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 on 03/02/2026 has been received and entered claims 96-116 are pending. Claims 105-112 and 115 are withdrawn from consideration, as being directed to a non-elected invention. Claims 96-104, 113-114, and 116 have been examined on the merits.
Status of Prior Rejections/Response to Arguments
RE: Objection to claim 112
Amendments to the claims overcome the objection. The objection is withdrawn.
RE: Rejection of claims 96-104, 113-114, and 116 under 35 U.S.C 112(a)
Claim 96 has been amended to specify the oligonucleotide guides editing by ADAR1 or ADAR2. Amendments to claim 96 overcome the rejection of claims 96-104. The rejection over claims 96-104 is withdrawn.
Claim 113 has not been amended. Claims 114 and 116 depend from claim 113 and thus inherit the deficiencies of claim 113. The rejection over claims 113-114 and 116 is maintained.
RE: Rejection of claims 96-104, 113-114, and 116 under 35 U.S.C. 103 as being unpatentable over Fukuda et al (Scientific Reports, 2017) in view of Fukutomi et al (Mol Cell Biol, 2014) and Moretti et al (Free Radical Biology and Medicine, 2020).
Applicants amended claim 96 to require an oligonucleotide comprising one or more 2’-F modified sugars; and an oligonucleotide that can guide editing of a target adenosine in a NRF2 transcript by ADAR1 or ADAR2.
Fukuda et al, Fukutomi et al, and Moretti et al do not disclose or suggest a motivation for modifying an oligonucleotide to comprise one or more 2’-F modified sugars. Thus, amendments to claim 96 overcome the rejection of claim 96 and dependent claims 97-104. The rejection over claims 96-104 is withdrawn.
Claims 113-114 and 116 have not been amended. Additionally, applicants have not presented any arguments regarding the rejection of the claims. The rejection over claims 113-114 and 116 is maintained.
New/Maintained Rejections
Claim Rejections - 35 USC § 112(a)
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 113-114, and 116 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 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.
Independent claim 113 is directed to a method comprising administering an oligonucleotide or composition capable of editing an adenosine in a nucleic acid encoding NRF2, wherein the edited nucleic acid encodes a protein that is different from the protein encoded by the unedited nucleic acid at least one amino acid residue involved in the interaction between NRF2 and KEAP1. Claims 114 and 116 depend from claim 113.
The issue at hand is the scope of ‘an oligonucleotide or composition capable of editing an adenosine in a nucleic acid’, and particularly whether or not Applicants were in possession of the full scope of this claimed genus of compounds. In giving the term ‘oligonucleotide or composition capable of editing an adenosine’ its broadest reasonable interpretation, the number and types of compounds which can be considered ‘oligonucleotide or composition capable of editing an adenosine’ covers any composition capable of editing an adenosine including, adenosine deaminases/adenosine base editors, compositions comprising an endonuclease and a template for homology directed repair such as CRISPR/Cas9, TALENs, and Zinc finger endonucleases, oligonucleotides used for site directed mutagenesis, compositions for performing Cre/LoxP mediated excision, and piggyBac transposons. Thus oligonucleotide or composition capable of editing an adenosine is a large genus of molecules.
To satisfy the written description aspect of 35 U.S.C. 112(a) for a claimed genus of molecules, it must be clear that: (1) the identifying characteristics of the claimed molecules have been disclosed, e.g., structure or other physical and/or chemical properties, by functional characteristics coupled with a known or disclosed cor-relation between function and structure, or by a com-bination of such identifying characteristics; or (2) a representative number of species within the genus must be disclosed. See Eli Lilly, 119 F.3d at 1568, 43 USPQ2d at 1406.
While Applicants’ claims cover the full genus of oligonucleotide or composition capable of editing an adenosine, Applicants’ disclosure of such oligonucleotides and compositions is limited to oligonucleotides which are used as guides for adenosine deaminase-based editing (See Example 1).
