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 .
Application Status
This action is written in response to applicant’s correspondence received 21 July 2025. Claims 1-20 are pending. Claims 16 is amended. Claims 10-12 remain withdrawn from consideration as being drawn to a non-elected invention. Accordingly, claims 1-9 and 13-20 are currently under examination.
Applicant’s arguments, filed 21 July 2025, have been fully considered but are not found persuasive for reasons outlined below (see “Response to Arguments” section).
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.
Claim(s) 1-3, 14, and 19-20 is/are rejected under 35 U.S.C. 103 as being unpatentable over Stirnweis (PG Pub No. EP 3,702,464 A1, published 2 September 2020) in view of Choy (Cell 98.1 (1999): 69-80). This rejection is maintained.
Regarding claims 1-2 and 19, Stirnweis is drawn to an invention concerned with methods and nucleic acid sequences for obtaining pathogen resistance in plants (Abstract). Stirnweis teaches that a CRISPR-Cas13 RNA editing complex may be used to alter the RNA coding potential in a programmable manner which allows a targeted knockdown of endogenous transcripts ([0096]). Stirnweis teaches the use of a fusion construct comprising a CRISPR/Cas system that can provide for subcellular localization of the site-specific base editor ([0034]). Stirnweis teaches that the CRISPR/Cas protein may be directly fused to different localization signals that allow for localization of the CRISPR/Cas protein to the mitochondria via a mitochondrial localization signal, the chloroplast via a chloroplast localization signal, and the endoplasmic reticulum (i.e., the ER) via an ER retention signal (i.e., Stirnweis teaches the use of fused, heterologous amino acid sequences that can direct the CRISPR/Cas protein to different subcellular organelle regions) ([0034]). Stirnweis teaches that the CRISPR/Cas protein can be provided to a plant cell, tissue, organ, seed, or plant material in order to generate pathogen resistance ([0019]).
Stirnweis does not teach or suggest the fusion of one or more lipidation motifs to a Cas protein (Claim 1). Stirnweis does not teach or suggest that the lipidation motif is post-translationally modified to anchor the lipidation motif and the fused Cas protein to a target cellular location (Claim 1), selected from a subcellular organelle (Claim 2) or a replication organelle (Claim 14).
However, one of ordinary skill in the art would have considered the teachings of Choy as both references are common fields of endeavor pertaining to the use of subcellular localization signals.
Choy is drawn to a study concerned with a CAAX motif (i.e., a lipidation motif) and its ability to target proteins to the ER (i.e., a subcellular region that comprises a replication organelle) (Abstract). Choy teaches that adding the CAAX motif alone to a GFP’s C-terminus (i.e., a direct fusion of the lipidation motif) was sufficient to target the GFP to the ER (i.e., the CAAX lipidation motif alone was able to be fused to a heterologous protein such that it was targeted to a subcellular region) (pg. 74). Choy teaches that the CAAX motif can be post-translationally modified by a myriad of enzymes such that a hydrophobic C terminal is generated on an otherwise hydrophilic molecule in order to localize the motif to the endomembrane system (i.e., anchor to a subcellular region/membrane of a subcellular organelle) (Claims 1-2) (pg. 69).
Therefore, it would have been obvious to one of ordinary skill in the art before the effective filing date of the claimed invention to substitute the fused, heterologous amino acid sequence that can direct the CRISPR/Cas protein to different subcellular regions, as described by Stirnweis, for a CAAX motif (i.e., a heterologous amino acid sequence that can direct a protein of interest to a membrane of a replication subcellular organelle), as described by Choy. A person of ordinary skill in the art would have had a reasonable expectation of success because both Stirnweis and Choy teach the use of an amino acid sequences that can be fused to a heterologous protein in order to direct the protein to a subcellular region. Therefore, substituting the fused, heterologous amino acid sequence that can direct the CRISPR/Cas protein to different subcellular regions, as described by Stirnweis, for a CAAX motif (i.e., a heterologous amino acid sequence that can direct a protein of interest to a membrane of a replication subcellular organelle), as described by Choy, would have resulted in the predictable outcome of success.
Regarding claims 3 and 19-20, Stirnweis teaches that the CRISPR/Cas protein can be utilized to known down target RNA levels of interest, as opposed to knocking them out, in order to prevent undesired side effects when imparting immunity to pathogens (i.e., the CRISPR/Cas protein can cleave a target nucleic acid as part of a treatment regimen for a subject) ([0096]).
