DETAILED ACTION
Status of the Application
Claims 1-3, 14-17, 21-22, 27-28, 31, 33, 36, 40-41, 47-48, 50, 53, 58-62, 85-93 are pending.
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 1-3, 85, 87, 89, 92, addition of claim 93, and amendments to the specification as submitted in a communication filed on 2/18/2026 is acknowledged.
A request for continued examination under 37 CFR 1.114, including the fee set forth in 37 CFR 1.17(e), was filed in this application after final rejection. Since this application is eligible for continued examination under 37 CFR 1.114, and the fee set forth in 37 CFR 1.17(e) has been timely paid, the finality of the previous Office action has been withdrawn pursuant to 37 CFR 1.114. Applicant's submission filed on 2/18/2026 has been entered.
Applicant elected Group I, drawn to a system for modifying nucleotides in an RNA target of interest, wherein said system comprises a dead C2c1 or a C2c1 nickase, a guide molecule, and an adenosine deaminase protein, and a cell that comprises said system, in a communication filed on 1/9/2023.
New claim 93 is directed to a non-elected invention. Claims 14-15, 21-22, 27-28, 31, 33, 36, 40-41, 47-48, 50, 53, 58-62, 93 are withdrawn from further consideration pursuant to 37 CFR 1.142(b) as being drawn to a nonelected invention, there being no allowable generic or linking claim. Election was made without traverse in the reply filed on 1/9/2023.
Claims 1-3, 16-17, 85-92 are at issue and will be examined only to the extent they encompass the elected invention.
The text of those sections of Title 35, U.S. Code not included in this action can be found in a prior Office action.
Rejections and/or objections not reiterated from previous office actions are hereby withdrawn.
Specification
The specification was objected to for failing to comply with sequence rules. In view of the amendments made to the specification, this objection is hereby withdrawn.
Claim Objections
Claim 89 remains objected to as failing to comply with sequence rules. Claim 89 recites an amino acid sequence which is longer than 4 amino acids without referring to its corresponding sequence identifier (e.g., “GGGGS”). Applicant is required to include the corresponding sequence identifier in the claim. See particularly 37 CFR 1.821(d). Appropriate correction is required.
Claim Rejections - 35 USC § 112(b) or Second Paragraph (pre-AIA )
Claims 1-3, 16-17, 85-92 remain 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 pre-AIA the applicant regards as the invention. New grounds of rejection are necessitated by amendment.
Claim 1 (claims 2-3, 16-17, 85-92 dependent thereon) is indefinite in the recitation of “a human adenosine deaminase 2…protein encoded by the ADARB1 gene that has 701 amino acids or catalytic domain thereof that comprise a mutation at position E488 and one or more mutations at position V351, T375 and R455” for the following reasons. The term “or catalytic domain thereof that comprises a mutation at….” is unclear because one cannot determine if the recited mutations are in the hADAR2 or in the catalytic domain thereof. In addition, the recitation of numerical positions is meaningless in the absence of a recitation indicating the specific sequence identifier associated with the positions recited. Please note that the term “protein encoded by the ADARB1 gene that has 701 amino acids” does not provide a sequence identifier for the numerical positions recited, does not limit the protein to solely 701 amino acids because “has” is equivalent to “comprises”, and does not provide a single sequence to be the reference for the numerical positions and for comparison. It is well known in the art that one could have naturally occurring variants of a protein encoded by the same gene, as well as more than one protein encoded by the same gene. Therefore, it is not known if there is a single amino acid sequence that has 701 amino acids associated with a protein encoded by the ADARB1 gene. It should be noted that the Examiner has previously referred to a single protein encoded by the human ADARB1 gene that consists of 701 amino acids which has a specific amino acid sequence disclosed by Mittaz et al. (Genomics 41:210-217, 1997) in Figure 1B. Moreover, it is noted that the term “a human adenosine… protein…that comprise a mutation..” encompasses a genus of variants of the human adenosine deaminase 2 protein that comprise a mutation. As such, said variants can have more or less than 701 amino acids, thus having different lengths. Therefore, even if one assumes that the “701” amino acids could somehow provide the required sequence identifier, positions 88, 351, 375 and 455 appear to be the positions in the variants of any length encompassed by the claim. For example, the claim appears to require a hADAR2 variant X having 1000 amino acids to have a substitution at position 88 of the variant X, which may not be the corresponding position 88 in the protein of 701 amino acids recited in the claim. In an alignment of variant X and the protein having the 701 amino acids, position 100 in the variant X can be the position corresponding to position 88 in the protein having 701 amino acids. Therefore, it is unclear if variant X should have a mutation at position 100, which is a position that corresponds to position 88 of the protein of 701 amino acids, or at position 88 of the variant X. For examination purposes, it will be assumed that the system requires a mutant of a human adenosine deaminase 2 protein or fragment thereof, wherein said mutant can have any function. Correction is required.
