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 amendment of claims 68, 77 and the addition of new claims 95-101, in the paper of 3/6/2026, is acknowledged. Claims 68-77, 80-82, 95-101 are still at issue and are present for examination.
Election/Restriction
Applicant’s election with traverse of the claims of Group I, claims 68-73, 75, 76, 95-101, drawn to an altered cytidine deaminase, in the paper of 3/6/3026 is acknowledged.
Applicants traverse the restriction requirement on the basis that groups I, II and III could be readily evaluated in one search without placing an undue burden on the examiner as all claims are so interrelated that a search of the claims of Group I will reveal art on the others. Applicants traversal of the restriction requirement is acknowledged, however, not found persuasive on the basis that while the search and examination of the different Groups I, II and III may overlap, they are not co-extensive. Thus the additional consideration and search would result in a burden on the examiner. The requirement is still deemed proper and is therefore made FINAL.
Applicants reference to the rejoinder of Group III is acknowledged and such will be considered at the time of identification of allowable subject matter.
Claims 74, 77, 80-82 are withdrawn from further consideration by the examiner, 37 CFR 1.142(b), as being drawn to a non-elected invention.
Information Disclosure Statement
The listing of references in the specification is not a proper information disclosure statement. 37 CFR 1.98(b) requires a list of all patents, publications, or other information submitted for consideration by the Office, and MPEP § 609 A(1) states, "the list may not be incorporated into the specification but must be submitted in a separate paper."
The information disclosure statements filed on 3/7/2025, are acknowledged. Those references considered have been indicated as such.
Specification
The disclosure is objected to because of the following informalities:
The use of the terms: Tween (page 90, line 22; page 91, line 27, page 92, line 22, page 93, line 15 and additional pages/lines), BLAST (paragraph [0087]) which is a trade name or a mark used in commerce, has been noted in this application. The term should be accompanied by the generic terminology; furthermore the term should be capitalized wherever it appears or, where appropriate, include a proper symbol indicating use in commerce such as ™, SM , or ® following the term.
Although the use of trade names and marks used in commerce (i.e., trademarks, service marks, certification marks, and collective marks) are permissible in patent applications, the proprietary nature of the marks should be respected and every effort made to prevent their use in any manner which might adversely affect their validity as commercial marks.
This application contains sequence disclosures that are encompassed by the definitions for nucleotide and/or amino acid sequences set forth in 37 CFR 1.821(a)(1) and (a)(2). However, this application fails to comply with the requirements of 37 CFR 1.821 through 1.825 for the reason(s) set forth: The following portions of the specification list sequences which appear to meet the definition for an nucleic acid sequence, but do not have an associated SEQ ID No: Figures 1D, 1E, 1F and 29.
Further applicants are advised that when an amino acid sequence or nucleic acid sequence appear in a figure that an associated sequence identifier must also appear in the figure itself or in the description of the figure.
Appropriate correction is required.
Claim Rejections - 35 USC § 112
The following is a quotation of the first paragraph of 35 U.S.C. 112(a):
(a) IN GENERAL.—The specification shall contain a written description of the invention, and of the manner and process of making and using it, in such full, clear, concise, and exact terms as to enable any person skilled in the art to which it pertains, or with which it is most nearly connected, to make and use the same, and shall set forth the best mode contemplated by the inventor or joint inventor of carrying out the invention.
The following is a quotation of the first paragraph of pre-AIA 35 U.S.C. 112:
The specification shall contain a written description of the invention, and of the manner and process of making and using it, in such full, clear, concise, and exact terms as to enable any person skilled in the art to which it pertains, or with which it is most nearly connected, to make and use the same, and shall set forth the best mode contemplated by the inventor of carrying out his invention.
Claim(s) 68-73, 75, 76 and 95-101 are rejected under 35 U.S.C. 112(a) or 35 U.S.C. 112 (pre-AIA ), first paragraph, as failing to comply with the written description requirement. The claim(s) contains subject matter which was not described in the specification in such a way as to reasonably convey to one skilled in the relevant art that the inventor or a joint inventor, or for pre-AIA the inventor(s), at the time the application was filed, had possession of the claimed invention.