Claim(s) 5 is/are rejected under 35 U.S.C. 103 as being unpatentable over Stirnweis (PG Pub No. EP 3,702,464 A1, published 2 September 2020) in view of Choy (Cell 98.1 (1999): 69-80) as applied to claims 1-3, 14, and 19-20 above, and further in view of Ai (Nucleic Acids Research 50.11 (4 March 2022): e65-e65). This rejection is maintained.
Regarding claim 5, Stirnweis in view of Choy renders obvious claims 1-3, 14, and 19-20 as described above.
Stirnweis in view of Choy does not teach or suggest that the target cellular location reduced cellular toxicity of the Cas protein (Claim 5).
However, one of ordinary skill in the art would have considered the teachings of Ai because the references are common fields of endeavor pertaining towards studies concerned with Cas13.
Ai is drawn to a study concerned with the off-target cleavage of CRISPR-Cas13 systems (Abstract). Ai teaches that the off-target effects of RxCas13d, a commonly used Cas13 effector, can be as strong as the level of on-target RNA knockdown when exposed to cellular RNA (Abstract). Ai teaches that RxCas13d in human HeLa cells was associated with reduced RNA yields, suggestive of cellular toxicity (pg. 14).
Therefore, it would have been obvious to a person of ordinary skill in the art before the effective filing date of the claimed invention to modify the method of Stirnweis in view of Choy such that cellular toxicity of the CRISPR-Cas nuclease is reduced by localizing the nuclease to the endoplasmic reticulum because less total cellular RNA could be accessed by the localized Cas13 nuclease when compared to a non-localized Cas 13 nuclease, as described by Ai. A person of ordinary skill in the art would have been motived to do so in order to reduce Cas13’s cellular toxicity. A person of ordinary skill in the art would have had a reasonable expectation of success because Ai teaches that when Cas13 is exposed to cellular RNA it is toxic while Stirnweis in view of Choy renders obvious the use of a Cas13 that is localized to a subcellular region of interest (i.e., not exposed to less cellular RNA when compared to a non-localized Cas13). Therefore, in localizing the Cas13 nuclease to a particular region of the cell, less total RNA could be accessed by the localized Cas13 nuclease compared to a non-localized Cas13 protein and the rate of off-target mutations (i.e., mutations associated with cellular toxicity) would also be reduced. Thus, a person of ordinary skill in the art would have had a reasonable expectation of success in reducing the cellular toxicity of a Cas13 nuclease by localizing it to the endoplasmic reticulum.
Claim(s) 6-7 and 13 is/are rejected under 35 U.S.C. 103 as being unpatentable over Stirnweis (PG Pub No. EP 3,702,464 A1, published 2 September 2020) in view of Choy (Cell 98.1 (1999): 69-80) as applied to claims 1-3, 14, and 19-20 above, and further in view of Al-Quadan (Trends in microbiology 19.12 (2011): 573-579). This rejection is maintained.
Regarding claims 6-7 and 13, Stirnweis in view of Choy renders obvious claims 1-3, 14, and 19-20 as described above.
Stirnweis further teaches that one or more amino acid localizations signals may be fused to the CRISPR/Cas protein ([0034]).
Stirnweis in view of Choy does not teach or suggest the use of a CTIL motif (Claim 6). Stirnweis in view of Choy does not teach or suggest the use of a CVIS motif (Claim 7). Stirnweis in view of Choy does not teach or suggest that a first lipidation motif will target a first cellular location and a second lipidation motif will target a second cellular location (Claim 13).
However, one of ordinary skill in the art would have considered the teachings of Al-Quadan because the references are analogous fields of endeavor pertaining to CAAX lipidation motifs.
Al-Quadan is drawn to a review study concerned with the anchoring of bacterial effector proteins to host membranes through host-mediated lipidation by prenylation (Abstract). Al-Quadan teaches that CAAX motifs are known in the art to be able to be utilized to anchor injected effector proteins to host cell membranes via the prenylation (i.e., post-translational modification) of the motif (Abstract). Al-Quadan teaches that CTIL and CVIS are both known CAAX lipidation motifs (pg. 576-577; see Table 1). Al-Quadan teaches that the CAAX motif is known to be able to be utilized to anchor both prokaryotic and eukaryotic proteins to eukaryotic membranes (pg. 578). Al-Quadan teaches that different CAAX motifs will target fusion proteins to different cellular locations in eukaryotic cells (pg. 578).