Regarding disclosure of identifying characteristics of the claimed molecules a review of the specification reveals various structural characteristics of modified oligonucleotides (i.e. modified sugars (e.g., 2' -F, 2' -OMe, etc.), modified bases (e.g., 8-oxo-dA), modified nucleobases (e.g., b008U), and modified internucleotide linkages), however the specification fails to provide a definition of what structural characteristics a ‘composition capable of editing an adenosine’ encompassed by the current claims must have. Applicants have not identified any particular core chemical structure or function (along with a correlation between function and a specific conserved structure) of a composition which must be shared by all covered compounds; and thus one of ordinary skill in the art would not immediately envisage all composition capable of editing an adenosine, as currently claimed. Therefore, Applicants have not disclosed the identifying characteristics of the claimed genus.
Regarding disclosure of a representative number of species within the genus a review of the specification shows that Applicants have disclosed various oligonucleotides which can be used with an ADAR (See Examples 1, and Examples 5-32). However, compositions comprising an oligonucleotide, per se, does not constitute a representative number for such a broad genus as is encompassed by the breadth of ‘or compositions capable of editing an adenosine’. Again, this scope covers, in addition to oligonucleotides, per se, adenosine deaminases/adenosine base editors, compositions comprising an endonuclease and a template for homology directed repair such as CRISPR/Cas9, TALENs, and Zinc finger endonucleases, oligonucleotides used for site directed mutagenesis, compositions for performing Cre/LoxP mediated excision, and piggyBac transposons. Therefore Applicants have not disclosed a representative number of species, as would be required to support description and to show possession of the entire genus.
Thus, one of ordinary skill in the art, in looking to the instant specification, would not be able to determine that Applicants were in possession of the invention, as claimed, at the time the invention was made. Accordingly, the claims are considered to lack sufficient written description and are properly rejected under 35 USC 112(a).
Dependent claims 114, and 116 do not further limit the scope of ‘oligonucleotides and compositions capable of editing an adenosine’ and thus inherit the lack of written description.
Claim Rejections - 35 USC § 112(b)
Claim Rejections - 35 USC § 112(b)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 96-104 are rejected under 35 U.S.C. 112(b) or 35 U.S.C. 112 (pre-AIA ), second paragraph, as being indefinite for failing to particularly point out and distinctly claim the subject matter which the inventor or a joint inventor (or for applications subject to pre-AIA 35 U.S.C. 112, the applicant), regards as the invention.
Claim 96 recites the limitation "the edited nucleic acid" in line three. There is insufficient antecedent basis for this limitation in the claim. It is acknowledged that line 7 of the claim states that the oligonucleotide that is administered can guide editing of a target adenosine, but (i) this is recited later in the claim, which is insufficient to provide antecedent basis, and (ii) because editing is not necessarily required (it is only possible), it is not clear that there is a nucleic acid edit. Appropriate correction is required.
Claims 97-104 depend from claim 96 and inherit the deficiency.
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.
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 113-114, and 116 are rejected under 35 U.S.C. 103 as being unpatentable over Fukuda et al (Scientific Reports, 2017) in view of Fukutomi et al (Mol Cell Biol, 2014) and Moretti et al (Free Radical Biology and Medicine, 2020).
Fukuda et al teaches a method of site-directed RNA mutagenesis using a guide RNA and adenosine deaminase acting on RNA (ADAR) to change an adenosine to an inosine (See abstract). Inosine is read as a guanosine by translation machinery thus, A-to-I RNA editing can regulate protein functions by changing target protein codons (See abstract). Additionally, Fukuda et al teaches ADAR2 is mainly expressed in neurons (See pg. 2 second paragraph). The AD-gRNAs of Fukuda et al are able to guide ADAR2 (See pg. 2 third paragraph).
Regarding claims 113, 114, and 116: Fukuda et al teaches a method of editing an adenosine which results in changing a codon in a target protein.
Fukuda et al does not teach editing an adenosine in a nucleic acid encoding NRF2 or modulating an interaction between NRF2 and KEAP proteins.
Fukutomi et al teaches binding of NRF2 and KEAP1 results in ubiquitination and degradation of NRF2 (See abstract). NRF2 interacts with KEAP1 through an extended DLG motif of NRF2 and an ETGE motif (See Fig. 1 and pg. 834, last paragraph). Fukutomi et al performs GST pulldown assays using NRF2 proteins which have been mutated in 19 different sites in the DLG motif (See Fig. 2). KEAP1 was not detected in pulldown assays performed with 13 out of the 19 mutants, including Q26E, D27Y, I28T, and D29G mutants (read on amino acids involved in the interaction between NRF2 and KEAP1) (See Fig. 2). Thus, mutation of any of the 13 identified mutants is sufficient to disrupt the interaction between NRF2 and KEAP1.
