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 .
Election/Restrictions
Restriction to one of the following inventions is required under 35 U.S.C. 121:
I. Claims 1-8, drawn to a pair of helper guide RNA/guide RNA for editing a human PCSK9 nucleic acid sequence , classified in C12N 15/113.
II. Claim 9, drawn to a method of inactivating a PCSK9 gene in a cell, classified in A61K 48/00.
Inventions I and II are related as product and process of use. The inventions can be shown to be distinct if either or both of the following can be shown: (1) the process for using the product as claimed can be practiced with another materially different product or (2) the product as claimed can be used in a materially different process of using that product. See MPEP § 806.05(h). In the instant case, the process of inactivating a PCSK9 gene as claimed in Group II can be practiced with a materially different product, such as a different gene-editing system like Zinc Finger Nucleases (ZNFs), Transcription Activator-Like Effectors (TALENS), RNA interference, or a standard CRISPR-Cas9 knockout system. Additionally, the product of Group I could be used in a materially different process, such as in vitro diagnostic assays (e.g., Targeted Sequencing Enrichment or Fluorescence In Situ Hybridization FISH)) to detect the presence or accessibility of the PCSK9 target sites, rather than for the functional inactivation of the gene in a live cell. Because the process can be practiced with a materially different product and the product can be used in a materially different process, the inventions are distinct.
Restriction for examination purposes as indicated is proper because all the inventions listed in this action are independent or distinct for the reasons given above and there would be a serious search and/or examination burden if restriction were not required because one or more of the following reasons apply:
the inventions have acquired a separate status in the art in view of their different classification;
the inventions have acquired a separate status in the art in view of their recognized divergent subject matter; and
the inventions require a different field of search (e.g., searching different classes/subclasses or electronic resources, or employing different search strategies or search queries).
Applicant is advised that the reply to this requirement to be complete must include (i) an election of an invention to be examined even though the requirement may be traversed (37 CFR 1.143) and (ii) identification of the claims encompassing the elected invention.
The election of an invention may be made with or without traverse. To reserve a right to petition, the election must be made with traverse. If the reply does not distinctly and specifically point out supposed errors in the restriction requirement, the election shall be treated as an election without traverse. Traversal must be presented at the time of election in order to be considered timely. Failure to timely traverse the requirement will result in the loss of right to petition under 37 CFR 1.144. If claims are added after the election, applicant must indicate which of these claims are readable upon the elected invention.
Should applicant traverse on the ground that the inventions are not patentably distinct, applicant should submit evidence or identify such evidence now of record showing the inventions to be obvious variants or clearly admit on the record that this is the case. In either instance, if the examiner finds one of the inventions unpatentable over the prior art, the evidence or admission may be used in a rejection under 35 U.S.C. 103 or pre-AIA 35 U.S.C. 103(a) of the other invention.
This application contains claims directed to the following patentably distinct species regarding claim 7,
Species 1: pair of helper guide RNA/guide SEQ ID NO:166 and 181;
Species 2: pair of helper guide RNA/guide SEQ ID NO:167 and 182;
Species 3: pair of helper guide RNA/guide SEQ ID NO:168 and 183;
Species 4: pair of helper guide RNA/guide SEQ ID NO:169 and 184;
Species 5: pair of helper guide RNA/guide SEQ ID NO:170 and 185;
Species 6: pair of helper guide RNA/guide SEQ ID NO:171 and 186;
Species 7: pair of helper guide RNA/guide SEQ ID NO:172 and 187;
Species 8: pair of helper guide RNA/guide SEQ ID NO:173 and 188;
Species 9: pair of helper guide RNA/guide SEQ ID NO:174 and 189;
Species 10: pair of helper guide RNA/guide SEQ ID NO:175 and 190;
Species 11: pair of helper guide RNA/guide SEQ ID NO:176 and 191;
Species 12: pair of helper guide RNA/guide SEQ ID NO:177 and 192;
Species 13: pair of helper guide RNA/guide SEQ ID NO:178 and 193;
Species 14: pair of helper guide RNA/guide SEQ ID NO:179 and 194;
Species 15: pair of helper guide RNA/guide: SEQ ID NO:180 and 195.
