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 .
Election/Restrictions
Applicant’s election without traverse of claims 1, 2, 4, 5, 7, 8, 10-14, 16, 18, 29, 32, 33, 35, and 47 (Group I) in the reply filed on 02/19/2026 is acknowledged.
Claim 37 is withdrawn from further consideration pursuant to 37 CFR 1.142(b) as being drawn to a nonelected invention, there being no allowable generic or linking claim.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 02/19/2026.
Accordingly, claims 1, 2, 4, 5, 7, 8, 10-14, 16, 18, 29, 32, 33, 35, and 47 are under consideration.
Priority
Applicant’s claim for the benefit of a prior-filed application under 35 U.S.C. 119(e) or under 35 U.S.C. 120, 121, 365(c), or 386(c) is acknowledged. The earliest effective filing date to which the instant application is entitled is 10/19/2021.
Information Disclosure Statement
Receipt of information disclosure statements on 01/17/2024, 12/02/2024, 05/19/2025, and 09/24/2025 is acknowledged. The signed and initialed PTO-1449‘s have been mailed with this action.
Drawings
The drawings are objected to because:
With regard to Figures 19 and 53, the grayscale keys for the Figures depicted therein are not readily distinguishable to one of ordinary skill in the art for purposes of identifying which data correspond to which category from the key. It would be remedial to ensure that the key readily facilitates interpretation of the depicted Figures.
With regard to Figures 22B, 27B, 28, 64E, and 76A-76C, the image quality is insufficient to be clearly legible. It would be remedial to increase the image quality such that it is clearly legible.
Corrected drawing sheets in compliance with 37 CFR 1.121(d) are required in reply to the Office action to avoid abandonment of the application. Any amended replacement drawing sheet should include all of the figures appearing on the immediate prior version of the sheet, even if only one figure is being amended. The figure or figure number of an amended drawing should not be labeled as “amended.” If a drawing figure is to be canceled, the appropriate figure must be removed from the replacement sheet, and where necessary, the remaining figures must be renumbered and appropriate changes made to the brief description of the several views of the drawings for consistency. Additional replacement sheets may be necessary to show the renumbering of the remaining figures. Each drawing sheet submitted after the filing date of an application must be labeled in the top margin as either “Replacement Sheet” or “New Sheet” pursuant to 37 CFR 1.121(d). If the changes are not accepted by the examiner, the applicant will be notified and informed of any required corrective action in the next Office action. The objection to the drawings will not be held in abeyance.
Nucleotide and/or Amino Acid Sequence Disclosures
Summary of Requirements for Patent Applications Filed On Or After July 1, 2022, That Have Sequence Disclosures
37 CFR 1.831(a) requires that patent applications which contain disclosures of nucleotide and/or amino acid sequences that fall within the definitions of 37 CFR 1.831(b) must contain a “Sequence Listing XML”, 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 1.831-1.835. This “Sequence Listing XML” part of the disclosure may be submitted:
1. In accordance with 37 CFR 1.831(a) using the symbols and format requirements of 37 CFR 1.832 through 1.834 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”) in XML format, together with an incorporation by reference statement of the material in the XML file in a separate paragraph of the specification (an incorporation by reference paragraph) as required by 37 CFR 1.835(a)(2) or 1.835(b)(2) identifying:
a. the name of the XML file
b. the date of creation; and
c. the size of the XML file in bytes; or
2. In accordance with 37 CFR 1.831(a) using the symbols and format requirements of 37 CFR 1.832 through 1.834 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 statement of the material in the XML format according to 37 CFR 1.52(e)(8) and 37 CFR 1.835(a)(2) or 1.835(b)(2) in a separate paragraph of the specification identifying:
a. the name of the XML file;
b. the date of creation; and
c. the size of the XML file in bytes.
SPECIFIC DEFICIENCIES AND THE REQUIRED RESPONSE TO THIS NOTICE ARE AS FOLLOWS:
Specific deficiency - Sequences appearing in the drawings are not identified by sequence identifiers in accordance with 37 CFR 1.831(c). Sequence identifiers for sequences (i.e., “SEQ ID NO:X” or the like) must appear either in the drawings or in the Brief Description of the Drawings. Specifically, Figure 28 appears to depict two sequences. However, the instant specification indicates that the Figure discloses SEQ ID NOs: 33555-33557, which encompasses three sequences. Given that the Figure appears to depict only two sequences, it is unclear which sequences are actually depicted. Similarly, Figure 73 appears to depict sixteen sequences. However, the instant specification indicates that the Figure discloses seventeen sequences. Given that the Figure appears to depict only sixteen sequences, it is unclear which sequences are actually depicted.
Required response – Applicant must provide:
Amended 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 (i.e., “SEQ ID NO:X” or the like) 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.
Specific deficiency - Sequences appearing in the specification are not identified by sequence identifiers (i.e., “SEQ ID NO:X” or the like) in accordance with 37 CFR 1.831(c). Paragraph [0135] appears to disclose an amino acid sequence at line 15 that requires a sequence identifier, as it comprises more than 4 specifically defined and enumerated residues.
Required response – Applicant must provide:
A substitute specification in compliance with 37 CFR 1.52, 1.121(b)(3), and 1.125 inserting the required sequence identifiers, 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.
Specification
The disclosure is objected to because of the following informalities:
Although the instant drawings are filed in black and white, the specification makes numerous references to color in the brief description of the drawings. See for example paragraphs [0064], [0075], [0080], [0084], [0131], [0133], [0137], [0139], [0140], and [0141], all of which disclose that the filed drawings include the color blue. There is no color in the instant drawings. It would be remedial to either provide color drawings, as set forth below, or to edit the instant specification to properly reflect the instant drawings.
Should applicant wish to provide color drawings, Color photographs and color drawings are not accepted in utility applications unless a petition filed under 37 CFR 1.84(a)(2) is granted. Any such petition must be accompanied by the appropriate fee set forth in 37 CFR 1.17(h), one set of color drawings or color photographs, as appropriate, if submitted via the USPTO patent electronic filing system or three sets of color drawings or color photographs, as appropriate, if not submitted via the via USPTO patent electronic filing system, and, unless already present, an amendment to include the following language as the first paragraph of the brief description of the drawings section of the specification:
The patent or application file contains at least one drawing executed in color. Copies of this patent or patent application publication with color drawing(s) will be provided by the Office upon request and payment of the necessary fee.
Color photographs will be accepted if the conditions for accepting color drawings and black and white photographs have been satisfied. See 37 CFR 1.84(b)(2).
Appropriate correction is required.
The lengthy specification has not been checked to the extent necessary to determine the presence of all possible minor errors. Applicant’s cooperation is requested in correcting any errors of which applicant may become aware in the specification.
Claim Objections
Claims 1, 4, 16, 18, and 47 are objected to because of the following informalities:
With regard to claims 1 and 4, both of which recite “nucleic acid insertion into the genome,” this recitation, while not strictly improper, nonetheless does not comport with standard linguistic conventions. For purposes of comporting with standard linguistic conventions, it would be remedial to amend the instant claim language such that it is more consistent with linguistic conventions. For example, claim 1 may recite “the insertion template comprises a nucleic acid sequence for insertion into the genome,” while claim 4 may recite “the nucleic acid sequence for insertion into the genome…”. These are merely examples set forth by the Examiner and are not intended to be limiting.
With regard to claims 16 and 18, both of which recite “the modified R2 element,” the Examiner notes that other claims recited the same species as “the modified R2 element enzyme” (bolded emphasis added). For purposes of internal consistency and clarity, it would be remedial to amend instant claims 16 and 18 to recite “the modified R2 element enzyme” (bolded emphasis added), as in the other claims.
With regard to claim 47, the recitation of “non-LTR-site specific retrotransposon element enzyme” (bolded and underlined emphasis added) at component ii) is inconsistent with the earlier-recited “non-LTR site specific retrotransposon element enzyme.” For purposes of internal consistency and clarity, it would be remedial to amend instant claim 47 to recite “non-LTR site specific retrotransposon element enzyme,” as earlier recited in the same claim.
With further regard to claim 47, the lack of a punctuation mark (such as a semicolon) separating components ii) and iii) does not comport with standard grammatical and/or linguistic conventions. It would be remedial to amend instant claim 47 to include a punctuation mark (such as a semicolon) separating components ii) and iii), as earlier recited in the same claim, thereby comporting with standard grammatical and/or linguistic conventions.
Appropriate correction is required.
Claim Rejections - 35 USC § 112
Claim 12 is 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 12 recites the limitation "the 28S rRNA locus" in lines 2-3. There is insufficient antecedent basis for this limitation in the claim. It would be remedial to amend the instant claim such that there is sufficient antecedent basis for every claimed limitation.
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.
Claims 1, 2, 4, 5, 7, 8, 10, 11, 13, 14, 16, 18, 35, and 47 are rejected under 35 U.S.C. 102(a)(1) and 35 U.S.C. 102(a)(2) as being anticipated by WO 2021/102042 A1 (hereinafter Zhang; as cited in the IDS filed 01/17/2024), as evidenced by Thompson and Christensen, 2011 (hereinafter Thompson) and Swarts and Jinek, 2018 (hereinafter Swarts; as cited in the IDS filed 09/24/2025).
With regard to claim 1, which recites “a genome editing system comprising: i) an R2 element enzyme; and ii) a payload RNA, wherein the payload RNA comprises an insertion template…wherein the insertion template comprises a sequence for a nucleic acid insertion into the genome, and wherein the R2 element enzyme comprises a reverse transcriptase domain and a nickase domain,” Zhang discloses engineered or non-naturally occurring compositions for targeted gene modification, targeted insertion, perturbation of gene transcripts, and nucleic acid editing, said compositions comprising a non-LTR retrotransposon polypeptide (i.e. R2) and a polynucleotide encoding a retrotransposon RNA, wherein the retrotransposon RNA comprises or encodes a donor polynucleotide (abstract; paragraphs [0006] and [0008]), as instantly claimed. Zhang further discloses that R2 elements (i.e. from Bombyx mori) encode a single ORF containing reverse transcriptase activity and a restriction enzyme-like domain, although nickase variants are also disclosed to have utility in the system disclosed therein (paragraphs [0082] and [0088]). Thus, the compositions comprising an R2 element enzyme with a reverse transcriptase domain and a nickase domain for targeted insertion of nucleic acids encoded by an R2 retrotransposon RNA disclosed in Zhang anticipate each and every limitation of instant claim 1.
With regard to claim 2, which recites “the genome editing system of claim 1, wherein the R2 element enzyme further comprises a targeting domain,” R2 elements, such as those disclosed in Zhang (paragraph [0008]), naturally comprise a targeting domain. As reviewed in Thompson, R2 retrotransposons encode DNA binding motifs, such as zinc fingers, to target insertion events to specific sites in the genome (page 29, column 2, paragraph 1). Thus, the naturally-occurring zinc finger domains encoded in R2 retrotransposon elements, such as those disclosed in Zhang, are considered to anticipate each and every limitation of instant claim 2.