Moretti et al teaches reactive oxygen species (ROS) production is elevated in Huntington’s disease (HD) (See pg. 243, Sec. Introduction, first paragraph). NRF2 is a key modulator of the antioxidant response. Under low ROS conditions, KEAP1 interacts with NRF2 and targets NRF2 for degradation. ROS target cysteine residues in KEAP1, causing modifications which result in release of NRF2, allowing NRF2 to translocate to the nuclease where it is able to activate transcription of antioxidant enzymes (See pg. 244, first and second paragraph). In experiments using small molecules which are able to block the interaction between NRF2 and KEAP1, Moretti reports ROS protection of astrocytes.
Given that Fukuda et al teaches a method of editing A-to-I (which is translated as a guanosine) in a target protein by using an AD-gRNA (reads on an oligonucleotide for editing an adenosine) and hADAR2, Fukutomi teaches a D29G (GAU or GAC to GGU or GGC modification) modification prevents NRF2-KEAP1 interactions, and Moretti teaches ROS are elevated in HD and disrupting NRF2-KEAP1 interactions allows NRF2 to modulate antioxidant response which has a cryoprotective effect on astrocytes, it would have been prima facie obvious, to use the editing method of Fukuda to edit D29 of NRF2 by modify the AD-gRNA of Fukuda et al to make a gRNA, which targets the adenosine in D29 of NRF2, in order to disrupt the interaction between NRF2 and KEAP1 in HD astrocytes (reads on a system that is a CNS cell). Administering AD-gRNA to astrocytes in order to edit an adenosine in D29 to cause a D29G mutation which disrupts NRF2-KEAP1 interactions reads on a method for modulating an interaction between NRF2 and KEAP1 proteins in a system comprising administering an oligonucleotide capable of editing an adenosine in a nucleic acid encoding NRF2 wherein the edited nucleic acid encodes a protein that is different from the protein encoded by the unedited nucleic acid at at least one amino acid residue involved in the interaction between NRF2 and KEAP1. One would have been motivated to modify the method of Fukuda et al to target D29 of NRF2 because Moretti et al teaches disrupting NRF2-KEAP1 interactions protects astrocytes from ROS. There is a reasonable expectation of success because Fukutomi et al teaches a D29G mutation disrupts the interaction between NRF2 and KEAP1.
Moretti et al further discloses inhibiting the interaction NRF2-KEAP1 interaction in astrocytes results in upregulation of NQO1 transcription which reads on one or more nucleic acids regulated by NRF2 are modulated. Therefore, inhibiting the interaction between NRF2 and KEAP1 in astrocytes by using an AD-gRNA to make a D29G edit in NRF2 would result in upregulation of NQO1 transcription which reads on a method of modulating expression level of one or more nucleic acids regulated by NRF2, wherein the method comprises administering to the system an oligonucleotide capable of editing an adenosine in a nucleic acid encoding NRF2, wherein the edited nucleic acid encodes a protein that is different from the protein encoded by the unedited nucleic acid at at least one amino acid residue involved in the interactions between NRF2 and KEAP1.
Claims 96-104, 113-114, and 116 are rejected under 35 U.S.C. 103 as being unpatentable over Fukuda et al (Scientific Reports, 2017) in view of Fukutomi et al (Mol Cell Biol, 2014), Moretti et al (Free Radical Biology and Medicine, 2020), and bioSYNTHESIS (2’ Fluoro RNA Modification, July, 2021).
The teachings of Fukuda et al, Fukutomi et al, and Moretti et al are set forth above.
Fukuda et al, Fukutomi et al, and Moretti et al render claims 113-114 and 116 obvious.
Regarding claims 96, 102, and 103: Fukuda et al teaches a method of editing an adenosine which results in changing a codon in a target protein.
Fukuda et al does not teach editing an adenosine in a nucleic acid encoding NRF2 or modulating an interaction between NRF2 and KEAP proteins.
