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
Applicant’s election of Group I (claims 1-12, 14, 33, 46, and 65; drawn to a method for testing whether a target protein regulates viral RNA translation) in the reply filed on 19 December 2025 is acknowledged. Applicant’s election of species (claims 9 – inhibitor, and claim 10 – KRAB) is acknowledged. Because applicant did not distinctly and specifically point out the supposed errors in the restriction requirement, the election has been treated as an election without traverse (MPEP § 818.01(a)).
Claims 23 and 55 withdrawn from further consideration pursuant to 37 CFR 1.142(b) as being drawn to a nonelected Group II of invention (drawn to a kit for testing whether a target protein regulates viral RNA translation), there being no allowable generic or linking claim. Claims 11 and 12 withdrawn from further consideration pursuant to 37 CFR 1.142(b) as being drawn to a nonelected species (activator), there being no allowable generic or linking claims.
Accordingly, claims 1-10, 14, 33, 46, and 65 are examined herein.
Priority
Acknowledgment is made of applicant's claim for priority based on a US Provisional Application
No. 63/002,576 filed on 31 March 2020.
Claim Objections
Claim 14 objected to because of the following informalities: the recitation of "nucleotide sequence a second reporter protein" line 7 is grammatically incorrect. Therefore, it should read as "nucleotide sequence encoding a second reporter protein". Appropriate correction is required.
Claim 14 objected to under 37 CFR 1.75 as being a substantial duplicate of claim 1. Claim 46 objected to under 37 CFR 1.75 as being a substantial duplicate of claim 33. When two claims in an application are duplicates or else are so close in content that they both cover the same thing, despite a slight difference in wording, it is proper after allowing one claim to object to the other as being a substantial duplicate of the allowed claim. See MPEP § 608.01(m).
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 1-10, 14, 33, 46, and 5 are rejected under 35 U.S.C. 103 as being unpatentable over Jaafar et al (Translation initiation by the hepatitis C virus IRES requires eIF1A and ribosomal complex remodeling; eLife, 2016, 5:e21198) in view of Dasgupta et al (US 6,833,254 B2; Published Date: 21 December 2004) and further in view of Gersbach et al (US 2019/0127713 A1; Published Date: 02 May, 2019).
Regarding claim 1, Jaafar teaches a method for testing whether eukaryotic initiation factor eIF1A (i.e., a target protein) is necessary for HCV IRES-based translation (i.e., regulates viral RNA translation) (pg. 3, second paragraph). Jaafar teaches the method comprises: a) introducing into rabbit reticulocyte lysate: i) a reporter nucleic acid comprising a nucleotide sequence encoding a bicistronic reporter (i.e., translation monitor) comprising "a cap-driven (Rluc) (i.e., a first reporter protein translated under the control of a Cap-dependent translation element) and a HCV IRES-driven (CAT) ORFs" (i.e., a second reporter protein translated under the control of a Cap-independent translation element) (pg. 5, third paragraph; Figure 2C); ii) an RNA aptamer α-eIF1A (i.e., a regulatory nucleic acid) that binds to eIF1A (pg. 5, third paragraph; Figure 2A) , thereby generating a test host cell; and b) detecting expression of Rluc and CAT from lysates treated with α-eIF1A (i.e., in the test host cell) to lysates treated with no RNA or a randomized 40 nucleotide RNA (i.e., in a control host cell that comprises the reporter nucleic acid but not the regulatory nucleic acid) (pg. 5, third paragraph; Figure 2C). Jaagar further teaches "the HCV IRES requires eIF1A for full function" (pg. 5, third paragraph) because Figure 2C demonstrated the expression of Rluc and CAT in lysate with the aptamer (i.e., test host cell) are reduced compared to their expression in lysate with no RNA or +N40 randomized RNA (i.e., control host cell), therefore, Jaagar positively teaches a method wherein a target protein is considered to regulate translation via the Cap-dependent or -independent element based on the expression of the first and second reporter proteins.
However, Jaagar teaches a method comprising introducing a bicistronic reporter into rabbit reticulocyte lysate, which is a cell-free system used for in vitro protein sythesis, rather than introducing the bicistronic reporter into a host cell.