With regard to claim 4, which recites “the genome editing system of claim 1, wherein the nucleic acid insertion into the genome is a DNA or RNA insertion template,” as set forth above, Zhang discloses retrotransposon RNA comprising or encoding a donor polynucleotide (paragraphs [0006] and [0008]). Said donor polynucleotide is further disclosed to be an RNA comprising a poly-A tail in some embodiments (paragraph [0012]), as instantly claimed. Thus, Zhang anticipates each and every limitation of instant claim 4.
With regard to claim 5, which recites “the R2 element enzyme [of the genome editing system of claim 1] is a modified R2 element enzyme,” as set forth above, Zhang discloses compositions for targeted gene editing, said compositions comprising an R2 element enzyme (abstract; paragraphs [0006] and [0008]). Zhang further discloses that the R2 element enzymes taught therein may be modified by fusion to a site-specific nuclease (paragraph [0009]) or subject to other modifications or truncations (paragraph [0010]), as instantly claimed. Thus, Zhang anticipates each and every limitation of instant claim 5.
With regard to claim 7, which recites “the modified R2 element enzyme [of the genome editing system of claim 5] is modified by an N-terminal or C-terminal truncation of the R2 element enzyme sequence,” as set forth above, Zhang discloses that the R2 element enzymes taught therein may be modified by modifications such as truncations (paragraph [0010]). These truncations are disclosed to impact a zinc finger region, a Myb region, a basic region, a reverse transcriptase domain, a cysteine-histidine rich motif, or an endonuclease domain (paragraph [0010]). As shown in Figure 1 of Thompson, R2 element enzymes comprise zinc finger domains at the N terminus and restriction-like endonuclease domains at the C terminus. Therefore, Zhang’s disclosure of truncation of a zinc finger region or endonuclease domain of R2 element enzymes must necessarily disclose truncation of the N terminus or C terminus of the R2 element enzyme of the genome editing compositions taught therein. Thus, it is considered that Zhang anticipates each and every limitation of instant claim 7.
With regard to claim 8, which recites “the modified R2 element enzyme [of the genome editing system of claim 5] comprises a linker,” as set forth above, that the R2 element enzymes taught therein may be modified by fusion to a site-specific nuclease (paragraph [0009]). Such fusion may be accomplished by connecting the non-LTR retrotransposon to the site-specific nuclease via a linker (paragraph [0078]). Thus, Zhang anticipates each and every limitation of instant claim 8.
With regard to claim 10, which recites “the genome editing system of claim 1, wherein the genome editing system targets a genomic locus,” as set forth above, Zhang discloses compositions for targeted gene editing (including targeted insertion), said compositions comprising an R2 element enzyme (abstract; paragraphs [0006] and [0008]). Furthermore, Zhang also discloses fusion of the R2 element enzymes taught therein to site-specific nucleases, such as CRISPR nucleases (paragraphs [0003], [0009], and [0010]), for purposes of targeting a specific site in a targeted polynucleotide within the genome (paragraphs [0010] and [0148]). Thus, Zhang anticipates each and every limitation of instant claim 10.
With regard to claim 11, which recites “the genome editing system of claim 1, wherein the genome editing system targets a genomic locus other than the 28S rRNA locus,” as set forth above, Zhang discloses fusion of the R2 element enzymes taught therein to site-specific nucleases, such as CRISPR nucleases (paragraphs [0003], [0009], and [0010]), for purposes of targeting a specific site in a targeted polynucleotide within the genome (paragraphs [0010] and [0148]). Such targeted sites may include “safe harbor” loci for directed transgene integration, such as CCR5 or AAVS1, or the TRAC locus may be targeted for transgene insertion (paragraph [0598]). Therefore, Zhang discloses targeting of a genomic locus other than the 28S rRNA locus with the compositions taught therein, as instantly claimed. Thus, Zhang anticipates each and every limitation of instant claim 11.
With regard to claim 13, which recites “the genome editing system of claim 11, wherein a non-naturally occurring targeting region is fused to the N-terminus of the R2 element enzyme or inserted into the R2 element enzyme,” as set forth above, Zhang discloses fusion of the R2 element enzymes taught therein to site-specific nucleases, such as CRISPR nucleases (paragraphs [0003], [0009], and [0010]). Specifically, the site-specific nuclease is disclosed to be fused to the N-terminus of the non-LTR retrotransposon polypeptide taught therein for purposes of targeted transposition of a donor sequence into targeted nucleic acids (paragraph [0009]). Thus, Zhang anticipates each and every limitation of instant claim 13.
With regard to claim 14, which recites “the genome editing system of claim 5, wherein the modified R2 element enzyme is a fusion protein,” as set forth above, Zhang discloses fusion of the R2 element enzymes taught therein to site-specific nucleases, such as CRISPR nucleases (paragraphs [0003], [0009], and [0010]). Thus, Zhang anticipates each and every limitation of instant claim 14.
With regard to claim 16, which recites “the modified R2 element [of the genome editing system of claim 5] is fused to a Cas12 protein that is fully active, catalytically dead, or functioning as a nickase,” as set forth above, Zhang discloses fusion of the R2 element enzymes taught therein to site-specific nucleases, such as CRISPR nucleases (paragraphs [0003], [0009], and [0010]). Such CRISPR nucleases include Cpf1, which may have endonuclease or nickase activity (paragraphs [0128] and [0129]). Per Swarts, Cpf1 is another term for Cas12a (abstract), which is a Cas12 protein, as instantly claimed. Thus, Zhang anticipates each and every limitation of instant claim 16.
With regard to claim 18, which recites “the modified R2 element [of the genome editing system of claim 5] is fused to a TALEN protein, zinc finger protein, argonaute, or meganuclease protein,” as set forth above, Zhang discloses fusion of the R2 element enzymes taught therein to site-specific nucleases, such as CRISPR nucleases (paragraphs [0003], [0009], and [0010]). However, the site-specific nucleases of this fusion are not limited to CRISPR nucleases (paragraph [0009]). Other exemplary site-specific nucleases for fusion include TALENS, zinc finger nucleases, and meganucleases (paragraph [0213]), as instantly claimed. Thus, Zhang anticipates each and every limitation of instant claim 18.
With regard to claim 35, which recites “the genome editing system of claim 1, wherein the R2 element enzyme comprises a nuclear localization signal (NLS),” Zhang discloses that the non-LTR retrotransposons (such as R2 elements) taught therein may comprise a nuclear localization signal (paragraph [0008] and [0244]), as instantly claimed. Thus, Zhang anticipates each and every limitation of instant claim 35.
With regard to claim 47, which recites “a genome editing system comprising: i) a payload RNA, wherein the payload RNA comprises an insertion template…wherein the insertion template comprises a sequence for a nucleic acid insertion into the genome; ii) a non-LTR site specific retrotransposon element enzyme; wherein the non-LTR site specific retrotransposon element enzyme comprises a reverse transcriptase domain…and wherein if the non-LTR-site specific retrotransposon element enzyme does not comprise the optional nuclease or nickase domain, the genome editing system further comprises iii) a nuclease or nickase enzyme,” as set forth above, Zhang discloses engineered or non-naturally occurring compositions for targeted gene modification, targeted insertion, perturbation of gene transcripts, and nucleic acid editing, said compositions comprising a non-LTR retrotransposon polypeptide (i.e. R2) and a polynucleotide encoding a retrotransposon RNA, wherein the retrotransposon RNA comprises or encodes a donor polynucleotide (abstract; paragraphs [0006] and [0008]), as instantly claimed. Zhang further discloses that R2 elements (i.e. from Bombyx mori) encode a single ORF containing reverse transcriptase activity and a restriction enzyme-like domain, although nickase variants are also disclosed to have utility in the system disclosed therein (paragraphs [0082] and [0088]). Thus, the compositions comprising an R2 element enzyme with a reverse transcriptase domain and a nickase domain for targeted insertion of nucleic acids encoded by an R2 retrotransposon RNA disclosed in Zhang anticipate each and every limitation of instant claim 47.
However, if one does not accept that these endogenous R2 domains do not read on the limitations of the instant claim, Zhang also discloses fusion of the R2 element enzymes taught therein to site-specific nucleases, such as CRISPR nucleases (paragraphs [0003], [0009], and [0010]). Such CRISPR nucleases include Cpf1, which may have endonuclease or nickase activity (paragraphs [0128] and [0129]). Thus, Zhang anticipates each and every limitation of instant claim 47.
Claims 1, 2, 4, 5, 7, 8, 10, 11, 12, 13, 14, 16, 18, ,35, and 47 are rejected under 35 U.S.C. 102(a)(1) and 35 U.S.C. 102(a)(2) as being anticipated by US 2020/0109398 A1 (hereinafter Rubens; as cited in the IDS filed 05/19/2025), as evidenced by Thompson and Christensen, 2011 (hereinafter Thompson) and Swarts and Jinek, 2018 (hereinafter Swarts; as cited in the IDS filed 09/24/2025).
With regard to claim 1, which recites “a genome editing system comprising: i) an R2 element enzyme; and ii) a payload RNA, wherein the payload RNA comprises an insertion template…wherein the insertion template comprises a sequence for a nucleic acid insertion into the genome, and wherein the R2 element enzyme comprises a reverse transcriptase domain and a nickase domain,” Rubens discloses methods and compositions for inserting sequences of interest to modulate a target genome (abstract; paragraph [0003]) using the retrotransposon-based Gene Writer™ system (paragraph [0114]; figure 1). Per the disclosure of Rubens, the elements of non-L TR retrotransposons (such as R2) can be functionally modularized to form the Gene Writer™ gene editor, which is capable of modifying, targeting, editing, modifying, or manipulating a target DNA sequence by reverse transcription (paragraphs [0116] and [0117]; Example 1). The Gene Writer™ gene editor system comprises a polypeptide (or a nucleic acid encoding the same) comprising a reverse transcriptase domain, an endonuclease domain (which may comprise a Cas9 nickase (paragraph [0105])), and a DNA binding domain (which targets different sites of the genome (paragraph [0090]; figure 3) (paragraph [0117]; figure 2). Additionally, Rubens discloses that the Gene Writer™ gene editing system comprises a template RNA (or DNA encoding the same), itself comprising a sequence that binds the polypeptide, a heterologous object sequence that encodes a therapeutic polypeptide (or a fragment or variant thereof) referred to as the payload domain for insertion into the target genome (paragraph [0178]), and a guide RNA (paragraphs [0007], [0117], and [0173]; figure 11). Thus, Rubens discloses a genome editing system comprising an R2 element enzyme, as set forth above, as well as a template RNA considered to read on the instantly claimed payload RNA, as it comprises an insertion template comprising a nucleic acid sequence for insertion into the genome, as instantly claimed. Thus, Rubens anticipates each and every limitation of instant claim 1.
