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 .
Applicant’s response of 07/16/2026, including replacement drawings and a substitute specification, has been received and entered into the application file.
Claims 135, 136, 139, 141, 144-147, 152, 153, and 154 were amended in the claim set filed 07/16/2026.
Claim 138 was cancelled in the claim set filed 07/16/2026.
Claims 135-137 and 139-154 are pending, of which claims 153 and 154 were previously withdrawn.
Accordingly, claims 135-137 and 139-152 are pending and under consideration.
Election/Restrictions
Applicant’s previous election without traverse of claims 135-152 (Group I) in the reply filed on 03/12/2026 is acknowledged.
Claims 153 and 154 were previously withdrawn from further consideration pursuant to 37 CFR 1.142(b) as being drawn to a nonelected invention, there being no allowable generic or linking claim.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 03/12/2026.
Claim 138 was cancelled in the claim set filed 07/16/2026.
Accordingly, claims 135-137 and 139-152 are pending and under consideration.
Information Disclosure Statement
Receipt of information disclosure statements on 04/15/2026, 07/16/2026, and 09/23/2026 is acknowledged. The signed and initialed PTO-1449‘s have been mailed with this action.
Prior Grounds of Objection/Rejection
RE: Drawings
►The drawings were previously objected to for various informalities.
The replacement drawings received 07/16/2026 have obviated the basis of the objections of record. The objections of record are hereby withdrawn.
RE: Specification
►The disclosure was previously objected to for containing an embedded hyperlink and/or other form of browser-executable code.
The substitute specification filed 07/16/2026 has obviated the basis of the objections of record. The objections of record are hereby withdrawn.
Claim Objections
►Claims 135, 136, 144, and 147 were previously objected to for various informalities.
The amendments to the instant claim set have obviated the basis of the objections of record. The objections of record are hereby withdrawn.
RE: Claim Rejections - 35 USC § 112(a)
►Claims 135-152 were previously rejected under 35 U.S.C. 112(a) or 35 U.S.C. 112 (pre-AIA ), first paragraph, as failing to comply with the written description requirement. The claim(s) contains subject matter which was not described in the specification in such a way as to reasonably convey to one skilled in the relevant art that the inventor or a joint inventor, or for applications subject to pre-AIA 35 U.S.C. 112, the inventor(s), at the time the application was filed, had possession of the claimed invention.
The cancellation of claim 138 renders the rejection thereof moot.
The amendments to the instant claim set have obviated the basis of the rejection of record. The rejection of record is hereby withdrawn.
►Claims 135-144 were previously rejected under 35 U.S.C. 112(a) or 35 U.S.C. 112 (pre-AIA ), first paragraph, as failing to comply with the written description requirement. The claim(s) contains subject matter which was not described in the specification in such a way as to reasonably convey to one skilled in the relevant art that the inventor or a joint inventor, or for applications subject to pre-AIA 35 U.S.C. 112, the inventor(s), at the time the application was filed, had possession of the claimed invention.
The cancellation of claim 138 renders the rejection thereof moot.
The amendments to the instant claim set have obviated the basis of the rejection of record. The rejection of record is hereby withdrawn.
RE: Claim Rejections - 35 USC § 112(b)
►Claims 136 and 152 were previously 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.
The amendments to the instant claim set have obviated the basis of the rejections of record. The rejections of record are hereby withdrawn.
RE: Claim Rejections - 35 USC § 103
►Claims 135-137, 139-144 and 146-152 were previously rejected under 35 U.S.C. 103 as being unpatentable over US 2019/0024090 A1 (hereinafter Cathomen; as cited in the IDS filed 02/27/2025) in view of Alerasool et al., 2020 (hereinafter Alerasool; as cited in the IDS filed 01/16/2024), UniProt Entry Q96PE6 (as cited in the IDS filed 12/23/2025), UniProt Entry Q9UJW3 (aligned sequence released 02/15/2017), and UniProt Entry A0A386IRG9_STAAU (aligned sequence released 12/05/2018), as evidenced by Barrangou and Doudna, 2016 (hereinafter Barrangou).
►Claim 145 was previously rejected under 35 U.S.C. 103 as being unpatentable over US 2019/0024090 A1 (hereinafter Cathomen; as cited in the IDS filed 02/27/2025) in view of Alerasool et al., 2020 (hereinafter Alerasool; as cited in the IDS filed 01/16/2024), UniProt Entry Q96PE6 (as cited in the IDS filed 12/23/2025), UniProt Entry Q9UJW3 (aligned sequence released 02/15/2017), and UniProt Entry A0A386IRG9_STAAU (aligned sequence released 12/05/2018), as evidenced by Barrangou and Doudna, 2016 (hereinafter Barrangou) as applied to claim 135 above, and further in view of US 2019/0032049 A1 (hereinafter Naldini; as cited in the IDS filed 01/16/2024), as evidenced by Eom et al., 2016 (hereinafter Eom).
Applicant has traversed the rejection of record, asserting that amended instant claim 135 includes the limitations of cancelled claim 138, which was not previously rejected under 35 U.S.C. § 103. All other claims depend directly or indirectly from claim 135.
In response, while the Examiner acknowledges that cancelled claim 138 was not previously rejected under 35 U.S.C. § 103, further review of the prior art has necessitated new grounds of rejection. Accordingly, this action is made non-final, with new grounds of rejection set forth in detail below.
RE: Double Patenting
►Claims 135-137, 139-144, and 146-151 were previously rejected on the ground of nonstatutory double patenting as being unpatentable over claims 1-11, 15-19 of U.S. Patent No. 12,390,538 B2. Although the claims at issue are not identical, they are not patentably distinct from each other.
Applicant has filed a terminal disclaimer, which obviates the basis of the rejection of record.
►Claims 135, 137, 139, 140, 141, 143, 146, 147, 148, 149, 150, and 152 were previously rejected on the ground of nonstatutory double patenting as being unpatentable over claims 1, 3, 4, 5, 10, 12, and 13 of U.S. Patent No. 12,558,437 B2. Although the claims at issue are not identical, they are not patentably distinct from each other.
Applicant has filed a terminal disclaimer, which obviates the basis of the rejection of record.
►Claims 135, 137, and 139-152 were previously provisionally rejected on the ground of nonstatutory double patenting as being unpatentable over claims 1, 2, 4, 6, 9, 10, 14, 17-23, 25, 38, and 40 of copending Application No. 18/861,783 (reference application; not yet published). Although the claims at issue are not identical, they are not patentably distinct from each other.
Applicant has traversed the rejection of record, asserting that according to MPEP § 804, if a provisional nonstatutory double patenting rejection is the only rejection remaining in an application having the earliest effective U.S. filing date (i.e. patent term filing date) compared to the reference application(s), the examiner should withdraw the rejection in the application having the earliest effective U.S. filing date and permit that application to issue as a patent.
In response, as set forth above, new grounds of rejection necessitated by a further review of the prior art are set forth below. Accordingly, the double patenting rejection of record is hereby updated to reflect these new grounds of rejection.
►Claims 135, 137, 139-143, and 145-149 were previously provisionally rejected on the ground of nonstatutory double patenting as being unpatentable over claims 1, 2, 3, 17, 20, and 21 of copending Application No. 18/877,796 (reference application; corresponds to US 2025/0387518 A1). Although the claims at issue are not identical, they are not patentably distinct from each other.
Applicant has traversed the rejection of record, asserting that according to MPEP § 804, if a provisional nonstatutory double patenting rejection is the only rejection remaining in an application having the earliest effective U.S. filing date (i.e. patent term filing date) compared to the reference application(s), the examiner should withdraw the rejection in the application having the earliest effective U.S. filing date and permit that application to issue as a patent.
In response, as set forth above, new grounds of rejection necessitated by a further review of the prior art are set forth below. Accordingly, the double patenting rejection of record is hereby updated to reflect these new grounds of rejection.
►Claims 135, 137, 139-143, 145-151 were previously provisionally rejected on the ground of nonstatutory double patenting as being unpatentable over claims 1-5, 13, 16, 17-22, 24, 26, 31, 33, 34, 36, 37, and 39 of copending Application No. 18/877,818 (reference application; corresponds to US 2025/0387514 A1). Although the claims at issue are not identical, they are not patentably distinct from each other.
Applicant has traversed the rejection of record, asserting that Application No. 18/877,818 is abandoned, thereby rendering the rejection moot.
In response, this is found persuasive. Application No. 18/877,818 was abandoned on 04/24/2026, as reflected in the application file.
►Claims 135, 136, 139-141, 143, 144, and 146-150 were previously provisionally rejected on the ground of nonstatutory double patenting as being unpatentable over claims 41, 46-51, 58, and 60 of copending Application No. 18/981,846 (reference application; corresponds to US 2025/0197818 A1; as cited in the IDS filed 07/02/2025). Although the claims at issue are not identical, they are not patentably distinct from each other.
Applicant has traversed the rejection of record, asserting that according to MPEP § 804, if a provisional nonstatutory double patenting rejection is the only rejection remaining in an application having the earliest effective U.S. filing date (i.e. patent term filing date) compared to the reference application(s), the examiner should withdraw the rejection in the application having the earliest effective U.S. filing date and permit that application to issue as a patent.
In response, as set forth above, new grounds of rejection necessitated by a further review of the prior art are set forth below. Accordingly, the double patenting rejection of record is hereby updated to reflect these new grounds of rejection.
►Claims 135, 139, and 140-143 were previously provisionally rejected on the ground of nonstatutory double patenting as being unpatentable over claims 148, 157, 158, 160, 161, 163, and 165 of copending Application No. 18/989,126 (reference application; corresponds to US 2025/0320478 A1). Although the claims at issue are not identical, they are not patentably distinct from each other.
Applicant has traversed the rejection of record, asserting that according to MPEP § 804, if a provisional nonstatutory double patenting rejection is the only rejection remaining in an application having the earliest effective U.S. filing date (i.e. patent term filing date) compared to the reference application(s), the examiner should withdraw the rejection in the application having the earliest effective U.S. filing date and permit that application to issue as a patent.
In response, as set forth above, new grounds of rejection necessitated by a further review of the prior art are set forth below. Accordingly, the double patenting rejection of record is hereby updated to reflect these new grounds of rejection.
►Claims 135-137, 139-146, and 146-149 were previously provisionally rejected on the ground of nonstatutory double patenting as being unpatentable over claims 1, 2, 7, 8, 13, 14, 19, and 20 of copending Application No. 19/060,404 (reference application; corresponds to US 2025/0236847 A1). Although the claims at issue are not identical, they are not patentably distinct from each other.
Applicant has traversed the rejection of record, asserting that according to MPEP § 804, if a provisional nonstatutory double patenting rejection is the only rejection remaining in an application having the earliest effective U.S. filing date (i.e. patent term filing date) compared to the reference application(s), the examiner should withdraw the rejection in the application having the earliest effective U.S. filing date and permit that application to issue as a patent.
In response, as set forth above, new grounds of rejection necessitated by a further review of the prior art are set forth below. Accordingly, the double patenting rejection of record is hereby updated to reflect these new grounds of rejection.
►Claims 135-137, 139-144, and 146-151 were previously provisionally rejected on the ground of nonstatutory double patenting as being unpatentable over claims 1-11 and 13-19 of copending Application No. 19/224,549 (reference application; corresponds to US 2025/0288691 A1). Although the claims at issue are not identical, they are not patentably distinct from each other.
Applicant has traversed the rejection of record, asserting that according to MPEP § 804, if a provisional nonstatutory double patenting rejection is the only rejection remaining in an application having the earliest effective U.S. filing date (i.e. patent term filing date) compared to the reference application(s), the examiner should withdraw the rejection in the application having the earliest effective U.S. filing date and permit that application to issue as a patent.
In response, as set forth above, new grounds of rejection necessitated by a further review of the prior art are set forth below. Accordingly, the double patenting rejection of record is hereby updated to reflect these new grounds of rejection.
►Claims 135, 137, 139-144, 146-150, and 152 were previously provisionally rejected on the ground of nonstatutory double patenting as being unpatentable over claims 1, 6-14, 16, and 21-29 of copending Application No. 19/390,246 (reference application; not yet published). Although the claims at issue are not identical, they are not patentably distinct from each other.
Applicant has traversed the rejection of record, asserting that according to MPEP § 804, if a provisional nonstatutory double patenting rejection is the only rejection remaining in an application having the earliest effective U.S. filing date (i.e. patent term filing date) compared to the reference application(s), the examiner should withdraw the rejection in the application having the earliest effective U.S. filing date and permit that application to issue as a patent.
In response, as set forth above, new grounds of rejection necessitated by a further review of the prior art are set forth below. Accordingly, the double patenting rejection of record is hereby updated to reflect these new grounds of rejection.
►Claims 135, 139-141, 143, and 145 were previously provisionally rejected on the ground of nonstatutory double patenting as being unpatentable over claims 1, 7, 10, 11, and 39 of copending Application No. 19/476,668 (reference application; not yet published). Although the claims at issue are not identical, they are not patentably distinct from each other.
Applicant has traversed the rejection of record, asserting that according to MPEP § 804, if a provisional nonstatutory double patenting rejection is the only rejection remaining in an application having the earliest effective U.S. filing date (i.e. patent term filing date) compared to the reference application(s), the examiner should withdraw the rejection in the application having the earliest effective U.S. filing date and permit that application to issue as a patent.
In response, as set forth above, new grounds of rejection necessitated by a further review of the prior art are set forth below. Accordingly, the double patenting rejection of record is hereby updated to reflect these new grounds of rejection.
►Claims 135, 137, and 139-152 were previously provisionally rejected on the ground of nonstatutory double patenting as being unpatentable over claims 1, 4-6, 9, 10, 14, 17-23, 32, 34, 35, 37, 38, and 40 of copending Application No. 19/480,313 (reference application; not yet published). Although the claims at issue are not identical, they are not patentably distinct from each other.
►Claims 135, 137, and 139-152 were previously provisionally rejected on the ground of nonstatutory double patenting as being unpatentable over claims 1-19, 21, 22, 26, 29-35, 44, 46, 47, 49, 50, 52, 74-80, 82, 83, 87, 90-96, 105, 107, 108, 110, 111, 113, and 115 of copending Application No. 19/483,765 (reference application; not yet published). Although the claims at issue are not identical, they are not patentably distinct from each other.
►Claims 135, 137, and 139-152 were previously provisionally rejected on the ground of nonstatutory double patenting as being unpatentable over claims 1-10, 14, 17-23, 32, 34, 35, 37, 38, and 40 of copending Application No. 19/515,156 (reference application; not yet published). Although the claims at issue are not identical, they are not patentably distinct from each other.
►Claims 135, 137, and 139-152 were previously provisionally rejected on the ground of nonstatutory double patenting as being unpatentable over claims 1-10, 14, 17-23, 32, 34, 35, 37, 38, and 40 of copending Application No. 19/515,205 (reference application; not yet published). Although the claims at issue are not identical, they are not patentably distinct from each other.
Applicant has traversed the rejections of record, asserting that according to MPEP § 804, if a provisional nonstatutory double patenting rejection is the only rejection remaining in an application having the earliest effective U.S. filing date (i.e. patent term filing date) compared to the reference application(s), the examiner should withdraw the rejection in the application having the earliest effective U.S. filing date and permit that application to issue as a patent.
In response, as set forth above, new grounds of rejection necessitated by a further review of the prior art are set forth below. Accordingly, the double patenting rejection of record is hereby updated to reflect these new grounds of rejection.
►Claims 135, 137, 139-143, and 145-152 were previously provisionally rejected on the ground of nonstatutory double patenting as being unpatentable over claims 1-8, 14, 17-23, 32, 34, 35, 37, 38, 40, and 62 of copending Application No. 19/502,682 (reference application; not yet published). Although the claims at issue are not identical, they are not patentably distinct from each other.
Applicant has traversed the rejection of record, asserting that according to MPEP § 804, if a provisional nonstatutory double patenting rejection is the only rejection remaining in an application having the earliest effective U.S. filing date (i.e. patent term filing date) compared to the reference application(s), the examiner should withdraw the rejection in the application having the earliest effective U.S. filing date and permit that application to issue as a patent.
In response, as set forth above, new grounds of rejection necessitated by a further review of the prior art are set forth below. Accordingly, the double patenting rejection of record is hereby updated to reflect these new grounds of rejection.
New/Maintained Grounds of Objection/Rejection
Claim Objections
Claim 135 is objected to because of the following informalities:
The penultimate line of claim 135 recites “to affect an epigenetic modification” (bolded emphasis added), which does not comport with standard grammatical and/or linguistic conventions. The proper verb to describe the action of an effector protein is “effect” not “affect.” It would be remedial to amend the instant claim language to recite “effect” in place of “affect.”
Appropriate correction is required.
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.
Claims 135-137, 139-144 and 146-152 are rejected under 35 U.S.C. 103 as being unpatentable over US 2019/0024090 A1 (hereinafter Cathomen; as cited in the IDS filed 02/27/2025; of record) in view of Alerasool et al., 2020 (hereinafter Alerasool; as cited in the IDS filed 01/16/2024; of record), UniProt Entry Q96PE6 (as cited in the IDS filed 12/23/2025; of record), UniProt Entry Q9UJW3 (aligned sequence released 02/15/2017; of record), and UniProt Entry A0A386IRG9_STAAU (aligned sequence released 12/05/2018; of record), as evidenced by Barrangou and Doudna, 2016 (hereinafter Barrangou; of record).
With regard to amended claim 135, which recites “an epigenetic editor comprising a fusion protein or a nucleic acid encoding the fusion protein thereof, wherein the fusion protein comprises:
a first DNA methyltransferase (DNMT) domain;
a DNA binding domain, wherein the DNA binding domain comprises (1) a zinc finger motif, or a zinc finger array, or (2) a nucleic acid guided DNA binding domain bound to a guide polynucleotide; and
a repressor domain, wherein the repressor domain is selected from the group consisting of: ZIM3…and wherein the repressor domain specifically binds to an epigenetic effector protein in a cell comprising a target gene and directs the epigenetic editor to the target gene to [e]ffect an epigenetic modification in a nucleotide in the target gene or a histone bound to the target gene.
Cathomen discloses a construct for editing epigenetic marks of genes governing the expression thereof, said construct comprising a Krϋppel-associated box (KRAB) zinc finger protein (or homologous), a DNA region capable of binding to the target gene (or homologous), and two DNA methyltransferases (DNMT) (human DNMT3A or homologous and murine Dnmt3L or homologous) (paragraphs [0012]-[0018]). Thus, Cathomen discloses an epigenetic editor comprising a fusion protein, said fusion protein comprising a first DNMT domain, a DNA binding domain, and a repressor domain, as instantly claimed. Regarding the instantly claimed repressor domain, per paragraph [0009], the KRAB zinc finger proteins taught therein include an effector motif called KRAB, wherein KRAB serves to recruit histone deacetylase complexes, thereby repressing gene expression. Per paragraphs [0071] and [0072] of the instant specification, KRAB is a known transcription repressor domain. Thus, it is considered that the KRAB zinc finger protein disclosed in Cathomen generally reads on the instantly claimed repressor domain. Per Cathomen, the KRAB domain taught therein recruits the scaffold protein KAP1 that in turn regulates transcription through the induction of histone modifications such as deacetylation or tri-methylation (paragraphs [0009] and [0044]).
However, Cathomen is silent as to the instantly claimed ZIM3 domain.
This deficiency is cured by Alerasool, which discloses CRISPR interference constructs comprising fusion of inactive Cas9 (dCas9) to the ZIM3 KRAB domain, which is an exceptionally potent repressor (abstract; page 1093, column 2, paragraph 2; Figures 1 and 2). Therefore, while Cathomen does not disclose that the KRAB fusion taught therein specifically comprises the ZIM3 KRAB domain, Alerasool discloses that the ZIM3 KRAB domain is a potent repressor compatible with targeted gene silencing by fusing it to dCas9 (i.e. a DNA binding domain, wherein said DNA binding domain is a nucleic acid DNA binding domain bound to a guide polynucleotide-see Figure 1). While Alerasool does not specify that the gRNA is bound to the dCas9 taught therein, it is known to those of ordinary skill in the art that gRNAs function by binding to their target sequences as well as to the Cas9 protein to assemble a functional editing complex (see Box 1 of Barrangou and Figure 1 of Alerasool). Alerasool further discloses that the ZIM3 KRAB domain interacts strongly with TRIM28/KAP1 (page 1093, column 2, paragraph 3; Figure 1).
Therefore, in aggregate, it is considered that Cathomen discloses a construct for editing epigenetic marks of genes governing the expression thereof, wherein said construct comprises a KRAB domain (such as ZIM3 as disclosed in Alerasool), a DNA region capable of binding to the target gene (i.e. a dCas9 bound to a gRNA as disclosed in Alerasool), and two DNMTs, wherein the ZIM3 KRAB domain strongly interacts with TRIM28/KAP1 (as disclosed in Alerasool) to induce histone modifications as per Cathomen. This strong, specific interaction of the ZIM3 KRAB domain with TRIM28/KAP1 is considered to read on the limitation of “the repressor domain specifically binds to an epigenetic effector protein in a cell comprising a target gene,” wherein the epigenetic effector protein is TRIM28/KAP1, which assembles a protein complex with chromatin regulators (as disclosed in Alerasool: page 1093, column 2, paragraph 3). As depicted in Figure 1B of Cathomen, said construct then effects an epigenetic modification in a nucleotide in the target gene or a histone bound to the target gene, specifically in the promoter region of the target gene (see also paragraph [0061]). Thus, it is considered that Cathomen and Alerasool collectively disclose each and every limitation of amended instant claim 135.
With regard to amended claim 136, which recites “the repressor domain [of the epigenetic editor of claim 135] is selected from the group consisting of: SEQ ID NOs: 67-595,” as set forth above, Cathomen discloses fusion of KRAB to a DNA binding domain and two DNMT domains for targeted silencing of genes via epigenetic modification, while Alerasool discloses fusion specifically of the ZIM3 KRAB domain to dCas9 to facilitate potent repression of gene expression. However, neither Cathomen nor Alerasool discloses the sequence of the ZIM3 repressor domain corresponding to SEQ ID NO: 67. This deficiency is cured by UniProt Entry Q96PE6. As shown in the alignment of Appendix I (previously provided), UniProt Entry Q96PE6 (corresponding to human ZIM3) comprises 100% identity to instant SEQ ID NO: 67. Thus, it is considered that UniProt Entry Q96PE6 discloses each and every additional limitation of instant claim 136.
With regard to claim 137, which recites “the DNA binding domain [of the epigenetic editor of claim 135] binds to a target sequence in a target chromosome comprising a target gene,” as set forth above, Cathomen discloses a fusion construct for epigenetic editing. Furthermore, as shown in Figures 1B and 2A of Cathomen, the DEM (designer epigenome modifier per paragraph [0013], the DNA binding portion of the DEM directs the DEM to a specific target site in the promoter or any other regulatory element of the target gene, leading to the methylation of the neighboring CpG di-residues and the deacetylation of neighboring histone tails, thereby silencing the target gene of interest (paragraphs [0061] and [0063]). This targeted binding reads on each and every additional limitation of instant claim 137. Thus, it is considered that Cathomen discloses each and every additional limitation of instant claim 137.
