DETAILED ACTION
The present application, filed on or after March 16, 2013, is being examined under the first inventor to file provisions of the AIA .
Applicant’s response to restriction requirement and amendments to the claims filed on May 4, 2026 have been received and entered. Claims 1, 4-5, 9, 12-15, 19 have been amended, while claims 2-3, 6-8, 24-25 have been canceled. Claims 1, 4-5, 9-23 and 26 are pending in the instant application.
Election/Restrictions
Applicant’s election of claims 1, 4, 9-20 and 26 (group I) in the reply filed on May 4, 2026 is acknowledged. Because applicant did not distinctly and specifically point out the supposed errors in the restriction requirement, the election has been treated as an election without traverse (MPEP § 818.01(a)).
Claims 5, 21-23 are withdrawn from further consideration pursuant to 37 CFR 1.142(b) as being drawn to a nonelected invention, there being no allowable generic or linking claim. Election was made without traverse in the reply filed on May 4, 2026
Priority
This application is a 371 of PCT/US2022/020899 filed on 03/18/2022, which claims priority form US provisional application no 63/163,532 filed on 03/19/2021.
Information Disclosure Statement
The information disclosure statements (IDS) submitted on 06/20/2024 and 05/04/2026 are in compliance with the provisions of 37 CFR 1.97. Accordingly, the information disclosure statement has been considered by the examiner.
Claims 1, 4, 9-20 and 26 are under consideration.
Specification
The abstract of the disclosure is objected to because it is too short (one sentence). The abstract should be a single paragraph between 50 to 150 words in length. The abstract should describe the disclosure sufficiently to assist readers in deciding whether there is a need for consulting the full patent text for details. A corrected abstract of the disclosure is required and must be presented on a separate sheet, apart from any other text. See MPEP § 608.01(b).
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, 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.
Claim 4 is rejected under 35 U.S.C. 103 as being unpatentable over Voytas et al (US2005048652, 3/3//2005) in view of Schumann (US20110045591, dated 02/24/2011)/ Kafri (US7220578, dated 05/22/2007).
Claim is directed toa template RNA comprising: a first retrotransposon LTR, a second retrotransposon LTR, a heterologous object sequence encoding a therapeutic effector for a human disease, positioned between the first LTR and the second LTR.
Claim interpretation: In absence of any specific structure, recitation of a therapeutic effector for a human disease in interpreted as any effector for intended use.
With respect to claim 4, Voytas teaches a templet RNA comprising a 5” mini-retrotransposon LTR, a heterologous coding sequence of NPTII and a 3’ mini-retrotransposon LTR that confers cells resistance to kanamycin and G418 (see figure 3b). Voytas differs from claimed invention by not disclosing heterologous cargo gene is not a therapeutic gene for human disease.
However, before the effective filing date of instant application, it was routine to use therapeutic gene are alternatively to heterologous insert in a gene delivery vector. For instance, Schumann teaches retrotransposon comprises a heterologous gene selected from the group consisting of a reporter gene, a therapeutic gene, and a selectable marker gene. (see claims 4-5 and figures). This is further evidenced by Kafri who teaches comprising a 5' retroviral LTR and a 3' retroviral LTR, a heterologous nucleotide sequence, a packaging signal, a rev responsive element, a polypurine tract, a eukaryotic promoter, a primer binding site, a bacterial origin of replication and a bacterial selection muter, wherein the bacterial origin of replication and bacterial selection marker are located between the two LTRs, and wherein the U3 region of the 3' LTR comprises a loxP site (see claim 6 of ‘578), wherein the heterologous nucleotide sequence can encode a polypeptide or peptide that can impart an immunogenic effect and/or therapeutic effect in a target cell in a subject including a reporter protein, green fluorescent protein (GFP), luciferase, human growth hormone (see col. 6, lines 43-60).
Therefore, it would have been prima facie obvious for a person of ordinary skill in the art to combine the teachings of prior art to modify the template RNA disclosed in Voytas by substituting heterologous marker gene with other known heterologous alternative gene insert as disclosed in Schumann or Kafri, in the method of modifying DNA, as instantly claimed, with a reasonable expectation of success, before the effective filing date of instant invention. Said modification amounting to combining prior art elements according to known methods to yield predictable results. One of ordinary skill in the art would be motivated to do so because swapping one heterologous insert with another was routine and conventional in gene delivery art as evident form the teaching of Schumann or Kafri. One of skill in the art would have been expected to have a reasonable expectation of success in substituting one effector gene with another heterologous gene was routine and was successfully practiced for delivering therapeutic gene in prior art as evident from Schumann or Kafri It should be noted that the KSR case forecloses the argument that a specific teaching, suggestion, or motivation is required to support a finding of obviousness See the recent Board decision Ex parte Smith, --USPQ2d--, slip op. at 20, (Bd. Pat. App. & Interf. June 25, 2007) (citing KSR, 82 USPQ2d at 1396) (available at http: www. uspto.gov/web/offices/dcom/bpai/prec/fd071925.pdf).