With regard to claim 2, which recites “the genome editing system of claim 1, wherein the R2 element enzyme further comprises a targeting domain,” R2 elements, such as those disclosed in Rubens (paragraphs [0116] and [0117]; Example 1), naturally comprise a targeting domain. As reviewed in Thompson, R2 retrotransposons encode DNA binding motifs, such as zinc fingers, to target insertion events to specific sites in the genome (page 29, column 2, paragraph 1). Thus, the naturally-occurring zinc finger domains encoded in R2 retrotransposon elements, such as those disclosed in Rubens, are considered to anticipate each and every limitation of instant claim 2.
However, if one does not accept that the naturally-occurring zinc finger domains encoded in R2 retrotransposon elements satisfy the limitations of instant claim 2, Rubens also discloses that the non-LTR retrotransposon elements taught therein can be functionally modularized and/or modified to target, edit, modify, or manipulate a target DNA sequence for purposes of inserting a heterologous nucleic acid sequence into a targeted genome site by reverse transcription, for example a genomic safe harbor site that is able to accommodate the integration of heterologous genetic material (paragraphs [0080] and [0117]). Thus, Rubens anticipates each and every limitation of instant claim 2.
With regard to claim 4, which recites “the genome editing system of claim 1, wherein the nucleic acid insertion into the genome is a DNA or RNA insertion template,” as set forth above, Rubens discloses that the Gene Writer™ gene editing system comprises a template RNA (or DNA encoding the same) (paragraph [0009]), itself comprising a sequence that binds the polypeptide, a heterologous object sequence that encodes a therapeutic polypeptide (or a fragment or variant thereof) referred to as the payload domain for insertion into the target genome (paragraph [0178]), and a guide RNA (paragraphs [0007], [0117], and [0173]; figure 11). Thus, Rubens anticipates each and every limitation of instant claim 4.
With regard to claim 5, which recites “the R2 element enzyme [of the genome editing system of claim 1] is a modified R2 element enzyme,” as set forth above, Rubens also discloses that the non-LTR retrotransposon elements taught therein can be functionally modularized and/or modified to target, edit, modify, or manipulate a target DNA sequence for purposes of inserting a heterologous nucleic acid sequence into a targeted genome site by reverse transcription, for example a genomic safe harbor site that is able to accommodate the integration of heterologous genetic material (paragraphs [0080] and [0117]). Thus, Rubens anticipates each and every limitation of instant claim 5.
With regard to claim 7, which recites “the modified R2 element enzyme [of the genome editing system of claim 5] is modified by an N-terminal or C-terminal truncation of the R2 element enzyme sequence,” Rubens further discloses experimentation with truncation of the 3’ UTR of R2Tg (an endogenous retrotransposon from the zebra finch) (paragraphs [0240] and [0266]), which is located at the C terminus of the R2 element enzyme sequence, as known to those of ordinary skill in the art. Thus, Rubens anticipates each and every limitation of instant claim 7.
With regard to claim 8, which recites “the modified R2 element enzyme [of the genome editing system of claim 5] comprises a linker,” Ruben further discloses that the components of the Gene Writer™ gene editing system taught therein may comprise domains (such as those derived from R2) joined by a linker (paragraph [0149]; Figure 18). Thus, Rubens anticipates each and every limitation of instant claim 8.
With regard to claim 10, which recites “the genome editing system [of claim 1] targets a genomic locus,” as set forth above, Rubens discloses that the non-LTR retrotransposon elements taught therein can be functionally modularized and/or modified to target, edit, modify, or manipulate a target DNA sequence for purposes of inserting a heterologous nucleic acid sequence into a targeted genome site by reverse transcription, for example a genomic safe harbor site that is able to accommodate the integration of heterologous genetic material (paragraphs [0080] and [0117]). Thus, Rubens anticipates each and every limitation of instant claim 10.
With regard to claim 11, which recites “the genome editing system [of claim 1] targets a genomic locus other than the 28S rRNA locus,” as set forth above, Rubens discloses that the non-LTR retrotransposon elements taught therein can be functionally modularized and/or modified to target, edit, modify, or manipulate a target DNA sequence for purposes of inserting a heterologous nucleic acid sequence into a targeted genome site by reverse transcription, for example a genomic safe harbor site that is able to accommodate the integration of heterologous genetic material (paragraphs [0080] and [0117]). Thus, Rubens anticipates each and every limitation of instant claim 11.
With regard to claim 12, which recites “the genome editing system of claim 11, wherein an N-terminal zinc finger domain of the R2 element enzyme is modified to target a genomic locus other than the 28S rRNA locus,” as set forth above, Rubens discloses that the non-LTR retrotransposon elements taught therein can be functionally modularized and/or modified to target, edit, modify, or manipulate a target DNA sequence for purposes of inserting a heterologous nucleic acid sequence into a targeted genome site by reverse transcription, for example a genomic safe harbor site that is able to accommodate the integration of heterologous genetic material (paragraphs [0080] and [0117]). Rubens further discloses a working example wherein the polypeptide component of the Gene Writer™ gene editing system is derived from R2 of Bombyx mori, which is modified by replacing its DNA binding domain in the amino terminus of the polypeptide (a zinc finger motif per Thompson: Figure 1; page 29, column 2, paragraph 1) with a heterologous zinc-finger DNA binding domain known to bind to DNA in the BmBLOS2 loci of B. mori cells (paragraph [0220]). Thus, Rubens anticipates each and every limitation of instant claim 12 regarding modification of an N-terminal zinc finger domain to target a genomic locus other than the 28S rRNA locus.
With regard to claim 13, which recites “the genome editing system of claim 11, wherein a non-naturally occurring targeting region is fused to the N-terminus of the R2 element enzyme or inserted into the R2 element enzyme,” as set forth above, Rubens discloses that the non-LTR retrotransposon elements taught therein can be functionally modularized and/or modified to target, edit, modify, or manipulate a target DNA sequence for purposes of inserting a heterologous nucleic acid sequence into a targeted genome site by reverse transcription, for example a genomic safe harbor site that is able to accommodate the integration of heterologous genetic material (paragraphs [0080] and [0117]). Rubens further discloses a working example wherein the polypeptide component of the Gene Writer™ gene editing system is derived from R2 of Bombyx mori, which is modified by replacing its DNA binding domain in the amino terminus of the polypeptide (a zinc finger motif per Thompson: Figure 1; page 29, column 2, paragraph 1) with a heterologous zinc-finger DNA binding domain known to bind to DNA in the BmBLOS2 loci of B. mori cells (paragraph [0220]). Thus, Rubens anticipates each and every limitation of instant claim 13 regarding insertion of a non-naturally occurring targeting region into the R2 element enzyme.
With regard to claim 14, which recites “the genome editing system of claim 5, wherein the modified R2 element enzyme is a fusion protein,” as set forth above, Rubens discloses the retrotransposon-based Gene Writer™ system (paragraph [0114]; figure 1), wherein the Gene Writer™ protein is a fusion protein comprising an R2-derived reverse transcriptase domain (which reads on the instantly claimed modified R2 element enzyme) fused to an endonuclease such as Cas protein (Figure 18). Thus, Rubens anticipates each and every limitation of instant claim 14.
With regard to claim 16, which recites “the modified R2 element [of the genome editing system of claim 5] is fused to a Cas12 protein that is fully active, catalytically dead, or functioning as a nickase,” as set forth above, Rubens discloses the retrotransposon-based Gene Writer™ system (paragraph [0114]; figure 1), wherein the Gene Writer™ protein is a fusion protein comprising an R2-derived reverse transcriptase domain (which reads on the instantly claimed modified R2 element enzyme) fused to an endonuclease such as Cas protein (Figure 18). Such Cas proteins include Cpf1 that may be altered to have no endonuclease activity (paragraph [0124]). Per Swarts, Cpf1 is another term for Cas12a (abstract), which is a Cas12 protein, as instantly claimed. Thus, Rubens anticipates each and every limitation of instant claim 16.
With regard to claim 18, which recites “the modified R2 element [of the genome editing system of claim 5] is fused to a TALEN protein, zinc finger protein, argonaute, or meganuclease protein,” not only does Rubens disclose fusion to Cas proteins (paragraph [0124]; Figure 18), but Rubens also discloses fusion to zinc finger elements, TAL effector elements, or fragments thereof (paragraph [0124]). Thus, Rubens anticipates each and every limitation of instant claim 18.
With regard to claim 35, which recites “the genome editing system of claim 1, wherein the R2 element enzyme comprises a nuclear localization signal (NLS),” Rubens further discloses that the Gene Writer™ polypeptide (which may be an R2Bm protein as set forth above) comprises a nuclear localization sequence or a nucleolar localization sequence which may also be a nuclear localization sequence at the N-terminus or C-terminus of the Gene Writer™ polypeptide (paragraph [0127]). Thus, Rubens anticipates each and every limitation of instant claim 35.
With regard to claim 47, which recites “a genome editing system comprising: i) a payload RNA, wherein the payload RNA comprises an insertion template…wherein the insertion template comprises a sequence for a nucleic acid insertion into the genome; ii) a non-LTR site specific retrotransposon element enzyme; wherein the non-LTR site specific retrotransposon element enzyme comprises a reverse transcriptase domain…and wherein if the non-LTR-site specific retrotransposon element enzyme does not comprise the optional nuclease or nickase domain, the genome editing system further comprises iii) a nuclease or nickase enzyme,” as set forth above, Rubens discloses methods and compositions for inserting sequences of interest to modulate a target genome (abstract; paragraph [0003]) using the retrotransposon-based Gene Writer™ system (paragraph [0114]; figure 1). Per the disclosure of Rubens, the elements of non-L TR retrotransposons (such as R2) can be functionally modularized to form the Gene Writer™ gene editor, which is capable of modifying, targeting, editing, modifying, or manipulating a target DNA sequence by reverse transcription (paragraphs [0116] and [0117]; Example 1). The Gene Writer™ gene editor system comprises a polypeptide (or a nucleic acid encoding the same) comprising a reverse transcriptase domain, an endonuclease domain (which may comprise a Cas9 nickase (paragraph [0105])), and a DNA binding domain (which targets different sites of the genome (paragraph [0090]; figure 3) (paragraph [0117]; figure 2). Additionally, Rubens discloses that the Gene Writer™ gene editing system comprises a template RNA (or DNA encoding the same), itself comprising a sequence that binds the polypeptide, a heterologous object sequence that encodes a therapeutic polypeptide (or a fragment or variant thereof) referred to as the payload domain for insertion into the target genome (paragraph [0178]), and a guide RNA (paragraphs [0007], [0117], and [0173]; figure 11). Thus, the Gene Writer™ system disclosed in Rubens anticipates each and every limitation of instant claim 47.