Therefore, it would have been obvious to one of ordinary skill in the art before the effective filing date of the claimed invention to substitute the one or more CAAX motifs rendered obvious by Stirnweis in view of Choy for a CTIL motif, a CVIS motif, or both a CTIL and CVIS motif, as described by Al-Quadan. A person of ordinary skill in the art would have had a reasonable expectation of success because Stirnweis in view of Choy rendered obvious the use of multiple CAAX motifs directly fused to a CRISPR/Cas protein and Al-Quadan teaches that CTIL and CVIS motifs were known CAAX motifs. Therefore, substituting the one or more CAAX motifs rendered obvious by Stirnweis in view of Choy for a CTIL motif, a CVIS motif, or both a CTIL and CVIS motif, as described by Al-Quadan, would have resulted in the predicable outcome of success.
Claim(s) 4, 8-9, 15-16, and 18 is/are rejected under 35 U.S.C. 103 as being unpatentable over Stirnweis (PG Pub No. EP 3,702,464 A1, published 2 September 2020) in view of Choy (Cell 98.1 (1999): 69-80) as applied to claims 1-3, 14, and 19-20 above, and further in view of Soveg (Elife 10 (2021): e71047). This rejection is maintained.
Regarding claims 8-9, 16, and 18, Stirnweis in view of Choy renders obvious claims 1-3, 14, and 19-20 as described above.
Stirnweis further teaches that the fusion protein may comprise a CRISPR/Cas protein fused to a targeting protein ([0034]).
Stirnweis in view of Choy does not teach or suggest that the target nucleic acid is a viral nucleic acid (Claim 4). Stirnweis in view of Choy does not teach or suggest that fusion one or more lipidation motifs to the Cas protein comprising inserting a linker to account for amino acids that affect the efficiency of the post-translational modification (Claim 8). Stirnweis in view of Choy does not teach or suggest that the linker is derived from a C-terminal end of an OAS1 protein (Claim 9). Stirnweis in view of Choy does not teach or suggest that the target cellular location comprises a location appropriated by a virus (Claim 15). Stirnweis in view of Choy does not teach or suggest that the linker comprises inserting one or more peptide linkers derived from the C-terminal end of an OAS1 human protein between a ribonucleotide complex and a CTIL motif (Claims 16 and 18).
However, one of ordinary skill in the art would have considered the teachings of Soveg because the references are analogous fields of endeavor pertaining to the targeting of proteins to target subcellular regions.
Soveg is drawn to a study concerning the function that the C-terminus of an OAS1 protein plays in subcellular localization of proteins (pg. 2). Soveg teaches that the C-terminus of an OAS1 protein (i.e., a linker to account for amino acids that affect the efficiency of the post-translational modification) comprises a CAAX motif and allows for the targeting of the OAS1 protein to the endomembrane such that protection against COVID-19 RNA may be imparted on the cell (Abstract; pg. 2). Soveg teaches OAS1 proteins containing a CaaX motif at their C-termini undergo prenylation and are targeted to (i.e., anchored to) the cytosolic face of intracellular organelle membranes of the endomembrane system following post-prenylation processing at the endoplasmic reticulum (pg. 2). Soveg teaches that the endomembrane system is a known cellular location that COVID-19 RNA appropriates in cells (pg. 23; see Figure 7).
Therefore, it would have been obvious to one of ordinary skill in the art before the effective filing date of the claimed invention to substitute the targeting protein present in the fusion protein rendered obvious by Stirnweis in view of Choy for a C-terminal end of an OAS1 protein such that the fusion protein is targeted to a location appropriated by a virus, as described by Soveg. A person of ordinary skill in the art would have had a reasonable expectation of success because both Soveg and Stirnweis in view of Choy teach the use of targeting proteins that can target proteins of interest to subcellar regions of interest. Therefore, substituting the targeting protein present in the fusion protein rendered obvious by Stirnweis in view of Choy for a C-terminal end of an OAS1 protein such that the fusion protein is targeted to a location appropriated by a virus, as described by Soveg, would have resulted in the predicable outcome of success.