Claim(s) 68-73, 75, 76 and 95-101 are directed to all possible altered cytidine deaminases comprising amino acid substitution mutations at positions functionally equivalent to Tyr130 and Tyr132 in a reference APOBEC3A of SEQ ID NO:3, wherein the altered cytidine deaminase comprises an activity of converting 5-methyl cytosine (5mC) to thymidine (T) by deamination at a greater rate than conversion of cytosine (C) to uracil (U) by deamination, and wherein the substitution mutation at the position functionally equivalent to Tyr132 comprises a mutation to His, Arg, Gln, or Lys. The specification, however, only provides the representative species of that altered cytidine deaminase comprising amino acid substitution mutations at positions Tyr130 and Tyr132 in a reference APOBEC3A of SEQ ID NO:3, wherein the altered cytidine deaminase comprises an activity of converting 5-methyl cytosine (5mC) to thymidine (T) by deamination at a greater rate than conversion of cytosine (C) to uracil (U) by deamination, and wherein the substitution mutation at the position functionally equivalent to Tyr132 comprises a mutation to His, Arg, Gln, or Lys, encompassed by these claims. There is no disclosure of any particular structure to function/activity relationship in the disclosed species. The specification also fails to describe additional representative species of these cytidine deaminases by any identifying structural characteristics or properties, for which no predictability of structure and function is apparent.
Regarding the level of skill and knowledge in the art of amino acid mutation, the reference of Singh et al. (Curr. Protein Pept. Sci. 18:1-11, 2017; cited on the attached Form PTO-892) reviews various protein engineering methods and discloses that despite the availability of an ever-growing database of protein structures and highly sophisticated computational algorithms, protein engineering is still limited by the incomplete understanding of protein functions, folding, flexibility, and conformational changes (see p. 7, column 1, top). Also, the unpredictability associated with amino acid mutations is exemplified by the reference of Zhang et al. (Structure 26:1474-1485, 2018; cited on the attached Form PTO-892), which discloses that even a mutation of a surface residue that was predicted to be benign caused significant structural changes and unexpected effects on the function of a polypeptide (p. 1475, column 1). Given this lack of additional representative species as encompassed by the claims, Applicants have failed to sufficiently describe the claimed invention, in such full, clear, concise, and exact terms that a skilled artisan would recognize Applicants were in possession of the claimed invention.
Applicant is referred to the revised guidelines concerning compliance with the written description requirement of U.S.C. 112, first paragraph, published in the Official Gazette and also available at www.uspto.gov.
Claim(s) 68-73, 75, 76 and 95-101 are rejected under 35 U.S.C. 112, first paragraph, because the specification, while being enabling for that altered cytidine deaminase comprising amino acid substitution mutations at positions Tyr130 and Tyr132 in a APOBEC3A of SEQ ID NO:3, wherein the altered cytidine deaminase comprises an activity of converting 5-methyl cytosine (5mC) to thymidine (T) by deamination at a greater rate than conversion of cytosine (C) to uracil (U) by deamination, and wherein the substitution mutation at the position functionally equivalent to Tyr132 comprises a mutation to His, Arg, Gln, or Lys, does not reasonably provide enablement for all possible altered cytidine deaminase comprising amino acid substitution mutations at positions functionally equivalent to Tyr130 and Tyr132 in a reference APOBEC3A of SEQ ID NO:3, wherein the altered cytidine deaminase comprises an activity of converting 5-methyl cytosine (5mC) to thymidine (T) by deamination at a greater rate than conversion of cytosine (C) to uracil (U) by deamination, and wherein the substitution mutation at the position functionally equivalent to Tyr132 comprises a mutation to His, Arg, Gln, or Lys. The specification does not enable any person skilled in the art to which it pertains, or with which it is most nearly connected, to make and use the invention commensurate in scope with these claims.
Factors to be considered in determining whether undue experimentation is required, are summarized in In re Wands (858 F.2d 731, 8 USPQ 2nd 1400 (Fed. Cir. 1988)) as follows: (1) the quantity of experimentation necessary, (2) the amount of direction or guidance presented, (3) the presence or absence of working examples, (4) the nature of the invention, (5) the state of the prior art, (6) the relative skill of those in the art, (7) the predictability or unpredictability of the art, and (8) the breadth of the claim(s).