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.
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 12 is rejected under 35 U.S.C. 103 as being unpatentable over WO 2021/102042 A1 (hereinafter Zhang; as cited in the IDS filed 01/17/2024), as evidenced by Thompson and Christensen, 2011 (hereinafter Thompson) and Swarts and Jinek, 2018 (hereinafter Swarts; as cited in the IDS filed 09/24/2025), as applied to claims 1 and 11 above, and further in view of US 2020/0109398 A1 (hereinafter Rubens; as cited in the IDS filed 05/19/2025).
The disclosure of Zhang is described above and applied as before. However, this disclosure does not teach the R2 zinc finger domain modification of instant claim 12.
With regard to claim 12, which recites “the genome editing system of claim 11, wherein an N-terminal zinc finger domain of the R2 element enzyme is modified to target a genomic locus other than the 28S rRNA locus,” as set forth above, Zhang discloses fusion of the R2 element enzymes taught therein to site-specific nucleases, such as CRISPR nucleases (paragraphs [0003], [0009], and [0010]), for purposes of targeting a specific site in a targeted polynucleotide within the genome (paragraphs [0010] and [0148]). Such targeted sites may include “safe harbor” loci for directed transgene integration, such as CCR5 or AAVS1, or the TRAC locus may be targeted for transgene insertion (paragraph [0598]). However, Zhang does not disclose targeting other sites in the genome by modifying the N-terminal zinc finger domain of the R2 element enzyme.
This deficiency is cured by Rubens. As set forth above, Rubens discloses that the non-LTR retrotransposon elements taught therein can be functionally modularized and/or modified to target, edit, modify, or manipulate a target DNA sequence for purposes of inserting a heterologous nucleic acid sequence into a targeted genome site by reverse transcription, for example a genomic safe harbor site that is able to accommodate the integration of heterologous genetic material (paragraphs [0080] and [0117]). Rubens further discloses a working example wherein the polypeptide component of the Gene Writer™ gene editing system is derived from R2 of Bombyx mori, which is modified by replacing its DNA binding domain in the amino terminus of the polypeptide (a zinc finger motif per Thompson: Figure 1; page 29, column 2, paragraph 1) with a heterologous zinc-finger DNA binding domain known to bind to DNA in the BmBLOS2 loci of B. mori cells (paragraph [0220]).
Given that both Zhang and Rubens disclose targeting sites in the genome other than the 28S rRNA locus with gene editing compositions comprising modified R2 retrotransposon element enzymes, and that Rubens specifically discloses targeting sites in the genome other than the 28S rRNA locus by modifying a zinc finger domain of said modified R2 retrotransposon element enzymes, it would have been obvious to someone of ordinary skill in the art before the effective filing date of the claimed invention to further modify the R2 retrotransposon element enzymes disclosed in Zhang as in Rubens such that an endogenous zinc finger domain is modified to target genomic sites other than the 28S rRNA locus to predictably target genomic sites other than the 28S rRNA locus. One would have been motivated to make such a modification in order to receive the expected benefit of targeting genomic sites other than the 28S rRNA locus.
Claim 29 is rejected under 35 U.S.C. 103 as being unpatentable over WO 2021/102042 A1 (hereinafter Zhang; as cited in the IDS filed 01/17/2024), as evidenced by Thompson and Christensen, 2011 (hereinafter Thompson) and Swarts and Jinek, 2018 (hereinafter Swarts; as cited in the IDS filed 09/24/2025), as applied to claim 1 above, and further in view of Christensen et al., 2006 (hereinafter Christensen).
The disclosure of Zhang is described above and applied as before. However, this disclosure does not teach the payload RNA UTR truncation(s) of instant claim 29.
With regard to claim 29, which recites “the payload RNA [of the genome editing system of claim 1] further comprises a 5’ untranslated region (UTR), a 3’ UTR, or both a 5’ and a 3’ UTR, wherein the UTRs are truncated,” as set forth above, Zhang discloses the genome editing system of claim 1. Zhang further discloses that R2 from Bombyx mori depends only on the UTR of the insertion template, thereby motivating experimentation with the same (paragraph [0042]). Such experimentation would be further motivated by Christensen, which discloses that removal of 5’ RNA (comprising the UTR) from the insertion template for R2 is implicated in controlling a complete integration reaction, thereby motivating experimental manipulation of the same (i.e. truncation of the 5’ UTR) for purposes of controlling such integration (page 17606, column 2, paragraph 3).
Given that Zhang discloses the genome editing system of claim 1, with specific disclosure that R2 from Bombyx mori depends only on the UTR of the insertion template, thereby motivating experimentation with the same, and that Christensen discloses that removal of 5’ RNA (comprising the UTR) from the insertion template for R2 is implicated in controlling a complete integration reaction, it would have been obvious to someone of ordinary skill in the art before the effective filing date of the claimed invention to experimentally manipulate the 5’ UTR of R2 by truncating it to predictably temporally control the complete integration reaction performed by R2. One would have been motivated to make such a modification in order to receive the expected benefit of temporally controlling the complete integration reaction performed by R2.
Claim 32 is rejected under 35 U.S.C. 103 as being unpatentable over WO 2021/102042 A1 (hereinafter Zhang; as cited in the IDS filed 01/17/2024), as evidenced by Thompson and Christensen, 2011 (hereinafter Thompson) and Swarts and Jinek, 2018 (hereinafter Swarts; as cited in the IDS filed 09/24/2025), as applied to claim 1 above, and further in view of Glass et al., 2018 (hereinafter Glass; as cited in the IDS filed 09/24/2025), WO 2021/046243 A2 (hereinafter Getts; as cited in the IDS filed 12/02/2024), and Palazzo and Lee, 2018 (hereinafter Palazza; as cited in the IDS filed 09/24/2025).
The disclosure of Zhang is described above and applied as before. However, this disclosure does not teach the nuclear retention element of instant claim 32.
With regard to claim 32, which recites “the payload RNA [of the genome editing system of claim 1] further comprises a nuclear retention element,” as set forth above, Zhang discloses the genome editing system of claim 1. However, Zhang does not disclose the instantly claimed nuclear retention element.
This deficiency is cured by Glass teaches that the components to edit a genome with CRISPR-Cas "must be transported directly to the nucleus of targeted cells" in order to access the genomic DNA and to function properly (abstract). One of ordinary skill in the art would certainly be aware that this requirement is not unique to CRISPR-Cas machinery, but rather an inherent hurdle to gene editing given that eukaryotic cells are well-known to store their genomic DNA in their nuclei. Therefore, in order to edit said genomic DNA, the editing machinery (such as the instantly claimed payload RNA with an insertion template) must be transported directly to the nucleus, as taught in Glass and set forth above. Nuclear localization signals are known in the art, as set forth above regarding instant claim 1.
However, there are other available tools to promote and maintain nuclear localization. Getts discloses that another measure to enhance integration or retrotransposition efficiency is to increase nuclear import or retention, for example by fusing nuclear retention signal sequences to the editing machinery being used (paragraph [00238]). While Getts discloses fusion of nuclear retention signal sequences to LINE-1 retrotransposons for purposes of genome editing (paragraph [00238]), there is nothing in the art to suggest that nuclear retention signal sequences are only compatible with LINE-1 retrotransposons. In fact, nuclear retention signal sequences (or elements) are known to be crucial for proper processing of mRNA within the nucleus prior to export to the cytoplasm, as disclosed in Palazzo (see section "Reporter mRNAs"-pages 2-3).
Given that Zhang discloses the genome editing system of claim 1 (as set forth above), that Glass discloses that gene editing components (such as CRISPR machinery) must be directly transported to the nucleus of targeted cells to access the genomic DNA and to function effectively, and that Getts and Palazzo both disclose that nuclear retention signal sequences (or elements) are useful to increase nuclear retention, it would have been obvious to someone of ordinary skill in the art before the effective filing date of the claimed invention to modify the payload RNA of Zhang to comprise a nuclear retention element, as disclosed in Getts and Palazzo to predictably generate a payload RNA (or template RNA) carrying a nucleic acid sequence for insertion and capable of being retained in the nucleus to facilitate said insertion. One would have been motivated to make such a modification in order to receive the expected benefit of generating a payload RNA (or template RNA) carrying a nucleic acid sequence for insertion and capable of being retained in the nucleus to facilitate said insertion.
Claim 32 is rejected under 35 U.S.C. 103 as being unpatentable over US 2020/0109398 A1 (hereinafter Rubens; as cited in the IDS filed 05/19/2025), as evidenced by Thompson and Christensen, 2011 (hereinafter Thompson) and Swarts and Jinek, 2018 (hereinafter Swarts; as cited in the IDS filed 09/24/2025), as applied to claim 1 above, and further in view of Glass et al., 2018 (hereinafter Glass; as cited in the IDS filed 09/24/2025), WO 2021/046243 A2 (hereinafter Getts; as cited in the IDS filed 12/02/2024), and Palazzo and Lee, 2018 (hereinafter Palazza; as cited in the IDS filed 09/24/2025).
The disclosure of Rubens is described above and applied as before. However, this disclosure does not teach the nuclear retention element of instant claim 32.
With regard to claim 32, which recites “the payload RNA [of the genome editing system of claim 1] further comprises a nuclear retention element,” as set forth above, Rubens discloses the genome editing system of claim 1. However, Zhang does not disclose the instantly claimed nuclear retention element.
This deficiency is cured by Glass teaches that the components to edit a genome with CRISPR-Cas "must be transported directly to the nucleus of targeted cells" in order to access the genomic DNA and to function properly (abstract). One of ordinary skill in the art would certainly be aware that this requirement is not unique to CRISPR-Cas machinery, but rather an inherent hurdle to gene editing given that eukaryotic cells are well-known to store their genomic DNA in their nuclei. Therefore, in order to edit said genomic DNA, the editing machinery (such as the instantly claimed payload RNA with an insertion template) must be transported directly to the nucleus, as taught in Glass and set forth above. Nuclear localization signals are known in the art, as set forth above regarding instant claim 1.
However, there are other available tools to promote and maintain nuclear localization. Getts discloses that another measure to enhance integration or retrotransposition efficiency is to increase nuclear import or retention, for example by fusing nuclear retention signal sequences to the editing machinery being used (paragraph [00238]). While Getts discloses fusion of nuclear retention signal sequences to LINE-1 retrotransposons for purposes of genome editing (paragraph [00238]), there is nothing in the art to suggest that nuclear retention signal sequences are only compatible with LINE-1 retrotransposons. In fact, nuclear retention signal sequences (or elements) are known to be crucial for proper processing of mRNA within the nucleus prior to export to the cytoplasm, as disclosed in Palazzo (see section "Reporter mRNAs"-pages 2-3).
