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 .
This action is in response to the amendment filed 10/14/2025, in which claims 47-49, 55, 56 and 58 were amended, claim 50 is previously presented, claims 51 and 57 was canceled and claims 59-69 were newly added. Claims 41-45, 47-50, 52-55, 56 and 58-69 are currently pending.
Applicant’s arguments have been thoroughly reviewed, but are not persuasive for the
reasons that follow. Any rejection and objections not reiterated in this action have been
withdrawn. This action is FINAL.
Election/Restrictions
Applicant elected the species of cytosine deaminase APOBEC1, mammalian cells, and C as the starting base and G as the ending base with traverse in the reply filed on 06/10/2025
Claims 41-45 and 52-54 are withdrawn from further consideration pursuant to 37 CFR 1.142(b), as being drawn to a nonelected species, there being no allowable generic or linking claim. Applicant timely traversed the restriction (election) requirement in the reply filed on 06/10/2025.
Claims 47-50, 55, 56 and 58-69 are currently under examination.
Response to Amendments - Claim Objections
The previous objection of claims 47 and 55 has been withdrawn in view of applicant’s amendments to the claims filed on 10/14/2025.
Response to Amendments – Improper Markush
The previous rejection of claims 55-57 as an improper Markush grouping has been withdrawn in view of Applicant’s amendments to the claims filed on 10/14/2025.
Claim Rejections - 35 USC § 112
The following is a quotation of the first paragraph of 35 U.S.C. 112(a):
(a) IN GENERAL.—The specification shall contain a written description of the invention, and of the manner and process of making and using it, in such full, clear, concise, and exact terms as to enable any person skilled in the art to which it pertains, or with which it is most nearly connected, to make and use the same, and shall set forth the best mode contemplated by the inventor or joint inventor of carrying out the invention.
The following is a quotation of the first paragraph of pre-AIA 35 U.S.C. 112:
The specification shall contain a written description of the invention, and of the manner and process of making and using it, in such full, clear, concise, and exact terms as to enable any person skilled in the art to which it pertains, or with which it is most nearly connected, to make and use the same, and shall set forth the best mode contemplated by the inventor of carrying out his invention.
Claims 47-50, 55, 56 and 58-69 are rejected under 35 U.S.C. 112(a) or pre-AIA 35 U.S.C. 112, first paragraph, as based on a disclosure which is not enabling. The disclosure does not enable one of ordinary skill in the art to practice the invention without the sequences outlined by accession numbers, which is/are critical or essential to the practice of the invention but not included in the claim(s) using the proper incorporation by reference, such as sequence identifiers corresponding the sequence listing. See In re Mayhew, 527 F.2d 1229, 188 USPQ 356 (CCPA 1976). This is a NEW rejection necessitated by the amendment filed on 10/14/2025.
Claims 47, 55, 58-62, 65 and 68 comprise the sequences defined by reference to Genbank Accession numbers AAH03792.1, Q99ZW2.1 and CAG46474.1 which are defined by reference to entries in an electronic database. "Essential material" may be incorporated by reference, but only by way of an incorporation by reference to a U.S. Patent or U.S. Patent application publication, which patent or patent application publication does not itself incorporate such essential material by reference.
In the instant case, the claims are, in effect, incorporating the sequence contained in an electronic database. See MPEP 608.01(p). Accordingly, the reference to the online genomic sequence does not provide the features that are critical or essential to the practice of the claimed invention.
Accordingly, claims 48-50, 56, 63, 64, 67 and 69 are included due to relying upon the rejected claims stated above.
The following is a quotation of 35 U.S.C. 112(b):
(b) CONCLUSION.—The specification shall conclude with one or more claims particularly pointing out and distinctly claiming the subject matter which the inventor or a joint inventor regards as the invention.
The following is a quotation of 35 U.S.C. 112 (pre-AIA ), second paragraph:
The specification shall conclude with one or more claims particularly pointing out and distinctly claiming the subject matter which the applicant regards as his invention.
Claims 48, 56, 58 and 66-69 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. This is a previous rejection made in the prior office action filed on 07/11/2025 and rewritten to address the amendments filed on 10/14/2025.