The species are independent or distinct because each of these species is defined by a unique set of nucleotide sequences that target specific, different genomic coordinates within the PCSK9 gene. These species are independent or distinct because each pair of sequences (helper gRNA and guide RNA) is structurally and chemically divergent from the others. A search for and/or prior art rejection of one specific sequence pair would not necessarily apply to or anticipate the others, as the biding affinity, off-target profile, and editing efficiency at one site are not predictive of the performance at a different site. Furthermore, the different species target distinct non-stop codons or different positions within the gene, which may result in varying degrees of gene inactivation or different truncated protein products. In addition, these species are not obvious variants of each other based on the current record.
Applicant is required under 35 U.S.C. 121 to elect a single disclosed species, or a single grouping of patentably indistinct species, for prosecution on the merits to which the claims shall be restricted if no generic claim is finally held to be allowable. Currently, claim 1 is generic.
There is a serious search and/or examination burden for the patentably distinct species as set forth above because at least the following reason(s) apply: each species requires a separate search of the patent and non-patent literature to identify the structural elements not shared with the other species.
Applicant is advised that the reply to this requirement to be complete must include (i) an election of a species to be examined even though the requirement may be traversed (37 CFR 1.143) and (ii) identification of the claims encompassing the elected species or grouping of patentably indistinct species, including any claims subsequently added. An argument that a claim is allowable or that all claims are generic is considered nonresponsive unless accompanied by an election.
The election may be made with or without traverse. To preserve a right to petition, the election must be made with traverse. If the reply does not distinctly and specifically point out supposed errors in the election of species requirement, the election shall be treated as an election without traverse. Traversal must be presented at the time of election in order to be considered timely. Failure to timely traverse the requirement will result in the loss of right to petition under 37 CFR 1.144. If claims are added after the election, applicant must indicate which of these claims are readable on the elected species or grouping of patentably indistinct species.
Should applicant traverse on the ground that the species, or groupings of patentably indistinct species from which election is required, are not patentably distinct, applicant should submit evidence or identify such evidence now of record showing them to be obvious variants or clearly admit on the record that this is the case. In either instance, if the examiner finds one of the species unpatentable over the prior art, the evidence or admission may be used in a rejection under 35 U.S.C. 103 or pre-AIA 35 U.S.C. 103(a) of the other species.
Upon the allowance of a generic claim, applicant will be entitled to consideration of claims to additional species which depend from or otherwise require all the limitations of an allowable generic claim as provided by 37 CFR 1.141.
Applicant is reminded that upon the cancelation of claims to a non-elected invention, the inventorship must be corrected in compliance with 37 CFR 1.48(a) if one or more of the currently named inventors is no longer an inventor of at least one claim remaining in the application. A request to correct inventorship under 37 CFR 1.48(a) must be accompanied by an application data sheet in accordance with 37 CFR 1.76 that identifies each inventor by his or her legal name and by the processing fee required under 37 CFR 1.17(i).
The examiner has required restriction between product or apparatus claims and process claims. Where applicant elects claims directed to the product/apparatus, and all product/apparatus claims are subsequently found allowable, withdrawn process claims that include all the limitations of the allowable product/apparatus claims should be considered for rejoinder. All claims directed to a nonelected process invention must include all the limitations of an allowable product/apparatus claim for that process invention to be rejoined.
In the event of rejoinder, the requirement for restriction between the product/apparatus claims and the rejoined process claims will be withdrawn, and the rejoined process claims will be fully examined for patentability in accordance with 37 CFR 1.104. Thus, to be allowable, the rejoined claims must meet all criteria for patentability including the requirements of 35 U.S.C. 101, 102, 103 and 112. Until all claims to the elected product/apparatus are found allowable, an otherwise proper restriction requirement between product/apparatus claims and process claims may be maintained. Withdrawn process claims that are not commensurate in scope with an allowable product/apparatus claim will not be rejoined. See MPEP § 821.04. Additionally, in order for rejoinder to occur, applicant is advised that the process claims should be amended during prosecution to require the limitations of the product/apparatus claims. Failure to do so may result in no rejoinder. Further, note that the prohibition against double patenting rejections of 35 U.S.C. 121 does not apply where the restriction requirement is withdrawn by the examiner before the patent issues. See MPEP § 804.01.
During a telephone conversation with Alex Nie on May 5, 2026, a provisional election was made without traverse to prosecute the invention of Group I, claims 1-8. Additionally, a provisional election was made without traverse to prosecute the invention of Species 1, pair of helper guide RNA/guide SEQ ID NO:166 and 181. Affirmation of this election must be made by applicant in replying to this Office action. Claim 9 is withdrawn from further consideration by the examiner, 37 CFR 1.142(b), as being drawn to a non-elected invention.