Given that Rubens discloses the genome editing system of claim 1 (as set forth above), that Glass discloses that gene editing components (such as CRISPR machinery) must be directly transported to the nucleus of targeted cells to access the genomic DNA and to function effectively, and that Getts and Palazzo both disclose that nuclear retention signal sequences (or elements) are useful to increase nuclear retention, it would have been obvious to someone of ordinary skill in the art before the effective filing date of the claimed invention to modify the payload RNA of Rubens to comprise a nuclear retention element, as disclosed in Getts and Palazzo to predictably generate a payload RNA (or template RNA) carrying a nucleic acid sequence for insertion and capable of being retained in the nucleus to facilitate said insertion. One would have been motivated to make such a modification in order to receive the expected benefit of generating a payload RNA (or template RNA) carrying a nucleic acid sequence for insertion and capable of being retained in the nucleus to facilitate said insertion.
Claim 33 is rejected under 35 U.S.C. 103 as being unpatentable over US 2020/0109398 A1 (hereinafter Rubens; as cited in the IDS filed 05/19/2025), as evidenced by Thompson and Christensen, 2011 (hereinafter Thompson) and Swarts and Jinek, 2018 (hereinafter Swarts; as cited in the IDS filed 09/24/2025), as applied to claim 1 above, and further in view of Anzalone et al., 2019 (hereinafter Anzalone; as cited in the IDS filed 09/24/2025).
The disclosure of Rubens is described above and applied as before. However, this disclosure does not teach the guide RNA extensions of instant claim 33.
With regard to claim 33, which recites “the payload RNA [of the genome editing system of claim 1] further comprises a Cas9 or Cas12 guide RNA, and wherein the Cas9 or Cas12 guide RNA comprises an extension with a 5’ homology sequence, a 3’ homology sequence a 5’ untranslated region (UTR), a 3’ UTR, an insertion template, or any combination thereof,” while Rubens discloses that the template RNA taught therein may comprise a guide RNA (paragraph [0173]), they do not disclose the instantly claimed modifications to said guide RNA.
This deficiency is cured by Anzalone. Anzalone discloses the prime editing method, in which prime editing guide RNA (peg RNA) that specifies both the desired target site and edit complexes with a prime editor comprising a reverse transcriptase domain and a Cas9 nickase (abstract; figure 1 b). The pegRNAs disclosed in Anzalone are capable of producing targeted small insertions (from 1 to 3 base pairs) specified by the peg RNA sequence, which as set forth above specifies both the desired target site and the edit (page 154, column 1, paragraph 5; figures 1 b and 4f). Finally, Anzalone discloses that the prime editing experiments disclosed therein performed 19 insertions up to 44 base pairs with single-nucleotide precision, facilitated by the flexibility of peg RNA template design (page 156, column 1, paragraph 7-column 2, paragraphs 2 and 3). Thus, Anzalone discloses a guide RNA compatible with Cas9 that comprises an insertion template, as instantly claimed.
Given that Rubens discloses the genome editing system of claim 1 editing system of claim 1 in which the payload RNA further comprises a guide RNA (as set forth above), and that Anzalone et al., 2019 discloses pegRNAs, which are compatible with Cas9 and comprise an insertion template for targeted insertion into the genome, it would have been obvious to someone of ordinary skill in the art before the effective filing date of the claimed invention to substitute the guide RNA disclosed in Rubens with the peg RNA disclosed in Anzalone to predictably generate a genome editing system capable of inserting DNA sequences with single-nucleotide precision. One would have been motivated to make such a modification in order to receive the expected benefit of generating a genome editing system capable of inserting DNA sequences with single-nucleotide precision.
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, 4, 5, 7, 8, 10, 11, 13, 14, 16, 33, and 47 are provisionally rejected on the ground of nonstatutory double patenting as being unpatentable over claims 1, 2, 13, 20, 21, and 24 of copending Application No. 19/333,523 (corresponds to US 2026/0008827 A1; claims amended 12/02/2025) in view of US 2020/0109398 A1 (hereinafter Rubens; as cited in the IDS filed 05/19/2025), WO 2021/102042 A1 (hereinafter Zhang; as cited in the IDS filed 01/17/2024), and Anzalone et al., 2019 (hereinafter Anzalone; as cited in the IDS filed 09/24/2025), as evidenced by Thompson and Christensen, 2011 (hereinafter Thompson).
Copending application ‘523 is drawn to systems and methods for targeted gene modification, said systems and methods comprising components of CRISPR systems and non-LTR retrotransposon elements (abstract).
Copending claim 1 recites “an engineered or non-naturally occurring composition for targeted transposition of a donor polynucleotide into a target polynucleotide, said composition comprising: (a) a programmable DNA-binding protein configured to bind a target sequence within a target polynucleotide; (b) a non-long terminal repeat (non-LTR) retrotransposon polypeptide fused to or otherwise capable of associating with the programmable DNA-binding protein, wherein the non-LTR retrotransposon polypeptide comprises one or more modifications or truncations relative to a wild-type non-LTR retrotransposon polypeptide; and (c) a donor construct comprising a donor polynucleotide for insertion into the target polynucleotide and an engineered binding element capable of forming a complex with the non-LTR retrotransposon polypeptide.”
The non-LTR retrotransposon polypeptide of copending claim 1 is further limited to R2 at copending claims 13 and 20. Furthermore, the non-LTR retrotransposon polypeptide of copending claim 1 is recited to be “fused to the programmable DNA-binding protein by means of a flexible linker” at copending claim 21.
The programmable DNA-binding protein of copending claim 1 is further limited to “a CRISPR-Cas system comprising a Cas protein and one or more guide molecules capable of forming a complex with the Cas protein and directing sequence-specific binding of the complex to the target sequence within the target polynucleotide…wherein the CRISPR-Cas system is…a Cas12i1 or Cas12i2 system, and…wherein the Cas protein is a nickase” at copending claim 2.
Finally, copending claim 24 further limits the donor construct of copending claim 1 to further comprise “a first homology region, a donor template for insertion into the target polynucleotide, and a second homology region.”
In comparison, instant claim 1 recites “a genome editing system comprising: i) an R2 element enzyme; and ii) a payload RNA, wherein the payload RNA comprises an insertion template…wherein the insertion template comprises a sequence for a nucleic acid insertion into the genome, and wherein the R2 element enzyme comprises a reverse transcriptase domain and a nickase domain.” This genome editing system comprises an R2 element enzyme and a payload RNA comprising an insertion template for nucleic acid insertion into the genome, as recited at copending claims 1 and 24. Copending claims 13 and 20 limit the non-LTR retrotransposon polypeptide claimed therein to R2, as instantly claimed. As set forth above, the claimed reverse transcriptase domain and nickase domain are considered to be endogenous properties of R2 element enzymes (as reviewed in Thompson). Thus, the recited subject matter of instant claim 1 is not patentably distinct from that of copending application ‘523.
While instant claim 2 further recites that the “R2 element enzyme further comprises a targeting domain,” this recitation is anticipated by copending claim 1, which recites a modified R2 element enzyme fused to a programmable DNA-binding protein, such as a Cas protein (as recited at copending claim 2). Thus, the recited subject matter of instant claim 2 is not patentably distinct from that of copending application ‘523.
Instant claim 4 recites that “the nucleic acid insertion into the genome is a DNA or RNA insertion template,” which is anticipated by the recitation of copending claim 1, as the claimed donor polynucleotide reads on either DNA or RNA nucleic acid species. However, even if one does not accept that the recitation of copending claim 1 anticipates instant claim 4, Rubens discloses that the Gene Writer™ gene editing system comprises a template RNA (or DNA encoding the same) (paragraph [0009]), itself comprising a sequence that binds the polypeptide, a heterologous object sequence that encodes a therapeutic polypeptide (or a fragment or variant thereof) referred to as the payload domain for insertion into the target genome (paragraph [0178]), and a guide RNA (paragraphs [0007], [0117], and [0173]; figure 11). Thus, the recited subject matter of instant claim 4 is not patentably distinct from that of copending application ‘523, particularly in view of Rubens. One would have looked to Rubens for guidance regarding suitable donor polynucleotide species for use in the instant invention based on the generic recitation of the “donor polynucleotide” of the copending application. The disclosure of Rubens establishes that there is a predictable expectation of success when inserting RNA or DNA donor polynucleotides into the genome, as instantly claimed and supported by the copending application.
Instant claim 5 recites that “the R2 element enzyme is a modified R2 element enzyme,” which is anticipated by copending claims 1, 2, 13, and 20, which recite that the non-LTR retrotransposon polypeptide claimed therein (i.e. R2) is both modified or truncated, as well as modified by association with a programmable DNA-binding protein such as a Cas12. Thus, the recited subject matter of instant claim 5 is not patentably distinct from that of copending application ‘523.
Instant claim 7 recites that “the modified R2 element enzyme is modified by an N-terminal or C-terminal truncation of the R2 element enzyme sequence,” as set forth above, copending claims 1, 13, and 20 collectively recite modification or truncation of a non-LTR retrotransposon polypeptide such as R2. However, the copending claims do not recite that said truncation is at the N-terminus or C-terminus specifically. This deficiency is cured by Rubens. As set forth above, Rubens further discloses experimentation with truncation of the 3’ UTR of R2Tg (an endogenous retrotransposon from the zebra finch) (paragraphs [0240] and [0266]) to increase efficiency of genome integration. As is known to those of ordinary skill in the art, the 3’ UTR is located at the C terminus of the R2 element enzyme sequence. Thus, the recited subject matter of instant claim 7 is not patentably distinct from that of copending application ‘523, particularly in view of Rubens. One would have looked to Rubens for guidance regarding specific truncations compatible with the claimed non-LTR retrotransposon polypeptide such as R2 based on the generic recitation of truncations to the same in the copending application. The disclosure of Rubens establishes that there is a predictable expectation of success when truncating the C-terminus of the claimed non-LTR retrotransposon polypeptide (i.e. R2), as instantly claimed.
Instant claim 8 recites that “the modified R2 element enzyme comprises a linker.” As set forth above, copending claims 1, 2, 13, and 20 recite that the non-LTR retrotransposon polypeptide claimed therein (i.e. R2) is fused to a programmable DNA-binding protein such as Cas12. This fusion is specifically recited to be accomplished via a flexible linker at copending claim 21. Thus, the recited subject matter of instant claim 8 is not patentably distinct from that of copending application ‘523.
