Notice of Pre-AIA or AIA Status
The examiner prosecuting the application has changed.
The present application, filed on or after March 16, 2013, is being examined under the first inventor to file provisions of the AIA .
DETAILED ACTION
Applicant’s response and claim amendments filed on 9/15/2025 are received and entered.
In the response to the most recent action, claims 1-4, 7-14, 23, 28-29, 49, 51, 52, 57, and 58 were previously under examination of the merits. In the instant action, claims 1, 23, 28, and 29 are currently amended. Claims 5-6, 15-22, 24-27, 30-48, 50, 53, 54, 60-63, and 66 are canceled without prejudice or disclaimer. Claims 55, 56, 59, 64, and 65 are withdrawn from consideration. Claim 67 is newly added, claims 3, 4, 8, and 10-13 are as originally presented. Regarding claim 67, no new matter has been added.
Claims 1-4, 7-14, 23, 28-29, 49, 51-52, 57-58 and 67 are currently under examination of the merits.
Any rejections/objections NOT repeated/presented here are withdrawn.
New Rejections
Claim Rejections - 35 USC § 112
Written Description
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 1-4, 7-14, 23, 28-29, 49, 51-52, 57-58 and 67 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.
The factors to be considered when analyzing claims for compliance with the written description requirement include: (A) actual reduction to practice; (B) disclosure of drawings or structural chemical formulas; (C) sufficient relevant identifying characteristics (e.g., complete structure, partial structure, physical and/or chemical properties, structure/function correlation); (D) level of skill and knowledge in the art; and (E) predictability in the art.
Reduction to Practice
The instant specification discloses fragments of a base editor (e.g., ABE, CBE) is fused to a split intein-N and a split intein-C for the delivery of a base editor. When fused to separate protein fragments, the inteins IntN and IntC recognize each other, splice themselves out and simultaneously ligate the flanking N- and C-terminal exteins of the protein fragments to which there were fused, thereby reconstituting a full-length protein from the two protein fragments.
Disclosure of Drawings or Structural Chemical Formulas
The instant specification discloses fragments of a fusion protein of the invention can vary in length, where in some embodiments, the protein fragments ranges from 2 amino acids to about 1000 amino acids.
Sufficient Relevant Identifying Characteristics
The instant specification does not provide sufficient relative identifying characteristics of an active fragment of an ABE or CBE. Applicant does not provide information or guidance on specific fragments of ABEs or CBEs, nor does the applicant disclose the specific sequence lengths, modifications, or limitations that would make a fragment of a base editor active, by itself.
Level of skill and Knowledge in the Art
The level of skill is high. One skilled in the art would need a proficient understanding of delivery of a polypeptide to a cell in conjunction with the functions of fusion proteins. The use of base editing fragments is known in the art, as evidenced by Joung et al. (US 2020/0172895 A1, published 6/4/2020) where Joung teaches truncated, catalytically inactive or deficient derivative fragments of a parental deaminase that when combined, forms a catalytically active base editor (see paragraph 0006). However, as mentioned in Joung, the split deaminases are not catalytically active until a fusion protein is formed.
In view of the totality of factors analyzed above, it is clear that the instant specification fails to reasonable convey that the instant inventors had possession of the instantly claimed subject matter (an active fragment of an adenosine deaminase domain or an active fragment of a cytidine deaminase domain) as of the effective filing date. The inventors do not describe structural or identifying characteristics of a standalone fragment that would exhibit deaminase activity without forming a fusion protein.
In view of the foregoing, claims 1-4, 7-14, 23, 28-29, 49, 51-52, 57-58 and 67 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 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 9-11 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.
Regarding claims 9-11, applicant amends claim 1 to recite where the multi-effector nucleobase editor comprises an adenosine deaminase and a cytidine deaminase (or a fragment thereof). Regarding claim 9, which is dependent on claim 1, applicant claims where the polypeptide comprises two adenosine deaminases, which are the same or different. Here, it is unclear whether the applicant claims a polynucleotide encoding two deaminases, wherein one deaminase is an adenosine deaminase and a second which is a cytidine deaminase, or where the polynucleotide encodes two adenosine deaminases. Therefore, the invention as claimed in claim 9 conflicts with the amendments proposed in claim 1.
Claims 10 and 11 are rejected as being dependent on claim 9.
The following is a quotation of 35 U.S.C. 112(d):
(d) REFERENCE IN DEPENDENT FORMS.—Subject to subsection (e), a claim in dependent form shall contain a reference to a claim previously set forth and then specify a further limitation of the subject matter claimed. A claim in dependent form shall be construed to incorporate by reference all the limitations of the claim to which it refers.