Claims 48, 56 and 66 recite the limitation "the human uracil DNA glycosidase UNG amino acid sequence from the N-terminal" in lines 3-5 in claim 48, lines 4-6 in claim 56 and lines 3-4 in claim 66. There is insufficient antecedent basis for this limitation in the claim. Claim 56 recites, “the uracil DNA glycosidase is a protein represented by an amino acid sequence obtained by deleting the amino acid sequence represented by positions 1 to 84 of the human uracil DNA glycosidase UNG amino acid sequence from the N-terminal”, however, the amino acid is not specified within the instant claims to be able to determine the deletion of positions 1 to 84 of the human uracil DNA glycosidase.
Claim 58 is drawn to a product, but improperly recites method steps, including “including introducing a coding gene of cytosine deaminase APOBEC, a coding gene of nCas9 nuclease, a coding gene of uracil DNA glycosidase and a coding sequence of sgRNA into receptor organism or the cells of a receptor organism, so that the coding gene of the cytosine deaminase APOBEC, a coding gene of nCas9 nuclease, a coding gene of uracil DNA glycosidase and a coding sequence of sgRNA are all expressed to mutate a target base C to G”. It is unclear whether infringement occurs upon manufacture of the product or upon performance of the recited steps using the product. Therefore, the scope of the claim is found to be indefinite.
Accordingly claims 66-69 also are found to be indefinite due to their relying on claim 58.
Response to Amendments - Claim Rejections - 35 USC § 112
The previous rejection of claims 55-57 under 35 U.S.C. 112(a) has been withdrawn in view of Applicant’s amendments to the claims filed on 10/14/2025.
The previous rejection of claim 58 under 35 U.S.C. 112(a) has been withdrawn in view of Applicant’s amendments to the claims filed on 10/14/2025.
The previous rejection of claims 49-51 and 58 under 35 U.S.C. 112(b) has been maintained and rewritten in view of Applicant’s amendments to the claims filed on 10/14/2025.
Applicants’ arguments have been considered but have not been found persuasive. Applicant argues that the amendments to claims 48, 49, 51 and 58 in the listing of claims are sufficient to address the issues noted by the office and render the claims sufficiently definite.
Applicant’s arguments are not found persuasive because, as stated above, claims 48, 56 and 66 recite limitations that show a lack of antecedent basis on that the amino acid sequence is not specified within the instant claims to be able to determine the deletion of positions 1 to 84 of the human uracil DNA glycosidase. Therefore, the claims are not in compliance with 35 U.S.C. 112 (b) for a lack of antecedent basis.
Claim Rejections - 35 USC § 102
In the event the determination of the status of the application as subject to AIA 35 U.S.C. 102 and 103 (or as subject to pre-AIA 35 U.S.C. 102 and 103) is incorrect, any correction of the statutory basis (i.e., changing from AIA to pre-AIA ) for the rejection will not be considered a new ground of rejection if the prior art relied upon, and the rationale supporting the rejection, would be the same under either status.
The following is a quotation of the appropriate paragraphs of 35 U.S.C. 102 that form the basis for the rejections under this section made in this Office action:
A person shall be entitled to a patent unless –
(a)(1) the claimed invention was patented, described in a printed publication, or in public use, on sale, or otherwise available to the public before the effective filing date of the claimed invention.
(a)(2) the claimed invention was described in a patent issued under section 151, or in an application for patent published or deemed published under section 122(b), in which the patent or application, as the case may be, names another inventor and was effectively filed before the effective filing date of the claimed invention.
Claim 58 is rejected under 35 U.S.C. 102(a)(1) as being anticipated by Liu et al (WO 2018/165629 A1). This rejection was made in the Office action mailed 07/11/2025 and has been rewritten to address the amendment to the claims in the reply filed 10/14/2025.
For the purposes of this rejection, claim 58 is interpreted as being drawn to a product comprising cytosine deaminase APOBEC, nCas9 nuclease and uracil DNA glycosidase. See the above rejection under 35 U.S.C. 112(b) or 35 U.S.C. 112 (pre-AIA ), second paragraph.