Instant claims 10 and 11 recite that “the genome editing system targets a genomic locus,” “other than the 28S rRNA locus,” which is not patentably distinct from the recitation of copending claim 1 in view of Rubens. As set forth above, copending claim 1 recites that the composition claimed therein is “for targeted transposition of a donor polynucleotide into a target polynucleotide,” which may broadly be considered to read on the instantly claimed targeting of a genomic locus. However, even if one does not accept that the broad recitation of copending claim 1 reads on the instantly claimed targeting of a genomic locus, this deficiency is cured by Rubens. As set forth above, Rubens discloses that the non-LTR retrotransposon elements taught therein can be functionally modularized and/or modified to target, edit, modify, or manipulate a target DNA sequence for purposes of inserting a heterologous nucleic acid sequence into a targeted genome site by reverse transcription, for example a genomic safe harbor site that is able to accommodate the integration of heterologous genetic material (paragraphs [0080] and [0117]). Thus, the recited subject matter of instant claims 10 and 11 is not patentably distinct from that of copending application ‘523, particularly in view of Rubens. One would have looked to Rubens for guidance regarding suitable genomic target sites compatible with the instantly claimed system and the system of the copending application. The disclosure of Rubens establishes that there is a predictable expectation of targeting genomic loci other than the 28S rRNA locus, as instantly claimed and supported by the copending application.
Instant claims 13 and 14 recite that “a non-naturally occurring targeting region is fused to the N-terminus of the R2 element enzyme or inserted into the R2 element enzyme,” and that “the modified R2 element enzyme is a fusion protein.” As set forth above, copending claims 1 and 2 recite modification of the non-LTR retrotransposon polypeptide claimed therein (R2 per copending claims 13 and 20) by association with a programmable DNA-binding protein such as a Cas12 (or a nickase thereof). This association is recited to be accomplished by fusion via a linker at copending claim 21 (which reads on the claimed fusion subject matter of instant claim 14). However, the copending claim set is silent as to the location of said fusion. This deficiency is cured by Zhang. As set forth above, Zhang discloses fusion of the R2 element enzymes taught therein to site-specific nucleases, such as CRISPR nucleases (paragraphs [0003], [0009], and [0010]). Specifically, the site-specific nuclease is disclosed to be fused to the N-terminus of the non-LTR retrotransposon polypeptide taught therein for purposes of targeted transposition of a donor sequence into targeted nucleic acids (paragraph [0009]). Thus, the recited subject matter of instant claims 13 and 14 is not patentably distinct from that of copending application ‘523, particularly in view of Zhang. One would have looked to Zhang for guidance regarding suitable locations for fusion to a non-naturally occurring targeting region compatible with the instantly claimed system and the system of the copending application. The disclosure of Zhang establishes that there is a predictable expectation of success when linking the non-naturally occurring targeting region to the R2 element enzyme at the N-terminus of the R2 element enzyme, as instantly claimed.
Instant claim 16 recites that “the modified R2 element is fused to a Cas12 protein that is fully active, catalytically dead, or functioning as a nickase,” as set forth above, copending claims 1 and 2 recite modification of the non-LTR retrotransposon polypeptide claimed therein (R2 per copending claims 13 and 20) by association with a programmable DNA-binding protein such as a Cas12 (or a nickase thereof). Thus, the recited subject matter of instant claim 16 is not patentably distinct from that of copending application ‘523.
Instant claim 33 further recites that the payload RNA “comprises a Cas9 or Cas12 guide RNA, and wherein the Cas9 or Cas12 guide RNA comprises an extension with a 5’ homology sequence a 3’ homology sequence, a 5’ untranslated region (UTR), a 3’ UTR, an insertion template, or any combination thereof.” As set forth above, copending claim 2 recites that the composition of copending claim 1 further comprises a guide molecule compatible with a Cas12 protein or a nickase variant thereof. While the copending claim set is silent as to the guide RNA modifications and incorporation into the payload RNA as in the instant application, this deficiency is cured by Anzalone and Rubens. As set forth above (see section Claim Rejection – 35 USC § 103), Rubens discloses that the template RNA taught therein may comprise a guide RNA (paragraph [0173]). Anzalone further discloses the prime editing method, in which prime editing guide RNA (peg RNA) that specifies both the desired target site and edit complexes with a prime editor comprising a reverse transcriptase domain and a Cas9 nickase (abstract; figure 1 b). The pegRNAs disclosed in Anzalone are capable of producing targeted small insertions (from 1 to 3 base pairs) specified by the peg RNA sequence, which as set forth above specifies both the desired target site and the edit (page 154, column 1, paragraph 5; figures 1 b and 4f). Finally, Anzalone discloses that the prime editing experiments disclosed therein performed 19 insertions up to 44 base pairs with single-nucleotide precision, facilitated by the flexibility of peg RNA template design (page 156, column 1, paragraph 7-column 2, paragraphs 2 and 3). Thus, the recited subject matter of instant claim 33 is not patentably distinct from that of copending application ‘523, particularly in view of Rubens and Anzalone. One would have looked to Rubens for guidance on how to incorporate the guide RNAs of the copending application into the systems of the instant and copending applications. Furthermore, based on the disclosure of Anzalone, one would have been motivated to modify the guide RNAs of the instantly claimed system to comprise at least an insertion template for purposes of making precise, defined, and targeted modifications to the genome, as instantly claimed. Rubens and Anzalone establish that this outcome is predictable when applying the methods taught therein.
Finally, instant claim 47 recites “a genome editing system comprising: i) a payload RNA, wherein the payload RNA comprises an insertion template…wherein the insertion template comprises a sequence for a nucleic acid insertion into the genome; ii) a non-LTR site specific retrotransposon element enzyme; wherein the non-LTR site specific retrotransposon element enzyme comprises a reverse transcriptase domain…and wherein if the non-LTR-site specific retrotransposon element enzyme does not comprise the optional nuclease or nickase domain, the genome editing system further comprises iii) a nuclease or nickase enzyme,” all of which is recited at instant claims 1, 2, and 24, as set forth above. Thus, the recited subject matter of instant claim 47 is not patentably distinct from that of copending application ‘523.
This is a provisional nonstatutory double patenting rejection.
Claims 1, 2, 4, 5, 8, 10, 11, 13, 16, and 47 are provisionally rejected on the ground of nonstatutory double patenting as being unpatentable over claims 1-3, 11, 19, and 21 of copending Application No. 18/276,471 (corresponds to US 2024/0132916 A1; claims amended 02/29/2024) in view of US 2020/0109398 A1 (hereinafter Rubens; as cited in the IDS filed 05/19/2025), WO 2021/102042 A1 (hereinafter Zhang; as cited in the IDS filed 01/17/2024), as evidenced by Thompson and Christensen, 2011 (hereinafter Thompson) and Swarts and Jinek, 2018 (hereinafter Swarts; as cited in the IDS filed 09/24/2025).
Copending application ‘471 is drawn to systems and methods for targeted gene modification and insertion (abstract).
Copending claim 1 recites “an engineered composition for non-native, targeted transposition of donor sequence into targeted nucleic acids, comprising: a. a first site-specific nuclease configured to bind a target sequence in a target polynucleotide; b. a first non-LTR retrotransposon polypeptide fused to or otherwise capable of forming a complex with the first site-specific nuclease; and c. a donor construct comprising, a donor polynucleotide for insertion into the target polynucleotide and comprising one or more elements capable of forming a complex with the non-LTR retrotransposon polypeptide.”
The claimed non-LTR retrotransposon is further limited to R2 at copending claim 11.
The claimed site-specific nuclease is further limited to a Cas polypeptide such as a Type V Cas polypeptide with optional nickase activity at copending claims 2 and 3.
Finally, the claimed donor construct is further limited to comprise “a first homology region, a donor template [or sequence] for insertion into the target polynucleotide, [and] a second homology region” at copending claims 19 and 21.
In comparison, instant claim 1 recites “a genome editing system comprising: i) an R2 element enzyme; and ii) a payload RNA, wherein the payload RNA comprises an insertion template…wherein the insertion template comprises a sequence for a nucleic acid insertion into the genome, and wherein the R2 element enzyme comprises a reverse transcriptase domain and a nickase domain.” This genome editing system comprises an R2 element enzyme and a payload RNA comprising an insertion template for nucleic acid insertion into the genome, as recited at copending claims 1, 11, 19, and 21. As set forth above, the claimed reverse transcriptase domain and nickase domain are considered to be endogenous properties of R2 element enzymes (as reviewed in Thompson). Thus, the recited subject matter of instant claim 1 is not patentably distinct from that of copending application ‘471.
While instant claim 2 further recites that the “R2 element enzyme further comprises a targeting domain,” this recitation is anticipated by copending claims 1-3 under broadest reasonable interpretation, as the fusion of the non-LTR retrotransposon polypeptide to a site-specific nuclease (such as a Cas polypeptide) reads on the further instantly claimed “targeting domain.” Thus, the recited subject matter of instant claim 2 is not patentably distinct from that of copending application ‘471.
Instant claim 4 recites that “the nucleic acid insertion into the genome is a DNA or RNA insertion template,” which is anticipated by the recitation of copending claim 1, as the claimed donor polynucleotide reads on either DNA or RNA nucleic acid species. However, even if one does not accept that the recitation of copending claim 1 anticipates instant claim 4, Rubens discloses that the Gene Writer™ gene editing system comprises a template RNA (or DNA encoding the same) (paragraph [0009]), itself comprising a sequence that binds the polypeptide, a heterologous object sequence that encodes a therapeutic polypeptide (or a fragment or variant thereof) referred to as the payload domain for insertion into the target genome (paragraph [0178]), and a guide RNA (paragraphs [0007], [0117], and [0173]; figure 11). Thus, the recited subject matter of instant claim 4 is not patentably distinct from that of copending application ‘471, particularly in view of Rubens. One would have looked to Rubens for guidance regarding suitable donor polynucleotide species for use in the instant invention based on the generic recitation of the “donor polynucleotide” of the copending application. The disclosure of Rubens establishes that there is a predictable expectation of success when inserting RNA or DNA donor polynucleotides into the genome, as instantly claimed and supported by the copending application.
Instant claim 5 recites that “the R2 element enzyme is a modified R2 element enzyme,” which is anticipated by copending claims 1 and 11, as under broadest reasonable interpretation, as the fusion of the non-LTR retrotransposon polypeptide (i.e. R2) to a site-specific nuclease reads on the further instantly claimed “modified R2 element enzyme.” Thus, the recited subject matter of instant claim 5 is not patentably distinct from that of copending application ‘471.
Instant claim 8 recites that “the modified R2 element enzyme comprises a linker.” While the copending application recites fusion of the non-LTR retrotransposon polypeptide (i.e. R2) to a site-specific nuclease, as set forth above, the claim set is silent as to this being accomplished via a linker. However, this deficiency is cured by Rubens. As set forth above, Ruben further discloses that the components of the Gene Writer™ gene editing system taught therein may comprise domains (such as those derived from R2) joined by a linker (paragraph [0149]; Figure 18). Thus, the recited subject matter of instant claim 8 is not patentably distinct from that of copending application ‘471, particularly in view of Rubens. One would have looked to Rubens for guidance regarding methods of linking or fusing the claimed non-LTR retrotransposon polypeptide (i.e. R2) to the claimed site-specific nuclease compatible with the instantly claimed system and the system of the copending application. The disclosure of Rubens establishes that there is a predictable expectation of successfully and functionally fusing R2 to a site-specific nuclease for purposes of targeted genome modification, as instantly claimed.