The following is a quotation of pre-AIA 35 U.S.C. 112, fourth paragraph:
Subject to the following paragraph [i.e., the fifth paragraph of pre-AIA 35 U.S.C. 112], a claim in dependent form shall contain a reference to a claim previously set forth and then specify a further limitation of the subject matter claimed. A claim in dependent form shall be construed to incorporate by reference all the limitations of the claim to which it refers.
Claim 9-11 are rejected under 35 U.S.C. 112(d) or pre-AIA 35 U.S.C. 112, 4th paragraph, as being of improper dependent form for failing to further limit the subject matter of the claim upon which it depends, or for failing to include all the limitations of the claim upon which it depends.
Regarding claim 9-11, applicant recites wherein the polynucleotide comprises two adenosine deaminase. However, claims 9-11 do not embody the limitations of claim 1, as recited and amended, wherein the polynucleotide encodes both an adenosine and cytidine deaminase.
Applicant may cancel the claim(s), amend the claim(s) to place the claim(s) in proper dependent form, rewrite the claim(s) in independent form, or present a sufficient showing that the dependent claim(s) complies with the statutory requirements.
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 1-4, 12-14, 23, 28-29, 49, 51-52, 57-58, and 67 are rejected under 35 U.S.C. 103 as being unpatentable over Liu1 et al. (US 20190225955 A1, published 7/25/2019, with an effective filing date of 10/22/2016) and Liu2 et al. (US 20180073012 A1, published 3/15/2018).
Regarding claim 1, Liu1 discloses proteins that are useful for editing nucleic acids comprising fusion proteins of Cas9 and nucleic acid editing enzymes or enzymatic domains (e.g., deaminase domains), wherein the Cas9 comprises an active or inactive DNA cleavage domain of Cas9 and/or the gRNA binding domain of Cas9 (see paragraphs [0013] and [0094]).
Regarding claim 2, Liu1 discloses that in some embodiments, any of the fusion proteins disclosed may comprise one or more nuclear localization sequence (NLS) (see paragraph [0159]), an effector domain (e.g., a deaminase, and a uracil glycosylase inhibitor (UGI)) (see paragraph [0063]), wherein suitable UGI protein and nucleotide sequences are known to those in the art, and include, for example, Uracil-DNA glycosylase inhibitor (see paragraph [0245]).
Regarding claims 3-4, Liu1 discloses that nuclear localization sequences are known in the art and would be apparent to the skilled artisan and that in some embodiments, a NLS comprises the amino acid sequence MDSLLMNRRKFLYQFKNVRWAKGRRETYLC of SEQ ID NO: 300. Sequence ID No: 300 disclosed by Liu is a bipartite NLS signal as evidenced by Ito et. al. Ito et al teaches that Seq ID No: 300 is a bipartite NLS (see Figure 1F), and that Cytidine deaminase has the bipartite NLS of Seq ID No: 300, which allows it to shuttle between cytoplasm and nucleus. Liu also discloses that the disclosed polypeptide may comprise one or more nuclear localization sequence (NLS) (see paragraph [0518]). Liu further discloses that any of the nuclear localization sequences may be fused to the disclosed polypeptide in any suitable localization, for example, to promote translocation of the polypeptide into a cell nucleus without compromising its function (see paragraph [0160]).
Regarding claim 12-14, Liu1 discloses programmable DNA-binding proteins such as such as zinc-finger domains, TALEs, and other Cas9 proteins could be fused to Cas9 to improve the ability to target nucleotide sequences having canonical or non-canonical PAMs (see paragraph [0330]). Liu further discloses that point mutations can be introduced into Cas9 to abolish nuclease activity, resulting in a dead Cas9 (dCas9) that still retains its ability to bind DNA in a sgRNA-programmed manner (see paragraph [0013]).
Regarding claim 23, Liu1 discloses proteins that are useful for editing nucleic acids comprising fusion proteins of Cas9 (napDNAbp) and nucleic acid editing enzymes or enzymatic domains (e.g., deaminase domains), wherein the Cas9 comprises an active or inactive DNA cleavage domain of Cas9 and/or the gRNA binding domain of Cas9 (see paragraphs [0013] and [0094]). Liu1 further discloses that in some embodiments, any of the fusion proteins disclosed may comprise one or more nuclear localization sequence (NLS) (see paragraph [0159]), an effector domain (e.g., a deaminase, and a uracil glycosylase inhibitor (UGI)) (see paragraph [0063]), wherein suitable UGI protein and nucleotide sequences are known to those in the art, and include, for example, Uracil-DNA glycosylase inhibitor (see paragraph [0245]). Liu1 also discloses a systematic series of fusions between Cas9 and deaminase domains (e.g., cytosine or adenosine deaminase enzymes) that has been generated in order to direct the enzymatic activities of these deaminases to a specific site in genomic DNA (see paragraph [0169]).