Regarding claim 58, Liu (‘629) teaches a system to contact a target region of a nucleic acid (e.g., a double- stranded DNA sequence) with a complex comprising a base editor (e.g., a Cas9 domain fused to a cytidine deaminase and a uracil binding protein) and a guide nucleic acid (e.g., RNA), wherein the target region comprises a targeted nucleobase pair, inducing strand separation of said target region, converting a first nucleobase of said target nucleobase pair in a single strand of the target region to a second nucleobase, excising the second nucleobase, thereby creating an abasic site, and replacing a third nucleobase complementary to the first nucleobase base with a fourth nucleobase that is a cytosine (C) [00253]. Liu teaches a C to G base editor includes a fusion protein containing a nucleic acid programmable DNA binding protein (e.g., a Cas9 domain), an uracil DNA glycosylase (UDG) domain, and a cytidine deaminase [0003]. Liu teaches expressed UDG and UdgX variants fused to APOBEC-Cas9 nickase and simultaneously overexpressed TLS polymerases in trans lead to C to G editing at the RNF2 site [00284]. Liu teaches the cytosine deaminase is a APOBEC1 [00176]. Liu teaches the Cas9 nickase comprises a DI0A mutation [0064] where the wildtype sequence is 100% identical to accession number: Q99ZW2.1 presented in the instant claim with the required mutation at the 10 amino acid position substituting aspartic acid (D) for alanine (A). Liu teaches a base editing fusion protein is capable of binding to a specific nucleic acid sequence (e.g., via the Cas9 domain), deaminating a cytosine within the nucleic acid sequence to a uridine, which can then be excised from the nucleic acid molecule by UDG and then replaced with another base [0003]. Liu teaches the C to G base editor system at the HEK2 site in WT Hapl cells [00274]. Liu teaches the fusion of various polymerases should lead to repair of the opposite strand based on polymerase preference for repair opposite an abasic sites leading to increased C to G base editing [00278].
Response to Arguments - Claim Rejections - 35 USC § 102
The previous rejection of claim 58 under 35 U.S.C. 102(a)(1) over Liu et al (WO 2018/165629 A1) has been maintained and rewritten to address Applicant’s amendments to the claims filed on 10/14/2025.
Applicant's arguments filed 10/14/2025 have been fully considered but they are not persuasive. Applicant argues that Liu’s examples UDG (or UDG variants such as udgx) were expressed alone or co-transfected with an editor but where never fused with APOBEC and nCas9 to form a single protein. Applicant contends, therefore, that Liu does not teach or suggest to one of ordinary skill in the art either the structure of the recited APOBEC- nCas9-UDG fusion within a single open reading frame (ORF) or the product formed by "co-introducing the genes encoding the three together with sgRNA into mammalian cells" to achieve C--G mutations.
Applicant contends that Liu does not disclose each and every element arranged as set forth in the pending claim and that Liu cannot, therefore, anticipate claim 58.
Applicant requests, therefore, that this rejection be reconsidered and withdrawn accordingly.
However, Applicant’s arguments are not found to be persuasive because claim 58 does not require the fusion of the UDG to the APOBEC and nCas9 as a fusion protein of all three components. Claim 58 recites “A product comprising: any of the following products described in cl)-c2): c1) a product for improving a base editing efficiency of mutating a target base C to G in a genome sequence, including a base editing system for mutating C to G; c2) a product for realizing a site-directed mutation from base C to base G in a genome sequence in eukaryotes, including a base editing system for mutating C to G; and wherein the base editing system for mutating C to G is a base editing for mutating C to G wherein the base editing system comprises cytosine deaminase APOBEC, nCas9 nuclease and Uracil DNA glycosidase, which including introducing a coding gene of cytosine deaminase APOBEC, a coding gene of nCas9 nuclease, a coding gene of uracil DNA glycosidase and a coding sequence of sgRNA into receptor organism or the cells of a receptor organism, so that the coding gene of cytosine deaminase, the coding gene of nCas9 nuclease, the coding gene of uracil DNA glycosidase and the coding sequence of sgRNA are all expressed to mutate a target base C to G; wherein, the receptor organism is a mammal and the cells of the receptor organism are mammalian cells; and the nCas9 nuclease is a Cas9 mutant nCas9-D10A with an amino acid sequence obtained by mutating aspartic acid (D) to alanine (A) at a site 10 from the N-terminal of an amino acid sequence of the Cas9 nuclease of Accession: Q99ZW2.1.” Therefore, the teachings of Liu anticipate claim 58 as it currently stands.
Claim Rejections - 35 USC § 103
In the event the determination of the status of the application as subject to AIA 35 U.S.C. 102 and 103 (or as subject to pre-AIA 35 U.S.C. 102 and 103) is incorrect, any correction of the statutory basis (i.e., changing from AIA to pre-AIA ) for the rejection will not be considered a new ground of rejection if the prior art relied upon, and the rationale supporting the rejection, would be the same under either status.