Claims 1-8 of the elected invention, Group I, read on the elected species.
STATUS OF CLAIMS
Claims 1-9 are pending.
Claims 1-8 are under examination in the instant office action.
Priority
Acknowledgment is made of applicant’s claim for foreign priority under 35 U.S.C. 119 (a)-(d). The certified copy has been filed in parent Application No. 17/427040, filed on 02/03/2020.
Receipt is acknowledged of certified copies of papers required by 37 CFR 1.55.
However, claims 1-8 are not entitled to the right of priority under 35 U.S.C. 119(a)-(d) and 365(a) to the prior filed foreign Application No. PCT/CN2019/074577 because the prior filed foreign application fails to provide adequate support for the claimed subject matter in the manner provided by 35 U.S.C. 122(a). Specifically, the earlier foreign application fails to disclose helper guide RNA and nucleic acid sequences of SEQ ID NOs: 166-195.
Applicant’s claim for the benefit of a prior-filed application under 35 U.S.C. 119(e) or under 35 U.S.C. 120, 121, 365(c), or 386(c) is acknowledged. Applicant states that the instant application: “is a continuation of U.S. Application No. 17/862,354, filed July 11, 2022, which is a continuation of U.S. Application No. 17/427,040, filed July 29, 2021, now U.S. Patent No. 11,384,353, which is a U.S. National Stage Application under 35 U.S.C. §371 of International Application No. PCT/CN2020/074218, filed February 3, 2020, which claims the priority to PCT/CN2019/074577, filed on February 2, 2019. The examiner finds support for all claimed limitations in the instant application within the previously filed Application No. PCT/CN2020/074218, filed 02/03/2020. Thus, the examiner is considering claims 1-8 of the instant application to have an effective filing date of February 3, 2020.
Information Disclosure Statement
The information disclosure statement (IDS) submitted on 09/29/2023 is in compliance with the provisions of 37 CFR 1.97. Accordingly, the information disclosure statement is being considered by the examiner.
Claim Rejections - 35 USC § 112
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 5-7 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. It is unclear as to how claim 5 further limits claim 1 since it reverses the binding sites for the guide and helper guide RNA. It is noted that claim 1 recites “…wherein the guide RNA specifically targets a first site…, and wherein the helper guide RNA specifically targets a second site…” For claim 5 to be a proper dependent claim, it has to further limit the invention of claim 1. Claims 6 and 7 inherit for the same reason above because they depend from claim 5.
To obviate this rejection, applicants could present claim 5 as an independent claim.
In the interest of compact prosecution, the wherein clause in claim 5 is being considered as not further limiting claim 1; therefore, claim 5 will merely be a reflection of claim 1 so the examiner can examine claims 6 and 7 on the merits.
Claim Rejections - 35 USC § 103
In the event the determination of the status of the application as subject to AIA 35 U.S.C. 102 and 103 (or as subject to pre-AIA 35 U.S.C. 102 and 103) is incorrect, any correction of the statutory basis (i.e., changing from AIA to pre-AIA ) for the rejection will not be considered a new ground of rejection if the prior art relied upon, and the rationale supporting the rejection, would be the same under either status.
The following is a quotation of 35 U.S.C. 103 which forms the basis for all obviousness rejections set forth in this Office action:
A patent for a claimed invention may not be obtained, notwithstanding that the claimed invention is not identically disclosed as set forth in section 102, if the differences between the claimed invention and the prior art are such that the claimed invention as a whole would have been obvious before the effective filing date of the claimed invention to a person having ordinary skill in the art to which the claimed invention pertains. Patentability shall not be negated by the manner in which the invention was made.
The factual inquiries for establishing a background for determining obviousness under 35 U.S.C. 103 are summarized as follows:
1. Determining the scope and contents of the prior art.
2. Ascertaining the differences between the prior art and the claims at issue.
3. Resolving the level of ordinary skill in the pertinent art.
4. Considering objective evidence present in the application indicating obviousness or nonobviousness.
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 1-3 and 5-8 are rejected under 35 U.S.C. 103 as being unpatentable over Lundberg A. et. al., (US20200248168A1) in view of Maianti J. et. al., (US20180237787A1) and Ran A. et. al., (Cell; 154(6):1380–1389 and supplemental material 01, published 2013 Aug 29).