Claim 2 (claim 3 dependent thereon) is indefinite in the recitation of “wherein the hADAR2 protein or catalytic domain thereof is mutated at one or more positions selected from N473…and N597” for the following reasons. The term “or catalytic domain thereof is further mutated at….” is unclear because one cannot determine if the recited mutations are in the hADAR2 or in the catalytic domain thereof. In addition, the recitation of numerical positions is meaningless in the absence of a recitation indicating the specific sequence identifier associated with the positions recited. Please note that the term “protein encoded by the ADARB1 gene that has 701 amino acids” recited in claim 1 does not provide a sequence identifier for the numerical positions recited, does not limit the protein to solely 701 amino acids because “has” is equivalent to “comprises”, and does not provide a single sequence to be the reference for the numerical positions and for comparison. It is well known in the art that one could have naturally occurring variants of a protein encoded by the same gene, as well as more than one protein encoded by the same gene. Therefore, it is not known if there is single amino acid sequence associated with a protein encoded by the ADAB1 gene. Moreover, as explained above, the claim encompasses a genus of variants of the human adenosine deaminase 2 protein that comprise a mutation. As such, said variants can have more or less than 701 amino acids, thus having different lengths. Therefore, even if one assumes that the “701” amino acids could somehow provide the required sequence identifier, positions 473, 474, 475, 481, 495, 510, 451, 396, 376, 486, 462, and 597 appear to be the positions in the variants of any length encompassed by the claim. For example, the claim appears to require a hADAR2 variant X having 1000 amino acids to have a substitution at position 473 of the variant X, which may not be the corresponding position 473 in the protein of 701 amino acids recited in claim 1. In an alignment of variant X and the protein having the 701 amino acids, position 500 in the variant X can be the position corresponding to position 473 in the protein having 701 amino acids. Therefore, it is unclear if variant X should have a mutation at position 500, which is a position that corresponds to position 473 of the protein of 701 amino acids, or at position 473 of the variant X. For examination purposes, it will be assumed that claim 2 is a duplicate of claim 1 as interpreted. Correction is required.
Claim 3 is indefinite in the recitation of “…wherein said guide molecule is capable….a portion of the guide molecule….hybridizing with the portion of the guide molecule…” for the following reasons. Claim 1 as amended now refers to a guide nucleic acid. Therefore, there is no antecedent basis for the guide molecule recited in claim 3. For examination purposes, claim 3 will be interpreted as a duplicate of claim 1. Correction is required.
Claim 85 is indefinite in the recitation of “wherein the portion of the guide molecule that forms the duplex comprises ..” for the following reasons. Claim 1 as amended now refers to a guide nucleic acid. Therefore, there is no antecedent basis for the guide molecule recited in claim 85. For examination purposes, claim 85 will be interpreted as a duplicate of claim 1. Correction is required.
Claim 87 is indefinite in the recitation of “wherein the portion of the guide molecule that forms the duplex with said RNA target of interest is at least 15” for the following reasons. Claim 1 as amended now refers to a guide nucleic acid. Therefore, there is no antecedent basis for the guide molecule recited in claim 87. In addition, it is unclear as to how the term “wherein the portion of the guide molecule…is 15” further limits the portion of the guide molecule recited (i.e., 15 what?). For examination purposes, claim 87 will be interpreted as a duplicate of claim 1. Correction is required.