The following is a quotation of 35 U.S.C. 103 which forms the basis for all obviousness rejections set forth in this Office action:
A patent for a claimed invention may not be obtained, notwithstanding that the claimed invention is not identically disclosed as set forth in section 102, if the differences between the claimed invention and the prior art are such that the claimed invention as a whole would have been obvious before the effective filing date of the claimed invention to a person having ordinary skill in the art to which the claimed invention pertains. Patentability shall not be negated by the manner in which the invention was made.
The factual inquiries for establishing a background for determining obviousness under 35 U.S.C. 103 are summarized as follows:
1. Determining the scope and contents of the prior art.
2. Ascertaining the differences between the prior art and the claims at issue.
3. Resolving the level of ordinary skill in the pertinent art.
4. Considering objective evidence present in the application indicating obviousness or nonobviousness.
Claims 47-49, 55, 56, 63 and 68 are rejected under 35 U.S.C. 103 as being unpatentable by Liu et al (WO 2018/165629 A1) in view of Koblan et al (Nature Biotechnology, Vol. 36, No. 9, Pgs. 843-846; May 29, 2018). This rejection was made in the Office action mailed 07/11/2025 and has been rewritten to address the amendment to the claims in the reply filed 10/14/2025.
Regarding claims 47, 49, 63 and 68, Liu teaches methods of modifying a polynucleotide (e.g., DNA), for example, generating a cytosine to guanine mutation in a polynucleotide [0002]. Liu teaches the method comprises the steps of: a) contacting a target region of a nucleic acid (e.g., a double-stranded DNA sequence) with a complex comprising a base editor (e.g., a Cas9 domain fused to a cytidine deaminase and a uracil binding protein) and a guide nucleic acid (e.g., gRNA), wherein the target region comprises a targeted nucleobase pair, b) inducing strand separation of said target region, c) converting a first nucleobase of said target nucleobase pair in a single strand of the target region to a second nucleobase, d) excising the second nucleobase, thereby creating an abasic site, and e) replacing a third nucleobase complementary to the first nucleobase base with a fourth nucleobase that is a cytosine (C) [00253]. Liu teaches a nucleic acid molecule encoding the fusion proteins, comprising: (1) a nucleic acid programmable DNA binding protein (napDNAbp), and (it) a cytidine deaminase domain, and (iii) a uracil binding protein (UBP) and a gRNA, and/or any of the vectors [00269 and Claim 1]. Liu teaches a C to G base editor includes a fusion protein containing a nucleic acid programmable DNA binding protein (e.g., a Cas9 domain), an uracil DNA glycosylase (UDG) domain, and a cytidine deaminase [0003]. Liu teaches expressed UDG and UdgX variants fused to APOBEC-Cas9 nickase and simultaneously overexpressed TLS polymerases in trans lead to C to G editing at the RNEF2 site [00284]. Liu teaches the cytosine deaminase is a APOBEC1 [00176]. Liu teaches the Cas9 nickase comprises a D10A mutation [0064] where the wildtype sequence is 100% identical to accession number: Q99ZW2.1 presented in the instant claim with the required mutation at the 10 amino acid position substituting aspartic acid (D) for alanine (A). Liu teaches a base editing fusion protein is capable of binding to a specific nucleic acid sequence (e.g., via the Cas9 domain), deaminating a cytosine within the nucleic acid sequence to a uridine, which can then be excised from the nucleic acid molecule by UDG and then replaced with another base [0003]. Liu teaches the target sequence is a sequence in the genome of a mammal [00239]. Liu teaches the fusion of various polymerases should lead to repair of the opposite strand based on polymerase preference for repair opposite an abasic sites leading to increased C to G base editing [00278].
Liu does not teach introducing a coding gene of cytosine deaminase AID, a coding gene of nCas9 nuclease, a coding gene of uracil DNA glycosidase and a coding sequence of ssRNA into a receptor organism or the cells of a receptor organism wherein the coding gene of the cytosine deaminase APOBEC, the coding gene of the nCas9 nuclease, and the coding gene of the uracil DNA glycosidase are introduced into the receptor organism or the cells of the receptor organism through a recombinant plasmid C.