Claim(s) 1-20 are so broad as to encompass all possible altered cytidine deaminase comprising amino acid substitution mutations at positions functionally equivalent to Tyr130 and Tyr132 in a reference APOBEC3A of SEQ ID NO:3, wherein the altered cytidine deaminase comprises an activity of converting 5-methyl cytosine (5mC) to thymidine (T) by deamination at a greater rate than conversion of cytosine (C) to uracil (U) by deamination, and wherein the substitution mutation at the position functionally equivalent to Tyr132 comprises a mutation to His, Arg, Gln, or Lys. The scope of the claims is not commensurate with the enablement provided by the disclosure with regard to the extremely large number of altered cytidine deaminases and variants broadly encompassed by the claims. The claims rejected under this section of U.S.C. 112, first paragraph, place minimal structural limits if any on the altered cytidine deaminase encompassed by the claims. Since the amino acid sequence of a protein determines its structural and functional properties, predictability of which changes can be tolerated in a protein's amino acid sequence and obtain the desired activity requires a knowledge of and guidance with regard to which amino acids in the protein's sequence, if any, are tolerant of modification and which are conserved (i.e. expectedly intolerant to modification), and detailed knowledge of the ways in which the proteins' structure relates to its function. However, in this case the disclosure is limited to that altered cytidine deaminase comprising amino acid substitution mutations at positions Tyr130 and Tyr132 in a APOBEC3A of SEQ ID NO:3, wherein the altered cytidine deaminase comprises an activity of converting 5-methyl cytosine (5mC) to thymidine (T) by deamination at a greater rate than conversion of cytosine (C) to uracil (U) by deamination, and wherein the substitution mutation at the position functionally equivalent to Tyr132 comprises a mutation to His, Arg, Gln, or Lys.
While recombinant and mutagenesis techniques are known, it is not routine in the art to screen for multiple substitutions or multiple modifications, as encompassed by the instant claims, and the positions within a protein's sequence where amino acid modifications can be made with a reasonable expectation of success in obtaining the desired activity/utility are limited in any protein and the result of such modifications is unpredictable. In addition, one skilled in the art would expect any tolerance to modification for a given protein to diminish with each further and additional modification, e.g. multiple substitutions.
The specification does not support the broad scope of the claims which encompass any possible altered cytidine deaminase comprising amino acid substitution mutations at positions functionally equivalent to Tyr130 and Tyr132 in a reference APOBEC3A of SEQ ID NO:3, wherein the altered cytidine deaminase comprises an activity of converting 5-methyl cytosine (5mC) to thymidine (T) by deamination at a greater rate than conversion of cytosine (C) to uracil (U) by deamination, and wherein the substitution mutation at the position functionally equivalent to Tyr132 comprises a mutation to His, Arg, Gln, or Lys, because the specification does not establish: (A) regions of the encompassed cytidine deaminases which may be modified effecting the cytidine deaminase activity; (B) the general tolerance of cytidine deaminases to modification and extent of such tolerance; (C) a rational and predictable scheme for modifying any amino acid residue of an cytidine deaminase with an expectation of obtaining the desired biological function; and (D) the specification provides insufficient guidance as to which of the essentially infinite possible choices is likely to be successful. Because of this lack of guidance, the extended experimentation that would be required to determine which substitutions would be acceptable to retain the required lipase activities and the fact that the relationship between the sequence of a peptide and its tertiary structure (i.e. its activity) are not well understood and are not predictable (e.g., see Ngo et al. in The Protein Folding Problem and Tertiary Structure Prediction, 1994, Merz et al. (ed.), Birkhauser, Boston, MA, pp. 433 and 492-495; Franceus et al., J. Ind. Microbiol. Biotechnol. Vol 44, pp 687-695, 2017), it would require undue experimentation for one skilled in the art to arrive at the majority of those altered cytidine deaminase comprising amino acid substitution mutations at positions functionally equivalent to Tyr130 and Tyr132 in a reference APOBEC3A of SEQ ID NO:3, wherein the altered cytidine deaminase comprises an activity of converting 5-methyl cytosine (5mC) to thymidine (T) by deamination at a greater rate than conversion of cytosine (C) to uracil (U) by deamination, and wherein the substitution mutation at the position functionally equivalent to Tyr132 comprises a mutation to His, Arg, Gln, or Lys of the claimed genus.