With regard to amended claim 139, which recites “the repressor domain [of the epigenetic editor of claim 135] is selected from the group consisting of: ZIM3…,” as set forth above, Alerasool discloses CRISPR interference constructs comprising fusion of inactive Cas9 (dCas9) to the ZIM3 KRAB domain, which is an exceptionally potent repressor (abstract; page 1093, column 2, paragraph 2; Figures 1 and 2). Thus, it is considered that Alerasool discloses each and every additional limitation of instant claim 139.
With regard to claim 140, which recites “the fusion protein [of the epigenetic editor of claim 135] further comprises a second DNMT domain,” as set forth above, Cathomen discloses a construct for epigenetic modification of genes, said construct comprising a Krϋppel-associated box (KRAB) zinc finger protein (or homologous), a DNA region capable of binding to the target gene (or homologous), and two DNA methyltransferases (DNMT) (human DNMT3A or homologous and murine Dnmt3L or homologous) (paragraphs [0012]-[0018]). Thus, it is considered that Cathomen discloses each and every additional limitation of instant claim 140.
With regard to amended claim 141, which recites “the first DNMT domain [of the epigenetic editor of claim 135] is selected from the group consisting of a DNMT3A domain, a DNMT3B domain, a DNMT3C domain, and a DNMT3L domain,” as set forth above, Cathomen discloses a construct for epigenetic modification of genes, said construct comprising a Krϋppel-associated box (KRAB) zinc finger protein (or homologous), a DNA region capable of binding to the target gene (or homologous), and two DNA methyltransferases (DNMT) (human DNMT3A or homologous and murine Dnmt3L or homologous) (paragraphs [0012]-[0018]). Thus, it is considered that Cathomen discloses each and every additional limitation of instant claim 141.
With regard to claim 142, which recites “the first DNMT domain [of the epigenetic editor of claim 135] is a human DNMT3A domain or a human DMNT3L domain,” as set forth above, Cathomen discloses a construct for epigenetic modification of genes, said construct comprising a Krϋppel-associated box (KRAB) zinc finger protein (or homologous), a DNA region capable of binding to the target gene (or homologous), and two DNA methyltransferases (DNMT) (human DNMT3A or homologous and murine Dnmt3L or homologous) (paragraphs [0012]-[0018]). Thus, it is considered that Cathomen discloses each and every additional limitation of instant claim 142.
With regard to claim 143, which recites “the first DNMT domain [of the epigenetic editor of claim 140] is a DNMT3A domain and the second DNMT domain is a DNMT3L domain, or a catalytic portion thereof,” as set forth above, Cathomen discloses a construct for epigenetic modification of genes, said construct comprising a Krϋppel-associated box (KRAB) zinc finger protein (or homologous), a DNA region capable of binding to the target gene (or homologous), and two DNA methyltransferases (DNMT) (human DNMT3A or homologous and murine Dnmt3L or homologous) (paragraphs [0012]-[0018]). Thus, it is considered that Cathomen discloses each and every additional limitation of instant claim 143.
With regard to amended instant claim 144, which recites “the first DNMT domain and the second DNMT domain [of the epigenetic editor of claim 140] are selected from the group consisting of: SEQ ID NOs: 32-66,” as set forth above, Cathomen discloses a construct for epigenetic modification of genes, said construct comprising a Krϋppel-associated box (KRAB) zinc finger protein (or homologous), a DNA region capable of binding to the target gene (or homologous), and two DNA methyltransferases (DNMT) (human DNMT3A or homologous and murine Dnmt3L or homologous) (paragraphs [0012]-[0018]). Additionally, Cathomen further discloses that the murine DNMT3L of the fusion protein taught therein may alternatively be human DNMT3L at paragraph [0051]. Cathomen further discloses that SEQ ID NO: 3 taught therein corresponds to human DNMT3A. As shown in the alignment of Appendix II (previously provided), SEQ ID NO: 3 of Cathomen comprises 100% identity to instant SEQ ID NO: 34. However, while Cathomen discloses that the murine DNMT3L may alternatively be human DNMT3L, Cathomen is silent as to the specific sequence of human DNMT3L. This deficiency is cured by UniProt Entry Q9UJW3, which discloses the human DNMT3L sequence. As shown in the alignment of Appendix III (previously provided), UniProt Entry Q9UJW3comprises 100% identity to instant SEQ ID NO: 38. Thus, it is considered that Cathomen and UniProt Entry Q9UJW3 collectively disclose each and every additional limitation of instant claim 144.
With regard to amended claim 146, which recites “the DNA binding domain [of the epigenetic editor of claim 135] comprises the nucleic acid guided DNA binding domain bound to the guide polynucleotide,” the construct of Cathomen is disclosed to comprise a TALE-derived DNA binding domain (paragraph [0044]) rather than the instantly claimed nucleic acid guided DNA binding domain bound to a guide polynucleotide. However, as set forth above, Alerasool discloses CRISPR interference constructs comprising fusion of inactive Cas9 (dCas9) to the ZIM3 KRAB domain, which is an exceptionally potent repressor (abstract; page 1093, column 2, paragraph 2; Figures 1 and 2). Alerasool further discloses that the CRISPR interference (CRISPRi) achieved therein using the fusion protein set forth above is particularly sensitive to guide RNA (gRNA) selection (page 1093, column 1, paragraphs 1-2). As depicted in Figure 1a of Alerasool, different gRNAs target the dCas9 to different loci. Furthermore, these gRNAs are indispensable to functioning of the system, as target genes are fully expressed in the absence of the gRNAs, as shown in Figure 2a. While Alerasool does not specify that the gRNA is bound to the dCas9 taught therein, it is known to those of ordinary skill in the art that gRNAs function by binding to their target sequences as well as to the Cas9 protein to assemble a functional editing complex (see Box 1 of Barrangou and Figure 1 of Alerasool). Thus, it is considered that Alerasool (as evidenced by Barrangou) discloses each and every additional limitation of instant claim 146.
With regard to amended claim 147, which recites “the DNA binding domain [of the epigenetic editor of claim 146] comprises a CRISPR-Cas protein bound to the guide polynucleotide,” as set forth above, Alerasool discloses CRISPRi achieved via fusion of ZIM3 to dCas9 (a CRISPR-Cas protein), which is guided to a target locus by the associated gRNA (Figure 1a). Furthermore, it is known to those of ordinary skill in the art that gRNAs function by binding to their target sequences as well as to the Cas9 protein to assemble a functional editing complex (see Box 1 of Barrangou). Thus, it is considered that Alerasool (as evidenced by Barrangou) discloses each and every additional limitation of instant claim 147.
With regard to claim 148, which recites “the guide polynucleotide [of the epigenetic editor of claim 146] hybridizes with a target sequence,” as set forth above, Alerasool discloses CRISPRi achieved via fusion of ZIM3 to dCas9 (a CRISPR-Cas protein), which is guided to a target locus by the associated gRNA (Figure 1a). Furthermore, it is known to those of ordinary skill in the art that gRNAs function by binding to their target sequences as well as to the Cas9 protein to assemble a functional editing complex (see Box 1 of Barrangou). Thus, it is considered that Alerasool (as evidenced by Barrangou) discloses each and every additional limitation of instant claim 148.
With regard to claims 149 and 150, which respectively recite “the CRISPR-Cas protein [of the epigenetic editor of claim 147] comprises a nuclease inactive Cas9 (dCas9),” specifically “dSpCas9,” as set forth above, Alerasool discloses CRISPRi achieved via fusion of ZIM3 to dCas9, which is guided to a target locus by the associated gRNA (Figure 1a). Alerasool specifically discloses that the dCas9 utilized therein is derived from Streptococcus pyogenes dCas9 (page 1097, column 1, paragraph 4). Thus, it is considered that Alerasool discloses each and every additional limitation of instant claims 149 and 150.
With regard to claim 151, which recites “the dSpCas9 [of the epigenetic editor of claim 150] is defined as SEQ ID NO: 3,” as set forth above Alerasool specifically discloses that the dCas9 utilized therein is derived from Streptococcus pyogenes dCas9 (page 1097, column 1, paragraph 4). However, Alerasool does not disclose that the sequence of said dSpCas9 is defined as instant SEQ ID NO: 3. This deficiency is cured by UniProt Entry A0A386IRG9_STAAU, which discloses the sequence of dSpCas9. As shown in the alignment of Appendix IV (previously provided), UniProt Entry A0A386IRG9_STAAU comprises 100% identity to instant SEQ ID NO: 3. Thus, it is considered that Alerasool and UniProt Entry A0A386IRG9_STAAU collectively disclose each and every additional limitation of instant claim 151.
With regard to amended claim 152, which recites “the first DNMT domain [of the epigenetic editor of claim 140] is a DNMT3A, the second DNMT domain is a DNMT3L, the DNA binding domain is a dSpCas9, and wherein the fusion protein comprises from N-terminus to C-terminus the DNMT3A-the DNMT3L-the dSpCas9-the repressor domain,” as set forth above, Cathomen discloses a construct for epigenetic modification of genes, said construct comprising a Krϋppel-associated box (KRAB) zinc finger protein (or homologous), a DNA region capable of binding to the target gene (or homologous), and two DNA methyltransferases (DNMT) (human DNMT3A or homologous and murine Dnmt3L or homologous) (paragraphs [0012]-[0018]). The structure of the epigenetic modifier construct of Cathomen is disclosed at Figure 1A, comprising the repressor domain, the DNA binding domain, and the DNMT domains. While the DNA binding domain of Cathomen is a TALE-derived DNA binding domain (paragraph [0044]), Alerasool discloses the utility of dSpCas9 fusion proteins for targeted epigenetic modification (abstract; Figures 1 and 2). While the N and C termini are not specified, it is known to those of ordinary skill in the art that proteins are typically written from left-to-right from the N terminus to the C terminus. Therefore, while Cathomen and Alerasool collectively disclose all the components of the claimed fusion protein, the order is opposite of that which is instantly claimed. However, per MPEP § 2144.04(VI)(C), it is not inventive to rearrange parts of an invention when all parts of the invention have been disclosed in the prior art, as in the instant case. Accordingly, it is considered that Cathomen and Alerasool collectively disclose the claimed fusion protein and that it would require routine experimentation by someone of ordinary skill in the art to optimize the order of domains in the claimed fusion protein.
Given that Cathomen discloses a construct for epigenetic modification of genes, said construct comprising a Krϋppel-associated box (KRAB) zinc finger protein (or homologous), a DNA region capable of binding to the target gene (or homologous), and two DNA methyltransferases (DNMT) (human DNMT3A or homologous and murine Dnmt3L or homologous), and that Alerasool discloses that the ZIM3 KRAB domain facilitates potent repression via CRISPRi when fused to dSpCas9, and further that the ZIM3 KRAB domain strongly interacts with TRIM28/KAP1, which reads on the instantly claimed “epigenetic effector protein” specifically bound to said ZIM3 KRAB repressor domain, it would have been obvious to someone of ordinary skill in the art before the effective filing date of the claimed invention to utilize the ZIM3 KRAB domain disclosed in Alerasool as the KRAB repressor domain disclosed in Cathomen as part of a construct for epigenetic modification and further to substitute the TALE-derived DNA binding domain of Cathomen for dCas9 (as disclosed in Alerasool) to predictably facilitate user-specified sequence-specific targeting for epigenetic modification (as reviewed in Barrangou). One would have been motivated to make such a modification in order to receive the expected benefit of facilitating user-specified sequence-specific targeting for epigenetic modification.
Claim 145 is rejected under 35 U.S.C. 103 as being unpatentable over US 2019/0024090 A1 (hereinafter Cathomen; as cited in the IDS filed 02/27/2025; of record) in view of Alerasool et al., 2020 (hereinafter Alerasool; as cited in the IDS filed 01/16/2024; of record), UniProt Entry Q96PE6 (as cited in the IDS filed 12/23/2025; of record), UniProt Entry Q9UJW3 (aligned sequence released 02/15/2017; of record), and UniProt Entry A0A386IRG9_STAAU (aligned sequence released 12/05/2018; of record), as evidenced by Barrangou and Doudna, 2016 (hereinafter Barrangou; of record) as applied to claim 135 above, and further in view of US 2019/0032049 A1 (hereinafter Naldini; as cited in the IDS filed 01/16/2024; of record), as evidenced by Eom et al., 2016 (hereinafter Eom; of record).
The combined disclosures of Cathomen, Alerasool, UniProt Entry Q96PE6, UniProt Entry Q9UJW3, UniProt Entry A0A386IRG9_STAAU, and Barrangou are described above and applied as before. However, these disclosures do not teach the DNA binding domain comprising a zinc finger motif or a zinc finger array of instant claim 145.
With regard to amended claim 145, which recites “the DNA binding domain [of the epigenetic editor of claim 135] comprises the zinc finger motif or the zinc finger array,” as set forth above, Cathomen discloses a construct for epigenetic modification of genes, said construct comprising a Krϋppel-associated box (KRAB) zinc finger protein (or homologous), a DNA region capable of binding to the target gene (or homologous), and two DNA methyltransferases (DNMT) (human DNMT3A or homologous and murine Dnmt3L or homologous) (paragraphs [0012]-[0018]). However, the DNA binding domain of Cathomen is a TALE-derived DNA binding domain (paragraph [0044]), which does not comprise a zinc finger motif or a zinc finger array. This deficiency is cured by Naldini.
Naldini discloses artificial transcription repressors that establish robust and permanent states of epigenetic repression, said artificial transcription repressors comprising a DNA-binding domain operably linked to a KRAB domain, a DNMT3A domain, and/or a DNMT3L domain (paragraphs [0014], [0016], and [0024]-[0029]). As depicted in Figure 1 of Naldini, this system facilitates epigenetic silencing of a targeted gene of interest. Naldini discloses that the DNA binding domain taught therein may be a zinc finger domain (paragraphs [0037] and [0253]). As is known to those of ordinary skill in the art, zinc finger domains comprise zinc finger motifs (reviewed in Eom: see especially page 2023, column 2, paragraph 2). Thus, Naldini discloses that zinc finger domains (comprising zinc finger motifs) are capable of functioning as a DNA binding domain that targets a locus of interest for epigenetic modification thereof, as instantly claimed.
Given that Cathomen discloses a construct for epigenetic modification of genes, said construct comprising a Krϋppel-associated box (KRAB) zinc finger protein (or homologous), a DNA region capable of binding to the target gene (or homologous), and two DNA methyltransferases (DNMT) (human DNMT3A or homologous and murine Dnmt3L or homologous), and that Naldini discloses that zinc finger domains are capable of functioning as a DNA binding domain that targets a locus of interest for epigenetic modification thereof, it would have been obvious to someone of ordinary skill in the art before the effective filing date of the claimed invention to utilize the zinc finger domains disclosed in Naldini as the DNA binding domain for use in the construct for epigenetic modification disclosed in Cathomen to predictably facilitate user-specified sequence-specific targeting for epigenetic modification. One would have been motivated to make such a modification in order to receive the expected benefit of facilitating user-specified sequence-specific targeting for epigenetic modification.
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.
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Claims 135-137, and 139-152 are provisionally rejected on the ground of nonstatutory double patenting as being unpatentable over claims 1, 2, 4, 6, 9, 10, 14, 17-23, 25, 38, and 40 of copending Application No. 18/861,783 (reference application; corresponds to US 2026/0250646 A1) in view of US 2019/0024090 A1 (hereinafter Cathomen; as cited in the IDS filed 02/27/2025; of record), Alerasool et al., 2020 (hereinafter Alerasool; as cited in the IDS filed 01/16/2024; of record), andUniProt Entry Q96PE6 (of record), as evidenced by Barrangou and Doudna, 2016 (hereinafter Barrangou; of record).
Copending application ‘783 is drawn to a system for repressing transcription of a human PCSK9 gene in a human cell, said system comprising one or more fusion proteins collectively comprising a DNMT3A domain, a DNMT3L domain, a DNA-binding domain derived from dead CRISPR Cas such as dCas9, and a ZIM3 transcriptional repressor that binds to a target sequence (as recited at copending claims 1, 2, 4, 14, 18-23, 25, 38, and 40). This epigenetic editor fusion protein reads on the epigenetic editor comprising a fusion protein recited at instant claims 135, 137, 139, 140-143, 146-150, and 152, which comprises a DNA binding domain comprising a CRISPR Cas protein (such as dSpCas9) guided by a guide polynucleotide that hybridizes with a target sequence, a ZIM3 repressor domain, and human DNMT3A and DNMT3L domains.
Regarding the amended claim limitations of instant claim 135, as set forth above, Cathomen also discloses a construct for editing epigenetic marks of genes governing the expression thereof, said construct comprising a Krϋppel-associated box (KRAB) zinc finger protein (or homologous), a DNA region capable of binding to the target gene (or homologous), and two DNA methyltransferases (DNMT) (human DNMT3A or homologous and murine Dnmt3L or homologous) (paragraphs [0012]-[0018]). Thus, Cathomen discloses an epigenetic editor comprising a fusion protein, said fusion protein comprising a first DNMT domain, a DNA binding domain, and a repressor domain, as instantly claimed. Regarding the instantly claimed repressor domain, per paragraph [0009], the KRAB zinc finger proteins taught therein include an effector motif called KRAB, wherein KRAB serves to recruit histone deacetylase complexes, thereby repressing gene expression. Per paragraphs [0071] and [0072] of the instant specification, KRAB is a known transcription repressor domain. Thus, it is considered that the KRAB zinc finger protein disclosed in Cathomen generally reads on the instantly claimed repressor domain. Per Cathomen, the KRAB domain taught therein recruits the scaffold protein KAP1 that in turn regulates transcription through the induction of histone modifications such as deacetylation or tri-methylation (paragraphs [0009] and [0044]). However, Cathomen is silent as to the instantly claimed ZIM3 domain.
This deficiency is cured by Alerasool, which discloses CRISPR interference constructs comprising fusion of inactive Cas9 (dCas9) to the ZIM3 KRAB domain, which is an exceptionally potent repressor (abstract; page 1093, column 2, paragraph 2; Figures 1 and 2). Therefore, while Cathomen does not disclose that the KRAB fusion taught therein specifically comprises the ZIM3 KRAB domain, Alerasool discloses that the ZIM3 KRAB domain is a potent repressor compatible with targeted gene silencing by fusing it to dCas9 (i.e. a DNA binding domain, wherein said DNA binding domain is a nucleic acid DNA binding domain bound to a guide polynucleotide-see Figure 1). While Alerasool does not specify that the gRNA is bound to the dCas9 taught therein, it is known to those of ordinary skill in the art that gRNAs function by binding to their target sequences as well as to the Cas9 protein to assemble a functional editing complex (see Box 1 of Barrangou and Figure 1 of Alerasool). Alerasool further discloses that the ZIM3 KRAB domain interacts strongly with TRIM28/KAP1 (page 1093, column 2, paragraph 3; Figure 1).
Therefore, in aggregate, it is considered that both the copending application and Cathomen discloses a construct for editing epigenetic marks of genes governing the expression thereof, wherein said construct comprises a KRAB domain (such as ZIM3 as disclosed in Alerasool), a DNA region capable of binding to the target gene (i.e. a dCas9 bound to a gRNA as disclosed in Alerasool), and two DNMTs, wherein the ZIM3 KRAB domain strongly interacts with TRIM28/KAP1 (as disclosed in Alerasool) to induce histone modifications as per Cathomen. This strong, specific interaction of the ZIM3 KRAB domain with TRIM28/KAP1 is considered to read on the limitation of “the repressor domain specifically binds to an epigenetic effector protein in a cell comprising a target gene,” wherein the epigenetic effector protein is TRIM28/KAP1, which assembles a protein complex with chromatin regulators (as disclosed in Alerasool: page 1093, column 2, paragraph 3). As depicted in Figure 1B of Cathomen, said construct then effects an epigenetic modification in a nucleotide in the target gene or a histone bound to the target gene, specifically in the promoter region of the target gene (see also paragraph [0061]).
Thus, the instantly claimed epigenetic editor and that of copending application ‘783 are not patentably distinct in view of Cathomen and Alerasool.
Regarding the sequence of the repressor domain of the instant (see instant claim 136) and copending applications, both the instant and copending applications are drawn to ZIM3 repressor domains. The sequence of ZIM3 repressor domains was known in the art prior to the effective filing date of the instant application. As set forth above (and shown in the alignment of Appendix I (previously presented), UniProt Entry Q96PE6 (corresponding to human ZIM3) comprises 100% identity to instant SEQ ID NO: 67
Regarding the sequence of the dCas9 species of the instant and copending applications, instant claim 151 defines the dSpCas9 claimed therein as SEQ ID NO: 3, which is identical to the copending dCas9 sequence of SEQ ID NO: 12 as recited at copending claim 6, as shown in the alignment of Appendix IX (previously presented).
Regarding the sequence of the DNMT3A domains of the instant and copending applications, instant claim 144 defines the DNMT3A and DNMT3L domains claimed therein as corresponding to SEQ ID NOs: 34 and 38 (as elected by Applicant), respectively. These sequences are identical to the DNMT3A domain sequence recited at copending claim 9 (SEQ ID NO: 574) and the DNMT3L domain sequence recited at copending claim 10 (SEQ ID NO: 579), as shown in the alignment of Appendices X and XI (previously presented).
Furthermore, instant claim 145 recites “the DNA binding domain comprises a zinc finger motif or a zinc finger array,” which is not patentably distinct from the recitation of copending claim 4, which also recites that the DNA binding domain claimed therein comprises a zinc finger protein domain.
Finally, copending claim 17 recites that the transcriptional repressor domain may be derived from species such as TOX3, which is also recited at instant claim 139. Accordingly, these recitations are not patentably distinct.
With regard to amended claim 136, which recites “the repressor domain [of the epigenetic editor of claim 135] is selected from the group consisting of: SEQ ID NOs: 67-595,” as set forth above, copending claims 1, 2, 4, 14, 18-23, 25, 38, and 40 are not patentably distinct.
Given that the copending application discloses compositions and methods for epigenetic regulation, and further that Cathomen discloses a construct for epigenetic modification of genes, said construct comprising a Krϋppel-associated box (KRAB) zinc finger protein (or homologous), a DNA region capable of binding to the target gene (or homologous), and two DNA methyltransferases (DNMT) (human DNMT3A or homologous and murine Dnmt3L or homologous), while Alerasool discloses that the ZIM3 KRAB (the sequence of which is disclosed by UniProt entry Q96PE6) domain facilitates potent repression via CRISPRi when fused to dSpCas9, and further that the ZIM3 KRAB domain strongly interacts with TRIM28/KAP1, which reads on the instantly claimed “epigenetic effector protein” specifically bound to said ZIM3 KRAB repressor domain, it would have been obvious to someone of ordinary skill in the art before the effective filing date of the claimed invention to utilize the ZIM3 KRAB domain disclosed in the copending application and Alerasool as the KRAB repressor domain disclosed in the copending application and Cathomen as part of a construct for epigenetic modification and further to substitute the TALE-derived DNA binding domain of Cathomen for dCas9 (as disclosed in the copending application and Alerasool) to predictably facilitate user-specified sequence-specific targeting for epigenetic modification (as reviewed in Barrangou). One would have been motivated to make such a modification in order to receive the expected benefit of facilitating user-specified sequence-specific targeting for epigenetic modification.