Claims 1, 4, 9-20 and 26 are rejected under 35 U.S.C. 103 as being unpatentable over Rubens et al (WO2020047124, dated 03/05/2023 or US20200109398, 04/09/2020, IDS), Voytas et al (US2005048652, 3/3//2005) as evidenced by Pachulska-Wieczorek et al (Viruses, 2016, 193, 1-16, IDS) and Wilhelm et al (CMLS, 2001, 1246-1262, IDS).
Claims are directed to a system for modifying DNA comprising: a) a template RNA comprising a first long terminal repeat (LTR), a second LTR, a heterologous object sequence encoding a therapeutic effector, positioned between the first LTR and the second LTR, and optionally a primer binding site (PBS); or a DNA molecule encoding the template RNA; b) an LTR retrotransposon structural polypeptide domain, or a nucleic acid molecule encoding the LTR retrotransposon structural polypeptide domain; and c) an LTR retrotransposon reverse transcriptase polypeptide domain capable of reverse transcribing the template RNA, thereby producing a template DNA, or a nucleic acid molecule encoding the LTR retrotransposon reverse transcriptase polypeptide domain.
With respect to claims 1, 4, Rubens teaches a system for modifying DNA (para. 5-18 of 398) comprising: a) a template RNA (para. 7, 9) comprising (a) a polypeptide or a nucleic acid encoding a polypeptide, wherein the polypeptide comprises (i) a reverse transcriptase domain (RT) and (ii) an endonuclease domain; and (b) a template RNA (or DNA encoding the template RNA) comprising (i) a sequence that binds the polypeptide and (ii) a heterologous object sequence that encodes a therapeutic polypeptide or that encodes a mammalian (e.g., human) polypeptide, or a fragment or variant thereof. It is further disclosed that the system may further comprise a structural polypeptide domain such as gag (see para. 118). It is further disclosed that a heterologous reverse transcriptase from a different retrovirus, LTR-retrotransposon, or non-L TR retrotransposon may be used (see para. 120). The reverse transcriptase domain is engineered to bind a heterologous template RNA (see para. 120), wherein the system reverse transcribes the template RNA sequence into the target DNA strand, thereby modifying the target DNA strand (see para. 48, 50, 58).
Regarding claims 9-10, 13, 14, Rubens teaches providing the template RNA, and the RT and/or a structural polypeptide such gag (see par. 118), as on same nucleic acid or separate nucleic acid (see para. 5-48).
With respect to claim19-20, Rubens teaches that the compositions and systems may be formulated as a lipid nanoparticle (see page 557 or para. 208).
Rubens explicitly teaches that RT from LTR-retrotransposon could be used but differs from claimed invention by not disclosing the use of a RNA template with LTRs, in combination with a RT from a LTR retrotransposon.
Before the effective filing date of instant application, it was known in prior art that the RNA template to be reverse transcribed by this RT from LTR-retrotransposon as contemplated by Ruben must necessarily have the LTR at the both ends that are used by the RT to translate the RNA into cDNA that is then inserted into the host cell genome. For instance, Voytas teaches a retrotransposon that are mobile genetic elements that replicate through reverse transcription of an mRNA intermediate(a RNA template) (see para. 3). It should be noted that the LTR-containing retrotransposons are structurally similar to the retroviruses. The 5' LTR acts as the promoter, whereas the 3' LTR provides the polyadenylation signal and the polyadenylation site. Between the LTRs are a Primer Binding Site (PBS), Poly purine Tract (PPT) and the mRNA packaging signal. Voytas teaches a mini-retrotransposon vector system has been established for integrating foreign DNA into cells ( para. 7, 80). It is further disclosed that the remainder of the retroelement including gag and pol (see para. 19) (limitation of claims 10-11). Voytas teaches a RNA molecule with a 5'LTR, a coding sequence for neomycin phosphotransferase (Nptll) and a 3'LTR. Nptll represents a gene marker which confers on a plant cell to kanamycin and the antibiotic G-418, (see para. 95, fig. 3B). This is further supported by the teaching of Pachulska-Wieczorek who teaches a Long-terminal repeat (LTR) retrotransposon that are transposable genetic elements that replicate intracellularly, and can be considered progenitors of retroviruses. Ty1 and Ty3 are the most extensively characterized LTR retrotransposons whose RNA genomes provide the template for both protein translation and genomic RNA that is packaged) and reverse transcribed. Like retroviruses, LTR-retrotransposons replicate via an RNA intermediate and insert their double-stranded DNA into the host genome (see abstract and page 1). In the instant case , both elements contain long terminal repeats (LTRs) and central coding region with two overlapping ORFs: GAG and POL. RNA contains untranslated regions (UTRs) and a primer binding sites (PBS) that binds initiator (see fig. 1) (limitation of claims 16-18, 26).