Koblan teaches plasmids encoding base editors that enable single-nucleotide conversions in genomic DNA of mammalian cells (e.g., Abstract). Koblan teaches a plasmid encoding a cyticine base editor, BE4, comprising APOBEC deaminase and Cas9n as a fusion protein (e.g., page 843, left column; page 843, paragraph bridging columns; Fig. 1A). Koblan teaches a plasmid encoding sgRNA (e.g., page 843, paragraph bridging columns). Koblan teaches a method of editing comprising introducing the plasmids into mammalian cells for expression of the fusion protein and sgRNA (e.g., page 843, paragraph bridging columns). Koblan teaches that transfection of cells with the plasmid was not limiting editing efficiency (e.g., page 843, right column, 1st full paragraph).
It would have been obvious to one of ordinary skill in the art before the effective filing date of the claimed invention to modify the method of base editing of Liu (‘629) to include introducing a coding gene of APOBEC1, a coding gene of nCas9 nuclease, a coding gene of uracil DNA glycosidase and a coding sequence of sgRNA into mammalian cells through a recombinant plasmid "C" as taught by Koblan, where the coding genes are introduced in plasmid vectors, because Liu (629) teaches it is within the ordinary skill in the art to provide polynucleotides and vectors encoding the fusion proteins (e.g., paragraph [00268]) and Koblan teaches that it is within the skill of the art to deliver a base editing fusion protein comprising APOBEC1 and Cas9n to mammalian cells by delivering plamsid vector comprising polynucleotides encoding the fusion protein and sgRNA to the cells. One would have had a reasonable expectation of success in providing the components of the system of Liu ('629) to the mammalian cell as plamsid capable of expressing the components due to the similar nature of the components used by Koblan.
One would have been motivated to make such a modification in order to receive the expected benefit of delivery of a nucleobase editor to a mammalian cell in a manner that is not limiting to the efficiency of base editing as taught by Koblan.
Regarding claims 48 and 56, Liu teaches the cytosine deaminase is an APOBEC1 [00176].
Regarding claim 55, Liu teaches methods of modifying a polynucleotide (e.g., DNA), for example, generating a cytosine to guanine mutation in a polynucleotide [0002]. Liu teaches the method comprises the steps of: a) contacting a target region of a nucleic acid (e.g., a double-stranded DNA sequence) with a complex comprising a base editor (e.g., a Cas9 domain fused to a cytidine deaminase and a uracil binding protein) and a guide nucleic acid (e.g., gRNA), wherein the target region comprises a targeted nucleobase pair, b) inducing strand separation of said target region, c) converting a first nucleobase of said target nucleobase pair in a single strand of the target region to a second nucleobase, d) excising the second nucleobase, thereby creating an abasic site, and e) replacing a third nucleobase complementary to the first nucleobase base with a fourth nucleobase that is a cytosine (C) [00253]. Liu teaches a nucleic acid molecule encoding the fusion proteins, comprising: (1) a nucleic acid programmable DNA binding protein (napDNAbp), and (it) a cytidine deaminase domain, and (iii) a uracil binding protein (UBP) and a gRNA, and/or any of the vectors [00269 and Claim 1]. Liu teaches a C to G base editor includes a fusion protein containing a nucleic acid programmable DNA binding protein (e.g., a Cas9 domain), an uracil DNA glycosylase (UDG) domain, and a cytidine deaminase [0003]. Liu teaches expressed UDG and UdgX variants fused to APOBEC-Cas9 nickase and simultaneously overexpressed TLS polymerases in trans lead to C to G editing at the RNEF2 site [00284]. Liu teaches the cytosine deaminase is a APOBEC1 [00176]. Liu teaches the Cas9 nickase comprises a D10A mutation [0064] where the wildtype sequence is 100% identical to accession number: Q99ZW2.1 presented in the instant claim with the required mutation at the 10 amino acid position substituting aspartic acid (D) for alanine (A). Liu teaches a base editing fusion protein is capable of binding to a specific nucleic acid sequence (e.g., via the Cas9 domain), deaminating a cytosine within the nucleic acid sequence to a uridine, which can then be excised from the nucleic acid molecule by UDG and then replaced with another base [0003]. Liu teaches the target sequence is a sequence in the genome of a mammal [00239]. Liu teaches the fusion of various polymerases should lead to repair of the opposite strand based on polymerase preference for repair opposite an abasic sites leading to increased C to G base editing [00278].
Claims 59, 61 and 65 are rejected under 35 U.S.C. 103 as being unpatentable by Liu et al (WO 2018/165629 A1) in view of Koblan et al (Nature Biotechnology, Vol. 36, No. 9, Pgs. 843-846; May 29, 2018) as applied to claims 47-49, 55, 56, 63 and 68 above, and further in view of Genbank Accession number AAH03792.1 (APOBEC1 Protein Mus musculus; Publicly available August of 2008, Pgs. ½-2/2). This is a NEW rejection necessitated by the amendments to the claims in the reply filed 10/14/2025.