This is a provisional nonstatutory double patenting rejection because the patentably indistinct claims have not in fact been patented.
Claims 135-137 and 139-152 are provisionally rejected on the ground of nonstatutory double patenting as being unpatentable over claims 1, 2, 3, 17, 20, and 21 of copending Application No. 18/877,796 (reference application; corresponds to US 2025/0387518 A1; of record) in view of US 2019/0024090 A1 (hereinafter Cathomen; as cited in the IDS filed 02/27/2025; of record), Alerasool et al., 2020 (hereinafter Alerasool; as cited in the IDS filed 01/16/2024; of record), UniProt Entry Q96PE6 (as cited in the IDS filed 12/23/2025; of record), UniProt Entry Q9UJW3 (aligned sequence released 02/15/2017; of record), and UniProt Entry A0A386IRG9_STAAU (aligned sequence released 12/05/2018; of record), as evidenced by Barrangou and Doudna, 2016 (hereinafter Barrangou; of record).
Copending application ‘796 is drawn to a system for repressing transcription of a human B2M gene in a human cell, said system comprising one or more fusion proteins that collectively comprise a human DNMT3A and/or a DNMT3L domain and a transcriptional repressor domain linked to a DNA-binding domain (i.e. dCas or a ZFP domain) that binds to a targeted genomic locus, wherein said transcriptional repressor domain is derived from a ZIM3 KRAB domain or a TOX3 transcriptional repressor domain (as recited at copending claims 1, 2, 17, 20, and 21). Copending application ‘796 further recites that when the DNA-binding domain claimed therein comprises a dCas9 domain, the system further comprises one or more guide RNAs to direct the fusion protein to the targeted genomic locus (copending claim 3).
This epigenetic editor fusion protein reads on the epigenetic editor comprising a fusion protein recited at instant claims 135, 137, 139-143, 145-149, which comprises a DNA binding domain comprising a CRISPR Cas protein (such as dSpCas9) guided by a guide polynucleotide that hybridizes with a target sequence in the genome or alternatively a zinc finger motif/array, a ZIM3 or TOX3 repressor domain, and human DNMT3A and DNMT3L domains.
Regarding the amended claim limitations of instant claim 135, as set forth above, Cathomen also discloses a construct for editing epigenetic marks of genes governing the expression thereof, said construct comprising a Krϋppel-associated box (KRAB) zinc finger protein (or homologous), a DNA region capable of binding to the target gene (or homologous), and two DNA methyltransferases (DNMT) (human DNMT3A or homologous and murine Dnmt3L or homologous) (paragraphs [0012]-[0018]). Thus, Cathomen discloses an epigenetic editor comprising a fusion protein, said fusion protein comprising a first DNMT domain, a DNA binding domain, and a repressor domain, as instantly claimed. Regarding the instantly claimed repressor domain, per paragraph [0009], the KRAB zinc finger proteins taught therein include an effector motif called KRAB, wherein KRAB serves to recruit histone deacetylase complexes, thereby repressing gene expression. Per paragraphs [0071] and [0072] of the instant specification, KRAB is a known transcription repressor domain. Thus, it is considered that the KRAB zinc finger protein disclosed in Cathomen generally reads on the instantly claimed repressor domain. Per Cathomen, the KRAB domain taught therein recruits the scaffold protein KAP1 that in turn regulates transcription through the induction of histone modifications such as deacetylation or tri-methylation (paragraphs [0009] and [0044]). However, Cathomen is silent as to the instantly claimed ZIM3 domain.
This deficiency is cured by Alerasool, which discloses CRISPR interference constructs comprising fusion of inactive Cas9 (dCas9) to the ZIM3 KRAB domain, which is an exceptionally potent repressor (abstract; page 1093, column 2, paragraph 2; Figures 1 and 2). Therefore, while Cathomen does not disclose that the KRAB fusion taught therein specifically comprises the ZIM3 KRAB domain, Alerasool discloses that the ZIM3 KRAB domain is a potent repressor compatible with targeted gene silencing by fusing it to dCas9 (i.e. a DNA binding domain, wherein said DNA binding domain is a nucleic acid DNA binding domain bound to a guide polynucleotide-see Figure 1). While Alerasool does not specify that the gRNA is bound to the dCas9 taught therein, it is known to those of ordinary skill in the art that gRNAs function by binding to their target sequences as well as to the Cas9 protein to assemble a functional editing complex (see Box 1 of Barrangou and Figure 1 of Alerasool). Alerasool further discloses that the ZIM3 KRAB domain interacts strongly with TRIM28/KAP1 (page 1093, column 2, paragraph 3; Figure 1).
Therefore, in aggregate, it is considered that both the copending application and Cathomen discloses a construct for editing epigenetic marks of genes governing the expression thereof, wherein said construct comprises a KRAB domain (such as ZIM3 as disclosed in Alerasool), a DNA region capable of binding to the target gene (i.e. a dCas9 bound to a gRNA as disclosed in Alerasool), and two DNMTs, wherein the ZIM3 KRAB domain strongly interacts with TRIM28/KAP1 (as disclosed in Alerasool) to induce histone modifications as per Cathomen. This strong, specific interaction of the ZIM3 KRAB domain with TRIM28/KAP1 is considered to read on the limitation of “the repressor domain specifically binds to an epigenetic effector protein in a cell comprising a target gene,” wherein the epigenetic effector protein is TRIM28/KAP1, which assembles a protein complex with chromatin regulators (as disclosed in Alerasool: page 1093, column 2, paragraph 3). As depicted in Figure 1B of Cathomen, said construct then effects an epigenetic modification in a nucleotide in the target gene or a histone bound to the target gene, specifically in the promoter region of the target gene (see also paragraph [0061]).
Thus, the instantly claimed epigenetic editor and that of copending application ‘783 are not patentably distinct.
Regarding the sequence of the repressor domain of the instant (see claim 136) and copending applications, both the instant and copending applications are drawn to ZIM3 repressor domains. The sequence of ZIM3 repressor domains was known in the art prior to the effective filing date of the instant application. As set forth above (and shown in the alignment of Appendix I (previously presented), UniProt Entry Q96PE6 (corresponding to human ZIM3) comprises 100% identity to instant SEQ ID NO: 67
With regard to amended instant claim 144, which recites “the first DNMT domain and the second DNMT domain [of the epigenetic editor of claim 140] are selected from the group consisting of: SEQ ID NOs: 32-66,” as set forth above, Cathomen discloses a construct for epigenetic modification of genes, said construct comprising a Krϋppel-associated box (KRAB) zinc finger protein (or homologous), a DNA region capable of binding to the target gene (or homologous), and two DNA methyltransferases (DNMT) (human DNMT3A or homologous and murine Dnmt3L or homologous) (paragraphs [0012]-[0018]). Additionally, Cathomen further discloses that the murine DNMT3L of the fusion protein taught therein may alternatively be human DNMT3L at paragraph [0051]. Cathomen further discloses that SEQ ID NO: 3 taught therein corresponds to human DNMT3A. As shown in the alignment of Appendix II (previously presented), SEQ ID NO: 3 of Cathomen comprises 100% identity to instant SEQ ID NO: 34. However, while Cathomen discloses that the murine DNMT3L may alternatively be human DNMT3L, Cathomen is silent as to the specific sequence of human DNMT3L. This deficiency is cured by UniProt Entry Q9UJW3, which discloses the human DNMT3L sequence. As shown in the alignment of Appendix III (previously presented), UniProt Entry Q9UJW3comprises 100% identity to instant SEQ ID NO: 38. Thus, it is considered that Cathomen and UniProt Entry Q9UJW3 collectively disclose each and every additional limitation of instant claim 144.
With regard to claim 150, which recites “the epigenetic editor of claim 149, wherein the dCas9 is a dSpCas9,” as set forth above, Alerasool discloses CRISPRi achieved via fusion of ZIM3 to dCas9, which is guided to a target locus by the associated gRNA (Figure 1a). Alerasool specifically discloses that the dCas9 utilized therein is derived from Streptococcus pyogenes dCas9 (page 1097, column 1, paragraph 4). Thus, it is considered that Alerasool discloses each and every additional limitation of instant claim 150.
With regard to claim 151, which recites “the dSpCas9 [of the epigenetic editor of claim 150] is defined as SEQ ID NO: 3,” as set forth above Alerasool specifically discloses that the dCas9 utilized therein is derived from Streptococcus pyogenes dCas9 (page 1097, column 1, paragraph 4). However, Alerasool does not disclose that the sequence of said dSpCas9 is defined as instant SEQ ID NO: 3. This deficiency is cured by UniProt Entry A0A386IRG9_STAAU, which discloses the sequence of dSpCas9. As shown in the alignment of Appendix IV (previously presented), UniProt Entry A0A386IRG9_STAAU comprises 100% identity to instant SEQ ID NO: 3. Thus, it is considered that Alerasool and UniProt Entry A0A386IRG9_STAAU collectively disclose each and every additional limitation of instant claim 151.
With regard to amended claim 152, which recites “the first DNMT domain [of the epigenetic editor of claim 140] is a DNMT3A, the second DNMT domain is a DNMT3L, the DNA binding domain is a dSpCas9, and wherein the fusion protein comprises from N-terminus to C-terminus the DNMT3A-the DNMT3L-the dSpCas9-the repressor domain,” as set forth above, Cathomen discloses a construct for epigenetic modification of genes, said construct comprising a Krϋppel-associated box (KRAB) zinc finger protein (or homologous), a DNA region capable of binding to the target gene (or homologous), and two DNA methyltransferases (DNMT) (human DNMT3A or homologous and murine Dnmt3L or homologous) (paragraphs [0012]-[0018]). The structure of the epigenetic modifier construct of Cathomen is disclosed at Figure 1A, comprising the repressor domain, the DNA binding domain, and the DNMT domains. While the DNA binding domain of Cathomen is a TALE-derived DNA binding domain (paragraph [0044]), Alerasool discloses the utility of dSpCas9 fusion proteins for targeted epigenetic modification (abstract; Figures 1 and 2). While the N and C termini are not specified, it is known to those of ordinary skill in the art that proteins are typically written from left-to-right from the N terminus to the C terminus. Therefore, while Cathomen and Alerasool collectively disclose all the components of the claimed fusion protein, the order is opposite of that which is instantly claimed. However, per MPEP § 2144.04(VI)(C), it is not inventive to rearrange parts of an invention when all parts of the invention have been disclosed in the prior art, as in the instant case. Accordingly, it is considered that Cathomen and Alerasool collectively disclose the claimed fusion protein and that it would require routine experimentation by someone of ordinary skill in the art to optimize the order of domains in the claimed fusion protein.
Given that the copending application discloses compositions and methods for epigenetic regulation, and further that Cathomen discloses a construct for epigenetic modification of genes, said construct comprising a Krϋppel-associated box (KRAB) zinc finger protein (or homologous), a DNA region capable of binding to the target gene (or homologous), and two DNA methyltransferases (DNMT) (human DNMT3A or homologous and murine Dnmt3L or homologous), while Alerasool discloses that the ZIM3 KRAB (the sequence of which is disclosed by UniProt entry Q96PE6) domain facilitates potent repression via CRISPRi when fused to dSpCas9, and further that the ZIM3 KRAB domain strongly interacts with TRIM28/KAP1, which reads on the instantly claimed “epigenetic effector protein” specifically bound to said ZIM3 KRAB repressor domain, it would have been obvious to someone of ordinary skill in the art before the effective filing date of the claimed invention to utilize the ZIM3 KRAB domain disclosed in the copending application and Alerasool as the KRAB repressor domain disclosed in the copending application and Cathomen as part of a construct for epigenetic modification and further to substitute the TALE-derived DNA binding domain of Cathomen for dCas9 (as disclosed in the copending application and Alerasool) to predictably facilitate user-specified sequence-specific targeting for epigenetic modification (as reviewed in Barrangou). One would have been motivated to make such a modification in order to receive the expected benefit of facilitating user-specified sequence-specific targeting for epigenetic modification.
This is a provisional nonstatutory double patenting rejection because the patentably indistinct claims have not in fact been patented.
Claims 135-137 and 139-152 are provisionally rejected on the ground of nonstatutory double patenting as being unpatentable over claims 41, 46-51, 58, and 60 of copending Application No. 18/981,846 (reference application; corresponds to US 2025/0197818 A1; as cited in the IDS filed 07/02/2025; of record) in view of US 2019/0024090 A1 (hereinafter Cathomen; as cited in the IDS filed 02/27/2025; of record), Alerasool et al., 2020 (hereinafter Alerasool; as cited in the IDS filed 01/16/2024; of record), UniProt Entry Q96PE6 (as cited in the IDS filed 12/23/2025; of record), UniProt Entry Q9UJW3 (aligned sequence released 02/15/2017; of record), UniProt Entry A0A386IRG9_STAAU (aligned sequence released 12/05/2018; of record), and US 2019/0032049 A1 (hereinafter Naldini; as cited in the IDS filed 01/16/2024; of record), as evidenced by Barrangou and Doudna, 2016 (hereinafter Barrangou; of record) and Eom et al., 2016 (hereinafter Eom; of record).
Copending application ‘846 is drawn to an epigenetic editing system, said system comprising a DNA-binding domain (i.e. dCas9 guided by a guide RNA), a DNMT3L domain, a DNMT3A domain, and a transcriptional repressor domain such as a ZIM3, ZFP28, or ZN627 KRAB domain (as recited at copending claims 41, 46-51, 58, and 60).
This epigenetic editor fusion protein reads on the epigenetic editor comprising a fusion protein recited at instant claims 135, 139-141, 143, 144, and 146-150, which comprises a DNA binding domain comprising a CRISPR Cas protein (such as dCas9) guided by a guide polynucleotide that hybridizes with a target sequence in the genome, a ZIM3, ZN627, or ZFP28 repressor domain, and DNMT3A and DNMT3L domains. Thus, the instantly claimed epigenetic editor and that of copending application ‘846 are not patentably distinct.
Furthermore, copending claim 50 recites that the ZIM3 claimed therein has a sequence with at least 90% identity to SEQ ID NO: 60. As shown in the alignment of Appendix XIII (previously presented), instant SEQ ID NO: 67 (recited at instant claim 136) is identical to copending SEQ ID NO: 60.
With regard to claim 137, which recites “the DNA binding domain [of the epigenetic editor of claim 135] binds to a target sequence in a target chromosome comprising a target gene,” as set forth above, the copending application and Cathomen both disclose a fusion construct for epigenetic editing. Furthermore, as shown in Figures 1B and 2A of Cathomen, the DEM (designer epigenome modifier per paragraph [0013], the DNA binding portion of the DEM directs the DEM to a specific target site in the promoter or any other regulatory element of the target gene, leading to the methylation of the neighboring CpG di-residues and the deacetylation of neighboring histone tails, thereby silencing the target gene of interest (paragraphs [0061] and [0063]). This targeted binding reads on each and every additional limitation of instant claim 137. Thus, it is considered that Cathomen discloses each and every additional limitation of instant claim 137.
With regard to claim 142, which recites “the first DNMT domain [of the epigenetic editor of claim 135] is a human DNMT3A domain or a human DMNT3L domain,” as set forth above, Cathomen discloses a construct for epigenetic modification of genes, said construct comprising a Krϋppel-associated box (KRAB) zinc finger protein (or homologous), a DNA region capable of binding to the target gene (or homologous), and two DNA methyltransferases (DNMT) (human DNMT3A or homologous and murine Dnmt3L or homologous) (paragraphs [0012]-[0018]). Thus, it is considered that Cathomen discloses each and every additional limitation of instant claim 142.
With regard to amended claim 145, which recites “the DNA binding domain [of the epigenetic editor of claim 135] comprises the zinc finger motif or the zinc finger array,” as set forth above, Cathomen discloses a construct for epigenetic modification of genes, said construct comprising a Krϋppel-associated box (KRAB) zinc finger protein (or homologous), a DNA region capable of binding to the target gene (or homologous), and two DNA methyltransferases (DNMT) (human DNMT3A or homologous and murine Dnmt3L or homologous) (paragraphs [0012]-[0018]). However, the DNA binding domain of Cathomen is a TALE-derived DNA binding domain (paragraph [0044]), which does not comprise a zinc finger motif or a zinc finger array. This deficiency is cured by Naldini.
Naldini discloses artificial transcription repressors that establish robust and permanent states of epigenetic repression, said artificial transcription repressors comprising a DNA-binding domain operably linked to a KRAB domain, a DNMT3A domain, and/or a DNMT3L domain (paragraphs [0014], [0016], and [0024]-[0029]). As depicted in Figure 1 of Naldini, this system facilitates epigenetic silencing of a targeted gene of interest. Naldini discloses that the DNA binding domain taught therein may be a zinc finger domain (paragraphs [0037] and [0253]). As is known to those of ordinary skill in the art, zinc finger domains comprise zinc finger motifs (reviewed in Eom: see especially page 2023, column 2, paragraph 2). Thus, Naldini discloses that zinc finger domains (comprising zinc finger motifs) are capable of functioning as a DNA binding domain that targets a locus of interest for epigenetic modification thereof, as instantly claimed.
With regard to claim 151, which recites “the dSpCas9 [of the epigenetic editor of claim 150] is defined as SEQ ID NO: 3,” as set forth above Alerasool specifically discloses that the dCas9 utilized therein is derived from Streptococcus pyogenes dCas9 (page 1097, column 1, paragraph 4). However, Alerasool does not disclose that the sequence of said dSpCas9 is defined as instant SEQ ID NO: 3. This deficiency is cured by UniProt Entry A0A386IRG9_STAAU, which discloses the sequence of dSpCas9. As shown in the alignment of Appendix IV (previously provided), UniProt Entry A0A386IRG9_STAAU comprises 100% identity to instant SEQ ID NO: 3. Thus, it is considered that Alerasool and UniProt Entry A0A386IRG9_STAAU collectively disclose each and every additional limitation of instant claim 151.
With regard to amended claim 152, which recites “the first DNMT domain [of the epigenetic editor of claim 140] is a DNMT3A, the second DNMT domain is a DNMT3L, the DNA binding domain is a dSpCas9, and wherein the fusion protein comprises from N-terminus to C-terminus the DNMT3A-the DNMT3L-the dSpCas9-the repressor domain,” as set forth above, Cathomen discloses a construct for epigenetic modification of genes, said construct comprising a Krϋppel-associated box (KRAB) zinc finger protein (or homologous), a DNA region capable of binding to the target gene (or homologous), and two DNA methyltransferases (DNMT) (human DNMT3A or homologous and murine Dnmt3L or homologous) (paragraphs [0012]-[0018]). The structure of the epigenetic modifier construct of Cathomen is disclosed at Figure 1A, comprising the repressor domain, the DNA binding domain, and the DNMT domains. While the DNA binding domain of Cathomen is a TALE-derived DNA binding domain (paragraph [0044]), Alerasool discloses the utility of dSpCas9 fusion proteins for targeted epigenetic modification (abstract; Figures 1 and 2). While the N and C termini are not specified, it is known to those of ordinary skill in the art that proteins are typically written from left-to-right from the N terminus to the C terminus. Therefore, while Cathomen and Alerasool collectively disclose all the components of the claimed fusion protein, the order is opposite of that which is instantly claimed. However, per MPEP § 2144.04(VI)(C), it is not inventive to rearrange parts of an invention when all parts of the invention have been disclosed in the prior art, as in the instant case. Accordingly, it is considered that Cathomen and Alerasool collectively disclose the claimed fusion protein and that it would require routine experimentation by someone of ordinary skill in the art to optimize the order of domains in the claimed fusion protein.
Given that the copending application discloses compositions and methods for epigenetic regulation, and further that Cathomen discloses a construct for epigenetic modification of genes, said construct comprising a Krϋppel-associated box (KRAB) zinc finger protein (or homologous), a DNA region capable of binding to the target gene (or homologous), and two DNA methyltransferases (DNMT) (human DNMT3A or homologous and murine Dnmt3L or homologous), while Alerasool discloses that the ZIM3 KRAB (the sequence of which is disclosed by UniProt entry Q96PE6) domain facilitates potent repression via CRISPRi when fused to dSpCas9, and further that the ZIM3 KRAB domain strongly interacts with TRIM28/KAP1, which reads on the instantly claimed “epigenetic effector protein” specifically bound to said ZIM3 KRAB repressor domain, it would have been obvious to someone of ordinary skill in the art before the effective filing date of the claimed invention to utilize the ZIM3 KRAB domain disclosed in the copending application and Alerasool as the KRAB repressor domain disclosed in the copending application and Cathomen as part of a construct for epigenetic modification and further to substitute the TALE-derived DNA binding domain of Cathomen for dCas9 (as disclosed in the copending application and Alerasool) to predictably facilitate user-specified sequence-specific targeting for epigenetic modification (as reviewed in Barrangou). One would have been motivated to make such a modification in order to receive the expected benefit of facilitating user-specified sequence-specific targeting for epigenetic modification.
Furthermore, given that Cathomen discloses a construct for epigenetic modification of genes, said construct comprising a Krϋppel-associated box (KRAB) zinc finger protein (or homologous), a DNA region capable of binding to the target gene (or homologous), and two DNA methyltransferases (DNMT) (human DNMT3A or homologous and murine Dnmt3L or homologous), and that Naldini discloses that zinc finger domains are capable of functioning as a DNA binding domain that targets a locus of interest for epigenetic modification thereof, it would have been obvious to someone of ordinary skill in the art before the effective filing date of the claimed invention to utilize the zinc finger domains disclosed in Naldini as the DNA binding domain for use in the construct for epigenetic modification disclosed in Cathomen to predictably facilitate user-specified sequence-specific targeting for epigenetic modification. One would have been motivated to make such a modification in order to receive the expected benefit of facilitating user-specified sequence-specific targeting for epigenetic modification.
This is a provisional nonstatutory double patenting rejection because the patentably indistinct claims have not in fact been patented.
Claims 135-137 and 139-152 are provisionally rejected on the ground of nonstatutory double patenting as being unpatentable over claims 148, 157, 158, 160, 161, 163, and 165 of copending Application No. 18/989,126 (reference application; corresponds to US 2025/0320478 A1; of record) in view of US 2019/0024090 A1 (hereinafter Cathomen; as cited in the IDS filed 02/27/2025; of record), Alerasool et al., 2020 (hereinafter Alerasool; as cited in the IDS filed 01/16/2024; of record), UniProt Entry Q96PE6 (as cited in the IDS filed 12/23/2025; of record), UniProt Entry Q9UJW3 (aligned sequence released 02/15/2017; of record), UniProt Entry A0A386IRG9_STAAU (aligned sequence released 12/05/2018; of record), and US 2019/0032049 A1 (hereinafter Naldini; as cited in the IDS filed 01/16/2024; of record), as evidenced by Barrangou and Doudna, 2016 (hereinafter Barrangou; of record) and Eom et al., 2016 (hereinafter Eom; of record).
Copending application ‘126 is drawn to an epigenetic editing system, said system comprising a fusion protein comprising a transcriptional repressor domain (i.e. a ZIM3 KRAB domain), a DNA-binding domain, and a first and second DNMT domain (i.e. human DNMT3A and DNMT3L) (as recited at copending claims 148, 157, 158, 160, 161, 163, and 165).