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Fig. 1 shows the structure of two LTR-retrotransposons. The RNA intermediate/template comprises a LTR at each end. Wilhelm who reported reverse transcription of retroviruses and LTR retrotransposons. Figure 1 shows the genetic organization of prototypic retrotransposons and retroviruses. Both comprise a LTR at each end.
Therefore, it would have been prima facie obvious for a person of ordinary skill in the art to combine the teachings of prior art to modify the system by using a RNA template with LTRs in combination with a reverse transcriptase from a LTR retrotransposon as disclosed Voytas and Wilhelm, as a matter of design choice, in the method of delivering a heterologous sequence to a target cell, as instantly claimed, with a reasonable expectation of success, before the effective filing date of instant invention. Said modification amounting to combining prior art elements according to known methods to yield predictable results. One of ordinary skill in the art would be motivated to do so because swapping in an LTR RT would allow accurate and longer stretches of RNA to be successfully transcribed into DNA (see page 5 and table II) . One of skill in the art would have been expected to have a reasonable expectation of success in using a RNA template with LTRs in combination with a reverse transcriptase from a LTR retrotransposon because prior art successfully reported using LTR-retrotransposons that replicate via an RNA intermediate and insert their double-stranded DNA into the host genome as evident from the teaching of Pachulska-Wieczorek. It should be noted that the KSR case forecloses the argument that a specific teaching, suggestion, or motivation is required to support a finding of obviousness See the recent Board decision Ex parte Smith, --USPQ2d--, slip op. at 20, (Bd. Pat. App. & Interf. June 25, 2007) (citing KSR, 82 USPQ2d at 1396) (available at http: www. uspto.gov/web/offices/dcom/bpai/prec/fd071925.pdf).
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.
Claims 1, 4, 9-20 and 26 are rejected under 35 U.S.C. 112(a) or 35 U.S.C. 112 (pre-AIA ), first paragraph, as failing to comply with the written description requirement. The claim(s) contains subject matter which was not described in the specification in such a way as to reasonably convey to one skilled in the relevant art that the inventor or a joint inventor, or for 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 are directed to a system for modifying a DNA, the system comprising: a genera of template RNAs or a genera of DNA encoding said genera template RNAs and a genera of heterologous “object sequences” having no specific structural elements , any or all LTR retrotransposon structural polypeptide domain, or any nucleic acid molecule encoding the LTR retrotransposon structural polypeptide domain or any or all LTR transposon reverse transcriptase domain capable of transcribing the template RNA including variants, mutants and homologs from any source i.e., derived from any retrotransposon of undefined and unlimited structures and able to bind/interact with a genera of template RNA sequences and heterologous “object sequences” of undefined and unlimited structures.
Dependent claims limit the base system, wherein the template RNA comprises one or more elements from IAP, MusD, Gypsy/Ty3, Copia/Ty1, Bel/Pao, Morgane, BARE2, Large Retrotransposon Derivative (LARD), Terminal-repeat Retrotransposon in Miniature (TRIM), or ETn, or a functional fragment or variant thereof, or a nucleic acid sequence having at least 75%, 80%, 85%, 90%, 95%, 96%, 97%, 98%, or 99% sequence identity thereto, or wherein the LTR retrotransposon structural polypeptide domain is a protein from IAP, MusD, Gypsy/Ty3, Copia/Ty1, Bel/Pao, Morgane, BARE2, Large Retrotransposon Derivative (LARD), Terminal-repeat Retrotransposon in Miniature (TRIM), or ETn, or a functional fragment or variant thereof, or a polypeptide having at least 75%, 80%, 85%, 90%, 95%, 96%, 97%, 98%, or 99% sequence identity thereto or wherein the LTR retrotransposon reverse transcriptase polypeptide domain is a protein from IAP, MusD, Gypsy/Ty3, Copia/Ty1, Bel/Pao, Morgane, BARE2, Large Retrotransposon Derivative (LARD), Terminal-repeat Retrotransposon in Miniature (TRIM), or ETn, or a functional fragment or variant thereof, or a polypeptide having at least 75%, 80%, 85%, 90%, 95%, 96%, 97%, 98%, or 99% sequence identity thereto.