Instant claims 10 and 11 recite that “the genome editing system targets a genomic locus,” “other than the 28S rRNA locus,” which is not patentably distinct from the recitation of copending claim 1 in view of Rubens. As set forth above, copending claim 1 recites that the composition claimed therein is “for targeted transposition of a donor polynucleotide into target nucleic acids,” which may broadly be considered to read on the instantly claimed targeting of a genomic locus. However, even if one does not accept that the broad recitation of copending claim 1 reads on the instantly claimed targeting of a genomic locus, this deficiency is cured by Rubens. As set forth above, Rubens discloses that the non-LTR retrotransposon elements taught therein can be functionally modularized and/or modified to target, edit, modify, or manipulate a target DNA sequence for purposes of inserting a heterologous nucleic acid sequence into a targeted genome site by reverse transcription, for example a genomic safe harbor site that is able to accommodate the integration of heterologous genetic material (paragraphs [0080] and [0117]). Thus, the recited subject matter of instant claims 10 and 11 is not patentably distinct from that of copending application ‘471, particularly in view of Rubens. One would have looked to Rubens for guidance regarding suitable genomic target sites compatible with the instantly claimed system and the system of the copending application. The disclosure of Rubens establishes that there is a predictable expectation of targeting genomic loci other than the 28S rRNA locus, as instantly claimed and supported by the copending application.
Instant claims 13 and 14 recite that “a non-naturally occurring targeting region is fused to the N-terminus of the R2 element enzyme or inserted into the R2 element enzyme,” and that “the modified R2 element enzyme is a fusion protein.” As set forth above, copending claims 1-3 recite modification of the non-LTR retrotransposon polypeptide claimed therein (R2 per copending claim 11) by fusion with a site-specific nuclease such as a Cas polypeptide (optionally Type II or Type V; or a nickase thereof). However, the copending claim set is silent as to the location of said fusion. This deficiency is cured by Zhang. As set forth above, Zhang discloses fusion of the R2 element enzymes taught therein to site-specific nucleases, such as CRISPR nucleases (paragraphs [0003], [0009], and [0010]). Specifically, the site-specific nuclease is disclosed to be fused to the N-terminus of the non-LTR retrotransposon polypeptide taught therein for purposes of targeted transposition of a donor sequence into targeted nucleic acids (paragraph [0009]). Thus, the recited subject matter of instant claims 13 and 14 is not patentably distinct from that of copending application ‘471, particularly in view of Zhang. One would have looked to Zhang for guidance regarding suitable locations for fusion to a non-naturally occurring targeting region compatible with the instantly claimed system and the system of the copending application. The disclosure of Zhang establishes that there is a predictable expectation of success when linking the non-naturally occurring targeting region to the R2 element enzyme at the N-terminus of the R2 element enzyme, as instantly claimed.
Instant claim 16 recites that “the modified R2 element is fused to a Cas12 protein that is fully active, catalytically dead, or functioning as a nickase,” as set forth above, copending claims 2 and 3 recite modification of the non-LTR retrotransposon polypeptide claimed therein (R2 per copending claims 11) by association with a site-specific nuclease such as a Cas polypeptide (optionally Type II or Type V; or a nickase thereof). However, the copending application is silent as to specific selection of the Cas12 protein. This deficiency is cured by Rubens. Rubens discloses the retrotransposon-based Gene Writer™ system (paragraph [0114]; figure 1), wherein the Gene Writer™ protein is a fusion protein comprising an R2-derived reverse transcriptase domain (which reads on the instantly claimed modified R2 element enzyme) fused to an endonuclease such as Cas protein (Figure 18). Such Cas proteins include Cpf1 that may be altered to have no endonuclease activity (paragraph [0124]). Per Swarts, Cpf1 is another term for Cas12a (abstract), which is a type V Cas protein (Figure 1), as instantly claimed. One would have looked to Swarts for guidance in selecting a powerful Type V Cas polypeptide compatible with the instantly claimed system and the system of the copending application. The disclosure of Rubens establishes that there is a predictable expectation of success when linking the R2 element enzyme to a Cas12 protein, as instantly claimed.
Finally, instant claim 47 recites “a genome editing system comprising: i) a payload RNA, wherein the payload RNA comprises an insertion template…wherein the insertion template comprises a sequence for a nucleic acid insertion into the genome; ii) a non-LTR site specific retrotransposon element enzyme; wherein the non-LTR site specific retrotransposon element enzyme comprises a reverse transcriptase domain…and wherein if the non-LTR-site specific retrotransposon element enzyme does not comprise the optional nuclease or nickase domain, the genome editing system further comprises iii) a nuclease or nickase enzyme,” all of which is recited at instant claims 1-3, 19, and 21, as set forth above. Thus, the recited subject matter of instant claim 47 is not patentably distinct from that of copending application ‘523.
This a provisional nonstatutory double patenting rejection.
Claims 1, 2, 4, 5, 7, 8, 10, 11, 16, 29, 33, 35, and 47 are provisionally rejected on the ground of nonstatutory double patenting as being unpatentable over claims 1, 7, 8, 11, 16, 20, 26, and 36 of copending Application No. 18/047,685 (corresponds to US 2023/0272434 A1; claims amended 01/14/2026) in view of WO 2021/102042 A1 (hereinafter Zhang; as cited in the IDS filed 01/17/2024) and Christensen et al., 2006 (hereinafter Christensen).
Copending application ‘685 is drawn to genome editing tools for use in systems designed to deliver large genetic elements (abstract).
Copending claim 1 recites “a genome editing system comprising: i) an R2 element enzyme having an N-terminus and a C-terminus, and wherein the R2 element enzyme comprises a reverse transcriptase domain, a nickase domain, a targeting domain, and a nuclear localization signal (NLS) at the N-terminus or the C-terminus, wherein the R2 element enzyme is fused to a Cas9 or Cas12 protein having nickase activity; ii) at least one guide RNA; and iii) a payload RNA, wherein the payload RNA comprises a protein binding element and an insertion template comprising a nucleic acid sequence for insertion into a genome, and wherein the payload RNA further comprises a Cas9 or Cas12 guide RNA, wherein the Cas9 or Cas12 guide RNA comprises an extension with a 5’ homology sequence, a 3’ homology sequence, a 5’ untranslated region (UTR), a 3’ UTR, an insertion template, or any combination thereof.”
The R2 element enzyme of the copending application is further recited to be “modified by an N-terminal truncation” at copending claim 7 and to comprise a linker at copending claim 8.
The genome editing system of the copending application is further recited to comprise “a sequence and/or structure for targeting a genomic locus other than a 28S rRNA locus” at copending claim 11.
The Cas12 protein of the system of the copending application (recited at copending claim 1) is further recited to be “fully active or catalytically dead” at copending claim 16.
The payload RNA of the copending application (recited at copending claim 1) is further recited to comprise “one or more of a 5’ homology region or a 3’ homology region” at copending claim 20 or “a 5’ untranslated region (UTR), a 3’ UTR, or both a 5’ UTR and a 3’ UTR” at copending claim 26.
Finally, the insertion template of the copending application (recited at copending claim 1) is further recited to comprise “a template for a reporter gene, a transcription factor gene, a transgene, an enzyme gene, or a therapeutic gene” at copending claim 36. As is known to those of ordinary skill in the art, DNA encodes all of the claimed genes recited at copending claim 36.
These limitations anticipate the limitations of instant claims
Instant claim 1 recites “a genome editing system comprising: i) an R2 element enzyme; and ii) a payload RNA, wherein the payload RNA comprises an insertion template…wherein the insertion template comprises a sequence for a nucleic acid insertion into the genome, and wherein the R2 element enzyme comprises a reverse transcriptase domain and a nickase domain.” Instant claim 2 further recites that “the R2 element enzyme further comprises a targeting domain.” All of these limitations are also recited at copending claim 1, as set forth above. Thus, the recited subject matter of instant claim 1 is not patentably distinct from that of copending application ‘685.
Instant claim 4 recites “the nucleic acid insertion into the genome is a DNA or RNA insertion template,” which is anticipated by copending claim 36, as DNA encodes all of the claimed genes for insertion recited at copending claim 36, as set forth above. Thus, the recited subject matter of instant claim 4 is not patentably distinct from that of copending application ‘685.
Instant claim 5 recites “the R2 element enzyme is a modified R2 element enzyme,” which is anticipated by copending claims 1, which recites modification to the R2 element enzyme by fusing to a Cas nuclease, and 7, which recites modification to the R2 element by an N-terminal truncation, as is also recited at instant claim 7. Thus, the recited subject matter of instant claims 5 and 7 is not patentably distinct from that of copending application ‘685.
Instant claim 8 recites “the modified R2 element enzyme comprises a linker,” which is anticipated by the recitation of the same at copending claim 8. Thus, the recited subject matter of instant claim 8 is not patentably distinct from that of copending application ‘685.
Instant claims 10 and 11 recite that “the genome editing system targets a genomic locus,” “other than the 28S rRNA locus,” which is not patentably distinct from the recitation of copending claim 11, which recites identical limitations. Thus, the recited subject matter of instant claims 10 and 11 is not patentably distinct from that of copending application ‘685.
Instant claim 16 further recites that “the modified R2 element [of the genome editing system of claim 5] is fused to a Cas12 protein that is fully active, catalytically dead, or functioning as a nickase,” as recited at copending claims 1 and 16. Thus, the recited subject matter of instant claim 16 is not patentably distinct from that of copending application ‘685.
Instant claim 29 further recites that “the payload RNA [of the genome editing system of claim 1] further comprises a 5’ untranslated region (UTR), a 3’ UTR, or both a 5’ and a 3’ UTR, wherein the UTRs are truncated.” In comparison, copending claim 26 recites that “the payload RNA further comprises a 5’ untranslated region (UTR), a 3’ UTR, or both a 5’ and a 3’ UTR.” Thus, the copending application recites all limitations of instant claim 29 and is not patentably distinct from the instant application with the exception of the truncation of the UTRs claimed therein. This deficiency is cured by Zhang and Christensen. As set forth above, Zhang discloses that R2 from Bombyx mori depends only on the UTR of the insertion template, thereby motivating experimentation with the same (paragraph [0042]). Such experimentation would be further motivated by Christensen, which discloses that removal of 5’ RNA (comprising the UTR) from the insertion template for R2 is implicated in controlling a complete integration reaction, thereby motivating experimental manipulation of the same (i.e. truncation of the 5’ UTR) for purposes of controlling such integration (page 17606, column 2, paragraph 3). One would have looked to Christensen for guidance regarding manipulation of the UTR of the insertion template, as motivated by Zhang. The disclosure of Christensen establishes that truncation of 5’ RNA from the R2 insertion template is implicated in controlling a complete integration reaction, thereby motivating experimental manipulation (i.e. truncation) of the same for purposes of controlling such integration, as instantly claimed.