This epigenetic editor fusion protein reads on the epigenetic editor comprising a fusion protein recited at instant claims 135, 139, and 140-143, which comprises a DNA binding domain, a ZIM3 repressor domain, and human DNMT3A and DNMT3L domains. Thus, the instantly claimed epigenetic editor and that of copending application ‘126 are not patentably distinct.
With regard to amended claim 136, which recites “the repressor domain [of the epigenetic editor of claim 135] is selected from the group consisting of: SEQ ID NOs: 67-595,” as set forth above, Cathomen discloses fusion of KRAB to a DNA binding domain and two DNMT domains for targeted silencing of genes via epigenetic modification, while Alerasool discloses fusion specifically of the ZIM3 KRAB domain to dCas9 to facilitate potent repression of gene expression. However, neither Cathomen nor Alerasool discloses the sequence of the ZIM3 repressor domain corresponding to SEQ ID NO: 67. This deficiency is cured by UniProt Entry Q96PE6. As shown in the alignment of Appendix I (previously provided), UniProt Entry Q96PE6 (corresponding to human ZIM3) comprises 100% identity to instant SEQ ID NO: 67. Thus, it is considered that UniProt Entry Q96PE6 discloses each and every additional limitation of instant claim 136.
With regard to claim 137, which recites “the DNA binding domain [of the epigenetic editor of claim 135] binds to a target sequence in a target chromosome comprising a target gene,” as set forth above, Cathomen discloses a fusion construct for epigenetic editing. Furthermore, as shown in Figures 1B and 2A of Cathomen, the DEM (designer epigenome modifier per paragraph [0013], the DNA binding portion of the DEM directs the DEM to a specific target site in the promoter or any other regulatory element of the target gene, leading to the methylation of the neighboring CpG di-residues and the deacetylation of neighboring histone tails, thereby silencing the target gene of interest (paragraphs [0061] and [0063]). This targeted binding reads on each and every additional limitation of instant claim 137. Thus, it is considered that Cathomen discloses each and every additional limitation of instant claim 137.
With regard to amended instant claim 144, which recites “the first DNMT domain and the second DNMT domain [of the epigenetic editor of claim 140] are selected from the group consisting of: SEQ ID NOs: 32-66,” as set forth above, Cathomen discloses a construct for epigenetic modification of genes, said construct comprising a Krϋppel-associated box (KRAB) zinc finger protein (or homologous), a DNA region capable of binding to the target gene (or homologous), and two DNA methyltransferases (DNMT) (human DNMT3A or homologous and murine Dnmt3L or homologous) (paragraphs [0012]-[0018]). Additionally, Cathomen further discloses that the murine DNMT3L of the fusion protein taught therein may alternatively be human DNMT3L at paragraph [0051]. Cathomen further discloses that SEQ ID NO: 3 taught therein corresponds to human DNMT3A. As shown in the alignment of Appendix II (previously provided), SEQ ID NO: 3 of Cathomen comprises 100% identity to instant SEQ ID NO: 34. However, while Cathomen discloses that the murine DNMT3L may alternatively be human DNMT3L, Cathomen is silent as to the specific sequence of human DNMT3L. This deficiency is cured by UniProt Entry Q9UJW3, which discloses the human DNMT3L sequence. As shown in the alignment of Appendix III (previously provided), UniProt Entry Q9UJW3comprises 100% identity to instant SEQ ID NO: 38. Thus, it is considered that Cathomen and UniProt Entry Q9UJW3 collectively disclose each and every additional limitation of instant claim 144.
With regard to amended claim 145, which recites “the DNA binding domain [of the epigenetic editor of claim 135] comprises the zinc finger motif or the zinc finger array,” as set forth above, Cathomen discloses a construct for epigenetic modification of genes, said construct comprising a Krϋppel-associated box (KRAB) zinc finger protein (or homologous), a DNA region capable of binding to the target gene (or homologous), and two DNA methyltransferases (DNMT) (human DNMT3A or homologous and murine Dnmt3L or homologous) (paragraphs [0012]-[0018]). However, the DNA binding domain of Cathomen is a TALE-derived DNA binding domain (paragraph [0044]), which does not comprise a zinc finger motif or a zinc finger array. This deficiency is cured by Naldini.
Naldini discloses artificial transcription repressors that establish robust and permanent states of epigenetic repression, said artificial transcription repressors comprising a DNA-binding domain operably linked to a KRAB domain, a DNMT3A domain, and/or a DNMT3L domain (paragraphs [0014], [0016], and [0024]-[0029]). As depicted in Figure 1 of Naldini, this system facilitates epigenetic silencing of a targeted gene of interest. Naldini discloses that the DNA binding domain taught therein may be a zinc finger domain (paragraphs [0037] and [0253]). As is known to those of ordinary skill in the art, zinc finger domains comprise zinc finger motifs (reviewed in Eom: see especially page 2023, column 2, paragraph 2). Thus, Naldini discloses that zinc finger domains (comprising zinc finger motifs) are capable of functioning as a DNA binding domain that targets a locus of interest for epigenetic modification thereof, as instantly claimed.
With regard to amended claim 146, which recites “the DNA binding domain [of the epigenetic editor of claim 135] comprises the nucleic acid guided DNA binding domain bound to the guide polynucleotide,” the construct of Cathomen is disclosed to comprise a TALE-derived DNA binding domain (paragraph [0044]) rather than the instantly claimed nucleic acid guided DNA binding domain bound to a guide polynucleotide. However, as set forth above, Alerasool discloses CRISPR interference constructs comprising fusion of inactive Cas9 (dCas9) to the ZIM3 KRAB domain, which is an exceptionally potent repressor (abstract; page 1093, column 2, paragraph 2; Figures 1 and 2). Alerasool further discloses that the CRISPR interference (CRISPRi) achieved therein using the fusion protein set forth above is particularly sensitive to guide RNA (gRNA) selection (page 1093, column 1, paragraphs 1-2). As depicted in Figure 1a of Alerasool, different gRNAs target the dCas9 to different loci. Furthermore, these gRNAs are indispensable to functioning of the system, as target genes are fully expressed in the absence of the gRNAs, as shown in Figure 2a. While Alerasool does not specify that the gRNA is bound to the dCas9 taught therein, it is known to those of ordinary skill in the art that gRNAs function by binding to their target sequences as well as to the Cas9 protein to assemble a functional editing complex (see Box 1 of Barrangou and Figure 1 of Alerasool). Thus, it is considered that Alerasool (as evidenced by Barrangou) discloses each and every additional limitation of instant claim 146.
With regard to amended claim 147, which recites “the DNA binding domain [of the epigenetic editor of claim 146] comprises a CRISPR-Cas protein bound to the guide polynucleotide,” as set forth above, Alerasool discloses CRISPRi achieved via fusion of ZIM3 to dCas9 (a CRISPR-Cas protein), which is guided to a target locus by the associated gRNA (Figure 1a). Furthermore, it is known to those of ordinary skill in the art that gRNAs function by binding to their target sequences as well as to the Cas9 protein to assemble a functional editing complex (see Box 1 of Barrangou). Thus, it is considered that Alerasool (as evidenced by Barrangou) discloses each and every additional limitation of instant claim 147.
With regard to claim 148, which recites “the guide polynucleotide [of the epigenetic editor of claim 146] hybridizes with a target sequence,” as set forth above, Alerasool discloses CRISPRi achieved via fusion of ZIM3 to dCas9 (a CRISPR-Cas protein), which is guided to a target locus by the associated gRNA (Figure 1a). Furthermore, it is known to those of ordinary skill in the art that gRNAs function by binding to their target sequences as well as to the Cas9 protein to assemble a functional editing complex (see Box 1 of Barrangou). Thus, it is considered that Alerasool (as evidenced by Barrangou) discloses each and every additional limitation of instant claim 148.
With regard to claims 149 and 150, which respectively recite “the CRISPR-Cas protein [of the epigenetic editor of claim 147] comprises a nuclease inactive Cas9 (dCas9),” specifically “dSpCas9,” as set forth above, Alerasool discloses CRISPRi achieved via fusion of ZIM3 to dCas9, which is guided to a target locus by the associated gRNA (Figure 1a). Alerasool specifically discloses that the dCas9 utilized therein is derived from Streptococcus pyogenes dCas9 (page 1097, column 1, paragraph 4). Thus, it is considered that Alerasool discloses each and every additional limitation of instant claims 149 and 150.
With regard to claim 151, which recites “the dSpCas9 [of the epigenetic editor of claim 150] is defined as SEQ ID NO: 3,” as set forth above Alerasool specifically discloses that the dCas9 utilized therein is derived from Streptococcus pyogenes dCas9 (page 1097, column 1, paragraph 4). However, Alerasool does not disclose that the sequence of said dSpCas9 is defined as instant SEQ ID NO: 3. This deficiency is cured by UniProt Entry A0A386IRG9_STAAU, which discloses the sequence of dSpCas9. As shown in the alignment of Appendix IV (previously provided), UniProt Entry A0A386IRG9_STAAU comprises 100% identity to instant SEQ ID NO: 3. Thus, it is considered that Alerasool and UniProt Entry A0A386IRG9_STAAU collectively disclose each and every additional limitation of instant claim 151.
With regard to amended claim 152, which recites “the first DNMT domain [of the epigenetic editor of claim 140] is a DNMT3A, the second DNMT domain is a DNMT3L, the DNA binding domain is a dSpCas9, and wherein the fusion protein comprises from N-terminus to C-terminus the DNMT3A-the DNMT3L-the dSpCas9-the repressor domain,” as set forth above, Cathomen discloses a construct for epigenetic modification of genes, said construct comprising a Krϋppel-associated box (KRAB) zinc finger protein (or homologous), a DNA region capable of binding to the target gene (or homologous), and two DNA methyltransferases (DNMT) (human DNMT3A or homologous and murine Dnmt3L or homologous) (paragraphs [0012]-[0018]). The structure of the epigenetic modifier construct of Cathomen is disclosed at Figure 1A, comprising the repressor domain, the DNA binding domain, and the DNMT domains. While the DNA binding domain of Cathomen is a TALE-derived DNA binding domain (paragraph [0044]), Alerasool discloses the utility of dSpCas9 fusion proteins for targeted epigenetic modification (abstract; Figures 1 and 2). While the N and C termini are not specified, it is known to those of ordinary skill in the art that proteins are typically written from left-to-right from the N terminus to the C terminus. Therefore, while Cathomen and Alerasool collectively disclose all the components of the claimed fusion protein, the order is opposite of that which is instantly claimed. However, per MPEP § 2144.04(VI)(C), it is not inventive to rearrange parts of an invention when all parts of the invention have been disclosed in the prior art, as in the instant case. Accordingly, it is considered that Cathomen and Alerasool collectively disclose the claimed fusion protein and that it would require routine experimentation by someone of ordinary skill in the art to optimize the order of domains in the claimed fusion protein.
Given that the copending application discloses compositions and methods for epigenetic regulation, and further that Cathomen discloses a construct for epigenetic modification of genes, said construct comprising a Krϋppel-associated box (KRAB) zinc finger protein (or homologous), a DNA region capable of binding to the target gene (or homologous), and two DNA methyltransferases (DNMT) (human DNMT3A or homologous and murine Dnmt3L or homologous), while Alerasool discloses that the ZIM3 KRAB (the sequence of which is disclosed by UniProt entry Q96PE6) domain facilitates potent repression via CRISPRi when fused to dSpCas9, and further that the ZIM3 KRAB domain strongly interacts with TRIM28/KAP1, which reads on the instantly claimed “epigenetic effector protein” specifically bound to said ZIM3 KRAB repressor domain, it would have been obvious to someone of ordinary skill in the art before the effective filing date of the claimed invention to utilize the ZIM3 KRAB domain disclosed in the copending application and Alerasool as the KRAB repressor domain disclosed in the copending application and Cathomen as part of a construct for epigenetic modification and further to substitute the TALE-derived DNA binding domain of Cathomen for dCas9 (as disclosed in the copending application and Alerasool) to predictably facilitate user-specified sequence-specific targeting for epigenetic modification (as reviewed in Barrangou). One would have been motivated to make such a modification in order to receive the expected benefit of facilitating user-specified sequence-specific targeting for epigenetic modification.
Furthermore, given that Cathomen discloses a construct for epigenetic modification of genes, said construct comprising a Krϋppel-associated box (KRAB) zinc finger protein (or homologous), a DNA region capable of binding to the target gene (or homologous), and two DNA methyltransferases (DNMT) (human DNMT3A or homologous and murine Dnmt3L or homologous), and that Naldini discloses that zinc finger domains are capable of functioning as a DNA binding domain that targets a locus of interest for epigenetic modification thereof, it would have been obvious to someone of ordinary skill in the art before the effective filing date of the claimed invention to utilize the zinc finger domains disclosed in Naldini as the DNA binding domain for use in the construct for epigenetic modification disclosed in Cathomen to predictably facilitate user-specified sequence-specific targeting for epigenetic modification. One would have been motivated to make such a modification in order to receive the expected benefit of facilitating user-specified sequence-specific targeting for epigenetic modification.
This is a provisional nonstatutory double patenting rejection because the patentably indistinct claims have not in fact been patented.
Claims 135-137 and 139-152 are provisionally rejected on the ground of nonstatutory double patenting as being unpatentable over claims 1, 2, 7, 8, 13, 14, 19, and 20 of copending Application No. 19/060,404 (reference application; corresponds to US 2025/0236847 A1; of record) in view of US 2019/0024090 A1 (hereinafter Cathomen; as cited in the IDS filed 02/27/2025; of record), Alerasool et al., 2020 (hereinafter Alerasool; as cited in the IDS filed 01/16/2024; of record), UniProt Entry Q96PE6 (as cited in the IDS filed 12/23/2025; of record), UniProt Entry Q9UJW3 (aligned sequence released 02/15/2017; of record), UniProt Entry A0A386IRG9_STAAU (aligned sequence released 12/05/2018; of record), and US 2019/0032049 A1 (hereinafter Naldini; as cited in the IDS filed 01/16/2024; of record), as evidenced by Barrangou and Doudna, 2016 (hereinafter Barrangou; of record) and Eom et al., 2016 (hereinafter Eom; of record).
MPEP 804(II)(B)(1) states:
The specification can be used as a dictionary to learn the meaning of a term in the patent claim. Toro Co. v. White Consol. Indus., Inc., 199 F.3d 1295, 1299, 53 USPQ2d 1065, 1067 (Fed. Cir. 1999)… Further, those portions of the specification which provide support for the patent claims may also be examined and considered when addressing the issue of whether a claim in the application defines an obvious variation of an invention claimed in the patent. In re Vogel, 422 F.2d 438, 441-42, 164 USPQ 619, 622 (CCPA 1970).
The following rejections are in view of the decision of the Court of Appeals for the Federal Circuit in Pfizer Inc, v Teva pharmaceuticals USA Inc., 86 USPQ2d 1001, at page 1008 (March 2008), which indicates that there is no patentable distinction between claims to a product and a method of using that product disclosed in the specification of the application and that the preclusion of such a double patenting rejection under 35 USC 121 does not apply where the present application is other than a divisional application of the patent application containing such patentably indistinct claims.
Copending application ‘404 is drawn to a method for repressing expression of an HBV genome, said method comprising contacting the HBV genome with an epigenetic editing system, said system comprising a fusion protein or a nucleic acid encoding the same, wherein the fusion protein comprises a catalytically inactive Cas9 DNA binding domain guided by a guide RNA to a target region of the HBV genome, a ZIM3 KRAB repression domain, and a DNMT3L and DNMT3L domain (as recited at copending claims 1, 2, 7, 8, 13, 14, 19, and 20).
This epigenetic editing system reads on the epigenetic editor comprising a fusion protein (or a nucleic acid encoding the same) recited at instant claims 135, 137, 139-143, and 146-149, which comprises a DNA binding domain, a ZIM3 repressor domain, and human DNMT3A and DNMT3L domains. Thus, the instantly claimed epigenetic editor and that of copending application ‘404 are not patentably distinct.
Furthermore, copending claims 2, 8, 14, and 20 recite that the ZIM3 claimed therein has a sequence with at least 90% identity to SEQ ID NO: 495. As shown in the alignment of Appendix XIV (previously presented) instant SEQ ID NO: 67 (recited at instant claim 136) is identical to copending SEQ ID NO: 495.
With regard to amended instant claim 144, which recites “the first DNMT domain and the second DNMT domain [of the epigenetic editor of claim 140] are selected from the group consisting of: SEQ ID NOs: 32-66,” as set forth above, Cathomen discloses a construct for epigenetic modification of genes, said construct comprising a Krϋppel-associated box (KRAB) zinc finger protein (or homologous), a DNA region capable of binding to the target gene (or homologous), and two DNA methyltransferases (DNMT) (human DNMT3A or homologous and murine Dnmt3L or homologous) (paragraphs [0012]-[0018]). Additionally, Cathomen further discloses that the murine DNMT3L of the fusion protein taught therein may alternatively be human DNMT3L at paragraph [0051]. Cathomen further discloses that SEQ ID NO: 3 taught therein corresponds to human DNMT3A. As shown in the alignment of Appendix II (previously provided), SEQ ID NO: 3 of Cathomen comprises 100% identity to instant SEQ ID NO: 34. However, while Cathomen discloses that the murine DNMT3L may alternatively be human DNMT3L, Cathomen is silent as to the specific sequence of human DNMT3L. This deficiency is cured by UniProt Entry Q9UJW3, which discloses the human DNMT3L sequence. As shown in the alignment of Appendix III (previously provided), UniProt Entry Q9UJW3comprises 100% identity to instant SEQ ID NO: 38. Thus, it is considered that Cathomen and UniProt Entry Q9UJW3 collectively disclose each and every additional limitation of instant claim 144.
With regard to amended claim 145, which recites “the DNA binding domain [of the epigenetic editor of claim 135] comprises the zinc finger motif or the zinc finger array,” as set forth above, Cathomen discloses a construct for epigenetic modification of genes, said construct comprising a Krϋppel-associated box (KRAB) zinc finger protein (or homologous), a DNA region capable of binding to the target gene (or homologous), and two DNA methyltransferases (DNMT) (human DNMT3A or homologous and murine Dnmt3L or homologous) (paragraphs [0012]-[0018]). However, the DNA binding domain of Cathomen is a TALE-derived DNA binding domain (paragraph [0044]), which does not comprise a zinc finger motif or a zinc finger array. This deficiency is cured by Naldini.
Naldini discloses artificial transcription repressors that establish robust and permanent states of epigenetic repression, said artificial transcription repressors comprising a DNA-binding domain operably linked to a KRAB domain, a DNMT3A domain, and/or a DNMT3L domain (paragraphs [0014], [0016], and [0024]-[0029]). As depicted in Figure 1 of Naldini, this system facilitates epigenetic silencing of a targeted gene of interest. Naldini discloses that the DNA binding domain taught therein may be a zinc finger domain (paragraphs [0037] and [0253]). As is known to those of ordinary skill in the art, zinc finger domains comprise zinc finger motifs (reviewed in Eom: see especially page 2023, column 2, paragraph 2). Thus, Naldini discloses that zinc finger domains (comprising zinc finger motifs) are capable of functioning as a DNA binding domain that targets a locus of interest for epigenetic modification thereof, as instantly claimed.
With regard to claim 150, which recites “the epigenetic editor of claim 149, wherein the dCas9 is a dSpCas9,” as set forth above, Alerasool discloses CRISPRi achieved via fusion of ZIM3 to dCas9, which is guided to a target locus by the associated gRNA (Figure 1a). Alerasool specifically discloses that the dCas9 utilized therein is derived from Streptococcus pyogenes dCas9 (page 1097, column 1, paragraph 4). Thus, it is considered that Alerasool discloses each and every additional limitation of instant claim 150.
With regard to claim 151, which recites “the dSpCas9 [of the epigenetic editor of claim 150] is defined as SEQ ID NO: 3,” as set forth above Alerasool specifically discloses that the dCas9 utilized therein is derived from Streptococcus pyogenes dCas9 (page 1097, column 1, paragraph 4). However, Alerasool does not disclose that the sequence of said dSpCas9 is defined as instant SEQ ID NO: 3. This deficiency is cured by UniProt Entry A0A386IRG9_STAAU, which discloses the sequence of dSpCas9. As shown in the alignment of Appendix IV (previously provided), UniProt Entry A0A386IRG9_STAAU comprises 100% identity to instant SEQ ID NO: 3. Thus, it is considered that Alerasool and UniProt Entry A0A386IRG9_STAAU collectively disclose each and every additional limitation of instant claim 151.
With regard to amended claim 152, which recites “the first DNMT domain [of the epigenetic editor of claim 140] is a DNMT3A, the second DNMT domain is a DNMT3L, the DNA binding domain is a dSpCas9, and wherein the fusion protein comprises from N-terminus to C-terminus the DNMT3A-the DNMT3L-the dSpCas9-the repressor domain,” as set forth above, Cathomen discloses a construct for epigenetic modification of genes, said construct comprising a Krϋppel-associated box (KRAB) zinc finger protein (or homologous), a DNA region capable of binding to the target gene (or homologous), and two DNA methyltransferases (DNMT) (human DNMT3A or homologous and murine Dnmt3L or homologous) (paragraphs [0012]-[0018]). The structure of the epigenetic modifier construct of Cathomen is disclosed at Figure 1A, comprising the repressor domain, the DNA binding domain, and the DNMT domains. While the DNA binding domain of Cathomen is a TALE-derived DNA binding domain (paragraph [0044]), Alerasool discloses the utility of dSpCas9 fusion proteins for targeted epigenetic modification (abstract; Figures 1 and 2). While the N and C termini are not specified, it is known to those of ordinary skill in the art that proteins are typically written from left-to-right from the N terminus to the C terminus. Therefore, while Cathomen and Alerasool collectively disclose all the components of the claimed fusion protein, the order is opposite of that which is instantly claimed. However, per MPEP § 2144.04(VI)(C), it is not inventive to rearrange parts of an invention when all parts of the invention have been disclosed in the prior art, as in the instant case. Accordingly, it is considered that Cathomen and Alerasool collectively disclose the claimed fusion protein and that it would require routine experimentation by someone of ordinary skill in the art to optimize the order of domains in the claimed fusion protein.
Given that the copending application discloses compositions and methods for epigenetic regulation, and further that Cathomen discloses a construct for epigenetic modification of genes, said construct comprising a Krϋppel-associated box (KRAB) zinc finger protein (or homologous), a DNA region capable of binding to the target gene (or homologous), and two DNA methyltransferases (DNMT) (human DNMT3A or homologous and murine Dnmt3L or homologous), while Alerasool discloses that the ZIM3 KRAB (the sequence of which is disclosed by UniProt entry Q96PE6) domain facilitates potent repression via CRISPRi when fused to dSpCas9, and further that the ZIM3 KRAB domain strongly interacts with TRIM28/KAP1, which reads on the instantly claimed “epigenetic effector protein” specifically bound to said ZIM3 KRAB repressor domain, it would have been obvious to someone of ordinary skill in the art before the effective filing date of the claimed invention to utilize the ZIM3 KRAB domain disclosed in the copending application and Alerasool as the KRAB repressor domain disclosed in the copending application and Cathomen as part of a construct for epigenetic modification and further to substitute the TALE-derived DNA binding domain of Cathomen for dCas9 (as disclosed in the copending application and Alerasool) to predictably facilitate user-specified sequence-specific targeting for epigenetic modification (as reviewed in Barrangou). One would have been motivated to make such a modification in order to receive the expected benefit of facilitating user-specified sequence-specific targeting for epigenetic modification.