Regarding claims 1-2 and 6-7, Lundberg teaches CRISPR-mediated editing of the PCSK9 gene using one or more sgRNAs comprising spacer sequences corresponding to SEQ ID NOs: 5,5305-28,696, including spacer sequences corresponding to applicants target sites, see [00015]-[00016], [00019], [00023], [00049], [000357]-[000359], table 5, table 6, claims 21-22, 28, and 32-35. The disclosed spacer sequences correspond exactly to the 20-mer protospacer portions of applicant’s claimed 23-nt target sequences (which include PAM), and therefore target the same genomic loci. For example, Lundberg teaches SEQ ID NOs: 14235 and 8517, which align with 100% identity to the 20-mer protospacer portions of the elected helper guide RNA/guide RNA pair targeting SED ID NOs: 166 and 181, of the instant case (see sequence search results attached to the file wrapper). Lundberg further teaches that the CRISPR-mediated editing of PCSK9 gene “can cause a shift in reading frame and/or the creation of a premature stop codon,” see [00080].
Regarding claim 8, Lundberg teaches “a DNA encoding the single-molecule guide polynucleotide,” see [00025].
Lundberg does not explicitly teach helper guide terminology or “paired guide” use such that one guide binds a first site and a second guide binds a second site that is 20-100 bases from the first site. Lundberg also does not explicitly teach the guide RNA enables base editing to convert a non-stop codon (i.e., CAG/CAA/CGA) to a stop codon.
Maianti teaches “systems, compositions, kits, and methods for modifying a polynucleotide (e.g., DNA) encoding a PCSK9 protein to produce loss-of-function PCSK9 variants,” see [0004]. Specifically, Maianti teaches “(i) a fusion protein comprising: (a) a guide nucleotide sequence-programmable DNA binding protein domain; and (b) a cytosine deaminase domain; and (ii) a guide nucleotide sequence targeting the fusion protein of (i) to a target cytosine (C) base in the PCSK9-encoding polynucleotide, wherein the contacting results in deamination of the target C base by the fusion protein, resulting in a cytosine (C) to thymine (T) change in the PCSK9-encoding polynucleotide,” see [0005]. Maianti further teaches that “the guide nucleotide sequence-programmable DNA binding protein domain” may be “a nuclease inactive Cas9 (dCas9) domain,” or “a Cas9 nickase,” see [0006]. Maianti further teaches that “the cytosine deaminase domain comprises an apolipoprotein B mRNA-editing complex (APOBEC) family deaminase,” see [0010]. Thus, Maianti teaches that when “the C to T change occurs in the coding sequence or on the coding strand of the PCSK9-encoding polynucleotide,” by the activity of the CRISPR/APOBEC fusion protein, a “loss-of-function mutation introduces a premature stop codon in the PCSK9 coding sequence that leads to a truncated or non-functional PCSK9 protein,” see [0016-0017]. Maianti further teaches that “the premature stop codon is generated from a CAG to TAG change via the deamination of the first C on the coding strand,” or “the premature stop codon is generated from a CGA to TGA change via the deamination of the first C on the coding strand” or “ the premature stop codon is generated from a CAA to TAA change via the deamination of the first C on the coding strand,” see [0018]. Maianti further teaches “the guide nucleotide sequence is selected from the guide nucleotide sequences listed in Table 6 (SEQ ID NO: 938-1123)” to enact a C to T mutation resulting in a pre-mature stop codon in PCSK9, many of which correspond with 100% identity to the 20-mer photospacer spacer within the claimed target sequences. For example, as a representative set, SEQ ID NO: 1094 taught by Maianti corresponds with 100% identity to the 20-mer photospacer spacer within the claimed target sequence SEQ ID NO: 195; SEQ ID NO: 1088 taught by Maianti corresponds with 100% identity to the 20-mer photospacer spacer within the claimed target sequence SEQ ID NO: 194; SEQ ID NO: 1079 taught by Maianti corresponds with 100% identity to the 20-mer photospacer spacer within the claimed target sequence SEQ ID NO: 193; SEQ ID NO: 1062 taught by Maianti corresponds with 100% identity to the 20-mer photospacer spacer within the claimed target sequence SEQ ID NO: 192; and among others, see sequence search results attached to the file wrapper.
