeptide and inserting into an appropriate expression vector. Expression vectors are routinely used to propagate and express recombinant polynucleotides encoding engineered proteins, including fusion proteins such as that taught by Jelinek, yielding entirely predictable results.
Claim 8 is rejected under 35 U.S.C. 103 as being unpatentable over Jelinek (US Patent Application Publication No. 2016/0115474 A1) as applied to claims 1, 20-21 above, and further in view of Sanchez et al. (“Sanchez”, Trends in Biochemical Sciences, July 2011, cited as reference 10 on IDS filed 06/30/2021).
The teachings of Jelinek are described above and applied similarly.
Jelinek does not teach a heterologous PHD type zinc finger domain and does not teach a PHD type zinc finger domain that is a transcription initiation factor TFIID subunit 3, as required by the instant claim. However, this is cured by Sanchez.
Sanchez teaches the plant homeodomain (PHD) zinc finger as a sequence specific histone recognition protein module. Sanchez teaches that histone modifications, acetylation of lysine and methylation of lysine or arginine play a direct role in orchestrating the recruitment of multiprotein complexes for changing chromatin structure at target gene loci (e.g., paragraph 2nd, page 364; Fig. 1). Sanchez teaches the transcription initiation factor TFIID subunit 3 (TAF3) (e.g., paragraph 1st, page 366; Fig. 1). Sanchez teaches that TAF3 reads H3K4me3 (e.g., paragraph 1st, left column, page 366; Fig. 2).
It would have been obvious to one of ordinary skill in the art before the effective filing date of the claimed invention to substitute the protein-binding domain ADD of ATRX of the fusion transposase protein taught by Jelinek with the PHD zinc finger TFIID subunit 3 taught by Sanchez, because Jelinek teachings it is within the skill of the art to make a chimeric transposase fused to a PHD domain TFIID subunit 3 protein that are functional. Jelinek discloses a transposase fused to a PHD-finger, such as ADD from ATRX and Sanchez discloses a TFIID subunit 3 capable of interacting with methylated histone proteins. Thus, one would have substituted the ADD from ATRX domain of the chimeric transposase disclosed by Jelinek with the TFIID subunit 3 disclosed by Sanchez for the fusion of the two proteins in order to obtain the predictable result of linking the two functional proteins transposase and TFIID subunit 3 together using linkage type known in the art to be functional for the recognition of methylated histones.
Claims 1, 8, 20-21, 39, 51, 57-61, 63 and 64 are rejected under 35 U.S.C. 103 as being unpatentable over Mitra et al. Mitra et al. (“Mitra”, The EMBO Journal, 2008) in view of further Sanchez et al. (“Sanchez”, Trends in Biochemical Sciences, July 2011, cited as reference 10 on IDS filed 06/30/2021), Ostertag et al. (“Ostertag”, US 8,399,643 B2) and Yusa et al. (“Yusa”, Microbiology Spectrum, 2014) .
Regarding claim 1, Mitra teaches a piggyBac transposase protein expressed and purified from Escherichia coli (e.g., paragraph 4th, left column, page 1108). Mitra teaches that a conserved feature of piggyBac transposases is the C-terminal C2C2CHC2 motif. Analysis of this region suggests that this region forms a Zn2+-binding PHD domain. PHD domains bind to chromatin. The C terminus is, however, dispensable for piggyBac recombination in vitro: PiggyBac 1–558, which lacks the C2C2CHC2 motif, is as active in vitro as the wild-type piggyBac 1–594 (e.g., left column, paragraph 2nd, page 1104; Supplementary Fig. 8).
Regarding claims 20-21, Mitra teaches that the transposase is encoded by a second plasmid containing the piggyBac transposase gene (e.g., right column, paragraph 2nd, page 1104).
Regarding claim 63-64, Mitra teaches unique for piggyBac transposition is the exclusive use of TTAA target sites (e.g., paragraph 4th, right column, page 1). Laptev (Applied Biochemistry and Microbiology, 2017) is cited only to show that PiggyBac is also known as IFP2 and recognize the TTAA sequence as a target site.
Mitra does not teach a heterologous PHD type zinc finger domain and does not teach a PHD type zinc finger domain that is a transcription initiation factor TFIID subunit 3, as required by the instant claims. Mitra does not teach a transposable element comprising a cloning site for inserting a polynucleotide of interest, as required by the instant claims. However, this is cured by Sanchez, Yusa and Ostertag.