Regarding claim 28-29, Liu1 discloses proteins that are useful for editing nucleic acids (see paragraph [0013]) comprising the following domains [NH.sub.2]-[UGI]-[Cas9]-[deaminase]-[second Cas9]-[COOH] (see paragraph [0241]). Liu1 further discloses that in some embodiments, the effector domain is fused to the N-terminus or the C-terminus of the Cas9 protein (see paragraph ([0145]).
Regarding claim 49 and 51-52, Liu discloses polynucleotides encoding any of the Cas9 proteins, Cas9 fusion proteins, or guide RNA bound to the Cas9 protein or Cas9 fusion disclosed (see paragraph [0070]). Liu1 further discloses vectors comprising such polynucleotides (see paragraph [0070]).
Regarding claim 57, Liu1 discloses proteins that are useful for editing nucleic acids comprising fusion proteins of Cas9 or a fragment thereof (e.g., a protein comprising an active or inactive DNA cleavage domain of Cas9, and/or the gRNA binding domain of Cas9) (see paragraph [0094]).
Regarding claim 58, Liu1 further discloses kits comprising a nucleic acid construct, comprising (a) a nucleotide sequence encoding a Cas9 protein or a Cas9 fusion disclosed (see paragraph [0069]).
Regarding claim 67, Liu1 teaches where in some embodiments, any of the Cas9 proteins provided herein may be fused to a protein that has an enzymatic activity, wherein the enzymatic activity is … glycosylase activity (see paragraph 0009). It is evidenced by Schomacher et al. (Neil DNA glycosylases promote substrate turnover by Tdg during DNA demethylation, Nature Structural and Molecular Biology, Volume 23, pgs. 116-124, published 2016) wherein they show DNA glycosylases coordinate abasic-site processing during base excision (see abstract). Therefore an enzyme with glycosylase activity is an abasic editor.
Regarding claims 1, 23, and 28, Liu1 does not disclose a base editor polypeptide that has an adenosine deaminase domain and a cytidine deaminase domain, however, Liu does disclose that the base editing polypeptide is capable of having multiple deaminase domains (see paragraph 0013) and where the deaminase domain can be a cytidine or adenosine deaminase (see paragraph 0062).
Regarding claim 9, Liu1 does not teach where the polypeptide comprises two adenosine deaminases that are the same or different.
Regarding claims 1, 23, and 28, Liu2 teaches fusion proteins that comprise a nucleic acid programmable DNA binding protein, and at least two adenosine deaminase domains. Furthermore, Liu teaches where any of the fusion proteins may comprise 2, 3, 4, or 5 adenosine deaminase domains (see paragraph 0329). One with ordinary skill and creativity in the art would understand that a base editor polypeptide could include two different deaminase domains for improved base editing efficiency and targeting.
It would have been obvious to one with ordinary skill in the art, before the effective filing date, to modify the teachings of Liu to arrive at the claimed invention, or a multi-effector nucleobase editor polypeptide comprising a domain with specific nucleic acid sequence binding activity, an adenosine deaminase domain or an active fragment thereof, and a cytidine deaminase or an active fragment thereof, wherein the base editor deaminates both A and C in a target nucleic acid.
One would expect a reasonable chance of success as Liu teaches a nucleic acid base editor or fusion protein useful for targeted binding/editing of nucleic acids, including editing a single site within a subject’s genome (see paragraph 0013). Furthermore, Liu teaches where fusion proteins of Cas9 and nucleic acid editing enzymes or enzymatic domains, e.g., deaminase domains are provided (see paragraph 0013) or where the Cas9 protein may be fused to one or more domains that confer an activity to the protein, such as nucleic acid editing activity (e.g., deaminase activity or transcriptional activation activity) (see paragraph 0044).