Regarding claims 59, 61 and 65, Liu teaches a C to G base editor includes a fusion protein containing a nucleic acid programmable DNA binding protein (e.g., a Cas9 domain), an uracil DNA glycosylase (UDG) domain, and a cytidine deaminase [0003]. Liu teaches expressed UDG and UdgX variants fused to APOBEC-Cas9 nickase and simultaneously overexpressed TLS polymerases in trans lead to C to G editing at the RNEF2 site [00284]. Liu teaches the cytosine deaminase is a APOBEC1 derived from mouse [00176 and 00205]. Liu teaches the Cas9 nickase comprises a D10A mutation [0064] where the wildtype sequence is 100% identical to accession number: Q99ZW2.1 presented in the instant claim with the required mutation at the 10 amino acid position substituting aspartic acid (D) for alanine (A). Liu teaches a base editing fusion protein is capable of binding to a specific nucleic acid sequence (e.g., via the Cas9 domain), deaminating a cytosine within the nucleic acid sequence to a uridine, which can then be excised from the nucleic acid molecule by UDG and then replaced with another base [0003]. Liu teaches the target sequence is a sequence in the genome of a mammal [00239]. Liu teaches the fusion of various polymerases should lead to repair of the opposite strand based on polymerase preference for repair opposite an abasic sites leading to increased C to G base editing [00278].
Liu does not teach the specific APOBEC1 protein as outlined in Genbank Accession number AAH03792.1. However, it would have been obvious to one of ordinary skill in the art before the effective filing date of the claimed invention to substitute the APOBEC1 protein sequence derived from Mus musculus of Liu to include the APOBEC1 protein also derived from Mus musculus identified as GenBank Accession Number AAH03792.1 and publicly available as of August of 2008 because Liu teaches it is within the ordinary skill in the art to use a fusion protein containing a nucleic acid programmable DNA binding protein (e.g., a Cas9 domain), an uracil DNA glycosylase (UDG) domain, and a cytidine deaminase for delivery to a cell and Genbank Accession number AAH03792.1 is a known APOBEC1 protein derived from Mus musculus and known publicly as of August of 2008.
Thus, substitution of the APOBEC1 protein of Liu, for the APOBEC1 protein known in the art as of August of 2008 would have been prima facie obvious to one of ordinary skill in the art, and thus the invention as claimed is unpatentable over the work of the prior art. Substitution of one known product for another known product, the methods having equivalent effect, is considered to be obvious, absent a showing that the result of the substitution yields more than predictable results. See MPEP 2143(I)(B).
Claims 60, 62 and 67 are rejected under 35 U.S.C. 103 as being unpatentable by Liu et al (WO 2018/165629 A1) in view of Koblan et al (Nature Biotechnology, Vol. 36, No. 9, Pgs. 843-846; May 29, 2018) as applied to claims 47-49, 55, 56, 63 and 68 above, and further in view of NCBI Accession number CAG46474.1 (UNG – Uracil DNA Glycosidase [Homo sapiens]; Publicly available June of 2004, Pgs. ½-2/2). This is a NEW rejection necessitated by the amendments to the claims in the reply filed 10/14/2025.
Regarding claims 60, 62 and 67, Liu teaches a C to G base editor includes a fusion protein containing a nucleic acid programmable DNA binding protein (e.g., a Cas9 domain), an uracil DNA glycosylase (UDG) domain, and a cytidine deaminase [0003]. Liu teaches expressed UDG and UdgX variants fused to APOBEC-Cas9 nickase and simultaneously overexpressed TLS polymerases in trans lead to C to G editing at the RNEF2 site [00284]. Liu teaches the cytosine deaminase is a APOBEC1 derived from mouse [00176 and 00205]. Liu teaches the Cas9 nickase comprises a D10A mutation [0064] where the wildtype sequence is 100% identical to accession number: Q99ZW2.1 presented in the instant claim with the required mutation at the 10 amino acid position substituting aspartic acid (D) for alanine (A). Liu teaches a base editing fusion protein is capable of binding to a specific nucleic acid sequence (e.g., via the Cas9 domain), deaminating a cytosine within the nucleic acid sequence to a uridine, which can then be excised from the nucleic acid molecule by UDG and then replaced with another base [0003]. Liu teaches the target sequence is a sequence in the genome of a mammal [00239]. Liu teaches the fusion of various polymerases should lead to repair of the opposite strand based on polymerase preference for repair opposite an abasic sites leading to increased C to G base editing [00278].