Fukutomi et al teaches binding of NRF2 and KEAP1 results in ubiquitination and degradation of NRF2 (See abstract). NRF2 interacts with KEAP1 through an extended DLG motif of NRF2 and an ETGE motif (See Fig. 1 and pg. 834, last paragraph). Fukutomi et al performs GST pulldown assays using NRF2 proteins which have been mutated in 19 different sites in the DLG motif (See Fig. 2). KEAP1 was not detected in pulldown assays performed with 13 out of the 19 mutants, including Q26E, D27Y, I28T, and D29G mutants (read on amino acids involved in the interaction between NRF2 and KEAP1) (See Fig. 2). Thus, mutation of any of the 13 identified mutants is sufficient to disrupt the interaction between NRF2 and KEAP1.
Moretti et al teaches reactive oxygen species (ROS) production is elevated in Huntington’s disease (HD) (See pg. 243, Sec. Introduction, first paragraph). NRF2 is a key modulator of the antioxidant response. Under low ROS conditions, KEAP1 interacts with NRF2 and targets NRF2 for degradation. ROS target cysteine residues in KEAP1, causing modifications which result in release of NRF2, allowing NRF2 to translocate to the nuclease where it is able to activate transcription of antioxidant enzymes (See pg. 244, first and second paragraph). In experiments using small molecules which are able to block the interaction between NRF2 and KEAP1, Moretti reports ROS protection of astrocytes.
Given that Fukuda et al teaches a method of editing A-to-I (which is translated as a guanosine) in a target protein by using an AD-gRNA (reads on an oligonucleotide for editing an adenosine) and hADAR2, Fukutomi teaches a D29G (GAU or GAC to GGU or GGC modification) modification prevents NRF2-KEAP1 interactions, and Moretti teaches ROS are elevated in HD and disrupting NRF2-KEAP1 interactions allows NRF2 to modulate antioxidant response which has a cryoprotective effect on astrocytes, it would have been prima facie obvious, to use the editing method of Fukuda to edit D29 of NRF2 by modify the AD-gRNA of Fukuda et al to make a gRNA, which targets the adenosine in D29 of NRF2, in order to disrupt the interaction between NRF2 and KEAP1 in HD astrocytes (reads on a system that is a CNS cell). Administering AD-gRNA to astrocytes in order to edit an adenosine in D29 to cause a D29G mutation which disrupts NRF2-KEAP1 interactions reads on a method for modulating an interaction between NRF2 and KEAP1 proteins in a system comprising administering an oligonucleotide capable of editing an adenosine in a nucleic acid encoding NRF2 wherein the edited nucleic acid encodes a protein that is different from the protein encoded by the unedited nucleic acid at at least one amino acid residue involved in the interaction between NRF2 and KEAP1. One would have been motivated to modify the method of Fukuda et al to target D29 of NRF2 because Moretti et al teaches disrupting NRF2-KEAP1 interactions protects astrocytes from ROS. There is a reasonable expectation of success because Fukutomi et al teaches a D29G mutation disrupts the interaction between NRF2 and KEAP1.
Additionally, Fukuda et al does not teach an oligonucleotide comprising one or more 2’-F modified sugars.
bioSYNTHESIS teaches 2’ Fluoro (reads on 2’-F modified sugar) RNA oligonucleotides contain a fluorine molecule at the 2’ ribose position which increases binding affinity and nuclease resistance resulting in higher stability (See first paragraph).
Given that Fukuda et al teaches a method of editing A-to-I (which is translated as a guanosine) in a target protein by using an AD-gRNA (reads on an RNA oligonucleotide) and biosynthesis teaches RNA oligonucleotides comprising 2’-Fluoro modifications have increased binding affinity, nuclease resistance and are more stable, it would have been prima facie obvious to modify the AD-gRNA of Fukuda et al by adding a 2’-F modification. One would have been motivated to modify the AD-gRNA of Fukuda et al by adding a 2’-F modification because bioSYNTHESIS teaches 2’-F modified RNA oligonucleotides have increased binding affinity, nuclease resistance, and stability. There is a reasonable expectation of success because bioSYNTHESIS teaches 2’F modified RNA oligonucleotides have increased binding affinity, nuclease resistance, and stability and the AD-gRNA of Fukuda et al is an RNA oligonucleotide.