Furthermore, given that Cathomen discloses a construct for epigenetic modification of genes, said construct comprising a Krϋppel-associated box (KRAB) zinc finger protein (or homologous), a DNA region capable of binding to the target gene (or homologous), and two DNA methyltransferases (DNMT) (human DNMT3A or homologous and murine Dnmt3L or homologous), and that Naldini discloses that zinc finger domains are capable of functioning as a DNA binding domain that targets a locus of interest for epigenetic modification thereof, it would have been obvious to someone of ordinary skill in the art before the effective filing date of the claimed invention to utilize the zinc finger domains disclosed in Naldini as the DNA binding domain for use in the construct for epigenetic modification disclosed in Cathomen to predictably facilitate user-specified sequence-specific targeting for epigenetic modification. One would have been motivated to make such a modification in order to receive the expected benefit of facilitating user-specified sequence-specific targeting for epigenetic modification.
This is a provisional nonstatutory double patenting rejection because the patentably indistinct claims have not in fact been patented.
Claims 135-137 and 139-152 are provisionally rejected on the ground of nonstatutory double patenting as being unpatentable over claims 1-11 and 13-19 of copending Application No. 19/224,549 (reference application; corresponds to US 2025/0288691 A1; of record) in view of US 2019/0024090 A1 (hereinafter Cathomen; as cited in the IDS filed 02/27/2025; of record), Alerasool et al., 2020 (hereinafter Alerasool; as cited in the IDS filed 01/16/2024; of record), UniProt Entry Q96PE6 (as cited in the IDS filed 12/23/2025; of record), UniProt Entry Q9UJW3 (aligned sequence released 02/15/2017; of record), UniProt Entry A0A386IRG9_STAAU (aligned sequence released 12/05/2018; of record), and US 2019/0032049 A1 (hereinafter Naldini; as cited in the IDS filed 01/16/2024; of record), as evidenced by Barrangou and Doudna, 2016 (hereinafter Barrangou; of record) and Eom et al., 2016 (hereinafter Eom; of record).
MPEP 804(II)(B)(1) states:
The specification can be used as a dictionary to learn the meaning of a term in the patent claim. Toro Co. v. White Consol. Indus., Inc., 199 F.3d 1295, 1299, 53 USPQ2d 1065, 1067 (Fed. Cir. 1999)… Further, those portions of the specification which provide support for the patent claims may also be examined and considered when addressing the issue of whether a claim in the application defines an obvious variation of an invention claimed in the patent. In re Vogel, 422 F.2d 438, 441-42, 164 USPQ 619, 622 (CCPA 1970).
The following rejections are in view of the decision of the Court of Appeals for the Federal Circuit in Pfizer Inc, v Teva pharmaceuticals USA Inc., 86 USPQ2d 1001, at page 1008 (March 2008), which indicates that there is no patentable distinction between claims to a product and a method of using that product disclosed in the specification of the application and that the preclusion of such a double patenting rejection under 35 USC 121 does not apply where the present application is other than a divisional application of the patent application containing such patentably indistinct claims.
Copending application ‘549 is drawn to a method, said method comprising administering an epigenetic editing system to a subject, said system comprising a fusion protein comprising a dCas9 protein domain (defined by SEQ ID NO: 12 and derived from Streptococcus pyogenes) guided by a guide RNA to a target sequence, a DNMT3A domain (defined by SEQ ID NO: 1029), a human DNMT3L domain (defined by SEQ ID NO: 1033), and a ZIM3 KRAB domain (defined by SEQ ID NO: 495) (as recited at copending claims 1-11 and 13-19).
This epigenetic editing system reads on the epigenetic editor comprising a fusion protein recited at instant claims 135, 137, 139-143, and 146-150, which comprises a DNA binding domain, a ZIM3 repressor domain, and human DNMT3A and DNMT3L domains. Thus, the instantly claimed epigenetic editor and that of copending application ‘549 are not patentably distinct.
Furthermore, copending claims 136, 144, and 151 recite that the ZIM3, DNMT3A and DNMT3L, and dSpCas9 claimed therein are defined by SEQ ID NOs: 67, 34, 38, and 3, respectively. As shown in the alignments of Appendices XV-XVIII (previously presented), these sequences are identical to those recited in the copending application.
With regard to amended claim 145, which recites “the DNA binding domain [of the epigenetic editor of claim 135] comprises the zinc finger motif or the zinc finger array,” as set forth above, Cathomen discloses a construct for epigenetic modification of genes, said construct comprising a Krϋppel-associated box (KRAB) zinc finger protein (or homologous), a DNA region capable of binding to the target gene (or homologous), and two DNA methyltransferases (DNMT) (human DNMT3A or homologous and murine Dnmt3L or homologous) (paragraphs [0012]-[0018]). However, the DNA binding domain of Cathomen is a TALE-derived DNA binding domain (paragraph [0044]), which does not comprise a zinc finger motif or a zinc finger array. This deficiency is cured by Naldini.
Naldini discloses artificial transcription repressors that establish robust and permanent states of epigenetic repression, said artificial transcription repressors comprising a DNA-binding domain operably linked to a KRAB domain, a DNMT3A domain, and/or a DNMT3L domain (paragraphs [0014], [0016], and [0024]-[0029]). As depicted in Figure 1 of Naldini, this system facilitates epigenetic silencing of a targeted gene of interest. Naldini discloses that the DNA binding domain taught therein may be a zinc finger domain (paragraphs [0037] and [0253]). As is known to those of ordinary skill in the art, zinc finger domains comprise zinc finger motifs (reviewed in Eom: see especially page 2023, column 2, paragraph 2). Thus, Naldini discloses that zinc finger domains (comprising zinc finger motifs) are capable of functioning as a DNA binding domain that targets a locus of interest for epigenetic modification thereof, as instantly claimed.
With regard to amended claim 152, which recites “the first DNMT domain [of the epigenetic editor of claim 140] is a DNMT3A, the second DNMT domain is a DNMT3L, the DNA binding domain is a dSpCas9, and wherein the fusion protein comprises from N-terminus to C-terminus the DNMT3A-the DNMT3L-the dSpCas9-the repressor domain,” as set forth above, Cathomen discloses a construct for epigenetic modification of genes, said construct comprising a Krϋppel-associated box (KRAB) zinc finger protein (or homologous), a DNA region capable of binding to the target gene (or homologous), and two DNA methyltransferases (DNMT) (human DNMT3A or homologous and murine Dnmt3L or homologous) (paragraphs [0012]-[0018]). The structure of the epigenetic modifier construct of Cathomen is disclosed at Figure 1A, comprising the repressor domain, the DNA binding domain, and the DNMT domains. While the DNA binding domain of Cathomen is a TALE-derived DNA binding domain (paragraph [0044]), Alerasool discloses the utility of dSpCas9 fusion proteins for targeted epigenetic modification (abstract; Figures 1 and 2). While the N and C termini are not specified, it is known to those of ordinary skill in the art that proteins are typically written from left-to-right from the N terminus to the C terminus. Therefore, while Cathomen and Alerasool collectively disclose all the components of the claimed fusion protein, the order is opposite of that which is instantly claimed. However, per MPEP § 2144.04(VI)(C), it is not inventive to rearrange parts of an invention when all parts of the invention have been disclosed in the prior art, as in the instant case. Accordingly, it is considered that Cathomen and Alerasool collectively disclose the claimed fusion protein and that it would require routine experimentation by someone of ordinary skill in the art to optimize the order of domains in the claimed fusion protein.
Given that the copending application discloses compositions and methods for epigenetic regulation, and further that Cathomen discloses a construct for epigenetic modification of genes, said construct comprising a Krϋppel-associated box (KRAB) zinc finger protein (or homologous), a DNA region capable of binding to the target gene (or homologous), and two DNA methyltransferases (DNMT) (human DNMT3A or homologous and murine Dnmt3L or homologous), while Alerasool discloses that the ZIM3 KRAB (the sequence of which is disclosed by UniProt entry Q96PE6) domain facilitates potent repression via CRISPRi when fused to dSpCas9, and further that the ZIM3 KRAB domain strongly interacts with TRIM28/KAP1, which reads on the instantly claimed “epigenetic effector protein” specifically bound to said ZIM3 KRAB repressor domain, it would have been obvious to someone of ordinary skill in the art before the effective filing date of the claimed invention to utilize the ZIM3 KRAB domain disclosed in the copending application and Alerasool as the KRAB repressor domain disclosed in the copending application and Cathomen as part of a construct for epigenetic modification and further to substitute the TALE-derived DNA binding domain of Cathomen for dCas9 (as disclosed in the copending application and Alerasool) to predictably facilitate user-specified sequence-specific targeting for epigenetic modification (as reviewed in Barrangou). One would have been motivated to make such a modification in order to receive the expected benefit of facilitating user-specified sequence-specific targeting for epigenetic modification.
Furthermore, given that Cathomen discloses a construct for epigenetic modification of genes, said construct comprising a Krϋppel-associated box (KRAB) zinc finger protein (or homologous), a DNA region capable of binding to the target gene (or homologous), and two DNA methyltransferases (DNMT) (human DNMT3A or homologous and murine Dnmt3L or homologous), and that Naldini discloses that zinc finger domains are capable of functioning as a DNA binding domain that targets a locus of interest for epigenetic modification thereof, it would have been obvious to someone of ordinary skill in the art before the effective filing date of the claimed invention to utilize the zinc finger domains disclosed in Naldini as the DNA binding domain for use in the construct for epigenetic modification disclosed in Cathomen to predictably facilitate user-specified sequence-specific targeting for epigenetic modification. One would have been motivated to make such a modification in order to receive the expected benefit of facilitating user-specified sequence-specific targeting for epigenetic modification.
This is a provisional nonstatutory double patenting rejection because the patentably indistinct claims have not in fact been patented.
Claims 135-137 and 139-152 are provisionally rejected on the ground of nonstatutory double patenting as being unpatentable over claims 1, 6-14, 16, and 21-29 of copending Application No. 19/390,246 (reference application; not yet published) in view of US 2019/0024090 A1 (hereinafter Cathomen; as cited in the IDS filed 02/27/2025; of record), Alerasool et al., 2020 (hereinafter Alerasool; as cited in the IDS filed 01/16/2024; of record), UniProt Entry Q96PE6 (as cited in the IDS filed 12/23/2025; of record), UniProt Entry Q9UJW3 (aligned sequence released 02/15/2017; of record), UniProt Entry A0A386IRG9_STAAU (aligned sequence released 12/05/2018; of record), and US 2019/0032049 A1 (hereinafter Naldini; as cited in the IDS filed 01/16/2024; of record), as evidenced by Barrangou and Doudna, 2016 (hereinafter Barrangou; of record) and Eom et al., 2016 (hereinafter Eom; of record).
MPEP 804(II)(B)(1) states:
The specification can be used as a dictionary to learn the meaning of a term in the patent claim. Toro Co. v. White Consol. Indus., Inc., 199 F.3d 1295, 1299, 53 USPQ2d 1065, 1067 (Fed. Cir. 1999)… Further, those portions of the specification which provide support for the patent claims may also be examined and considered when addressing the issue of whether a claim in the application defines an obvious variation of an invention claimed in the patent. In re Vogel, 422 F.2d 438, 441-42, 164 USPQ 619, 622 (CCPA 1970).
The following rejections are in view of the decision of the Court of Appeals for the Federal Circuit in Pfizer Inc, v Teva pharmaceuticals USA Inc., 86 USPQ2d 1001, at page 1008 (March 2008), which indicates that there is no patentable distinction between claims to a product and a method of using that product disclosed in the specification of the application and that the preclusion of such a double patenting rejection under 35 USC 121 does not apply where the present application is other than a divisional application of the patent application containing such patentably indistinct claims.
Copending application ‘246 recites a method of administering an epigenetic editing system comprising a fusion protein with a configuration of DNMT3A-DNMT3L-dCas9-ZIM3 KRAB, wherein the dCas9 is from Streptococcus pyogenes and guided to a target sequence by an associated guide RNA, and DNMT3A and DNTM3L are defined by SEQ ID NOs: 1029 and 1033 (as recited at copending claims 1, 6-14, 16, and 21-29).
This epigenetic editing system reads on the epigenetic editor comprising a fusion protein recited at instant claims 135, 137, 139-144, 146-150, and 152 which comprises a DNA binding domain, a ZIM3 repressor domain, and human DNMT3A and DNMT3L domains. Thus, the instantly claimed epigenetic editor and that of copending application ‘246 are not patentably distinct.
With regard to the copending and instantly claimed sequences, copending claim 144 recites that DNMT3A and DNMT3L are defined by SEQ ID NOs: 34 and 38, which are identical to copending SEQ ID NOs: 1029 and 1033, as shown in the alignments of Appendices XIX and XX (previously presented).
With regard to amended claim 136, which recites “the repressor domain [of the epigenetic editor of claim 135] is selected from the group consisting of: SEQ ID NOs: 67-595,” as set forth above, Cathomen discloses fusion of KRAB to a DNA binding domain and two DNMT domains for targeted silencing of genes via epigenetic modification, while Alerasool discloses fusion specifically of the ZIM3 KRAB domain to dCas9 to facilitate potent repression of gene expression. However, neither Cathomen nor Alerasool discloses the sequence of the ZIM3 repressor domain corresponding to SEQ ID NO: 67. This deficiency is cured by UniProt Entry Q96PE6. As shown in the alignment of Appendix I (previously provided), UniProt Entry Q96PE6 (corresponding to human ZIM3) comprises 100% identity to instant SEQ ID NO: 67. Thus, it is considered that UniProt Entry Q96PE6 discloses each and every additional limitation of instant claim 136.
With regard to amended claim 145, which recites “the DNA binding domain [of the epigenetic editor of claim 135] comprises the zinc finger motif or the zinc finger array,” as set forth above, Cathomen discloses a construct for epigenetic modification of genes, said construct comprising a Krϋppel-associated box (KRAB) zinc finger protein (or homologous), a DNA region capable of binding to the target gene (or homologous), and two DNA methyltransferases (DNMT) (human DNMT3A or homologous and murine Dnmt3L or homologous) (paragraphs [0012]-[0018]). However, the DNA binding domain of Cathomen is a TALE-derived DNA binding domain (paragraph [0044]), which does not comprise a zinc finger motif or a zinc finger array. This deficiency is cured by Naldini.
Naldini discloses artificial transcription repressors that establish robust and permanent states of epigenetic repression, said artificial transcription repressors comprising a DNA-binding domain operably linked to a KRAB domain, a DNMT3A domain, and/or a DNMT3L domain (paragraphs [0014], [0016], and [0024]-[0029]). As depicted in Figure 1 of Naldini, this system facilitates epigenetic silencing of a targeted gene of interest. Naldini discloses that the DNA binding domain taught therein may be a zinc finger domain (paragraphs [0037] and [0253]). As is known to those of ordinary skill in the art, zinc finger domains comprise zinc finger motifs (reviewed in Eom: see especially page 2023, column 2, paragraph 2). Thus, Naldini discloses that zinc finger domains (comprising zinc finger motifs) are capable of functioning as a DNA binding domain that targets a locus of interest for epigenetic modification thereof, as instantly claimed.
With regard to claim 151, which recites “the dSpCas9 [of the epigenetic editor of claim 150] is defined as SEQ ID NO: 3,” as set forth above Alerasool specifically discloses that the dCas9 utilized therein is derived from Streptococcus pyogenes dCas9 (page 1097, column 1, paragraph 4). However, Alerasool does not disclose that the sequence of said dSpCas9 is defined as instant SEQ ID NO: 3. This deficiency is cured by UniProt Entry A0A386IRG9_STAAU, which discloses the sequence of dSpCas9. As shown in the alignment of Appendix IV (previously provided), UniProt Entry A0A386IRG9_STAAU comprises 100% identity to instant SEQ ID NO: 3. Thus, it is considered that Alerasool and UniProt Entry A0A386IRG9_STAAU collectively disclose each and every additional limitation of instant claim 151.
Given that the copending application discloses compositions and methods for epigenetic regulation, and further that Cathomen discloses a construct for epigenetic modification of genes, said construct comprising a Krϋppel-associated box (KRAB) zinc finger protein (or homologous), a DNA region capable of binding to the target gene (or homologous), and two DNA methyltransferases (DNMT) (human DNMT3A or homologous and murine Dnmt3L or homologous), while Alerasool discloses that the ZIM3 KRAB (the sequence of which is disclosed by UniProt entry Q96PE6) domain facilitates potent repression via CRISPRi when fused to dSpCas9, and further that the ZIM3 KRAB domain strongly interacts with TRIM28/KAP1, which reads on the instantly claimed “epigenetic effector protein” specifically bound to said ZIM3 KRAB repressor domain, it would have been obvious to someone of ordinary skill in the art before the effective filing date of the claimed invention to utilize the ZIM3 KRAB domain disclosed in the copending application and Alerasool as the KRAB repressor domain disclosed in the copending application and Cathomen as part of a construct for epigenetic modification and further to substitute the TALE-derived DNA binding domain of Cathomen for dCas9 (as disclosed in the copending application and Alerasool) to predictably facilitate user-specified sequence-specific targeting for epigenetic modification (as reviewed in Barrangou). One would have been motivated to make such a modification in order to receive the expected benefit of facilitating user-specified sequence-specific targeting for epigenetic modification.
Furthermore, given that Cathomen discloses a construct for epigenetic modification of genes, said construct comprising a Krϋppel-associated box (KRAB) zinc finger protein (or homologous), a DNA region capable of binding to the target gene (or homologous), and two DNA methyltransferases (DNMT) (human DNMT3A or homologous and murine Dnmt3L or homologous), and that Naldini discloses that zinc finger domains are capable of functioning as a DNA binding domain that targets a locus of interest for epigenetic modification thereof, it would have been obvious to someone of ordinary skill in the art before the effective filing date of the claimed invention to utilize the zinc finger domains disclosed in Naldini as the DNA binding domain for use in the construct for epigenetic modification disclosed in Cathomen to predictably facilitate user-specified sequence-specific targeting for epigenetic modification. One would have been motivated to make such a modification in order to receive the expected benefit of facilitating user-specified sequence-specific targeting for epigenetic modification.
This is a provisional nonstatutory double patenting rejection because the patentably indistinct claims have not in fact been patented.
Claims 135-137 and 139-152 are provisionally rejected on the ground of nonstatutory double patenting as being unpatentable over claims 1, 7, 10, 11, and 39 of copending Application No. 19/476,668 (reference application; corresponds to US 2026/0286319 A1) in view of Alerasool et al., 2020 (hereinafter Alerasool; as cited in the IDS filed 01/16/2024; of record), UniProt Entry Q96PE6 (as cited in the IDS filed 12/23/2025; of record), UniProt Entry Q9UJW3 (aligned sequence released 02/15/2017; of record), and UniProt Entry A0A386IRG9_STAAU (aligned sequence released 12/05/2018; of record), as evidenced by Barrangou and Doudna, 2016 (hereinafter Barrangou; of record).
Copending application ‘668 recites a fusion protein (and a nucleic acid encoding the same) comprising one or more DNMT domains (such as DNMT3A and/or DNMT3L), two or more DNA-binding zinc finger domains, and one or more transcriptional repressor domains (such as ZIM3 or TOX3) (as recited at copending claims 1, 7, 10, 11, and 39.
This fusion protein reads on the epigenetic editor comprising a fusion protein (and a nucleic acid encoding the same) recited at instant claims 135, 139-141, 143, and 145, which comprises a zinc finger DNA binding domain, a ZIM3 or TOX3 repressor domain, and DNMT3A and DNMT3L domains. Thus, the instantly claimed epigenetic editor and that of copending application ‘668 are not patentably distinct.
With regard to amended claim 136, which recites “the repressor domain [of the epigenetic editor of claim 135] is selected from the group consisting of: SEQ ID NOs: 67-595,” as set forth above, Cathomen discloses fusion of KRAB to a DNA binding domain and two DNMT domains for targeted silencing of genes via epigenetic modification, while Alerasool discloses fusion specifically of the ZIM3 KRAB domain to dCas9 to facilitate potent repression of gene expression. However, neither Cathomen nor Alerasool discloses the sequence of the ZIM3 repressor domain corresponding to SEQ ID NO: 67. This deficiency is cured by UniProt Entry Q96PE6. As shown in the alignment of Appendix I (previously provided), UniProt Entry Q96PE6 (corresponding to human ZIM3) comprises 100% identity to instant SEQ ID NO: 67. Thus, it is considered that UniProt Entry Q96PE6 discloses each and every additional limitation of instant claim 136.
With regard to claim 137, which recites “the DNA binding domain [of the epigenetic editor of claim 135] binds to a target sequence in a target chromosome comprising a target gene,” as set forth above, Cathomen discloses a fusion construct for epigenetic editing. Furthermore, as shown in Figures 1B and 2A of Cathomen, the DEM (designer epigenome modifier per paragraph [0013], the DNA binding portion of the DEM directs the DEM to a specific target site in the promoter or any other regulatory element of the target gene, leading to the methylation of the neighboring CpG di-residues and the deacetylation of neighboring histone tails, thereby silencing the target gene of interest (paragraphs [0061] and [0063]). This targeted binding reads on each and every additional limitation of instant claim 137. Thus, it is considered that Cathomen discloses each and every additional limitation of instant claim 137.
With regard to claim 142, which recites “the first DNMT domain [of the epigenetic editor of claim 135] is a human DNMT3A domain or a human DMNT3L domain,” as set forth above, Cathomen discloses a construct for epigenetic modification of genes, said construct comprising a Krϋppel-associated box (KRAB) zinc finger protein (or homologous), a DNA region capable of binding to the target gene (or homologous), and two DNA methyltransferases (DNMT) (human DNMT3A or homologous and murine Dnmt3L or homologous) (paragraphs [0012]-[0018]). Thus, it is considered that Cathomen discloses each and every additional limitation of instant claim 142.
With regard to amended instant claim 144, which recites “the first DNMT domain and the second DNMT domain [of the epigenetic editor of claim 140] are selected from the group consisting of: SEQ ID NOs: 32-66,” as set forth above, Cathomen discloses a construct for epigenetic modification of genes, said construct comprising a Krϋppel-associated box (KRAB) zinc finger protein (or homologous), a DNA region capable of binding to the target gene (or homologous), and two DNA methyltransferases (DNMT) (human DNMT3A or homologous and murine Dnmt3L or homologous) (paragraphs [0012]-[0018]). Additionally, Cathomen further discloses that the murine DNMT3L of the fusion protein taught therein may alternatively be human DNMT3L at paragraph [0051]. Cathomen further discloses that SEQ ID NO: 3 taught therein corresponds to human DNMT3A. As shown in the alignment of Appendix II (previously provided), SEQ ID NO: 3 of Cathomen comprises 100% identity to instant SEQ ID NO: 34. However, while Cathomen discloses that the murine DNMT3L may alternatively be human DNMT3L, Cathomen is silent as to the specific sequence of human DNMT3L. This deficiency is cured by UniProt Entry Q9UJW3, which discloses the human DNMT3L sequence. As shown in the alignment of Appendix III (previously provided), UniProt Entry Q9UJW3comprises 100% identity to instant SEQ ID NO: 38. Thus, it is considered that Cathomen and UniProt Entry Q9UJW3 collectively disclose each and every additional limitation of instant claim 144.