Liu does not teach the specific APOBEC1 protein as outlined in Genbank Accession number CAG46474.1. However, it would have been obvious to one of ordinary skill in the art before the effective filing date of the claimed invention to substitute the UNG protein sequence derived from Homo sapiens of Liu to include the UNG protein also derived from Homo sapiens identified as GenBank Accession Number CAG46474.1 and publicly available as of June of 2004 because Liu teaches it is within the ordinary skill in the art to use a fusion protein containing a nucleic acid programmable DNA binding protein (e.g., a Cas9 domain), an uracil DNA glycosylase (UDG) domain, and a cytidine deaminase for delivery to a cell and Genbank Accession number CAG46474.1 is a known UNG protein derived from Homo sapiens and known publicly as of June of 2004.
Thus, substitution of the UNG protein of Liu, for the UNG protein known in the art as of June of 2004 would have been prima facie obvious to one of ordinary skill in the art, and thus the invention as claimed is unpatentable over the work of the prior art. Substitution of one known product for another known product, the methods having equivalent effect, is considered to be obvious, absent a showing that the result of the substitution yields more than predictable results. See MPEP 2143(I)(B).
Response to Arguments - Claim Rejections - 35 USC § 103
The previous rejection of claims 51 and 57 under 35 U.S.C. 103 as being unpatentable by Liu et al (WO 2018/165629 A1) in view of Koblan et al (Nature Biotechnology, Vol. 36, No. 9, Pgs. 843-846; May 29, 2018) has been moot in view of Applicant’s cancellation of the claims filed on 10/14/2025.
The previous rejection of claims 47-49 and 55-56 under 35 U.S.C. 103 as being unpatentable by Liu et al (WO 2018/165629 A1) in view of Koblan et al (Nature Biotechnology, Vol. 36, No. 9, Pgs. 843-846; May 29, 2018) has been maintained and rewritten in view of Applicant’s amendments filed on 10/14/2025.
Applicant's arguments filed 10/14/2025 have been fully considered but they are not persuasive. Applicant provides a table for the comparison and contrast of Liu, Koban and the instant invention.
Applicant argues that the core editing features differ between the two sources from the instant invention such as the instant invention shows efficient and high-purity C-to-G editing whereas Liu is the “first public C-to-G editing” and Koblan shows “only optimize the efficiency of the C-to-T and A-to-G (transition mutation) editors”.
Applicant argues that the current invention differs in the technical pathway and mechanism from Liu in that Liu teaches the UDG is used to excise U bases, but relies on exogenous overexpression of translesion polymerase (TLS) to guide repair toward C-to-G, making the system complex and Koblan shows the “UGI (inhibitor) is used to inhibit UDG activity, preventing U from being removed, thereby achieving C-to-T. Its pathway is to inhibit repair” whereas the instant invention does not use an exogenous TLS polymerase.
This argument is not found persuasive. The claims do not exclude the presence of a TLS. Further, Applicant provides no experimental data proving the absence of the TLS element provided unexpected and improved results in comparison to the closest prior art in which the TLS element was used.
Applicant argues the editor construction differs in that Liu shows “the concept of a fusion protein (deaminase + nCas9 +UDG) is taught, but not specific implementation may involve separate or additional components. Repair must be driven by a nick on the antisense strand” and Koblan shows the “focus on optimizing the expression levels of dual-component editors (deaminase +nCas9+UGI) such as BE4max” whereas the instant invention only requires a single triple fusion protein (deaminase +nCas9+UDG) integrates all functions into a single protein, ensuring high synergy using a specific UDG variant (human UNGΔ84) is used to optimize nuclear function.
In response to applicant's arguments against the references individually, one cannot show nonobviousness by attacking references individually where the rejections are based on combinations of references. See In re Keller, 642 F.2d 413, 208 USPQ 871 (CCPA 1981); In re Merck & Co., 800 F.2d 1091, 231 USPQ 375 (Fed. Cir. 1986). In response to applicant's argument that the instant invention only requires a single triple fusion protein (deaminase +nCas9+UDG), the fact that the inventor has recognized another advantage which would flow naturally from following the suggestion of the prior art cannot be the basis for patentability when the differences would otherwise be obvious. See Ex parte Obiaya, 227 USPQ 58, 60 (Bd. Pat. App. & Inter. 1985).