Claim 90 (claim 91 dependent thereon) is indefinite in the recitation of “wherein said dead …and said guide molecule ….protein comprises an aptamer sequence capable of binding to said adaptor protein” for the following reasons. There is no antecedent basis for the term guide molecule. In addition, an aptamer sequence is a graphical representation of the order in which monomers (nucleotides or amino acids) are arranged in an aptamer molecule. Therefore, sequences cannot bind to proteins. If the intended limitation refers to a protein that comprises an aptamer capable of binding to an adaptor protein, the claim should be amended accordingly. Correction is required.
When amending the claims, applicant is advised to carefully review all examined claims and make the necessary changes to ensure proper antecedent basis and dependency.
Claim Rejections - 35 USC § 112(a) or First Paragraph (pre-AIA )
Claims 1-3, 16-17, 85-92 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. This rejection is necessitated by the introduction of new matter.
As set forth in MPEP 2163 (I)(B), new or amended claims which introduce elements or limitations that are not supported by the as-filed disclosure violate the written description requirement. See, e.g., In re Lukach, 442 F.2d 967, 169 USPQ 795 (CCPA 1971) (subgenus range was not supported by generic disclosure and specific example within the subgenus range); In re Smith, 458 F.2d 1389, 1395, 173 USPQ 679, 683 (CCPA 1972) (an adequate description of a genus may not support claims to a subgenus or species within the genus). Claim 1 and dependent claims 2-3, 16-17, 85-92 now refer to a human adenosine deaminase 2 encoded by the ADARB1 gene that has 701 amino acids. In addition, claim 1 and dependent claims 2-3, 16-17, 85-92 now require a genus of dead A. acidoterrestris C2c1 proteins having at least 99% sequence identity to the polypeptide of SEQ ID NO: 88. The Examiner has not been able to find any mention of an ADARB1 gene that encodes a protein that has 701 amino acids or of a human adenosine deaminase 2 that has 701 amino acids. Furthermore, while the Examiner has found support for a genus of dead A. acidoterrestris C2c1 proteins having at least 95% sequence identity to the polypeptide of SEQ ID NO: 88, the Examiner has not been able to locate support for a genus of dead A. acidoterrestris C2c1 proteins having at least 99% sequence identity to the polypeptide of SEQ ID NO: 88.
Thus, there is no indication that a system that requires (i) a genus of dead A. acidoterrestris C2c1 proteins having at least 99% sequence identity to the polypeptide of SEQ ID NO: 88, and (ii) a variant of a protein encoded by an ADARB1 gene that has 701 amino acids, or a variant of a 701 amino acid-long human adenosine deaminase 2, was within the scope of the invention as conceived by Applicant at the time of the invention. Accordingly, Applicant is required to cancel the new matter in the response to this Office action.
Claims 1-3, 16-17, 85-92 remain 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.
This rejection has been discussed at length in prior Office actions. It is maintained for the reasons of record and those set forth below.
Applicant argues that the specification provides extensive disclosure of human ADAR2 proteins and their modifications in specific paragraphs of the specification, and refers to paragraph [0374] as specifically referring to mutations at one or more positions 351, 375, 455, or 488 and C to U deamination activity. Applicant states that the amended claims now recite that the hADAR2 protein is encoded by the ADARB1 gene, which ties the claims to a well-characterized specific gene that produces the human ADAR2 protein. Applicant states that Kuttan et al. demonstrates that positions numbering in human ADAR2 is well established in the art. Applicant states that the admission by the Examiner that there is a human ADAR2 isoform that has a valine at position 351, a threonine at position 375, an arginine at the position 455 and a glutamate at position 4888 confirms that the specification adequately describes these variants. Applicant points out that Applicant was in possession of the claimed dead A. acidoterrestris C2c1 proteins having at least 99% sequence identity to the protein of SEQ ID NO: 88. Applicant states that the % sequence identity limitation accommodates the catalytically inactivating mutations and that a protein having 99% sequence identity to the polypeptide of SEQ ID NO: 88 can differ by no more than 11 amino acid positions. Applicant states that the specification provides extensive detail on guide molecules for C2c1 proteins including their structure, function and design principles. Applicant states that the basic architecture of C2c1 guide molecules comprising a targeting domain and direct repeat sequences was known by those skilled in the art.