With regard to amended claim 146, which recites “the DNA binding domain [of the epigenetic editor of claim 135] comprises the nucleic acid guided DNA binding domain bound to the guide polynucleotide,” the construct of Cathomen is disclosed to comprise a TALE-derived DNA binding domain (paragraph [0044]) rather than the instantly claimed nucleic acid guided DNA binding domain bound to a guide polynucleotide. However, as set forth above, Alerasool discloses CRISPR interference constructs comprising fusion of inactive Cas9 (dCas9) to the ZIM3 KRAB domain, which is an exceptionally potent repressor (abstract; page 1093, column 2, paragraph 2; Figures 1 and 2). Alerasool further discloses that the CRISPR interference (CRISPRi) achieved therein using the fusion protein set forth above is particularly sensitive to guide RNA (gRNA) selection (page 1093, column 1, paragraphs 1-2). As depicted in Figure 1a of Alerasool, different gRNAs target the dCas9 to different loci. Furthermore, these gRNAs are indispensable to functioning of the system, as target genes are fully expressed in the absence of the gRNAs, as shown in Figure 2a. While Alerasool does not specify that the gRNA is bound to the dCas9 taught therein, it is known to those of ordinary skill in the art that gRNAs function by binding to their target sequences as well as to the Cas9 protein to assemble a functional editing complex (see Box 1 of Barrangou and Figure 1 of Alerasool). Thus, it is considered that Alerasool (as evidenced by Barrangou) discloses each and every additional limitation of instant claim 146.
With regard to amended claim 147, which recites “the DNA binding domain [of the epigenetic editor of claim 146] comprises a CRISPR-Cas protein bound to the guide polynucleotide,” as set forth above, Alerasool discloses CRISPRi achieved via fusion of ZIM3 to dCas9 (a CRISPR-Cas protein), which is guided to a target locus by the associated gRNA (Figure 1a). Furthermore, it is known to those of ordinary skill in the art that gRNAs function by binding to their target sequences as well as to the Cas9 protein to assemble a functional editing complex (see Box 1 of Barrangou). Thus, it is considered that Alerasool (as evidenced by Barrangou) discloses each and every additional limitation of instant claim 147.
With regard to claim 148, which recites “the guide polynucleotide [of the epigenetic editor of claim 146] hybridizes with a target sequence,” as set forth above, Alerasool discloses CRISPRi achieved via fusion of ZIM3 to dCas9 (a CRISPR-Cas protein), which is guided to a target locus by the associated gRNA (Figure 1a). Furthermore, it is known to those of ordinary skill in the art that gRNAs function by binding to their target sequences as well as to the Cas9 protein to assemble a functional editing complex (see Box 1 of Barrangou). Thus, it is considered that Alerasool (as evidenced by Barrangou) discloses each and every additional limitation of instant claim 148.
With regard to claims 149 and 150, which respectively recite “the CRISPR-Cas protein [of the epigenetic editor of claim 147] comprises a nuclease inactive Cas9 (dCas9),” specifically “dSpCas9,” as set forth above, Alerasool discloses CRISPRi achieved via fusion of ZIM3 to dCas9, which is guided to a target locus by the associated gRNA (Figure 1a). Alerasool specifically discloses that the dCas9 utilized therein is derived from Streptococcus pyogenes dCas9 (page 1097, column 1, paragraph 4). Thus, it is considered that Alerasool discloses each and every additional limitation of instant claims 149 and 150.
With regard to claim 151, which recites “the dSpCas9 [of the epigenetic editor of claim 150] is defined as SEQ ID NO: 3,” as set forth above Alerasool specifically discloses that the dCas9 utilized therein is derived from Streptococcus pyogenes dCas9 (page 1097, column 1, paragraph 4). However, Alerasool does not disclose that the sequence of said dSpCas9 is defined as instant SEQ ID NO: 3. This deficiency is cured by UniProt Entry A0A386IRG9_STAAU, which discloses the sequence of dSpCas9. As shown in the alignment of Appendix IV (previously provided), UniProt Entry A0A386IRG9_STAAU comprises 100% identity to instant SEQ ID NO: 3. Thus, it is considered that Alerasool and UniProt Entry A0A386IRG9_STAAU collectively disclose each and every additional limitation of instant claim 151.
With regard to amended claim 152, which recites “the first DNMT domain [of the epigenetic editor of claim 140] is a DNMT3A, the second DNMT domain is a DNMT3L, the DNA binding domain is a dSpCas9, and wherein the fusion protein comprises from N-terminus to C-terminus the DNMT3A-the DNMT3L-the dSpCas9-the repressor domain,” as set forth above, Cathomen discloses a construct for epigenetic modification of genes, said construct comprising a Krϋppel-associated box (KRAB) zinc finger protein (or homologous), a DNA region capable of binding to the target gene (or homologous), and two DNA methyltransferases (DNMT) (human DNMT3A or homologous and murine Dnmt3L or homologous) (paragraphs [0012]-[0018]). The structure of the epigenetic modifier construct of Cathomen is disclosed at Figure 1A, comprising the repressor domain, the DNA binding domain, and the DNMT domains. While the DNA binding domain of Cathomen is a TALE-derived DNA binding domain (paragraph [0044]), Alerasool discloses the utility of dSpCas9 fusion proteins for targeted epigenetic modification (abstract; Figures 1 and 2). While the N and C termini are not specified, it is known to those of ordinary skill in the art that proteins are typically written from left-to-right from the N terminus to the C terminus. Therefore, while Cathomen and Alerasool collectively disclose all the components of the claimed fusion protein, the order is opposite of that which is instantly claimed. However, per MPEP § 2144.04(VI)(C), it is not inventive to rearrange parts of an invention when all parts of the invention have been disclosed in the prior art, as in the instant case. Accordingly, it is considered that Cathomen and Alerasool collectively disclose the claimed fusion protein and that it would require routine experimentation by someone of ordinary skill in the art to optimize the order of domains in the claimed fusion protein.
Given that the copending application discloses compositions and methods for epigenetic regulation, and further that Cathomen discloses a construct for epigenetic modification of genes, said construct comprising a Krϋppel-associated box (KRAB) zinc finger protein (or homologous), a DNA region capable of binding to the target gene (or homologous), and two DNA methyltransferases (DNMT) (human DNMT3A or homologous and murine Dnmt3L or homologous), while Alerasool discloses that the ZIM3 KRAB (the sequence of which is disclosed by UniProt entry Q96PE6) domain facilitates potent repression via CRISPRi when fused to dSpCas9, and further that the ZIM3 KRAB domain strongly interacts with TRIM28/KAP1, which reads on the instantly claimed “epigenetic effector protein” specifically bound to said ZIM3 KRAB repressor domain, it would have been obvious to someone of ordinary skill in the art before the effective filing date of the claimed invention to utilize the ZIM3 KRAB domain disclosed in the copending application and Alerasool as the KRAB repressor domain disclosed in the copending application and Cathomen as part of a construct for epigenetic modification and further to substitute the TALE-derived DNA binding domain of Cathomen for dCas9 (as disclosed in the copending application and Alerasool) to predictably facilitate user-specified sequence-specific targeting for epigenetic modification (as reviewed in Barrangou). One would have been motivated to make such a modification in order to receive the expected benefit of facilitating user-specified sequence-specific targeting for epigenetic modification.
This is a provisional nonstatutory double patenting rejection because the patentably indistinct claims have not in fact been patented.
Claims 135-137, and 139-152 are provisionally rejected on the ground of nonstatutory double patenting as being unpatentable over claims 1, 5, 9, 14, 18, 19, and 23 of copending Application No. 19/480,313 (reference application; corresponds to US 2026/0284228 A1) in view of Alerasool et al., 2020 (hereinafter Alerasool; as cited in the IDS filed 01/16/2024; of record), UniProt Entry Q96PE6 (as cited in the IDS filed 12/23/2025; of record), UniProt Entry Q9UJW3 (aligned sequence released 02/15/2017; of record), and UniProt Entry A0A386IRG9_STAAU (aligned sequence released 12/05/2018; of record), as evidenced by Barrangou and Doudna, 2016 (hereinafter Barrangou; of record).
Copending application ‘313 is drawn to a system for repressing transcription of a human PCSK9 gene, said system comprising one or more fusion proteins (or nucleic acids encoding the same) that collectively comprise a human DNMT3A and/or a DNMT3L domain and a transcriptional repressor domain (such as ZIM3, ZFP28, ZN627, or TOX3) linked to a DNA binding domain (such as a dCas9 or zinc finger domain) that binds to a target region in the human PCSK9 gene (as recited at copending claims 1, 14, 18, 19, and 23).
This fusion protein reads on the epigenetic editor comprising a fusion protein (and a nucleic acid encoding the same) recited at instant claims 135, 137, 139-143, and 145-150, which comprises a DNA binding domain comprising a zinc finger domain or a dCas9 domain, DNMT3A and DNMT3L domains that may be from humans, and a transcriptional repressor domain such as ZIM3, ZFP28, ZN627, or TOX3.
Additionally, the DNMT3A and DNMT3L sequences of the copending application are recited to comprise SEQ ID NOs: 575 and 579 (as recited at copending claim 9), which are identical to instant SEQ ID NOs: 34 and 38 (as recited at instant claim 144), respectively, as shown in the alignments of Appendices XXII and XXIII (previously presented).
With regard to amended claim 136, which recites “the repressor domain [of the epigenetic editor of claim 135] is selected from the group consisting of: SEQ ID NOs: 67-595,” as set forth above, Cathomen discloses fusion of KRAB to a DNA binding domain and two DNMT domains for targeted silencing of genes via epigenetic modification, while Alerasool discloses fusion specifically of the ZIM3 KRAB domain to dCas9 to facilitate potent repression of gene expression. However, neither Cathomen nor Alerasool discloses the sequence of the ZIM3 repressor domain corresponding to SEQ ID NO: 67. This deficiency is cured by UniProt Entry Q96PE6. As shown in the alignment of Appendix I (previously provided), UniProt Entry Q96PE6 (corresponding to human ZIM3) comprises 100% identity to instant SEQ ID NO: 67. Thus, it is considered that UniProt Entry Q96PE6 discloses each and every additional limitation of instant claim 136.
With regard to claim 151, which recites “the dSpCas9 [of the epigenetic editor of claim 150] is defined as SEQ ID NO: 3,” as set forth above Alerasool specifically discloses that the dCas9 utilized therein is derived from Streptococcus pyogenes dCas9 (page 1097, column 1, paragraph 4). However, Alerasool does not disclose that the sequence of said dSpCas9 is defined as instant SEQ ID NO: 3. This deficiency is cured by UniProt Entry A0A386IRG9_STAAU, which discloses the sequence of dSpCas9. As shown in the alignment of Appendix IV (previously provided), UniProt Entry A0A386IRG9_STAAU comprises 100% identity to instant SEQ ID NO: 3. Thus, it is considered that Alerasool and UniProt Entry A0A386IRG9_STAAU collectively disclose each and every additional limitation of instant claim 151.
With regard to amended claim 152, which recites “the first DNMT domain [of the epigenetic editor of claim 140] is a DNMT3A, the second DNMT domain is a DNMT3L, the DNA binding domain is a dSpCas9, and wherein the fusion protein comprises from N-terminus to C-terminus the DNMT3A-the DNMT3L-the dSpCas9-the repressor domain,” as set forth above, Cathomen discloses a construct for epigenetic modification of genes, said construct comprising a Krϋppel-associated box (KRAB) zinc finger protein (or homologous), a DNA region capable of binding to the target gene (or homologous), and two DNA methyltransferases (DNMT) (human DNMT3A or homologous and murine Dnmt3L or homologous) (paragraphs [0012]-[0018]). The structure of the epigenetic modifier construct of Cathomen is disclosed at Figure 1A, comprising the repressor domain, the DNA binding domain, and the DNMT domains. While the DNA binding domain of Cathomen is a TALE-derived DNA binding domain (paragraph [0044]), Alerasool discloses the utility of dSpCas9 fusion proteins for targeted epigenetic modification (abstract; Figures 1 and 2). While the N and C termini are not specified, it is known to those of ordinary skill in the art that proteins are typically written from left-to-right from the N terminus to the C terminus. Therefore, while Cathomen and Alerasool collectively disclose all the components of the claimed fusion protein, the order is opposite of that which is instantly claimed. However, per MPEP § 2144.04(VI)(C), it is not inventive to rearrange parts of an invention when all parts of the invention have been disclosed in the prior art, as in the instant case. Accordingly, it is considered that Cathomen and Alerasool collectively disclose the claimed fusion protein and that it would require routine experimentation by someone of ordinary skill in the art to optimize the order of domains in the claimed fusion protein.
Given that the copending application discloses compositions and methods for epigenetic regulation, and further that Cathomen discloses a construct for epigenetic modification of genes, said construct comprising a Krϋppel-associated box (KRAB) zinc finger protein (or homologous), a DNA region capable of binding to the target gene (or homologous), and two DNA methyltransferases (DNMT) (human DNMT3A or homologous and murine Dnmt3L or homologous), while Alerasool discloses that the ZIM3 KRAB (the sequence of which is disclosed by UniProt entry Q96PE6) domain facilitates potent repression via CRISPRi when fused to dSpCas9, and further that the ZIM3 KRAB domain strongly interacts with TRIM28/KAP1, which reads on the instantly claimed “epigenetic effector protein” specifically bound to said ZIM3 KRAB repressor domain, it would have been obvious to someone of ordinary skill in the art before the effective filing date of the claimed invention to utilize the ZIM3 KRAB domain disclosed in the copending application and Alerasool as the KRAB repressor domain disclosed in the copending application and Cathomen as part of a construct for epigenetic modification and further to substitute the TALE-derived DNA binding domain of Cathomen for dCas9 (as disclosed in the copending application and Alerasool) to predictably facilitate user-specified sequence-specific targeting for epigenetic modification (as reviewed in Barrangou). One would have been motivated to make such a modification in order to receive the expected benefit of facilitating user-specified sequence-specific targeting for epigenetic modification.
This is a provisional nonstatutory double patenting rejection because the patentably indistinct claims have not in fact been patented.
Claims 135-137 and 139-152 are provisionally rejected on the ground of nonstatutory double patenting as being unpatentable over claims 1-19, 21, 22, 26, 29-35, 44, 46, 47, 49, 50, 52, 74-80, 82, 83, 87, 90-96, 105, 107, 108, 110, 111, 113, and 115 of copending Application No. 19/483,765 (reference application; not yet published) in view of Alerasool et al., 2020 (hereinafter Alerasool; as cited in the IDS filed 01/16/2024; of record), UniProt Entry Q96PE6 (as cited in the IDS filed 12/23/2025; of record), UniProt Entry Q9UJW3 (aligned sequence released 02/15/2017; of record), and UniProt Entry A0A386IRG9_STAAU (aligned sequence released 12/05/2018; of record), as evidenced by Barrangou and Doudna, 2016 (hereinafter Barrangou; of record).
Copending application ‘765 is drawn to systems for repressing transcription of target genes such as CD3D, said systems comprising one or more fusion proteins (or nucleic acids encoding the same) that collectively comprise a human DNMT3A and/or a DNMT3L domain and a transcriptional repressor domain (such as ZIM3, ZFP28, ZN627, or TOX3) linked to a DNA binding domain (such as a dCas9 or zinc finger domain) that binds to a target region in the targeted human gene (as recited at copending claims 1-18, 26, 29-35, 44, 46, 47, 49, 50, 52, 74-79, 87, 90-96, 105, 107, 108, 110, 111, 113, and 115).
This fusion protein reads on the epigenetic editor comprising a fusion protein (and a nucleic acid encoding the same) recited at instant claims 135, 137, 139-143, 145-150, and 152, which comprises a DNA binding domain comprising a zinc finger domain or a dCas9 domain, DNMT3A and DNMT3L domains that may be from humans, and a transcriptional repressor domain such as ZIM3, ZFP28, ZN627, or TOX3. Per instant claim 152, these domains are ordered from the N to C terminus as DNMT3A-DNMT3L-dSpCas9-the repressor domain, which is identical to the order recited at copending claims 44, 47, 50, 105, 108, and 111.
With regard to the copending and instantly claimed sequences, the DNA binding domain of the copending application is recited to comprise a dCas9 domain corresponding to copending SEQ ID NO: 12 (as recited at copending claims 19 and 80), which is identical to instant SEQ ID NO: 3 (derived from dSpCas9; as recited at instant claim 151), as shown in the alignment of Appendix XXIV (previously provided).
Additionally, the DNMT3A and DNMT3L sequences of the copending application are recited to comprise SEQ ID NOs: 575 and 579 (as recited at copending claims 21, 22, 82, and 83), which are identical to instant SEQ ID NOs: 34 and 38 (as recited at instant claim 144), respectively, as shown in the alignments of Appendices XXV and XXVI (previously provided).
With regard to amended claim 136, which recites “the repressor domain [of the epigenetic editor of claim 135] is selected from the group consisting of: SEQ ID NOs: 67-595,” as set forth above, Cathomen discloses fusion of KRAB to a DNA binding domain and two DNMT domains for targeted silencing of genes via epigenetic modification, while Alerasool discloses fusion specifically of the ZIM3 KRAB domain to dCas9 to facilitate potent repression of gene expression. However, neither Cathomen nor Alerasool discloses the sequence of the ZIM3 repressor domain corresponding to SEQ ID NO: 67. This deficiency is cured by UniProt Entry Q96PE6. As shown in the alignment of Appendix I (previously provided), UniProt Entry Q96PE6 (corresponding to human ZIM3) comprises 100% identity to instant SEQ ID NO: 67. Thus, it is considered that UniProt Entry Q96PE6 discloses each and every additional limitation of instant claim 136.
Given that the copending application discloses compositions and methods for epigenetic regulation, and further that Cathomen discloses a construct for epigenetic modification of genes, said construct comprising a Krϋppel-associated box (KRAB) zinc finger protein (or homologous), a DNA region capable of binding to the target gene (or homologous), and two DNA methyltransferases (DNMT) (human DNMT3A or homologous and murine Dnmt3L or homologous), while Alerasool discloses that the ZIM3 KRAB (the sequence of which is disclosed by UniProt entry Q96PE6) domain facilitates potent repression via CRISPRi when fused to dSpCas9, and further that the ZIM3 KRAB domain strongly interacts with TRIM28/KAP1, which reads on the instantly claimed “epigenetic effector protein” specifically bound to said ZIM3 KRAB repressor domain, it would have been obvious to someone of ordinary skill in the art before the effective filing date of the claimed invention to utilize the ZIM3 KRAB domain disclosed in the copending application and Alerasool as the KRAB repressor domain disclosed in the copending application and Cathomen as part of a construct for epigenetic modification and further to substitute the TALE-derived DNA binding domain of Cathomen for dCas9 (as disclosed in the copending application and Alerasool) to predictably facilitate user-specified sequence-specific targeting for epigenetic modification (as reviewed in Barrangou). One would have been motivated to make such a modification in order to receive the expected benefit of facilitating user-specified sequence-specific targeting for epigenetic modification.
This is a provisional nonstatutory double patenting rejection because the patentably indistinct claims have not in fact been patented.
Claims 135-137 and 139-152 are provisionally rejected on the ground of nonstatutory double patenting as being unpatentable over claims 1-8, 14, 17-23, 32, 34, 35, 37, 38, 40, and 62 of copending Application No. 19/502,682 (reference application; not yet published) in view of Alerasool et al., 2020 (hereinafter Alerasool; as cited in the IDS filed 01/16/2024; of record), UniProt Entry Q96PE6 (as cited in the IDS filed 12/23/2025; of record), UniProt Entry Q9UJW3 (aligned sequence released 02/15/2017; of record), and UniProt Entry A0A386IRG9_STAAU (aligned sequence released 12/05/2018; of record), as evidenced by Barrangou and Doudna, 2016 (hereinafter Barrangou; of record).
Copending application ‘682 is drawn to systems for repressing transcription of target genes such as RFXAP, said systems comprising one or more fusion proteins (or nucleic acids encoding the same) that collectively comprise a human DNMT3A and/or a DNMT3L domain and a transcriptional repressor domain (such as ZIM3, ZFP28, ZN627, or TOX3) linked to a DNA binding domain (such as a dCas9 or zinc finger domain) that binds to a target region in the targeted human gene (as recited at copending claims 1-6, 8, 14, 17, 18, 22, 23, 34, 37, 40, and 62).
This fusion protein reads on the epigenetic editor comprising a fusion protein (and a nucleic acid encoding the same) recited at instant claims 135, 137, 139-143, 145-150, and 152, which comprises a DNA binding domain comprising a zinc finger domain or a dCas9 domain, DNMT3A and DNMT3L domains that may be from humans, and a transcriptional repressor domain such as ZIM3, ZFP28, ZN627, or TOX3. Per instant claim 152, these domains are ordered from the N to C terminus as DNMT3A-DNMT3L-dSpCas9-the repressor domain, which is identical to the order recited at copending claims 32, 35, and 38.
With regard to the copending and instantly claimed sequences, the DNA binding domain of the copending application is recited to comprise a dCas9 domain corresponding to copending SEQ ID NO: 12 (as recited at copending claim7), which is identical to instant SEQ ID NO: 3 (derived from dSpCas9; as recited at instant claim 151), as shown in the alignment of Appendix XXVII (previously provided).
With regard to amended claim 136, which recites “the repressor domain [of the epigenetic editor of claim 135] is selected from the group consisting of: SEQ ID NOs: 67-595,” as set forth above, Cathomen discloses fusion of KRAB to a DNA binding domain and two DNMT domains for targeted silencing of genes via epigenetic modification, while Alerasool discloses fusion specifically of the ZIM3 KRAB domain to dCas9 to facilitate potent repression of gene expression. However, neither Cathomen nor Alerasool discloses the sequence of the ZIM3 repressor domain corresponding to SEQ ID NO: 67. This deficiency is cured by UniProt Entry Q96PE6. As shown in the alignment of Appendix I (previously provided), UniProt Entry Q96PE6 (corresponding to human ZIM3) comprises 100% identity to instant SEQ ID NO: 67. Thus, it is considered that UniProt Entry Q96PE6 discloses each and every additional limitation of instant claim 136.
With regard to amended instant claim 144, which recites “the first DNMT domain and the second DNMT domain [of the epigenetic editor of claim 140] are selected from the group consisting of: SEQ ID NOs: 32-66,” as set forth above, Cathomen discloses a construct for epigenetic modification of genes, said construct comprising a Krϋppel-associated box (KRAB) zinc finger protein (or homologous), a DNA region capable of binding to the target gene (or homologous), and two DNA methyltransferases (DNMT) (human DNMT3A or homologous and murine Dnmt3L or homologous) (paragraphs [0012]-[0018]). Additionally, Cathomen further discloses that the murine DNMT3L of the fusion protein taught therein may alternatively be human DNMT3L at paragraph [0051]. Cathomen further discloses that SEQ ID NO: 3 taught therein corresponds to human DNMT3A. As shown in the alignment of Appendix II (previously provided), SEQ ID NO: 3 of Cathomen comprises 100% identity to instant SEQ ID NO: 34. However, while Cathomen discloses that the murine DNMT3L may alternatively be human DNMT3L, Cathomen is silent as to the specific sequence of human DNMT3L. This deficiency is cured by UniProt Entry Q9UJW3, which discloses the human DNMT3L sequence. As shown in the alignment of Appendix III (previously provided), UniProt Entry Q9UJW3comprises 100% identity to instant SEQ ID NO: 38. Thus, it is considered that Cathomen and UniProt Entry Q9UJW3 collectively disclose each and every additional limitation of instant claim 144.