Dasgupta teaches a method to identify trans-acting translation factors, e.g., eIF1A, (i.e., target protein) using a bicistronic reporter in cells, and the bicistronic reporter comprises an enhanced blue fluorescent protein under the control of a CMV promoter (i.e., a Cap-dependent translation element) and an enhanced green fluorescent protein under the control of viral IRES (i.e., a Cap-independent translation element) (Abstract, Figure 1A).
Thus, it would have been obvious to one of ordinary skill in the art before the effective filling date of the invention to have modified Jaagar's method and introduced the bicistronic reporter in cells as taught by Dasgupta because it would have merely amounted to a simple substitution of prior art elements according to known methods to yield predictable results. One would have been motivated to have done so for the advantage of avoiding promiscuous translations that occur in vitro. One would have had a reasonable expectation of success in doing so because Dasgupta also teaches a method of using similar bicistronic reporter expression systems in cells to identify host factors involved in IRES-based translation.
Further, Jaagar does not teach generating a test host cell comprising a catalytically inactive CRISPR/Cas effector polypeptide and a regulatory nucleic acid that comprises a nucleotide sequence encoding a single guide RNA (sgRNA) that comprises a targeting sequence that specifically binds to a target sequence within a nucleic acid encoding the target protein.
Gersbach teaches a method of introducing a catalytically inactive CRISPR Cas9 (dCas9) effector and a regulatory nucleic acid comprising a sgRNA (FIG. 3A) into a host cell for silencing gene targets (i.e., target protein) in vivo (Abstract).
Thus, it would have been obvious to one of ordinary skill in the art before the effective filling date of the invention to have further modified Jaagar's method to substitute the RNA aptamer for the target protein eIF1A with CRISPR dCas9 effector and sgRNA to silence transcription of the target protein as taught by Gersbach because it would have merely amounted to a simple substitution of prior art elements according to known methods to yield predictable results. One would have been motivated to have done so for the advantage of specific silencing of target protein genes without the potential risk of the RNA aptamer binding to other proteins and subsequently inhibiting related proteins and pathways. One would have had a reasonable expectation of success in doing so because Gersbach teaches a method of modulating expression of a gene in vivo using CRISPR dCas9 and sgRNA.
Regarding claims 2 and 3, Jaafar teaches the Cap-dependent translation element is a CMV promoter from cytomegalovirus (pg. 17, "pDBS" subsection), and the Cap-independent translation element is from hepatitis C virus (pg. 5, third paragraph).
Regarding claim 4, Jaagar recites "cap-driven (Rluc) and HCV IRES-driven (CAT) ORFs of a bicistronic reporter" (pg. 5, third paragraph), thus Jaagar teaches a method wherein the first reporter protein is luciferase and the second reporter protein is a protein that confers antibiotic resistance.
Regarding claim 5, the obviousness to modify Jaagar's method with teachings of Dasgupta and Gersbach is discussed above as applied to claim 1. Both Dasgupta (Col. 3, line 31) and Gersbach ([0511]) teach wherein the host cell is HEK293 cells .
Regarding claims 6 and 7, the obviousness to modify Jaagar's method with teachings of Dasgupta and Gersbach is discussed above as applied to claim 1. Gersbach further teaches wherein the regulatory nucleic acid is in a vector and further comprises: i) a third reporter nucleic acid comprising a nucleotide sequence encoding a third reporter protein (e.g., GFP), ii) a selectable marker gene (e.g., Kanamycin resistance protein); and iii) a promoter driving the expression of the sgRNA (e.g., U6 promoter) (FIG. 3A).
Regarding claims 8-10, the obviousness to modify Jaagar's method with teachings of Dasgupta and Gersbach is discussed above as applied to claim 1. Gersbach further teaches dCas9 is fused to a transcription inhibitor, KRAB (FIG. 3A).
Regarding claim 14, it does not further distinguish over claim 1, as it recites the same subject matter. Accordingly, claim 14 is rejected for the same reasons set forth above in the rejection of claim 1.