Applicant’s arguments have been fully considered but not deemed persuasive to overcome the instant rejection. The Examiner acknowledges the teachings of the specification, the teachings of the prior art, and the amendments made to the claims. However, contrary to Applicant’s assertions, the claims as amended do not meet the written description requirement.
Claims 1-3, 16-17, 85-92 as interpreted are directed in part to a system that requires a dead C2c1 which has at least 99% sequence to the polypeptide of SEQ ID NO: 88, a guide molecule having any structure, and a mutant of a human ADAR2 having any structure, or a fragment of said mutant, wherein said mutant or said fragment can have any function. See Claim Rejections - 35 USC § 112(b) or Second Paragraph (pre-AIA ), for claim interpretation.
For the reasons extensively discussed above, the recitation of positions for the mutations without a sequence identifier has been found indefinite, even with the recitation of “protein encoded by the ADARB1 gene that has 701 amino acids”. In addition, even if the argument is made that the recited numerical positions could be linked to a specific and defined amino acid sequence, the claims do not exclude additional modifications at other positions. There is absolutely no limitation with regard to additional modifications that could be made to the naturally occurring human ADAR2 protein. The claims simply require any variant of the naturally occurring human ADAR2 protein having a mutation (deletion, insertion or substitution) at the positions recited. Therefore, the genus of variants of a human adenosine deaminase 2 encompassed by the claims can have any structure so long as the variants have a mutation at the recited positions. There is absolutely no recitation of function with regard to the variants of a human adenosine deaminase 2 recited. As such, even if the argument is made that the “protein encoded by the ADARB1 gene that has 701 amino acids” as recited in claim 1 is well defined by an amino sequence which is completely defined, it is unclear as to how one could possibly conclude that this “protein” ties the claims to a well-characterized specific gene that produces the human ADAR2 protein when the variants can have any structure and function. The variants are not limited solely to variants that comprise the entire amino acid sequence of the “protein encoded by the ADARB1 gene that has 701 amino acids” except for substitutions at the recited positions. With regard to the argument that the admission by the Examiner that there is a human ADAR2 isoform that has a valine at position 351, a threonine at position 375, an arginine at the position 455 and a glutamate at position 4888 confirms that the specification adequately describes these variants, it is unclear as to how a single protein having the amino acid sequence disclosed by Mittaz et al. can show that the specification adequately describes the entire genus of variants required by the claims, when (a) the specification does not even disclose the amino acid sequence of the protein of Mittaz et al. or the “protein encoded by the ADARB1 gene that has 701 amino acids” recited in claim 1, (b) the specification is silent with regard to which amino acids should be conserved and which ones can be modified in the protein of Mittaz et al. beyond those recited in the claim to obtain a variant as claimed with the desired deaminase activity, and (c) there is no structure/function correlation that would allow one of skill in the art to determine from an infinite number of variants, those most likely to have the desired deaminase activity. Therefore, contrary to Applicant’s assertions, the entire genus of variants of a human ADAR2 required by the claims is not deemed adequately described by the teachings of the specification and/or the prior art.