Sanchez teaches the plant homeodomain (PHD) zinc finger as a sequence specific histone recognition protein module. Sanchez teaches that histone modifications, acetylation of lysine and methylation of lysine or arginine play a direct role in orchestrating the recruitment of multiprotein complexes for changing chromatin structure at target gene loci (e.g., paragraph 2nd, page 364; Fig. 1). Sanchez teaches the transcription initiation factor TFIID subunit 3 (TAF3) (e.g., paragraph 1st, page 366; Fig. 1). Sanchez teaches that TAF3 reads H3K4me3 (e.g., paragraph 1st, left column, page 366; Fig. 2).
Yusa teaches that the broad host range of the piggyBac transposon is currently the most widely used transposon system for genetic manipulations (e.g., abstract). Yusa teaches that PHD fingers bind to chromatin, the C-terminus of piggyBac transposases may facilitate binding to transposon DNA in a chromatin context (e.g., paragraph 1st, right column, page 4). Yusa teaches transposase variants have also been generated by fusing functional protein domains. These fusion transposes are not only active but also able to integrate transposons into sites that are in close proximity to their respective binding sites, thereby allowing site-directed transposition (e.g., paragraph 2nd, right column, page 9).
It would have been obvious to one of ordinary skill in the art before the effective filing date of the claimed invention to substitute the transposase-disposable carboxy terminus PHD domain of PiggyBac taught by Mitra with the heterologous plant homeodomain (PHD) zinc finger TFIID subunit 3 (TFIID subunit 3 binds to H3K4me3 taught by Sanchez to generate a fusional protein as taught by Yusa, because 1) Mitra discloses a PiggyBac transposase carrying a PHD domain at the C-terminus end, 2) Sanchez discloses sequence specific histone recognition protein the TFIID 3 subunit, 3) Yusa discloses transposase variants have also been generated by fusing functional protein domains, and that PHD fingers bind to chromatin, the C-terminus of piggyBac transposases may facilitate binding to transposon DNA in a chromatin context. Thus, a person of ordinary skill in the art would have substituted the endogenous PHD zing finger in the piggyBac transposase disclosed by Mitra with a zinc finger from TFIID 3 to obtain the fusion of the two proteins in order to obtain the predictable result of linking the two functional proteins to allow site directed transposition at methylated histones.
Regarding claims 39, 51, 57-61, Ostertag teaches PiggyBac transposase proteins (It reads on transposase polypeptide), nucleic acids encoding the same (It reads on a polynucleotide encoding a PiggyBac transposase protein), compositions comprising the same, kits comprising the same, non-human transgenic animals comprising the same, and methods of using the same (e.g., abstract). Ostertag teaches the PiggyBac transposons can include a wide variety of inserted nucleic acids, where the nucleic acids can include a sequence of bases that is endogenous and/or exogenous to a multicellular or unicellular organism (it reads transposable element comprising a polynucleotide of interest) (e.g., line 30, column 14). Ostertag teaches the transposon containing the inverted repeats also comprises at least one restriction endonuclease recognized site, e.g. restriction site, located between the flanking inverted repeats, which serves as a site for insertion of an exogenous nucleic acid (e.g., line 18, column 15) (it reads transposable element comprising a cloning site for inserting the polynucleotide of interest). Ostertag teaches a variety of applications in which it is desired to introduce and stably integrate an exogenous nucleic acid into the genome of a target cell (e.g., line 6, column 16).
It would have been prima facie obvious to one of ordinary skill in the art, before the effective filing date of the claimed invention, to develop the piggyBac transposon variant fused to TFIID subunit 3, comprising a cloning site for a gene of interest for insertion, because 1) Mitra discloses that a conserved feature of piggyBac transposases is the C-terminal C2C2CHC2 motif. Analysis of this region suggests that this region forms a Zn2+-binding PHD domain. PHD domains bind to chromatin 2) Ostertag discloses a targeting system comprising a PiggyBac transposase protein or a vector encoding the PiggyBac transposase and a transposon carrying and exogenous DNA sequence, 3) Sanchez discloses sequence specific histone recognition protein the TFIID 3 subunit, and 4) Yusa, discloses transposase variants have also been generated by fusing functional protein domains and that PHD fingers bind to chromatin, the C-terminus of piggyBac transposases may facilitate binding to transposon DNA in a chromatin context, then it would have been obvious to develop a PiggyBac-TFIID 3 transposase-based targeting system to guide the transposon integration toward chromatin genomic regions carrying methylated histones.
One of ordinary skill in the art before the effective filing date of the invention would have been motivated to develop a targeting transposon-based insertion system of a transgene using a polypeptide comprising of histone recognition domain such as TFIID3 and a piggyBac transposase in order to guide the transposon integration toward chromatin genomic regions carrying methylated histones.
Conclusion
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/JULIO WASHINGTON GOMEZ RODRIGUEZ/Examiner, Art Unit 1637
/NEIL P HAMMELL/Supervisory Patent Examiner, Art Unit 1636
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