Instant claim 33 further recites that the payload RNA “comprises a Cas9 or Cas12 guide RNA, and wherein the Cas9 or Cas12 guide RNA comprises an extension with a 5’ homology sequence a 3’ homology sequence, a 5’ untranslated region (UTR), a 3’ UTR, an insertion template, or any combination thereof.” This is anticipated by the recitation of the same at copending claim 1. Thus, the recited subject matter of instant claim 33 is not patentably distinct from that of copending application ‘685.
Instant claim 35 further recites that “the R2 element [of the genome editing system of claim 1] comprises a nuclear localization signal (NLS),” which is anticipated by copending claim 1, which also recites that the R2 element enzyme claimed therein comprises an NLS. Thus, the recited subject matter of instant claim 35 is not patentably distinct from that of copending application ‘685.
Finally, instant claim 47 recites “a genome editing system comprising: i) a payload RNA, wherein the payload RNA comprises an insertion template…wherein the insertion template comprises a sequence for a nucleic acid insertion into the genome; ii) a non-LTR site specific retrotransposon element enzyme; wherein the non-LTR site specific retrotransposon element enzyme comprises a reverse transcriptase domain…and wherein if the non-LTR-site specific retrotransposon element enzyme does not comprise the optional nuclease or nickase domain, the genome editing system further comprises iii) a nuclease or nickase enzyme,” all of which is recited in the copending application, as set forth above, with the exception of the payload RNA further comprising one or more of a 5’ homology region or a 3’ homology region, as is recited at copending claim 20. Thus, the recited subject matter of instant claim 47 is not patentably distinct from that of copending application ‘685.
This a provisional nonstatutory double patenting rejection.
Claims 1, 2, 10, 11, 14, 16, 33, 35, and 47 are provisionally rejected on the ground of nonstatutory double patenting as being unpatentable over claims 1, 6, 7, 13, 17, 52, and 57 of copending Application No. 17/778,192 (corresponds to US 2023/0040216 A1; claims amended 01/27/2026) in view of US 2020/0109398 A1 (hereinafter Rubens; as cited in the IDS filed 05/19/2025) and Anzalone et al., 2019 (hereinafter Anzalone; as cited in the IDS filed 09/24/2025), as evidenced by Thompson and Christensen, 2011 (hereinafter Thompson) and Swarts and Jinek, 2018 (hereinafter Swarts; as cited in the IDS filed 09/24/2025).
Copending application ‘192 is drawn to systems and methods for targeted gene modification or insertion (abstract).
Copending claim 1 recites “an engineered or non-naturally occurring composition comprising: a. a site-specific nuclease polypeptide, or a polynucleotide comprising a coding sequence thereof; b. a non-LTR retrotransposon polypeptide connected to or otherwise capable of forming a complex with the site-specific nuclease polypeptide or a polynucleotide comprising a coding sequence thereof; c. a guide molecule capable of forming a complex with the site-specific nuclease polypeptide and directing site-specific binding to a target sequence of a target polynucleotide; and d. a polynucleotide encoding a retrotransposon RNA, wherein the retrotransposon RNA comprises or encodes a donor polynucleotide.”
The donor polynucleotide of the copending application is further recited to be “configured for insertion at, or adjacent to, the target nucleotide sequence” at copending claim 6, as well as to comprise “a homology sequence of the target sequence” at copending claim 52. Finally, the donor polynucleotide is recited to comprise a “homology sequence…on a region on a strand that binds to the guide,” meaning the donor polynucleotide of the copending application must associate with the guide molecule.
The site-specific nuclease polypeptide is further recited to be a nickase at copending claim 7.
The non-LTR retrotransposon polypeptide is further recited to be an R2 polypeptide at copending claim 13 and to comprise a nuclear localization signal at copending claim 17.
In comparison, instant claim 1 recites “a genome editing system comprising: i) an R2 element enzyme; and ii) a payload RNA, wherein the payload RNA comprises an insertion template…wherein the insertion template comprises a sequence for a nucleic acid insertion into the genome, and wherein the R2 element enzyme comprises a reverse transcriptase domain and a nickase domain.” Instant claim 2 further recites that “the R2 element enzyme further comprises a targeting domain.” As set forth above, copending application ‘192 claims a non-LTR retrotransposon polypeptide (i.e. R2 as recited at copending claim 13) modified to form a complex with a site-specific nuclease polypeptide (which also reads on the fusion protein claimed at instant claim 14). Thus, the instant recitation is anticipated by the copending application, as the complex of the non-LTR retrotransposon polypeptide to a site-specific nuclease polypeptide reads on the further instantly claimed “targeting domain.” Furthermore, as set forth above, the claimed reverse transcriptase domain and nickase domain are considered to be endogenous properties of R2 element enzymes (as reviewed in Thompson). Thus, the recited subject matter of instant claims 1 and 2 is not patentably distinct from that of copending application ‘192.
Instant claims 10 and 11 recite that “the genome editing system targets a genomic locus,” “other than the 28S rRNA locus,” which is not patentably distinct from the subject matter recited at copending claim 6 in view of Rubens. As set forth above, copending claim 6 recites targeting of a nucleotide sequence by the donor polynucleotide, which may be a genomic locus such as a safe harbor locus, as disclosed in Rubens. As set forth above, Rubens discloses that the non-LTR retrotransposon elements taught therein can be functionally modularized and/or modified to target, edit, modify, or manipulate a target DNA sequence for purposes of inserting a heterologous nucleic acid sequence into a targeted genome site by reverse transcription, for example a genomic safe harbor site that is able to accommodate the integration of heterologous genetic material (paragraphs [0080] and [0117]). Thus, the recited subject matter of instant claims 10 and 11 is not patentably distinct from that of copending application ‘192, particularly in view of Rubens. One would have looked to Rubens for guidance regarding suitable genomic target sites compatible with the instantly claimed system and the system of the copending application. The disclosure of Rubens establishes that there is a predictable expectation of targeting genomic loci other than the 28S rRNA locus, as instantly claimed and supported by the copending application.
Instant claim 16 recites “the modified R2 element is fused to a Cas12 protein that is fully active, catalytically dead, or functioning as a nickase,” which while not fully anticipated by the copending claims is nonetheless obvious over them. Copending claim 7 recites that the site-specific nuclease polypeptide complexed with the non-LTR retrotransposon polypeptide claimed therein is a nickase or lacks endonuclease activity. However, the exact species of Cas12 is not disclosed. This deficiency is cured by Rubens. as set forth above, Rubens discloses the retrotransposon-based Gene Writer™ system (paragraph [0114]; figure 1), wherein the Gene Writer™ protein is a fusion protein comprising an R2-derived reverse transcriptase domain (which reads on the instantly claimed modified R2 element enzyme) fused to an endonuclease such as Cas protein (Figure 18). Such Cas proteins include Cpf1 that may be altered to have no endonuclease activity (paragraph [0124]). Per Swarts, Cpf1 is another term for Cas12a (abstract), which is a Cas12 protein, as instantly claimed. One would have looked to Rubens for guidance in selecting a site-specific nuclease with nickase activity. The disclosure of Rubens establishes that Cas12 (with or without nickase activity) is a Cas polypeptide compatible with the instantly claimed system and the system of the copending application. The disclosure of Rubens establishes that there is a predictable expectation of success when linking the R2 element enzyme to a Cas12 protein, as instantly claimed.
Instant claim 33 further recites that the payload RNA “comprises a Cas9 or Cas12 guide RNA, and wherein the Cas9 or Cas12 guide RNA comprises an extension with a 5’ homology sequence a 3’ homology sequence, a 5’ untranslated region (UTR), a 3’ UTR, an insertion template, or any combination thereof.” As set forth above regarding copending claim 57, the donor polynucleotide of the copending application must associate with the guide molecule, as instantly claimed. However, the copending application is silent as to the claimed guide modifications. This deficiency is cured by Anzalone. Anzalone discloses the prime editing method, in which prime editing guide RNA (peg RNA) that specifies both the desired target site and edit complexes with a prime editor comprising a reverse transcriptase domain and a Cas9 nickase (abstract; figure 1 b). The pegRNAs disclosed in Anzalone are capable of producing targeted small insertions (from 1 to 3 base pairs) specified by the peg RNA sequence, which as set forth above specifies both the desired target site and the edit (page 154, column 1, paragraph 5; figures 1 b and 4f). Finally, Anzalone discloses that the prime editing experiments disclosed therein performed 19 insertions up to 44 base pairs with single-nucleotide precision, facilitated by the flexibility of peg RNA template design (page 156, column 1, paragraph 7-column 2, paragraphs 2 and 3). Thus, the recited subject matter of instant claim 33 is not patentably distinct from that of copending application ‘523, particularly in view of Anzalone. Based on the disclosure of Anzalone, one would have been motivated to modify the guide RNAs of the instantly claimed system to comprise at least an insertion template for purposes of making precise, defined, and targeted modifications to the genome, as instantly claimed. Anzalone establishes that this outcome is predictable when applying the methods taught therein.
Instant claim 35 further recites that “the R2 element [of the genome editing system of claim 1] comprises a nuclear localization signal (NLS),” which is also recited at copending claim 17, as set forth above. Thus, the subject matter of instant claim 35 is not patentably distinct from that of copending application ‘192.
Finally, instant claim 47 recites “a genome editing system comprising: i) a payload RNA, wherein the payload RNA comprises an insertion template…wherein the insertion template comprises a sequence for a nucleic acid insertion into the genome; ii) a non-LTR site specific retrotransposon element enzyme; wherein the non-LTR site specific retrotransposon element enzyme comprises a reverse transcriptase domain…and wherein if the non-LTR-site specific retrotransposon element enzyme does not comprise the optional nuclease or nickase domain, the genome editing system further comprises iii) a nuclease or nickase enzyme.” Copending application ‘192 further recites that the donor polynucleotide claimed therein comprises a homology sequence at copending claim 52, which reads on the instantly claimed payload RNA and modifications thereof. Furthermore, the copending application recites that the genome editing system claimed therein comprises a nuclease or nickase enzyme, as set forth above. Thus, the subject matter of instant claim 47 is not patentably distinct from that of copending application ‘192.
This a provisional nonstatutory double patenting rejection.
Conclusion
No claims are allowed.
Claims 1, 4, 16, 18, and 47 are objected to.
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/SARAH E ALLEN/ Examiner, Art Unit 1637
/J. E. ANGELL/ Primary Examiner, Art Unit 1637