Regarding claim 33, Jaagar teaches a method for testing whether eIF1A (i.e., a target protein) is required for full activity of HCV IRES-based translation (i.e., regulates viral RNA translation), the method comprising: a) introducing into HeLa cell lysate: i) "a firefly luciferase (Fluc)-based monocistronic reporter" comprising a Fluc reporter protein translated under the control of a viral IRES translation element (Figure 2D and 2H; pg. 5, third paragraph; pg. 7, first paragraph), ii) a regulatory nucleic acid which is an RNA aptamer (α-eIF1A) that binds to eIF1A (pg. 5, third paragraph); and b) detecting expression of Fluc from lysates treated with α-eIF1A (i.e., in the test host cell) to lysates treated with a negative control antisense aptamer (AS) (i.e., in the control host cell that comprises the reporter nucleic acid but not the regulatory nucleic acid (pg. 7, first paragraph). Jaagar further teaches "eIF1A depletion reduced translation initiation by the HCV and CSFV IRES" (Figure 2H), where expression of the Fluc reporter protein in lysates with α-eIF1A is different compared to the expression of the Fluc reporter protein in lysates with negative control AS aptamer (pg. 7, first paragraph).
However, Jaagar teaches a method comprising introducing a monocistronic reporter into rabbit reticulocyte or HeLa cell lysate, and does not teach introducing this reporter into a host cell.
Dasgupta teaches a method to identify trans-acting translation factors, e.g., eIF1A, (i.e., target protein) using a monocistronic reporter in HeLa extracts, wherein a firefly luciferase reporter protein is under the control of an IRES element (Col. 12, lines 1-5). Dasgupta further teaches that conversion of the monocistronic reporter into a bicistronic reporter in vivo results in measured IRES activity that is comparable to that observed in HeLa extracts (Col. 12, lines 13-30). These teachings demonstrated that the IRES element functions similarly in vitro and in vivo.
Thus, it would have been obvious to one of ordinary skill in the art before the effective filling date of the invention to have modified Jaagar's method and introduced the monocistronic reporter in cells as taught by Dasgupta because it would have merely amounted to a simple substitution of prior art elements according to known methods to yield predictable results. One would have been motivated to have done so for the advantage of avoiding promiscuous translations that occur in vitro. One would have had a reasonable expectation of success in doing so because Dasgupta teaches that in vitro and cellular assays yield similar IRES activity; hence, introducing a monocistronic reporter in cells would also allow measurement of the IRES activity or reporter protein expression levels.
Further, Jaagar does not teach generating a test host cell comprising a catalytically inactive CRISPR/Cas effector polypeptide and a regulatory nucleic acid that comprises a nucleotide sequence encoding a single guide RNA (sgRNA) that comprises a targeting sequence that specifically binds to a target sequence within a nucleic acid encoding the target protein.
Gersbach teaches a method of introducing a catalytically inactive CRISPR Cas9 (dCas9) effector and a regulatory nucleic acid comprising a sgRNA (FIG. 3A) into a host cell for silencing gene targets (i.e., target protein) in vivo (Abstract).
Thus, it would have been obvious to one of ordinary skill in the art before the effective filling date of the invention to have further modified Jaagar's method to substitute the RNA aptamer for the target protein eIF1A with CRISPR dCas9 effector and sgRNA to silence transcription of the target protein as taught by Gersbach because it would have merely amounted to a simple substitution of prior art elements according to known methods to yield predictable results. One would have been motivated to have done so for the advantage of specific silencing of target protein genes without the potential risk of the RNA aptamer binding to other proteins and subsequently inhibiting related proteins and pathways. One would have had a reasonable expectation of success in doing so because Gersbach teaches a method of modulating expression of a gene in cells using CRISPR dCas9 and sgRNA.
Regarding claim 46, it does not further distinguish over claim 33, as it recites the same subject matter. Accordingly, claim 14 is rejected for the same reasons set forth above in the rejection of claim 33.
Regarding claim 65, Jaagar teaches the Cap-independent translation element is HCV IRES (pg. 5, third paragraph; Figure 2C).
Conclusion
No claims are allowable.
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QIWEN SU-TOBON
Examiner
Art Unit 1636
/NEIL P HAMMELL/Supervisory Patent Examiner, Art Unit 1636