With regard to the arguments that the recited % sequence identity limitation accommodates the catalytically inactivating mutations and that a protein having 99% sequence identity to the polypeptide of SEQ ID NO: 88 can differ by no more than 11 amino acid positions, it is noted that using the previously provided equation, the total number of structural variants having 99% sequence identity to the protein of SEQ ID NO: 88 that result solely from amino acid substitutions is 1129!x1912/(1129-12)!/12! or 5.43x1073 variants (12 = 0.01x1129; SEQ ID NO: 88 has 1129 amino acids). While one could argue that the genus of variants of the protein of SEQ ID NO: 88 having at least 99% sequence identity allows no more than 12 amino acid modifications with respect to the polypeptide of SEQ ID NO: 88, the claims do not limit the genus to those having the modifications known to produce a dead A. acidoterrestris C2c1 protein. Instead, the structural variants recited can comprise modifications in any of the amino acids of the polypeptide of SEQ ID NO: 88. As previously argued by Applicant, not all amino acid positions can be freely substituted while maintaining protein structure and guide RNA binding capability. As previously stated, the specification and the art are silent with regard to a structure/function correlation that would allow one of skill in the art to determine a priori those structural variants of the polypeptide of SEQ ID NO: 88 that are catalytically inactive and can bind to a guide RNA. While the specification discloses a limited number of substitutions that, if present in the polypeptide of SEQ ID NO: 88, would render a catalytically inactive (dead) variant of the polypeptide of SEQ ID NO: 88, neither the specification nor the prior art disclose additional modifications that would allow one of skill in the art to determine a priori from an essentially infinite number of variants those that are catalytically inactive. Moreover, while these variants are required to form a complex with a guide molecule, there is no information as to which structural modifications should not be made that would disrupt the interaction of the variant with a guide molecule. Therefore, contrary to Applicant’s assertions, the entire genus of variants of the polypeptide of SEQ ID NO: 88 recited in the claims is not found adequately described by the teachings of the specification and/or the prior art.
With regard to the argument that the specification provides extensive detail on guide molecules for C2c1 proteins including their structure, function and design principles, and that the basic architecture of C2c1 guide molecules comprising a targeting domain and direct repeat sequences was known by those skilled in the art, it is noted that it is well known in the art that there is specificity with regard to the guide molecules that can bind to a particular C2c1 protein. While it is agreed that the specification provides a few examples of guide molecules that would be functional with a particular Cas protein, there is no indication that these few species of guide RNAs could function with any of the structural variants of the polypeptide of SEQ ID NO: 88 recited in the claims, or which are the structural variants of the polypeptide of SEQ ID NO: 88 that meet the recited % sequence identity that would bind to any of the guide RNA molecules disclosed. Simply describing the generic structure of a guide RNA as one that comprises a sequence which is complementary to a target sequence, a sequence linked to a direct repeat sequence and/or tracr sequence cannot be construed as providing extensive detail on the structure of guide molecules for C2c1 proteins. There is no structure/function correlation that would allow one of skill in the art to determine the structure of a functional guide RNA for a particular variant of the polypeptide of SEQ ID NO: 88 having the recited % sequence identity. Therefore, contrary to Applicant’s assertions, the entire genus of guide molecules recited is not deemed adequately described by the teachings of the specification and/or the prior art.
Claims 1-3, 16-17 remain rejected and new claims 85-92 are rejected under 35 U.S.C. 112(a) or 35 U.S.C. 112 (pre-AIA ), first paragraph, because the specification, while being enabling for (a) a system that comprises (i) a variant of the Alicylobacillus acidoterrestris C2c1 protein of SEQ ID NO: 88 that comprises all of SEQ ID NO: 88 except for the substitutions D570A, E848A, D977A, R911A, R1000A, or R1015A in SEQ ID NO: 88, (ii) a guide nucleic acid that can form a complex with the variant of (i), and (iii) a human adenosine deaminase disclosed by Mittaz et al. (Genomics 41:210-217, 1997) encoded by the ADARB1 gene that has 701 amino acids and comprises the amino acid sequence shown in Figure 1B (page 213 of Mittaz et al.), and (b) a cell that comprises the system of (a), does not reasonably provide enablement for (a) a system that comprises (i) any variant of the protein of SEQ ID NO: 88 having at least 99% sequence identity to the protein of SEQ ID NO: 88 which is catalytically inactive (dead), (ii) any guide nucleic acid, and (iii) any variant of a human ADAR2 protein or fragment thereof, or (b) a host cell comprising said system. 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/or use the invention commensurate in scope with these claims.