Regarding claim 97: Following the discussion of claim 96 above. Fukuda et al in view of Fukutomi et al and Moretti et al disclose a method for modifying D29 of NRF2 (reads on an amino acid residue involved in the interaction between NRF2 and KEAP1) using AD-gRNA which results in an aspartic acid to glycine modification (reads on the editing changed the amino acid to a different amino acid).
Regarding claim 98: Following the discussion of claim 96 above. Fukuda et al in view of Fukutomi et al and Moretti et al disclose a method for making a D29G modification of NRF2 using AD-gRNA. Fukutomi et al discloses a D29G modification of NRF2 inhibits the interaction of NRF2 and KEAP1 which reads on the protein-protein interaction is reduced.
Regarding claims 99 and 100: Following the discussion of claim 96 above. Fukuda et al in view of Fukutomi et al and Moretti et al disclose a method for making a D29G modification of NRF2 using AD-gRNA. Moretti et al further discloses inhibiting the interaction NRF2-KEAP1 interaction in astrocytes results in upregulation of NQO1 transcription which reads on one or more nucleic acids regulated by NRF2 are modulated (See Fig. 3). Therefore, inhibiting the interaction between NRF2 and KEAP1 in astrocytes by using an AD-gRNA to make a D29G edit in NRF2 would result in upregulation of NQO1 transcription.
Regarding claim 101: Following the discussion of claim 96 above. Fukuda et al in view of Fukutomi et al and Moretti et al disclose a method for making a D29G modification of NRF2 using AD-gRNA. Fukutomi et al Further discloses Asp27 of NRF2 supplies hydrogen bonds to the side chain of Arg380, Asn382, and Asn414 of KEAP1 and a D27Y mutation inhibits NRF2-KEAP1 interactions (See Sec. Structural characteristics of KEAP10DC and DLG long-peptide interaction, first paragraph).
While a D27Y mutation does not involve editing an adenosine, it would have been prima facie obvious to use the method of Fukutomi et al to edit the adenosine in D27 (reads on Asp27) of NRF2. One would be motivated to use the method of Fukuda et al to edit D27 of NRF2 because Fukutomi et al discloses D27 supplies hydrogen bonds which are important for the interaction between NRF2 and KEAP1. There is a reasonable expectation of success because Fukutomi et al discloses somatic mutations of D27 prevent NRF2-KEAP1 interactions and editing the adenosine of D27 with the AD-gRNA of Fukuda et al would result in a D27G mutation would alter the structure of the DLG binding motif of NRF2.
Regarding claim 104: Following the discussion of claim 96 above, Fukuda et al in view of Fukutomi et al and Moretti et al disclose a method for making a D29G modification of NRF2, in astrocytes isolated from a HD mouse model, using AD-gRNA. Fukuda et al further teaches using a plasmid to express the AD-gRNA (See pg. 11, Sec. preparation of the AD-gRNA expression plasmid).
Fukuda et al in view of Fukutomi et al and Moretti et al do not disclose editing an adenosine that modifies a NRF2-KEAP1 interaction in a tissue.
Although Fukuda et al in view of Fukutomi et al and Moretti et al do not disclose editing an adenosine in a tissue, it would have been prima facie obvious to administer a plasmid expressing the modified AD-gRNA, which targets D29 for ADAR2 mediated adenosine base editing, directly to the mouse model, to perform editing of the astrocytes in vivo (reads on editing an adenosine in a tissue). One would have been motivated to modify the method of Fukutomi et al by administering a plasmid expressing the AD-gRNA to an HD mouse model in order to test the effects of editing an adenosine in vivo for use as a treatment for HD. There is a reasonable expectation of success because using plasmids to express oligonucleotides in mouse models is a known technique in the field and Fukutomi et al discloses the AD-gRNA guides ADAR2 which is expressed in neuronal cells.
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.
Any inquiry concerning this communication or earlier communications from the examiner should be directed to MARISOL A O'NEILL whose telephone number is (571)272-2490. The examiner can normally be reached Monday - Friday 7:30 - 5:00 EST.
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/MARISOL ANN O'NEILL/ Examiner, Art Unit 1633
/ALLISON M FOX/Primary Examiner, Art Unit 1633
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