Maianti further teaches that the CRISPR/cytosine deaminase fusion system to edit PCSK9 has a more favorable safety profile, due to the low probability of off-target effects,” and thus has “ low impact on genomic stability, including oncogene activation or tumor suppressor inactivation,” see [0004]. Maianti further teaches “the loss-of-function variants” in PCSK9 have “a cardioprotective function” by reducing “LDL levels…, LDL cholesterol levels…, and overall cholesterol levels” while also increasing HDL levels, see [0004].
While Maianti teaches targeting PCSK9 with a CRISPR/APOBEC fusion protein to introduce pre-mature stop codons via base-editing, Maianti does not teach helper guide terminology or “paired guide” use such that one guide binds a first site and a second guide binds a second site that is 20-100 bases from the first site.
However, Ran teaches combining “a Cas9 nickase mutant with pairs of guide RNAs to introduce targeted double-strand breaks” with reduced “off-target activity by 50–1,000 fold,” and claims that “this versatile strategy thus enables a wide variety of genome editing applications with higher levels of specificity,” see abstract. Ran teaches that “The Cas9 nuclease from Streptococcus pyogenes can be directed by a chimeric single guide RNA (sgRNA) to any genomic locus followed by a 5′-NGG protospacer-adjacent motif (PAM),” and that “a 20-nt guide sequence within the sgRNA directs Cas9 to the genomic target via Watson-Crick base pairing and can be easily engineered to target a desired genomic locus.” Ran further teaches “that although each base within the 20-nt guide sequence contributes to overall specificity, multiple mismatches between the guide RNA and its complementary target DNA sequence can be tolerated depending on the quantity, position, and base identity of mismatches,” and that “these unwanted mutations can potentially limit the utility of Cas9 for genome editing applications that require high levels of precision, such as generation of isogenic cell lines for testing causal genetic variations or in vivo and ex vivo genome editing-based therapies,” see introduction second paragraph. “To improve the specificity of Cas9-mediated genome editing,” Ran teaches “a novel strategy that combines the D10A mutant nickase version of Cas9 (Cas9n) with a pair of offset sgRNAs complementary to opposite strands of the target site,” and that “this strategy minimizes off-target mutagenesis by each individual Cas9n-sgRNA complex while maintaining on-target modification rates similar to those of wild type Cas9,” see introduction third paragraph.
To identify the optimal spacing/offset of the sgRNAs, Ran further teaches a “designed sets of sgRNA pairs targeted against the human EMX1 genomic locus separated by a range of offset distances from approximately -200 to 200 bp,” and observed “robust NHEJ (up to 40%)…for sgRNA pairs with offsets from -4 to 20 bp, with modest indels forming in pairs offset by up to 100-bp,” see results: Cas9 nickase generates efficient NHEJ with paired, offset guide RNAs, second paragraph, and Table S1 supplemental material 01. Ran further teaches an exemplary sgRNA pair with a 23bp offset, see Figure 3A (provided below for convenience) and Results: Double nicking mediates highly specific genome editing, paragraph one. This offset squarely falls within the claimed range, 20-100 bases, as recited in claim 1 of the instant case. Furthermore, the paired guide RNAs Ran teaches are 20-mers, as shown in Figure 3A, and thus bind to a sequence that is 7-23 nucleotides in length. Ran additionally conducted
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“off-target analysis by deep sequencing for two sgRNA pairs (offsets of 16 and 20 bp) targeting the VEGFA locus, with similar results,” see Figure 3E and Results: Double nicking mediates highly specific genome editing, paragraph two. Ran emphasises “that the relative positions of the guide pairs are the most important parameters…,” see Results: Double nicking mediates highly specific genome editing, paragraph three.
It would have been obvious to a person having ordinary skill in the art (PHOSITA) before the effective filing date to modify the CRISPR-mediated PCSK9 editing system taught by Lundberg by employing the known CRISPR/cytosine deaminase base-editing fusion system taught by Maianti to introduce a premature stop codon in PCSK9, and further by using paired guide RNAs targeting nearby offset sites as taught by Ran such that one guide binds a first site and a second guide binds a second site located 20-100 bases from the first site. A PHOSITA would have been motivated to do so because both Lundberg and Maianti are directed to CRISPR-mediated editing of the same gene, PCSK9, and Maianti expressly teaches that bases editing of PCSK9 to convert non-stop codons (CAG, CAA, or CGA) into stop codons creates desirable loss-of-function variants while providing a more favorable safety profile due to the low probability of off-target effects and reduced impact on genomic instability. Maianti further motivates by teaching that such PCSK9 loss-of-function variants are therapeutically beneficial because they reduce LDL and overall cholesterol levels and increase HDL level. Additionally, Ran motivated by teaching that paired nearby guide RNAs improve editing specificity while maintaining robust on-target editing efficiency. Thus, a PHOSITA would have been motivated to combine these techniques to achieve therapeutically beneficial PCSK9 distribution with improved editing precision and safety. A PHOSITA would have had a reasonable expectation of success because all three employ the same underlying CRISPR/Cas platform using standard 20-nucleotide guide sequences directed to known genomic loci, and both Lundberg and Maianti demonstrate successful targeting and editing of the same PCSK9 locus using CRISPR-based systems, thereby evidencing that PCSK9 was a known and predictable target for CRISPR modification. Ran further demonstrates that paired offset guide RNAs function effectively over offsets including those within the claimed 20-100 base range, thereby providing a reasonable expectation that the combined system would successfully edit PCSK9 with less off target effects.