Vas-Cath Inc. v. Mahurkar, 19USPQ2d 1111, clearly states that "applicant must convey with reasonable clarity to those skilled in the art that, as of the filing date sought, he or she was in possession of the invention. The invention is, for purposes of the 'written description' inquiry, whatever is now darned." (See page 1117.) The specification does not "clearly allow persons of ordinary skill in the art to recognize that [he or she] invented what is claimed." (See Vas-Cath at page 1116).
No information, beyond the characterization of specific polypeptides having specific structural elements i.e., reverse transcriptase domains with defined structures (for details see Table S5, pages 396-432 of specification) in the claimed DNA modifying system has been provided by the specification, which would indicate that they had possession of the claimed system with full length driver and templet construct element for modifying a DNA, the system comprising: a genera of template RNAs or a genera of DNA encoding said genera template RNAs and a genera of heterologous “object sequences” having no specific structural elements , any or all LTR retrotransposon structural polypeptide domain, or any nucleic acid molecule encoding the LTR retrotransposon structural polypeptide domain or any or all LTR transposon reverse transcriptase domain capable of transcribing the template RNA including variants, mutants and homologs from any source i.e., derived from any retrotransposon of undefined and unlimited structures and able to bind/interact with a genera of template RNA sequences and heterologous “object sequences” of undefined and unlimited structures.
The prior art summarize by the reference of Ribet (Journal of Virology, 2007 1888-98) teaches activity of MusD depends on intact gag, pro and pol organization that includes RT in pol. The art teaches defection and/or mutation in these results in strong inhibition in mobility (see page 1895, col. 1, para. 1). Although there may be RT that is homologous to MusD or IAP derived but mixing RT derived from one species with arbitrary LTR retrotransposon RNA would be unpredictable for the contemplated biological activity because a variant of RT or RT homologous to known LTR transposon does not automatically efficiently copy any LTR as generally retrotransposon are cis preferential and dependent on sequence specific RNA packaging signal and use of different species between LTR system is nether disclosed in the specification nor contemplated in prior art for the contemplated biological activity. Nowak (Nature Structural & Molecular Biology, 2014, 21, 389-396) teaches Ty3 RT adopts an asymmetric homodimer structure whose assembly is substrate dependent. Nowak reported that Ty3 RT submits A and B have identical sequence (see page 390, col. 2, para. 2) but one contribute DNA polymerase activity, while other has RNase H activity (see page 390, col. 2, to 391, col. 1). The study of Nowak shows that same polypeptide could perform different function depending on the structural state of the dimer. This is further evident from the teaching in prior art that reported preserving the catalytic motif of an RT fragment is not sufficient to predict retro transposition activity because RNA binding, dimerization, RNase H positioning , primer utilization and substrate induced conformational changes would all contribute to the resulting function (see Uzun et al Journal of Virology, 2001, 6337-6347l; Pallan et al Cell Cycle 7:16, 2562-2569, 2008; Nowak, Li et al (JBC, 2016, 291, 26566-26585 and Corley et al Mol. Cell, 2020, 78(1), 9-29).
As the claimed system for modifying a DNA, the system comprising: genera of template RNAs or a genera of DNA encoding said genera template RNAs and a genera of heterologous “object sequences” having no specific structural element., any or all reverse transcriptase domains including variants, mutants and homologs from any source i.e., derived from any retrotransposon of undefined and unlimited structures and able to bind/interact with a genera of template RNA sequences and heterologous “object sequences” of undefined and unlimited structures having widely variable structures and associated function in the claimed system, since minor changes in structure may result in changes affecting function and no additional information correlating structure with function has been provided. Furthermore, “Possession may not be shown by merely describing how to obtain possession of members of the claimed genus or how to identify their common structural features” (See University of Rochester, 358 F.3d at 927, 69 USPQ2d at 1895).