Applicant argues the editing efficiency differs in that Liu shows “C-to-G efficiency is limited, and significant effects are heavily dependent on the assistance of exogenous TLS polymerase. Data demonstrating near-complete editing have not been disclosed” and Koblan shows the “optimized known C-to-T editing efficiency from ~50% to ~90%, but limited to C-to-T editing” whereas the instant invention editing efficiency shows achieving >95% C-to-G editing efficiency without the need for exogenous polymerase (a significant progress over Liu’s protocol). Applicant continues to argue that one would not have been able to predictably apply Koblan’s vector strategy.
Applicant does not provide any experimental data or analysis to prove unexpected and improved results. Applicant cannot broadly claim unexpected and improved results but instead must provide a comparison with the closest prior art as well as the unexpected and improved results of the present invention. An affidavit or declaration under 37 CFR 1.132 must compare the claimed subject matter with the closest prior art to be effective to rebut a prima facie case of obviousness. In re Burckel, 592 F.2d 1175, 201 USPQ 67 (CCPA 1979). See MPEP §716.02(e).
Applicant argues the edit purity/byproducts differs in that Liu shows “due to the involvement of double-stranded repair and the possible introduction of exogenous polymerase, a higher proportion of insertion/deletion (indels) and other byproducts may be generated” and Koblan shows that “after optimization, the purity of C-to-T was improved, but the purity of C-to-G was not affected” whereas the instant invention shows the editing products were extremely pure with almost no unintended indels or other base substitution byproducts.
Applicant does not provide any experimental data or analysis to prove unexpected and improved results. Applicant cannot broadly claim unexpected and improved results but instead must provide a comparison with the closest prior art as well as the unexpected and improved results of the present invention. An affidavit or declaration under 37 CFR 1.132 must compare the claimed subject matter with the closest prior art to be effective to rebut a prima facie case of obviousness. In re Burckel, 592 F.2d 1175, 201 USPQ 67 (CCPA 1979). See MPEP §716.02(e).
Applicant argues the system combination concept differs in that Liu and Koblan do not show the system combination concept whereas the instant invention shows purposes of a combinatorial toolbox: combining C-to-A and C-to-G system with existing C-to-T and A-to-G systems to theoretically achieve any-to-any base conversion, provides mathematical calculations and preliminary experimental evidence.
In response to applicant's argument that the references fail to show certain features of the invention, it is noted that the features upon which applicant relies (i.e., a combinatorial toolbox: combining C-to-A and C-to-G system with existing C-to-T and A-to-G systems to theoretically achieve any-to-any base conversion) are not recited in the rejected claim(s). Although the claims are interpreted in light of the specification, limitations from the specification are not read into the claims. See In re Van Geuns, 988 F.2d 1181, 26 USPQ2d 1057 (Fed. Cir. 1993).
In response to applicant’s argument that the system combination concept differs of Liu and Koblan from the instant invention, the test for obviousness is not whether the features of a secondary reference may be bodily incorporated into the structure of the primary reference; nor is it that the claimed invention must be expressly suggested in any one or all of the references. Rather, the test is what the combined teachings of the references would have suggested to those of ordinary skill in the art. See In re Keller, 642 F.2d 413, 208 USPQ 871 (CCPA 1981).
Conclusion
Applicant's amendment necessitated the new ground(s) of rejection presented in this Office action. Accordingly, THIS ACTION IS MADE FINAL. See MPEP § 706.07(a). Applicant is reminded of the extension of time policy as set forth in 37 CFR 1.136(a).
A shortened statutory period for reply to this final action is set to expire THREE MONTHS from the mailing date of this action. In the event a first reply is filed within TWO MONTHS of the mailing date of this final action and the advisory action is not mailed until after the end of the THREE-MONTH shortened statutory period, then the shortened statutory period will expire on the date the advisory action is mailed, and any nonprovisional extension fee (37 CFR 1.17(a)) pursuant to 37 CFR 1.136(a) will be calculated from the mailing date of the advisory action. In no event, however, will the statutory period for reply expire later than SIX MONTHS from the mailing date of this final action.
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/ALEXANDRA ROSE LIPPOLIS/Examiner, Art Unit 1637
/Jennifer Dunston/Supervisory Patent Examiner, Art Unit 1637
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