This rejection has been discussed at length in prior Office actions. It is maintained for the reasons of record and those set forth below.
Applicant argues that claim 1 has been amended to recite “a dead A. acidoterrestris C2c1 protein having at least 99% sequence identity to SEQ ID NO: 88…a human adenosine deaminase 2…encoded by the ADARB1 gene that has 701 amino acids ….and R455”. Applicant states that the recited system has been found as enabled and that the rejection should be withdrawn.
Applicant’s arguments have been fully considered but not deemed persuasive to overcome the instant rejection. The Examiner acknowledges the amendments made to the claims. However, contrary to Applicant’s assertions, the scope of the claims as currently presented is not limited to what was previously indicated as enabled.
The claims as currently presented require a genus of variants of the polypeptide of SEQ ID NO: 88 having at least 99% sequence identity to the polypeptide of SEQ ID NO: 88. As indicated above and also stated in the final action of 11/18/2025, only variants of the Alicylobacillus acidoterrestris C2c1 protein of SEQ ID NO: 88 that comprises all of SEQ ID NO: 88 except for the substitutions D570A, E848A, D977A, R911A, R1000A, or R1015A in SEQ ID NO: 88 have been found enabled. Therefore, contrary to Applicant’s assertions, the genus of variants of the polypeptide of SEQ ID NO: 88 currently recited is not what was found enabled.
The claims as currently presented require a genus of mutants of a human ADAR2 having any structure, or a fragment of said mutant, wherein said mutant or said fragment can have any function. See Claim Rejections - 35 USC § 112(b) or Second Paragraph (pre-AIA ), for claim interpretation. For the reasons extensively discussed above, the recitation of positions for the mutations without a sequence identifier has been found indefinite, even with the recitation of “protein encoded by the ADARB1 gene that has 701 amino acids”. In addition, even if the argument is made that the recited numerical positions could be linked to a specific and defined amino acid sequence, the claims do not exclude additional modifications at other positions. There is absolutely no limitation with regard to additional modifications that could be made to the naturally occurring human ADAR2 protein. The claims simply require any mutant of the naturally occurring human ADAR2 protein having a mutation (deletion, insertion or substitution) at the positions recited. Therefore, the genus of mutants of a human adenosine deaminase 2 encompassed by the claims can have any structure so long as the mutants have a mutation at the recited positions. There is absolutely no recitation of function with regard to the mutants of a human adenosine deaminase 2 recited. As indicated above and also stated in the final action of 11/18/2025, only the human adenosine deaminase disclosed by Mittaz et al. (Genomics 41:210-217, 1997) encoded by the ADARB1 gene that has 701 amino acids and comprises the amino acid sequence shown in Figure 1B (page 213 of Mittaz et al.) has been found enabled. Therefore, contrary to Applicant’s assertions, the genus of mutants of a human ADAR2 currently recited is not what was found enabled.
The number of variants of a human ADAR2, variants of the polypeptide of SEQ ID NO: 88 and guide molecules required by the claimed system is essentially infinite. The amount of experimentation required to find those variants and guide molecules encompassed by the claims is not routine. Thus, one cannot reasonably conclude that the entire scope of the claims is fully enabled by the teachings of the specification and/or the prior art.
Conclusion
No claim is in condition for allowance.
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Any inquiry concerning this communication or earlier communications from the examiner should be directed to DELIA M RAMIREZ, Ph.D., whose telephone number is (571) 272-0938. The examiner can normally be reached on Monday-Friday from 8:30 AM to 5:00 PM. If attempts to reach the examiner by telephone are unsuccessful, the examiner’s supervisor, Robert B. Mondesi, can be reached at (408) 918-7584. The fax phone number for the organization where this application or proceeding is assigned is 571-273-8300.
/DELIA M RAMIREZ/Primary Examiner, Art Unit 1652
DR
May 1, 2026
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