Claim 4 is rejected under 35 U.S.C. 103 as being unpatentable over Lundberg A. et. al., (US20200248168A1) in view of Maianti J. et. al., (US20180237787A1) and Ran A. et. al., (Cell; 154(6):1380–1389 and supplemental material 01, published 2013 Aug 29) as applied to claims 1-3 and 5-8 above, and further in view of Rose J. et. al., (bioRxiv 597849 and supplemental information, published 2019 April 03).
While Ran teaches paired 20-mer guide RNAs targeting nearby offset sites, neither Lundberg, Maianti, nor Ran explicitly teach co-administering a catalytically inactive truncated helper guide RNA, such as an 8-15 nucleotide guide, to improve editing specificity and reduce off-target effects.
Rose teaches “suppression of unwanted CRISPR/Cas9 editing by co-administration of catalytically inactivating truncated guide RNAs,” see title. That is, Rose teaches “off-target sites can be shielded from the active Cas9•single guide RNA (sgRNA) complex through the co-administration of dead-RNAs (dRNAs), truncated guide RNAs that direct Cas9 binding but not cleavage,” and thus Rose enables “precise genome editing by establishing a novel and flexible approach for suppressing unwanted editing of both off-targets and HDR-corrected sites ,” see abstract. Rose further teaches that the “off-target suppression approach is based on the observation that sgRNAs with target recognition sequences 16 or fewer bases in length direct Cas9 binding to DNA target sites but do not promote cleavage,” and that the approach yields “up to a ∼40-fold increase in specificity,” with minimal optimization of the truncated guide. Rose provides exemplary truncated guide RNA as 15-bp in length, see supplemental material Figure S1. Rose suggest the approach “can be combined with other approaches for improving specificity,” see introduction paragraph two and Figure 1. Rose further teaches that these methods are “easy-to-implement, effective and complementary methods for refining genome editing in both research and clinical applications,” thereby expressly encouraging their combination with existing CRISPR editing systems.
It would have been obvious to a person having ordinary skill in the art (PHOSITA) before the effective filing date to further modify the Lundberg/Maianti/Ran combined system by employing one of the paired guide RNAs as a catalytically inactive truncated helper guide RNA having a spacer length of 5-15 nucleotides, as taught by Rose. A PHOSITA would have been motivated to do so because Rose expressly teaches that truncated guide RNAs of 16 nucleotides or fewer bind target DNA without promoting cleavage, thereby suppressing unwanted editing at the helper target site and improving specificity up to approximately 40-fold, and further teaches that this approach can be combined with other specificity-improving CRISPR strategies as an easy-to-implement and complementary method for refining genome editing. A PHOSITA would have had a reasonable expectation of success because Rose demonstrated successful co-administration of active sgRNAs and truncated dead guide RNAs within he same CRISPR/Cas9 platform, using standard guide design principles, and therefore a PHOSITA would reasonably have expected that substituting one of Ran’s paired guides with a known 15-nucleotide truncated helper guide would preserve target binding while reducing undesired editing.