One would be motivated to do so as Liu2 teaches where “without wishing to be bound by any theory, dimerization of adenosine deaminases (e.g., in cis or in trans) may improve the ability (e.g., efficiency) of the fusion protein to modify a nucleic acid base (see paragraph 0329). Though neither Liu teach the specific combination of an adenosine and cytidine deaminase together, it is already known in the art that a base editor polynucleotide fusion protein can contain multiple deaminases as evidenced by Liu2 and Liu1 contemplates the use of adenosine or cytidine deaminases. Therefore, one with ordinary skill and creativity would have motivation to create a base editor polynucleotide comprising of multiple different deaminases, for the purpose of being able to target multiple bases as well as being more efficient.
Furthermore, the Federal Circuit has recognized that an implicit motivation to combine exists not only when a suggestion may be gleaned from the prior art as a whole, but when the “improvement” is technology-independent and the combination of references results in a product or process that is more desirable, for example, because it is stronger, cheaper, cleaner, faster, lighter, smaller, more durable, or more efficient. See DyStar Textilfarben GmBH & Co. Deutschland KG v. C. H. Patrick Co., 464 F.3d 1356, 1368 (Fed. Cir. 2006).
In view of the foregoing, claims 1-4, 12-14, 23, 28-29, 49, 51-52, and 57-58 are rejected under 35 U.S.C. 103 as being prima facie obvious, before the effective filing date.
Claims 7-8 are rejected under 35 U.S.C. 103 as being unpatentable over Liu1 et. al. (US 20190225955 A1, Published: 7/25/2019; EFD: 10/22/2016), in view of Gaudelli et. al. (Nature, Vol. 551, pages 464-471, 2017).
Regarding claims 7-8, The teachings of Liu as applied to claim 1 are discussed in the 102 rejection above.
Liu does not teach the polypeptide of claim 1 wherein the adenosine deaminase is a TadA deaminase wherein the TadA deaminase is a modified adenosine deaminase that does not occur in nature.
Gaudelli teaches ABEs (such as TadA deaminases) introduce point mutations more efficiently and cleanly, and with less off-target genome modification, than a current Cas9 nuclease-based method, and can install disease-correcting or disease-suppressing mutations in human cells, and that introducing mutations at or near TadA D108 enable TadA to perform adenine deamination on DNA substrates (see page 456, column 2, paragraphs 1-2).
It would have been prima facie obvious to one of ordinary skill in the art before the effective filing date of the claimed invention to have modified the polypeptide of Liu with the TadA deaminase of Gaudelli wherein the TadA deaminase is a modified adenosine deaminase that does not occur in nature. One of ordinary skill in the art would have been motivated to do so because Gaudelli teaches that TadA introduces point mutations efficiently and cleanly, and with less off-target genome modification compared to current Cas9 nuclease-based methods, and can install disease-correcting or disease-suppressing mutations in human cells, and that modifying TadA enables TadA to perform adenine deamination on DNA substrates.
Response to Arguments
Applicant’s arguments have been fully considered but are not found persuasive. Applicant does not directly argue the 103 rejection for claims 7 and 8 using the art of Liu et al. and Guadelli et al., however, applicant does argue that by amending claims 1, 23, and 28 to recite a multi-effector base editor polynucleotide comprising both an adenosine and cytidine deaminase renders, the art of Liu which only teaches either an adenosine or cytidine deaminase, insufficient as not all limitations are taught. This argument is rendered moot in view of new rejections necessitated by amendments.
Examiner argues that one skilled in the art and with ordinary creativity would apply both the arts of Liu, as described above, to reach the claimed invention. Liu2 clearly disclose the use of multiple adenosine base editors, which could enhance the efficiency (see paragraph 0329), and Liu1 describes the use of adenosine or cytidine base editors. One would envision that the combination of both an adenosine and cytidine deaminase would allow one to modify two bases at once, leading to improved efficiency of base editing.
The Federal Circuit has recognized that an implicit motivation to combine exists not only when a suggestion may be gleaned from the prior art as a whole, but when the “improvement” is technology-independent and the combination of references results in a product or process that is more desirable, for example, because it is stronger, cheaper, cleaner, faster, lighter, smaller, more durable, or more efficient. See DyStar Textilfarben GmBH & Co. Deutschland KG v. C. H. Patrick Co., 464 F.3d 1356, 1368 (Fed. Cir. 2006).
Conclusion
No claims are allowed.
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 DAVID YU whose telephone number is (571)272-1118. The examiner can normally be reached Monday-Friday 7:30 am -5 pm.
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/D.T.Y./Examiner, Art Unit 1635
/RAM R SHUKLA/Supervisory Patent Examiner, Art Unit 1635
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