Given that the copending application discloses compositions and methods for epigenetic regulation, and further that Cathomen discloses a construct for epigenetic modification of genes, said construct comprising a Krϋppel-associated box (KRAB) zinc finger protein (or homologous), a DNA region capable of binding to the target gene (or homologous), and two DNA methyltransferases (DNMT) (human DNMT3A or homologous and murine Dnmt3L or homologous), while Alerasool discloses that the ZIM3 KRAB (the sequence of which is disclosed by UniProt entry Q96PE6) domain facilitates potent repression via CRISPRi when fused to dSpCas9, and further that the ZIM3 KRAB domain strongly interacts with TRIM28/KAP1, which reads on the instantly claimed “epigenetic effector protein” specifically bound to said ZIM3 KRAB repressor domain, it would have been obvious to someone of ordinary skill in the art before the effective filing date of the claimed invention to utilize the ZIM3 KRAB domain disclosed in the copending application and Alerasool as the KRAB repressor domain disclosed in the copending application and Cathomen as part of a construct for epigenetic modification and further to substitute the TALE-derived DNA binding domain of Cathomen for dCas9 (as disclosed in the copending application and Alerasool) to predictably facilitate user-specified sequence-specific targeting for epigenetic modification (as reviewed in Barrangou). One would have been motivated to make such a modification in order to receive the expected benefit of facilitating user-specified sequence-specific targeting for epigenetic modification.
This is a provisional nonstatutory double patenting rejection because the patentably indistinct claims have not in fact been patented.
Claims 135-137 and 139-152 are provisionally rejected on the ground of nonstatutory double patenting as being unpatentable over claims 1-10, 14, 17-23, 32, 34, 35, 37, 38, and 40 of copending Application No. 19/515,156 (reference application; not yet published) in view of Alerasool et al., 2020 (hereinafter Alerasool; as cited in the IDS filed 01/16/2024; of record), UniProt Entry Q96PE6 (as cited in the IDS filed 12/23/2025; of record), UniProt Entry Q9UJW3 (aligned sequence released 02/15/2017; of record), and UniProt Entry A0A386IRG9_STAAU (aligned sequence released 12/05/2018; of record), as evidenced by Barrangou and Doudna, 2016 (hereinafter Barrangou; of record).
Copending application ‘156 is drawn to systems for repressing transcription of target genes such as TGFBR2, said systems comprising one or more fusion proteins (or nucleic acids encoding the same) that collectively comprise a human DNMT3A and/or a DNMT3L domain and a transcriptional repressor domain (such as ZIM3, ZFP28, ZN627, or TOX3) linked to a DNA binding domain (such as a dCas9 or zinc finger domain) that binds to a target region in the targeted human gene (as recited at copending claims 1-6, 8, 14, 17-23, 32, 34, 35, 37, 38, and 40).
This fusion protein reads on the epigenetic editor comprising a fusion protein (and a nucleic acid encoding the same) recited at instant claims 135, 137, 139-143, 145-150, and 152, which comprises a DNA binding domain comprising a zinc finger domain or a dCas9 domain, DNMT3A and DNMT3L domains that may be from humans, and a transcriptional repressor domain such as ZIM3, ZFP28, ZN627, or TOX3. Per instant claim 152, these domains are ordered from the N to C terminus as DNMT3A-DNMT3L-dSpCas9-the repressor domain, which is identical to the order recited at copending claims 32, 35, and 38.
With regard to the copending and instantly claimed sequences, the DNA binding domain of the copending application is recited to comprise a dCas9 domain corresponding to copending SEQ ID NO: 12 (as recited at copending claim 7), which is identical to instant SEQ ID NO: 3 (derived from dSpCas9; as recited at instant claim 151), as shown in the alignment of Appendix XXVIII (previously provided).
Additionally, the DNMT3A and DNMT3L sequences of the copending application are recited to comprise SEQ ID NOs: 575 and 579 (as recited at copending claims 9 and 10), which are identical to instant SEQ ID NOs: 34 and 38 (as recited at instant claim 144), respectively, as shown in the alignments of Appendices XXIX and XXX (previously provided).
With regard to amended claim 136, which recites “the repressor domain [of the epigenetic editor of claim 135] is selected from the group consisting of: SEQ ID NOs: 67-595,” as set forth above, Cathomen discloses fusion of KRAB to a DNA binding domain and two DNMT domains for targeted silencing of genes via epigenetic modification, while Alerasool discloses fusion specifically of the ZIM3 KRAB domain to dCas9 to facilitate potent repression of gene expression. However, neither Cathomen nor Alerasool discloses the sequence of the ZIM3 repressor domain corresponding to SEQ ID NO: 67. This deficiency is cured by UniProt Entry Q96PE6. As shown in the alignment of Appendix I (previously provided), UniProt Entry Q96PE6 (corresponding to human ZIM3) comprises 100% identity to instant SEQ ID NO: 67. Thus, it is considered that UniProt Entry Q96PE6 discloses each and every additional limitation of instant claim 136.
Given that the copending application discloses compositions and methods for epigenetic regulation, and further that Cathomen discloses a construct for epigenetic modification of genes, said construct comprising a Krϋppel-associated box (KRAB) zinc finger protein (or homologous), a DNA region capable of binding to the target gene (or homologous), and two DNA methyltransferases (DNMT) (human DNMT3A or homologous and murine Dnmt3L or homologous), while Alerasool discloses that the ZIM3 KRAB (the sequence of which is disclosed by UniProt entry Q96PE6) domain facilitates potent repression via CRISPRi when fused to dSpCas9, and further that the ZIM3 KRAB domain strongly interacts with TRIM28/KAP1, which reads on the instantly claimed “epigenetic effector protein” specifically bound to said ZIM3 KRAB repressor domain, it would have been obvious to someone of ordinary skill in the art before the effective filing date of the claimed invention to utilize the ZIM3 KRAB domain disclosed in the copending application and Alerasool as the KRAB repressor domain disclosed in the copending application and Cathomen as part of a construct for epigenetic modification and further to substitute the TALE-derived DNA binding domain of Cathomen for dCas9 (as disclosed in the copending application and Alerasool) to predictably facilitate user-specified sequence-specific targeting for epigenetic modification (as reviewed in Barrangou). One would have been motivated to make such a modification in order to receive the expected benefit of facilitating user-specified sequence-specific targeting for epigenetic modification.
This is a provisional nonstatutory double patenting rejection because the patentably indistinct claims have not in fact been patented.
Claims 135-137 and 139-152 are provisionally rejected on the ground of nonstatutory double patenting as being unpatentable over claims 1-10, 14, 17-23, 32, 34, 35, 37, 38, and 40 of copending Application No. 19/515,205 (reference application; not yet published) in view of Alerasool et al., 2020 (hereinafter Alerasool; as cited in the IDS filed 01/16/2024; of record), UniProt Entry Q96PE6 (as cited in the IDS filed 12/23/2025; of record), UniProt Entry Q9UJW3 (aligned sequence released 02/15/2017; of record), and UniProt Entry A0A386IRG9_STAAU (aligned sequence released 12/05/2018; of record), as evidenced by Barrangou and Doudna, 2016 (hereinafter Barrangou; of record).
Copending application ‘205 is drawn to systems for repressing transcription of target genes such as ADORA2A, said systems comprising one or more fusion proteins (or nucleic acids encoding the same) that collectively comprise a human DNMT3A and/or a DNMT3L domain and a transcriptional repressor domain (such as ZIM3, ZFP28, ZN627, or TOX3) linked to a DNA binding domain (such as a dCas9 or zinc finger domain) that binds to a target region in the targeted human gene (as recited at copending claims 1-6, 8, 14, 17-23, 32, 34, 35, 37, 38, and 40).
This fusion protein reads on the epigenetic editor comprising a fusion protein (and a nucleic acid encoding the same) recited at instant claims 135, 137, 139-143, 145-150, and 152, which comprises a DNA binding domain comprising a zinc finger domain or a dCas9 domain, DNMT3A and DNMT3L domains that may be from humans, and a transcriptional repressor domain such as ZIM3, ZFP28, ZN627, or TOX3. Per instant claim 152, these domains are ordered from the N to C terminus as DNMT3A-DNMT3L-dSpCas9-the repressor domain, which is identical to the order recited at copending claims 32, 35, and 38.
With regard to the copending and instantly claimed sequences, the DNA binding domain of the copending application is recited to comprise a dCas9 domain corresponding to copending SEQ ID NO: 12 (as recited at copending claim 7), which is identical to instant SEQ ID NO: 3 (derived from dSpCas9; as recited at instant claim 151), as shown in the alignment of Appendix XXXI (previously provided).
Additionally, the DNMT3A and DNMT3L sequences of the copending application are recited to comprise SEQ ID NOs: 575 and 579 (as recited at copending claims 9 and 10), which are identical to instant SEQ ID NOs: 34 and 38 (as recited at instant claim 144), respectively, as shown in the alignments of Appendices XXXII and XXXIII (previously provided).
With regard to amended claim 136, which recites “the repressor domain [of the epigenetic editor of claim 135] is selected from the group consisting of: SEQ ID NOs: 67-595,” as set forth above, Cathomen discloses fusion of KRAB to a DNA binding domain and two DNMT domains for targeted silencing of genes via epigenetic modification, while Alerasool discloses fusion specifically of the ZIM3 KRAB domain to dCas9 to facilitate potent repression of gene expression. However, neither Cathomen nor Alerasool discloses the sequence of the ZIM3 repressor domain corresponding to SEQ ID NO: 67. This deficiency is cured by UniProt Entry Q96PE6. As shown in the alignment of Appendix I (previously provided), UniProt Entry Q96PE6 (corresponding to human ZIM3) comprises 100% identity to instant SEQ ID NO: 67. Thus, it is considered that UniProt Entry Q96PE6 discloses each and every additional limitation of instant claim 136.
Given that the copending application discloses compositions and methods for epigenetic regulation, and further that Cathomen discloses a construct for epigenetic modification of genes, said construct comprising a Krϋppel-associated box (KRAB) zinc finger protein (or homologous), a DNA region capable of binding to the target gene (or homologous), and two DNA methyltransferases (DNMT) (human DNMT3A or homologous and murine Dnmt3L or homologous), while Alerasool discloses that the ZIM3 KRAB (the sequence of which is disclosed by UniProt entry Q96PE6) domain facilitates potent repression via CRISPRi when fused to dSpCas9, and further that the ZIM3 KRAB domain strongly interacts with TRIM28/KAP1, which reads on the instantly claimed “epigenetic effector protein” specifically bound to said ZIM3 KRAB repressor domain, it would have been obvious to someone of ordinary skill in the art before the effective filing date of the claimed invention to utilize the ZIM3 KRAB domain disclosed in the copending application and Alerasool as the KRAB repressor domain disclosed in the copending application and Cathomen as part of a construct for epigenetic modification and further to substitute the TALE-derived DNA binding domain of Cathomen for dCas9 (as disclosed in the copending application and Alerasool) to predictably facilitate user-specified sequence-specific targeting for epigenetic modification (as reviewed in Barrangou). One would have been motivated to make such a modification in order to receive the expected benefit of facilitating user-specified sequence-specific targeting for epigenetic modification.
This is a provisional nonstatutory double patenting rejection because the patentably indistinct claims have not in fact been patented.
Claims 135-137 and 139-152 are provisionally rejected on the ground of nonstatutory double patenting as being unpatentable over claims 1, 2, 6-10, 13, 14, and 18-23 of copending Application No. 19/162,223 (reference application; not yet published), as evidenced by Barrangou and Doudna, 2016 (hereinafter Barrangou; of record), Eom et al., 2016 (hereinafter Eom; of record), and UniProt Entry A0A386IRG9_STAAU (aligned sequence released 12/05/2018; of record).
Copending claim 1 is drawn to “a system for repressing transcription of a human PCSK9 gene in a human cell…comprising…one or more fusion proteins that collectively comprise a DNA methyltransferase (DNMT) domain…wherein the DNMT domain…comprise[s] a DNMT3A domain and/or a DNMT3L domain…and a transcriptional repressor domain, each domain being linked to a DNA-binding domain that binds to a target sequence in the human PCSK9 gene…”. Copending claim 2 further recites that the DNA-binding domain comprises a dead CRISPR Cas domain, and further that the “system comprises a guide RNA that targets the fusion protein to one or more sequences in the PCSK9 gene…”. Copending claim 14 recites “the transcriptional repressor domain comprises a KRAB domain derived from KOX1, ZIM3, ZFP28, or ZN627.”
Collectively, these claims read on instant claims 135, 139, 140, 141, 143, and 146-148. While the copending claim set is silent as to the guide polynucleotide being bound to the nucleic acid guided DNA binding domain, Barrangou teaches that gRNAs function by binding to their target sequences as well as to the Cas9 protein to assemble a functional editing complex (see Box 1 of Barrangou). Furthermore, the recitation of copending claim 2 reads on the recitation of instant claims 137 and 148, which require that “the DNA binding domain binds to a target sequence in a target chromosome comprising a target gene” and that “the guide polynucleotide hybridizes with a target sequence.” In the copending application, the target gene sequence is PCSK9.
Copending claim 13 recites “the transcriptional repressor domain comprises a sequence with at least 90% identity to a sequence selected from SEQ ID NOs: 33-570.” As shown in the alignment of the Appendix, SEQ ID NO: 33 of the copending application comprises 100% identity to instant SEQ ID NO: 67 as recited as instant claim 136.
Copending claim 18 further recites that the system claimed therein “comprises…a fusion protein comprising the DNMT3A domain, the DNMT3L domain, the transcriptional repressor domain, and the DNA-binding domain, optionally wherein one or both of the DNTM3A and the DNMT3L domain are human, and wherein the DNA-binding domain is a dead CRISPR Cas domain or a ZFP domain.” Human DNMT3A and DNMT3L domains are also recited at instant claim 142.
Copending claims 9 and 10 respectively recite “wherein the DNMT3A domain comprises a sequence with at least 90% identity to SEQ ID No: 574 or 575” and “wherein the DNMT3L domain comprises a sequence with at least 90% identity to a sequence selected from SEQ ID NOs: 578-581.” As shown in the alignments of the Appendix, SEQ ID NOs: 34 and 38 of the instant application (as recited at instant claim 144) comprise 100% identity to copending SEQ ID NOs: 575 and 579, respectively.
Copending claims 7 and 8 further limit the DNA binding domain claimed therein to a ZFP domain. Instant claim 145 recites “the DNA binding domain comprises the zinc finger motif or the zinc finger array.” As is known to those of ordinary skill in the art, zinc finger domains comprise zinc finger motifs (reviewed in Eom: see especially page 2023, column 2, paragraph 2). Thus, copending claims 7 and 8 are not patentably distinct from instant claim 145.
Copending claim 6 recites “the dCas9 comprises a dCas9 sequence, optionally a sequence with at least 90% identity to SEQ ID NO: 12 or 13.” This recitation reads on the recitations of instant claims 149-151. As shown in the alignment of the Appendix, copending SEQ ID NO: 12 comprises 100% identity to instant SEQ ID NO: 3, as recited at instant claim 151. Regarding the recitation of instant claim 150, which requires that the dCas9 is a dSpCas9, the Examiner notes that copending SEQ ID NO: 12 and instant SEQ ID NO: 3 (which are identical) correspond to dSpCas9 per UniProt Entry A0A386IRG9_STAAU (see previously provided Appendix). Thus, it is considered that the copending claim set recites a dSpCas9, as instantly claimed.
Finally, copending claims 19-23 recite that the fusion protein claimed therein comprises “from N-terminus to C-terminus, the DNMT3A domain…the DNMT3L domain…the DNA-binding domain” which is recited to be dSpCas9, as set forth above, “and the transcriptional repressor domain.” This order reads on the order recited at instant claim 152.
Accordingly, it is considered that the copending and instant applications are not patentably distinct, particularly given the evidentiary disclosures of Barrangou, Eom, and UniProt.
Given that the copending application recites each and every limitation of the instant application, with the exception of the explicit recitation of a guide RNA bound to a CRISPR nuclease (an inherent property as evidenced by Barrangou), a zinc finger domain explicitly comprising a zinc finger motif or array (an inherent property as evidenced by Eom), and explicit recitation of dSpCas9 (although the sequence claimed therein corresponds to dSpCas9 per UniProt Entry A0A386IRG9_STAAU), it would have been obvious to someone of ordinary skill in the art before the effective filing date of the claimed invention that the instant and copending applications are not patentably distinct from each other.
This is a provisional nonstatutory double patenting rejection because the patentably indistinct claims have not in fact been patented.
Claims 135-137 and 139-152 are provisionally rejected on the ground of nonstatutory double patenting as being unpatentable over claims 1-7, 10, 11, 14, and 15 of copending Application No. 19/483,778 (reference application; not yet published), in view of US 2019/0024090 A1 (hereinafter Cathomen; as cited in the IDS filed 02/27/2025; of record), Alerasool et al., 2020 (hereinafter Alerasool; as cited in the IDS filed 01/16/2024; of record), UniProt Entry Q96PE6 (as cited in the IDS filed 12/23/2025; of record), UniProt Entry Q9UJW3 (aligned sequence released 02/15/2017; of record), and UniProt Entry A0A386IRG9_STAAU (aligned sequence released 12/05/2018; of record), as evidenced by Barrangou and Doudna, 2016 (hereinafter Barrangou; of record), Eom et al., 2016 (hereinafter Eom; of record), and UniProt Entry A0A386IRG9_STAAU (aligned sequence released 12/05/2018; of record).
Copending claim 1 is drawn to “a system for repressing transcription…comprising… a first fusion protein that collectively comprises a first DNA methyltransferase (DNMT) domain…wherein the first DNMT domain…comprise[s] a first DNMT3A domain and…a first DNMT3L domain…and a first transcriptional repressor domain…linked to a first DNA-binding domain that binds to a target region in one or more human genes…”. Copending claim 2 further recites “wherein the first…DNA-binding domain…comprise[s] a dead CRISPR Cas (dCas) domain, a ZFP domain, or a TALE domain.” Copending claim 3 further recites “wherein the first…DNA-binding domain comprises a dCas9 domain and the system further comprises…one or more guide RNAs.” Copending claims 4-6 recite an identical system. Copending claims 10 and 11 further recite the sequence corresponding to the first DNMT3A and/or DNMT3L domains. Copending claim 15 further recites that “the first…transcriptional repressor domain comprises a KRAB domain derived from…ZIM3…”.
Collectively, these claims read on instant claims 135, 137, 139-141, 143, 145-147, and 149. While the copending claim set is silent as to the guide polynucleotide being bound to the nucleic acid guided DNA binding domain, Barrangou teaches that gRNAs function by binding to their target sequences as well as to the Cas9 protein to assemble a functional editing complex (see Box 1 of Barrangou). Additionally, instant claim 145 recites “the DNA binding domain comprises the zinc finger motif or the zinc finger array.” As is known to those of ordinary skill in the art, zinc finger domains comprise zinc finger motifs (reviewed in Eom: see especially page 2023, column 2, paragraph 2).
Regarding the sequences recited at copending claims 10 and 11, as shown in the alignments of the Appendix, copending SEQ ID NOs: 575 and 579 respectively comprise 100% identity to instant SEQ ID NOs: 34 and 38, as recited at instant claim 144.
Copending claim 14 further recites “wherein the…transcriptional repressor domain comprises a sequence with at least 90% identity to a sequence selected from SEQ ID NOs: 33-570.” As shown in the alignment of the Appendix, copending SEQ ID NO: 33 comprises 100% sequence identity to instant SEQ ID NO: 67, as recited at instant claim 136.
Copending claim 7 further recites “wherein the…dCas domain comprises a dCas9 sequence, optionally as equence with at least 90% identity to SEQ ID NO: 12 or 13.” As shown in the alignment of the Appendix, copending SEQ ID NO: 12 comprises 100% identity to instant SEQ ID NO:3, as recited at instant claim 151. Regarding the recitation of instant claim 150, which requires that the dCas9 is a dSpCas9, the Examiner notes that copending SEQ ID NO: 12 and instant SEQ ID NO: 3 (which are identical) correspond to dSpCas9 per UniProt Entry A0A386IRG9_STAAU (see previously provided Appendix). Thus, it is considered that the copending claim set recites a dSpCas9, as instantly claimed.
With regard to claim 142, which recites “the first DNMT domain [of the epigenetic editor of claim 135] is a human DNMT3A domain or a human DMNT3L domain,” as set forth above, Cathomen discloses a construct for epigenetic modification of genes, said construct comprising a Krϋppel-associated box (KRAB) zinc finger protein (or homologous), a DNA region capable of binding to the target gene (or homologous), and two DNA methyltransferases (DNMT) (human DNMT3A or homologous and murine Dnmt3L or homologous) (paragraphs [0012]-[0018]). Thus, it is considered that Cathomen discloses each and every additional limitation of instant claim 142.
With regard to claim 148, which recites “the guide polynucleotide [of the epigenetic editor of claim 146] hybridizes with a target sequence,” as set forth above, Alerasool discloses CRISPRi achieved via fusion of ZIM3 to dCas9 (a CRISPR-Cas protein), which is guided to a target locus by the associated gRNA (Figure 1a). Furthermore, it is known to those of ordinary skill in the art that gRNAs function by binding to their target sequences as well as to the Cas9 protein to assemble a functional editing complex (see Box 1 of Barrangou). Thus, it is considered that Alerasool (as evidenced by Barrangou) discloses each and every additional limitation of instant claim 148.
With regard to amended claim 152, which recites “the first DNMT domain [of the epigenetic editor of claim 140] is a DNMT3A, the second DNMT domain is a DNMT3L, the DNA binding domain is a dSpCas9, and wherein the fusion protein comprises from N-terminus to C-terminus the DNMT3A-the DNMT3L-the dSpCas9-the repressor domain,” as set forth above, Cathomen discloses a construct for epigenetic modification of genes, said construct comprising a Krϋppel-associated box (KRAB) zinc finger protein (or homologous), a DNA region capable of binding to the target gene (or homologous), and two DNA methyltransferases (DNMT) (human DNMT3A or homologous and murine Dnmt3L or homologous) (paragraphs [0012]-[0018]). The structure of the epigenetic modifier construct of Cathomen is disclosed at Figure 1A, comprising the repressor domain, the DNA binding domain, and the DNMT domains. While the DNA binding domain of Cathomen is a TALE-derived DNA binding domain (paragraph [0044]), Alerasool discloses the utility of dCas9 fusion proteins for targeted epigenetic modification (abstract; Figures 1 and 2). While the N and C termini are not specified, it is known to those of ordinary skill in the art that proteins are typically written from left-to-right from the N terminus to the C terminus. Therefore, while Cathomen and Alerasool collectively disclose all the components of the claimed fusion protein, the order is opposite of that which is instantly claimed. However, per MPEP § 2144.04(VI)(C), it is not inventive to rearrange parts of an invention when all parts of the invention have been disclosed in the prior art, as in the instant case. Accordingly, it is considered that Cathomen and Alerasool collectively disclose the claimed fusion protein and that it would require routine experimentation by someone of ordinary skill in the art to optimize the order of domains in the claimed fusion protein.