Double Patenting
The nonstatutory double patenting rejection is based on a judicially created doctrine grounded in public policy (a policy reflected in the statute) so as to prevent the unjustified or improper timewise extension of the “right to exclude” granted by a patent and to prevent possible harassment by multiple assignees. A nonstatutory double patenting rejection is appropriate where the conflicting claims are not identical, but at least one examined application claim is not patentably distinct from the reference claim(s) because the examined application claim is either anticipated by, or would have been obvious over, the reference claim(s). See, e.g., In re Berg, 140 F.3d 1428, 46 USPQ2d 1226 (Fed. Cir. 1998); In re Goodman, 11 F.3d 1046, 29 USPQ2d 2010 (Fed. Cir. 1993); In re Longi, 759 F.2d 887, 225 USPQ 645 (Fed. Cir. 1985); In re Van Ornum, 686 F.2d 937, 214 USPQ 761 (CCPA 1982); In re Vogel, 422 F.2d 438, 164 USPQ 619 (CCPA 1970); In re Thorington, 418 F.2d 528, 163 USPQ 644 (CCPA 1969).
A timely filed terminal disclaimer in compliance with 37 CFR 1.321(c) or 1.321(d) may be used to overcome an actual or provisional rejection based on nonstatutory double patenting provided the reference application or patent either is shown to be commonly owned with the examined application, or claims an invention made as a result of activities undertaken within the scope of a joint research agreement. See MPEP § 717.02 for applications subject to examination under the first inventor to file provisions of the AIA as explained in MPEP § 2159. See MPEP § 2146 et seq. for applications not subject to examination under the first inventor to file provisions of the AIA . A terminal disclaimer must be signed in compliance with 37 CFR 1.321(b).
The filing of a terminal disclaimer by itself is not a complete reply to a nonstatutory double patenting (NSDP) rejection. A complete reply requires that the terminal disclaimer be accompanied by a reply requesting reconsideration of the prior Office action. Even where the NSDP rejection is provisional the reply must be complete. See MPEP § 804, subsection I.B.1. For a reply to a non-final Office action, see 37 CFR 1.111(a). For a reply to final Office action, see 37 CFR 1.113(c). A request for reconsideration while not provided for in 37 CFR 1.113(c) may be filed after final for consideration. See MPEP §§ 706.07(e) and 714.13.
The USPTO Internet website contains terminal disclaimer forms which may be used. Please visit www.uspto.gov/patent/patents-forms. The actual filing date of the application in which the form is filed determines what form (e.g., PTO/SB/25, PTO/SB/26, PTO/AIA /25, or PTO/AIA /26) should be used. A web-based eTerminal Disclaimer may be filled out completely online using web-screens. An eTerminal Disclaimer that meets all requirements is auto-processed and approved immediately upon submission. For more information about eTerminal Disclaimers, refer to www.uspto.gov/patents/apply/applying-online/eterminal-disclaimer.
Claims 1-8 are rejected on the ground of nonstatutory double patenting as being unpatentable over claims 1-4 of U.S. Patent No. US11840685B2 in view Lundberg A. et. al., (US20200248168A1) and Maianti J. et. al., (US20180237787A1).
Claims 1-4 of U.S. Patent No. US11840685B2 teach a dual guide RNA system comprising a target single guide RNA having sequence complementarity to a first target nucleic acid sequence proximate to a first PAM site, a helper single guide RNA having complementarity to a second target nucleic acid sequence proximate to a second PAM site, wherein said second spacer is 8-15 bases in length, together with a clustered regularly interspaced short palindromic repeats (CRISPR)-associated (Cas) protein and a nucleobase deaminase, and wherein the second PAM site is from 10 to 150 bases from the first PAM site, thereby teaching the same general dual-guide/helper guide architecture as presently claimed. The patented claims differ from the instant claims in that they do not expressly limit the target nucleic acid sequence to human PCSK9, do not expressly recite the specific claimed PCSK9 target sequences , and do not expressly recite conversion of a non-stop codon to a stop codon. However, as discussed above and incorporated herein by reference to the 103 rejection above, Lundberg teaches CRISPR-mediated editing of the human PCSK9 gene using guide RNAs corresponding to the presently claimed and elected target sequences, and Maianti teaches CRISPR/deaminase-mediated base editing of PCSK9 to convert non-stop codons including CAG, CAA, and CGA into stop codons. Therefore, it would have been obvious to a person having ordinary skill in the art before the effective filing date to modify the claimed dual guide RNA system of U.S. Patent No. US11840685B2 to target human PCSK9 using the known guide sequences and base-editing objectives taught by Lundberg and Maianti, resulting in the presently claimed pair of helper guide RNA/guide RNA for editing a human PCS K9 nucleic acid sequence.
Conclusion
No claims are allowed.
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/COREY LANE BRETZ/Patent Examiner, 1635
/RAM R SHUKLA/Supervisory Patent Examiner, Art Unit 1635
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