The claimed invention as a whole is not adequately described if the claims require essential or critical elements that are not adequately described in the specification and that is not conventional in the art as of applicants effective filing date. Possession may be shown by actual reduction to practice, clear depiction of the invention in a detailed drawing, or by describing the invention with sufficient relevant identifying characteristics such that a person skilled in the art would recognize that the inventor had possession of the claimed invention. Pfaff v. Wells Electronics, Inc.. 48USPQ2d 1641,1646 (1998).
With the exception of the sequence referred to above, the skilled artisan cannot envision the detailed chemical structure of the encompassed polynucleotides or polypeptides, and therefore conception is not achieved until reduction to practice has occurred regardless of the complexity or simplicity of the method of isolation. The skilled artisan cannot envision the detailed chemical structure of the encompassed nucleic acid molecules and therefore conception is not achieved until reduction to practice has occurred, regardless of the complexity or simplicity of the method of isolation. Adequate written description requires more than a mere statement that it is part of the invention and reference to a potential method of isolating it. The nucleic acid itself is required. See Fiers v. Revel, 25 USPQ2d 1601 at 1606 (CAFC 1993) and Amgen Inc. v. Chugai Pharmaceutical Co. Ltd., 18 USPQ2d 1016.
One cannot describe what one has not conceived. See Fiddes v. Bard, 30 USPQ2d 1481 at 1483. In Fiddes, claims directed to mammalian FGF's were found to be unpatentable due to lack of written description for that broad class. The specification provided only the bovine sequence.
In view of the above considerations one of skill in the art would not recognize that applicant was in possession of the necessary common features or attributes possessed by any member of the genus encompassed by the claims other than those specifically disclosed in Table S5. University of California v. Eli Lilly and Co.. 43 USPQ2d 1398,1404, 1405 held that "to fulfill the written description requirement, a patent specification must describe an invention and do so in sufficient detail that one skilled in the art can clearly conclude "the inventor invented the claimed invention".
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, 9-20 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.
Claim limitation “A system” intended for modifying DNA invokes 35 U.S.C. 112(f) or pre-AIA 35 U.S.C. 112, sixth paragraph. However, the written description fails to disclose the corresponding structure, material, or acts for performing the entire claimed function and to clearly link the structure, material, or acts to the function. It is emphasized that A system is a non-structural term and therefore, the scope of the claim is indefinite and is rejected under 35 U.S.C. 112(b) or pre-AIA 35 U.S.C. 112, second paragraph.
Applicant may:
(a) Amend the claim so that the claim limitation will no longer be interpreted as a limitation under 35 U.S.C. 112(f) or pre-AIA 35 U.S.C. 112, sixth paragraph;
(b) Amend the written description of the specification such that it expressly recites what structure, material, or acts perform the entire claimed function, without introducing any new matter (35 U.S.C. 132(a)); or
(c) Amend the written description of the specification such that it clearly links the structure, material, or acts disclosed therein to the function recited in the claim, without introducing any new matter (35 U.S.C. 132(a)).
If applicant is of the opinion that the written description of the specification already implicitly or inherently discloses the corresponding structure, material, or acts and clearly links them to the function so that one of ordinary skill in the art would recognize what structure, material, or acts perform the claimed function, applicant should clarify the record by either:
(a) Amending the written description of the specification such that it expressly recites the corresponding structure, material, or acts for performing the claimed function and clearly links or associates the structure, material, or acts to the claimed function, without introducing any new matter (35 U.S.C. 132(a)); or
(b) Stating on the record what the corresponding structure, material, or acts, which are implicitly or inherently set forth in the written description of the specification, perform the claimed function. For more information, see 37 CFR 1.75(d) and MPEP §§ 608.01(o) and 2181.
For the sake of compact prosecution, claims 1, 9-20 and 26 are interpreted to encompass a composition for modifying DNA, said composition comprising: a) a template RNA comprising a first long terminal repeat (LTR), a second LTR, a heterologous object sequence encoding a therapeutic effector, positioned between the first LTR and the second LTR, or a DNA molecule encoding the template RNA ;b) an LTR retrotransposon structural polypeptide domain, or a nucleic acid molecule encoding the LTR retrotransposon structural polypeptide domain; and c) an LTR retrotransposon reverse transcriptase polypeptide domain capable of reverse transcribing the template RNA, thereby producing a template DNA, or a nucleic acid molecule encoding the LTR retrotransposon reverse transcriptase polypeptide domain.
Conclusion
No claims allowed.
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/ANOOP K SINGH/ Primary Examiner, Art Unit 1632
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