Given that the copending application discloses compositions and methods for epigenetic regulation, and further that Cathomen discloses a construct for epigenetic modification of genes, said construct comprising a Krϋppel-associated box (KRAB) zinc finger protein (or homologous), a DNA region capable of binding to the target gene (or homologous), and two DNA methyltransferases (DNMT) (human DNMT3A or homologous and murine Dnmt3L or homologous), while Alerasool discloses that the ZIM3 KRAB (the sequence of which is disclosed by UniProt entry Q96PE6) domain facilitates potent repression via CRISPRi when fused to dSpCas9, and further that the ZIM3 KRAB domain strongly interacts with TRIM28/KAP1, which reads on the instantly claimed “epigenetic effector protein” specifically bound to said ZIM3 KRAB repressor domain, it would have been obvious to someone of ordinary skill in the art before the effective filing date of the claimed invention to utilize the ZIM3 KRAB domain disclosed in the copending application and Alerasool as the KRAB repressor domain disclosed in the copending application and Cathomen as part of a construct for epigenetic modification and further to substitute the TALE-derived DNA binding domain of Cathomen for dCas9 (as disclosed in the copending application and Alerasool) to predictably facilitate user-specified sequence-specific targeting for epigenetic modification (as reviewed in Barrangou). One would have been motivated to make such a modification in order to receive the expected benefit of facilitating user-specified sequence-specific targeting for epigenetic modification.
This is a provisional nonstatutory double patenting rejection because the patentably indistinct claims have not in fact been patented.
Claims 135-137 and 139-152 are provisionally rejected on the ground of nonstatutory double patenting as being unpatentable over claims 1, 27, 33, 39, 52, 55, 58, 61, and 75 of copending Application No. 19/710,948 (reference application; not yet published) in view of US 2019/0024090 A1 (hereinafter Cathomen; as cited in the IDS filed 02/27/2025; of record), Alerasool et al., 2020 (hereinafter Alerasool; as cited in the IDS filed 01/16/2024; of record), UniProt Entry Q96PE6 (as cited in the IDS filed 12/23/2025; of record), UniProt Entry Q9UJW3 (aligned sequence released 02/15/2017; of record), UniProt Entry A0A386IRG9_STAAU (aligned sequence released 12/05/2018; of record), and US 2019/0032049 A1 (hereinafter Naldini; as cited in the IDS filed 01/16/2024; of record), as evidenced by Barrangou and Doudna, 2016 (hereinafter Barrangou; of record) and Eom et al., 2016 (hereinafter Eom; of record).
Copending claims 1, 27, 33, 39, 52, 55, 58, 61, and 75 are all drawn to an epigenetic editing system, wherein said epigenetic editing system comprises a DNA binding domain, at least one DNA methyltransferase domain, and a repressor domain. This editing system broadly reads on the instantly claimed epigenetic editor. When applying the prior art, this editing system reads on the instantly claimed epigenetic editor, as set forth below.
With regard to amended claim 135, which recites “an epigenetic editor comprising a fusion protein or a nucleic acid encoding the fusion protein thereof, wherein the fusion protein comprises:
a first DNA methyltransferase (DNMT) domain;
a DNA binding domain, wherein the DNA binding domain comprises (1) a zinc finger motif, or a zinc finger array, or (2) a nucleic acid guided DNA binding domain bound to a guide polynucleotide; and
a repressor domain, wherein the repressor domain is selected from the group consisting of: ZIM3…and wherein the repressor domain specifically binds to an epigenetic effector protein in a cell comprising a target gene and directs the epigenetic editor to the target gene to [e]ffect an epigenetic modification in a nucleotide in the target gene or a histone bound to the target gene.
Cathomen discloses a construct for editing epigenetic marks of genes governing the expression thereof, said construct comprising a Krϋppel-associated box (KRAB) zinc finger protein (or homologous), a DNA region capable of binding to the target gene (or homologous), and two DNA methyltransferases (DNMT) (human DNMT3A or homologous and murine Dnmt3L or homologous) (paragraphs [0012]-[0018]). Thus, Cathomen discloses an epigenetic editor comprising a fusion protein, said fusion protein comprising a first DNMT domain, a DNA binding domain, and a repressor domain, as instantly claimed. Regarding the instantly claimed repressor domain, per paragraph [0009], the KRAB zinc finger proteins taught therein include an effector motif called KRAB, wherein KRAB serves to recruit histone deacetylase complexes, thereby repressing gene expression. Per paragraphs [0071] and [0072] of the instant specification, KRAB is a known transcription repressor domain. Thus, it is considered that the KRAB zinc finger protein disclosed in Cathomen generally reads on the instantly claimed repressor domain. Per Cathomen, the KRAB domain taught therein recruits the scaffold protein KAP1 that in turn regulates transcription through the induction of histone modifications such as deacetylation or tri-methylation (paragraphs [0009] and [0044]). However, Cathomen is silent as to the instantly claimed ZIM3 domain.
This deficiency is cured by Alerasool, which discloses CRISPR interference constructs comprising fusion of inactive Cas9 (dCas9) to the ZIM3 KRAB domain, which is an exceptionally potent repressor (abstract; page 1093, column 2, paragraph 2; Figures 1 and 2). Therefore, while Cathomen does not disclose that the KRAB fusion taught therein specifically comprises the ZIM3 KRAB domain, Alerasool discloses that the ZIM3 KRAB domain is a potent repressor compatible with targeted gene silencing by fusing it to dCas9 (i.e. a DNA binding domain, wherein said DNA binding domain is a nucleic acid DNA binding domain bound to a guide polynucleotide-see Figure 1). While Alerasool does not specify that the gRNA is bound to the dCas9 taught therein, it is known to those of ordinary skill in the art that gRNAs function by binding to their target sequences as well as to the Cas9 protein to assemble a functional editing complex (see Box 1 of Barrangou and Figure 1 of Alerasool). Alerasool further discloses that the ZIM3 KRAB domain interacts strongly with TRIM28/KAP1 (page 1093, column 2, paragraph 3; Figure 1).
Therefore, in aggregate, it is considered that Cathomen discloses a construct for editing epigenetic marks of genes governing the expression thereof, wherein said construct comprises a KRAB domain (such as ZIM3 as disclosed in Alerasool), a DNA region capable of binding to the target gene (i.e. a dCas9 bound to a gRNA as disclosed in Alerasool), and two DNMTs, wherein the ZIM3 KRAB domain strongly interacts with TRIM28/KAP1 (as disclosed in Alerasool) to induce histone modifications as per Cathomen. This strong, specific interaction of the ZIM3 KRAB domain with TRIM28/KAP1 is considered to read on the limitation of “the repressor domain specifically binds to an epigenetic effector protein in a cell comprising a target gene,” wherein the epigenetic effector protein is TRIM28/KAP1, which assembles a protein complex with chromatin regulators (as disclosed in Alerasool: page 1093, column 2, paragraph 3). As depicted in Figure 1B of Cathomen, said construct then effects an epigenetic modification in a nucleotide in the target gene or a histone bound to the target gene, specifically in the promoter region of the target gene (see also paragraph [0061]). Thus, it is considered that Cathomen and Alerasool collectively disclose each and every limitation of amended instant claim 135.
With regard to amended claim 136, which recites “the repressor domain [of the epigenetic editor of claim 135] is selected from the group consisting of: SEQ ID NOs: 67-595,” as set forth above, Cathomen discloses fusion of KRAB to a DNA binding domain and two DNMT domains for targeted silencing of genes via epigenetic modification, while Alerasool discloses fusion specifically of the ZIM3 KRAB domain to dCas9 to facilitate potent repression of gene expression. However, neither Cathomen nor Alerasool discloses the sequence of the ZIM3 repressor domain corresponding to SEQ ID NO: 67. This deficiency is cured by UniProt Entry Q96PE6. As shown in the alignment of Appendix I (previously provided), UniProt Entry Q96PE6 (corresponding to human ZIM3) comprises 100% identity to instant SEQ ID NO: 67. Thus, it is considered that UniProt Entry Q96PE6 discloses each and every additional limitation of instant claim 136.
With regard to claim 137, which recites “the DNA binding domain [of the epigenetic editor of claim 135] binds to a target sequence in a target chromosome comprising a target gene,” as set forth above, Cathomen discloses a fusion construct for epigenetic editing. Furthermore, as shown in Figures 1B and 2A of Cathomen, the DEM (designer epigenome modifier per paragraph [0013], the DNA binding portion of the DEM directs the DEM to a specific target site in the promoter or any other regulatory element of the target gene, leading to the methylation of the neighboring CpG di-residues and the deacetylation of neighboring histone tails, thereby silencing the target gene of interest (paragraphs [0061] and [0063]). This targeted binding reads on each and every additional limitation of instant claim 137. Thus, it is considered that Cathomen discloses each and every additional limitation of instant claim 137.
With regard to amended claim 139, which recites “the repressor domain [of the epigenetic editor of claim 135] is selected from the group consisting of: ZIM3…,” as set forth above, Alerasool discloses CRISPR interference constructs comprising fusion of inactive Cas9 (dCas9) to the ZIM3 KRAB domain, which is an exceptionally potent repressor (abstract; page 1093, column 2, paragraph 2; Figures 1 and 2). Thus, it is considered that Alerasool discloses each and every additional limitation of instant claim 139.
With regard to claim 140, which recites “the fusion protein [of the epigenetic editor of claim 135] further comprises a second DNMT domain,” as set forth above, Cathomen discloses a construct for epigenetic modification of genes, said construct comprising a Krϋppel-associated box (KRAB) zinc finger protein (or homologous), a DNA region capable of binding to the target gene (or homologous), and two DNA methyltransferases (DNMT) (human DNMT3A or homologous and murine Dnmt3L or homologous) (paragraphs [0012]-[0018]). Thus, it is considered that Cathomen discloses each and every additional limitation of instant claim 140.
With regard to amended claim 141, which recites “the first DNMT domain [of the epigenetic editor of claim 135] is selected from the group consisting of a DNMT3A domain, a DNMT3B domain, a DNMT3C domain, and a DNMT3L domain,” as set forth above, Cathomen discloses a construct for epigenetic modification of genes, said construct comprising a Krϋppel-associated box (KRAB) zinc finger protein (or homologous), a DNA region capable of binding to the target gene (or homologous), and two DNA methyltransferases (DNMT) (human DNMT3A or homologous and murine Dnmt3L or homologous) (paragraphs [0012]-[0018]). Thus, it is considered that Cathomen discloses each and every additional limitation of instant claim 141.
With regard to claim 142, which recites “the first DNMT domain [of the epigenetic editor of claim 135] is a human DNMT3A domain or a human DMNT3L domain,” as set forth above, Cathomen discloses a construct for epigenetic modification of genes, said construct comprising a Krϋppel-associated box (KRAB) zinc finger protein (or homologous), a DNA region capable of binding to the target gene (or homologous), and two DNA methyltransferases (DNMT) (human DNMT3A or homologous and murine Dnmt3L or homologous) (paragraphs [0012]-[0018]). Thus, it is considered that Cathomen discloses each and every additional limitation of instant claim 142.
With regard to claim 143, which recites “the first DNMT domain [of the epigenetic editor of claim 140] is a DNMT3A domain and the second DNMT domain is a DNMT3L domain, or a catalytic portion thereof,” as set forth above, Cathomen discloses a construct for epigenetic modification of genes, said construct comprising a Krϋppel-associated box (KRAB) zinc finger protein (or homologous), a DNA region capable of binding to the target gene (or homologous), and two DNA methyltransferases (DNMT) (human DNMT3A or homologous and murine Dnmt3L or homologous) (paragraphs [0012]-[0018]). Thus, it is considered that Cathomen discloses each and every additional limitation of instant claim 143.
With regard to amended instant claim 144, which recites “the first DNMT domain and the second DNMT domain [of the epigenetic editor of claim 140] are selected from the group consisting of: SEQ ID NOs: 32-66,” as set forth above, Cathomen discloses a construct for epigenetic modification of genes, said construct comprising a Krϋppel-associated box (KRAB) zinc finger protein (or homologous), a DNA region capable of binding to the target gene (or homologous), and two DNA methyltransferases (DNMT) (human DNMT3A or homologous and murine Dnmt3L or homologous) (paragraphs [0012]-[0018]). Additionally, Cathomen further discloses that the murine DNMT3L of the fusion protein taught therein may alternatively be human DNMT3L at paragraph [0051]. Cathomen further discloses that SEQ ID NO: 3 taught therein corresponds to human DNMT3A. As shown in the alignment of Appendix II (previously provided), SEQ ID NO: 3 of Cathomen comprises 100% identity to instant SEQ ID NO: 34. However, while Cathomen discloses that the murine DNMT3L may alternatively be human DNMT3L, Cathomen is silent as to the specific sequence of human DNMT3L. This deficiency is cured by UniProt Entry Q9UJW3, which discloses the human DNMT3L sequence. As shown in the alignment of Appendix III (previously provided), UniProt Entry Q9UJW3comprises 100% identity to instant SEQ ID NO: 38. Thus, it is considered that Cathomen and UniProt Entry Q9UJW3 collectively disclose each and every additional limitation of instant claim 144.
With regard to amended claim 145, which recites “the DNA binding domain [of the epigenetic editor of claim 135] comprises the zinc finger motif or the zinc finger array,” as set forth above, Cathomen discloses a construct for epigenetic modification of genes, said construct comprising a Krϋppel-associated box (KRAB) zinc finger protein (or homologous), a DNA region capable of binding to the target gene (or homologous), and two DNA methyltransferases (DNMT) (human DNMT3A or homologous and murine Dnmt3L or homologous) (paragraphs [0012]-[0018]). However, the DNA binding domain of Cathomen is a TALE-derived DNA binding domain (paragraph [0044]), which does not comprise a zinc finger motif or a zinc finger array. This deficiency is cured by Naldini.
Naldini discloses artificial transcription repressors that establish robust and permanent states of epigenetic repression, said artificial transcription repressors comprising a DNA-binding domain operably linked to a KRAB domain, a DNMT3A domain, and/or a DNMT3L domain (paragraphs [0014], [0016], and [0024]-[0029]). As depicted in Figure 1 of Naldini, this system facilitates epigenetic silencing of a targeted gene of interest. Naldini discloses that the DNA binding domain taught therein may be a zinc finger domain (paragraphs [0037] and [0253]). As is known to those of ordinary skill in the art, zinc finger domains comprise zinc finger motifs (reviewed in Eom: see especially page 2023, column 2, paragraph 2). Thus, Naldini discloses that zinc finger domains (comprising zinc finger motifs) are capable of functioning as a DNA binding domain that targets a locus of interest for epigenetic modification thereof, as instantly claimed.
With regard to amended claim 146, which recites “the DNA binding domain [of the epigenetic editor of claim 135] comprises the nucleic acid guided DNA binding domain bound to the guide polynucleotide,” the construct of Cathomen is disclosed to comprise a TALE-derived DNA binding domain (paragraph [0044]) rather than the instantly claimed nucleic acid guided DNA binding domain bound to a guide polynucleotide. However, as set forth above, Alerasool discloses CRISPR interference constructs comprising fusion of inactive Cas9 (dCas9) to the ZIM3 KRAB domain, which is an exceptionally potent repressor (abstract; page 1093, column 2, paragraph 2; Figures 1 and 2). Alerasool further discloses that the CRISPR interference (CRISPRi) achieved therein using the fusion protein set forth above is particularly sensitive to guide RNA (gRNA) selection (page 1093, column 1, paragraphs 1-2). As depicted in Figure 1a of Alerasool, different gRNAs target the dCas9 to different loci. Furthermore, these gRNAs are indispensable to functioning of the system, as target genes are fully expressed in the absence of the gRNAs, as shown in Figure 2a. While Alerasool does not specify that the gRNA is bound to the dCas9 taught therein, it is known to those of ordinary skill in the art that gRNAs function by binding to their target sequences as well as to the Cas9 protein to assemble a functional editing complex (see Box 1 of Barrangou and Figure 1 of Alerasool). Thus, it is considered that Alerasool (as evidenced by Barrangou) discloses each and every additional limitation of instant claim 146.
With regard to amended claim 147, which recites “the DNA binding domain [of the epigenetic editor of claim 146] comprises a CRISPR-Cas protein bound to the guide polynucleotide,” as set forth above, Alerasool discloses CRISPRi achieved via fusion of ZIM3 to dCas9 (a CRISPR-Cas protein), which is guided to a target locus by the associated gRNA (Figure 1a). Furthermore, it is known to those of ordinary skill in the art that gRNAs function by binding to their target sequences as well as to the Cas9 protein to assemble a functional editing complex (see Box 1 of Barrangou). Thus, it is considered that Alerasool (as evidenced by Barrangou) discloses each and every additional limitation of instant claim 147.
With regard to claim 148, which recites “the guide polynucleotide [of the epigenetic editor of claim 146] hybridizes with a target sequence,” as set forth above, Alerasool discloses CRISPRi achieved via fusion of ZIM3 to dCas9 (a CRISPR-Cas protein), which is guided to a target locus by the associated gRNA (Figure 1a). Furthermore, it is known to those of ordinary skill in the art that gRNAs function by binding to their target sequences as well as to the Cas9 protein to assemble a functional editing complex (see Box 1 of Barrangou). Thus, it is considered that Alerasool (as evidenced by Barrangou) discloses each and every additional limitation of instant claim 148.
With regard to claims 149 and 150, which respectively recite “the CRISPR-Cas protein [of the epigenetic editor of claim 147] comprises a nuclease inactive Cas9 (dCas9),” specifically “dSpCas9,” as set forth above, Alerasool discloses CRISPRi achieved via fusion of ZIM3 to dCas9, which is guided to a target locus by the associated gRNA (Figure 1a). Alerasool specifically discloses that the dCas9 utilized therein is derived from Streptococcus pyogenes dCas9 (page 1097, column 1, paragraph 4). Thus, it is considered that Alerasool discloses each and every additional limitation of instant claims 149 and 150.
With regard to claim 151, which recites “the dSpCas9 [of the epigenetic editor of claim 150] is defined as SEQ ID NO: 3,” as set forth above Alerasool specifically discloses that the dCas9 utilized therein is derived from Streptococcus pyogenes dCas9 (page 1097, column 1, paragraph 4). However, Alerasool does not disclose that the sequence of said dSpCas9 is defined as instant SEQ ID NO: 3. This deficiency is cured by UniProt Entry A0A386IRG9_STAAU, which discloses the sequence of dSpCas9. As shown in the alignment of Appendix IV (previously provided), UniProt Entry A0A386IRG9_STAAU comprises 100% identity to instant SEQ ID NO: 3. Thus, it is considered that Alerasool and UniProt Entry A0A386IRG9_STAAU collectively disclose each and every additional limitation of instant claim 151.
With regard to amended claim 152, which recites “the first DNMT domain [of the epigenetic editor of claim 140] is a DNMT3A, the second DNMT domain is a DNMT3L, the DNA binding domain is a dSpCas9, and wherein the fusion protein comprises from N-terminus to C-terminus the DNMT3A-the DNMT3L-the dSpCas9-the repressor domain,” as set forth above, Cathomen discloses a construct for epigenetic modification of genes, said construct comprising a Krϋppel-associated box (KRAB) zinc finger protein (or homologous), a DNA region capable of binding to the target gene (or homologous), and two DNA methyltransferases (DNMT) (human DNMT3A or homologous and murine Dnmt3L or homologous) (paragraphs [0012]-[0018]). The structure of the epigenetic modifier construct of Cathomen is disclosed at Figure 1A, comprising the repressor domain, the DNA binding domain, and the DNMT domains. While the DNA binding domain of Cathomen is a TALE-derived DNA binding domain (paragraph [0044]), Alerasool discloses the utility of dCas9 fusion proteins for targeted epigenetic modification (abstract; Figures 1 and 2). While the N and C termini are not specified, it is known to those of ordinary skill in the art that proteins are typically written from left-to-right from the N terminus to the C terminus. Therefore, while Cathomen and Alerasool collectively disclose all the components of the claimed fusion protein, the order is opposite of that which is instantly claimed. However, per MPEP § 2144.04(VI)(C), it is not inventive to rearrange parts of an invention when all parts of the invention have been disclosed in the prior art, as in the instant case. Accordingly, it is considered that Cathomen and Alerasool collectively disclose the claimed fusion protein and that it would require routine experimentation by someone of ordinary skill in the art to optimize the order of domains in the claimed fusion protein.
Given that the copending application discloses compositions and methods for epigenetic regulation, and further that Cathomen discloses a construct for epigenetic modification of genes, said construct comprising a Krϋppel-associated box (KRAB) zinc finger protein (or homologous), a DNA region capable of binding to the target gene (or homologous), and two DNA methyltransferases (DNMT) (human DNMT3A or homologous and murine Dnmt3L or homologous), while Alerasool discloses that the ZIM3 KRAB (the sequence of which is disclosed by UniProt entry Q96PE6) domain facilitates potent repression via CRISPRi when fused to dSpCas9, and further that the ZIM3 KRAB domain strongly interacts with TRIM28/KAP1, which reads on the instantly claimed “epigenetic effector protein” specifically bound to said ZIM3 KRAB repressor domain, it would have been obvious to someone of ordinary skill in the art before the effective filing date of the claimed invention to utilize the ZIM3 KRAB domain disclosed in the copending application and Alerasool as the KRAB repressor domain disclosed in the copending application and Cathomen as part of a construct for epigenetic modification and further to substitute the TALE-derived DNA binding domain of Cathomen for dCas9 (as disclosed in the copending application and Alerasool) to predictably facilitate user-specified sequence-specific targeting for epigenetic modification (as reviewed in Barrangou). One would have been motivated to make such a modification in order to receive the expected benefit of facilitating user-specified sequence-specific targeting for epigenetic modification.
Furthermore, given that Cathomen discloses a construct for epigenetic modification of genes, said construct comprising a Krϋppel-associated box (KRAB) zinc finger protein (or homologous), a DNA region capable of binding to the target gene (or homologous), and two DNA methyltransferases (DNMT) (human DNMT3A or homologous and murine Dnmt3L or homologous), and that Naldini discloses that zinc finger domains are capable of functioning as a DNA binding domain that targets a locus of interest for epigenetic modification thereof, it would have been obvious to someone of ordinary skill in the art before the effective filing date of the claimed invention to utilize the zinc finger domains disclosed in Naldini as the DNA binding domain for use in the construct for epigenetic modification disclosed in Cathomen to predictably facilitate user-specified sequence-specific targeting for epigenetic modification. One would have been motivated to make such a modification in order to receive the expected benefit of facilitating user-specified sequence-specific targeting for epigenetic modification.
This is a provisional nonstatutory double patenting rejection because the patentably indistinct claims have not in fact been patented.
Conclusion
No claims are allowed.
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/SARAH E ALLEN/ Examiner, Art Unit 1637
/J. E. ANGELL/ Primary Examiner, Art Unit 1637