Thus, applicants have not provided sufficient guidance to enable one of ordinary skill in the art to make and use the claimed invention in a manner reasonably correlated with the scope of the claims broadly including any altered cytidine deaminase comprising amino acid substitution mutations at positions functionally equivalent to Tyr130 and Tyr132 in a reference APOBEC3A of SEQ ID NO:3, wherein the altered cytidine deaminase comprises an activity of converting 5-methyl cytosine (5mC) to thymidine (T) by deamination at a greater rate than conversion of cytosine (C) to uracil (U) by deamination, and wherein the substitution mutation at the position functionally equivalent to Tyr132 comprises a mutation to His, Arg, Gln, or Lys. The scope of the claims must bear a reasonable correlation with the scope of enablement (In re Fisher, 166 USPQ 19 24 (CCPA 1970)). Without sufficient guidance, determination of those altered cytidine deaminases having the desired biological characteristics is unpredictable and the experimentation left to those skilled in the art is unnecessarily, and improperly, extensive and undue. See In re Wands 858 F.2d 731, 8 USPQ2nd 1400 (Fed. Cir, 1988).
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.
Claims 68-73, 75, 76, 95-101 is/are rejected under 35 U.S.C. 103 as being unpatentable over Chen et al. (US 2021/163913) and Univ Shangai Tech (WO 2019/042284).
Chen et al. (US 2021/163913) teach a fusion protein comprising an APOBEC3A protein and a Cas protein. The APOBEC3 may be a mutant, comprising amino acid substitutions at Y130 and Y132. Examples of combinatory mutations include Y130F+D131E+Y132D, Y130F+D131Y+Y132D, Y130E-D131E-Y132D, and Y130E-D131Y-Y132D (see claims 1, 4, 5 and paragraph 0084). Chen et al. further teach the above APOBEC3 substitution mutants in the SEQ ID NO:16 and SEQ ID NO:40 which are 100% identical to instant SEQ ID NO:3. Chen et al. further teach the use of the above APOBEC3 mutant fusion proteins in methods of editing a target polynucleotide including the use of the mutant APOBEC3 mutant in a composition comprising a DNA comprising a 5-nethyl cytosine
Univ Shangai Tech (WO 2019/042284) teach fusion proteins comprising a cytidine deaminase such as APOBEC3A and a catalytically active Cpf1. The APOBEC3A may have one or more mutations, examples including Y130F-D131E-Y132D, Y130F-D131Y-Y132D (see paragraph 0051 and 0072).
One of skill in the art before the effective filing date of the invention would have been motivated to combine the teachings and methods of Chen et al. and Univ Shangai Tech to create additional substitutions at positions Y130 and Y132 of APOBEC3A to create additional creatine deaminases with altered properties since positions 130 and 132 were known determinators of enzyme specificity and activity. Included in these additional substitutions is Y132R (Arg) since like Y132D as taught by both Chen et al. and Univ Shangai Tech, Y132R is a substitution with an amino acid with a similar hydrophilic side group (D versus R). It would be further obvious to screen such obvious double mutants for favorable activities and use them in the methods of editing taught by Chen et al.. The functional limitations of claims 95-97 are considered inherent to the obvious cytidine deaminase mutants based upon the high degree of sequence identity of the obvious cytidine deaminase mutants. The expectation of success is high based upon the high level of expertise in the art as illustrated by both Chen et al. and Univ Shangai Tech who teach all methodology and substrates required to create the obvious mutants.
Thus, claims 68-73, 75, 76, 95-101 is/are rejected under 35 U.S.C. 103 as being unpatentable over Chen et al. (US 2021/163913) and Univ Shangai Tech (WO 2019/042284).
Remarks
No claim is allowed.
Any inquiry concerning this communication or earlier communications from the examiner should be directed to RICHARD G HUTSON whose telephone number is (571)272-0930. The examiner can normally be reached on 6-3 EST Mon-Fri.
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rgh
4/15/2026
/RICHARD G HUTSON/Primary Examiner, Art Unit 1652
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