Claim(s) 17 is/are rejected under 35 U.S.C. 103 as being unpatentable over Stirnweis (PG Pub No. EP 3,702,464 A1, published 2 September 2020) in view of Choy (Cell 98.1 (1999): 69-80) and Soveg (Elife 10 (2021): e71047) as applied to claims 4, 8-9, 15-16, and 18 above, and further in view of Kmiec (PLoS Pathogens 17.10 (2021): e1009726). This rejection is maintained.
Regarding claim 17, Stirnweis in view of Choy and Soveg renders obvious claims 4, 8-9, 15-16, and 18 as described above.
Stirnweis in view of Choy and Soveg does not teach or suggest that the linker is derived from the C-terminal end of a ZAP-L human protein between a ribonucleoprotein and a CVIL motif (Claim 17).
However, one of ordinary skill in the art would have considered the teachings of Kmiec because the references are analogous fields of endeavor pertaining to the targeting of proteins to target subcellular regions.
Kmiec is drawn to a study concerned with the localization of ZAP proteins (Abstract). Kmiec teaches that the C-terminus of a ZAP-L protein comprises a well-conserved CVIS motif (pg. 7; see Fig. 3). Kmiec teaches that the CVIS motif is essential for the antiviral activity of ZAP-L because the CVIS motif allows for the localization of the ZAP-L protein to endosomes and lysosomes of the cell which are often times single-membrane viral replication factories (pg. 7).
Therefore, it would have been obvious to one of ordinary skill in the art before the effective filing date of the claimed invention to substitute the targeting protein present in the fusion protein rendered obvious by Stirnweis in view of Choy and Soveg for a C-terminal end of a ZAP-L human protein comprising a CVIL motif, as described by Kmiec. A person of ordinary skill in the art would have had a reasonable expectation of success because both Kmiec and Stirnweis in view of Choy and Soveg teach the use of targeting proteins that can target proteins of interest to subcellar regions of interest. Therefore, substituting the targeting protein present in the fusion protein rendered obvious by Stirnweis in view of Choy for a C-terminal end of a ZAP-L human protein comprising a CVIL motif, as described by Kmiec, would have resulted in the predicable outcome of success.
Response to Arguments
Applicant’s arguments, filed 21 July 2025, have been fully considered but are not deemed persuasive for the following reasons.
Applicant alleges that Stirnweis is non-analogous art (Remarks; pg. 6-7). Applicant alleges that Stirnweis is not in the same field of endeavor as the claimed invention because the claimed invention’s technical field of endeavor is engineering CRISPR-Cas effectors for programmable subcellular delivery within animal virus replication organelles while Stirnweis’s filed of endeavor is in plant biotechnology (Remarks; pg. 6). Applicant alleges that Stirnweis is not reasonably pertinent to the problem faced by the inventor because the problem the inventors of the instant application set out to solve is how to localize programmable CRISPR-Cas nucleases precisely to viral replication organelles in eukaryotic cells—anchoring RNA-targeting effectors (e.g. Cas13 or Cas7-11) via tailored lipidation motifs so as to enhance antiviral efficacy and limit collateral damage in the cytosol while Stirnweis, by contrast, addresses an entirely different challenge: boosting innate pathogen resistance in crop plants by tinkering with the prenylation of endogenous CPL3-type phosphatase-like proteins to modulate immune signaling (Remarks; pg. 7).
In response to applicant's argument that Stirnweis is non-analogous art, it has been held that a prior art reference must either be in the field of the inventor' s endeavor or, if not, then be reasonably pertinent to the particular problem with which the inventor was concerned, in order to be relied upon as a basis for rejection of the claimed invention. See In re Oetiker, 977 F.2d 1443, 24 USPQ2d 1443 (Fed. Cir. 1992). In this case, both Stirnweis and the inventors of the instant application are directed towards methods of fusing CRISPR proteins to different localization signals that allow for localization of the CRISPR/Cas protein to eukaryotic subcellular regions of interest (see above 35 USC 103 rejection of record). Thus, Stirnweis is both in the same filed of endeavor as, and is reasonably pertinent to the problem faced by the inventor. Further, the claims do not claim that the method is performed within animal cells. Accordingly, the arguments pertaining to the inventor’s methods being performed in animal cells, and not plant cells, are not found persuasive.
Applicant alleges that a person of ordinary skill in the art would not have been motivated to modify the teachings of Stirnweis, which is directed to plant gene editing for pathogen resistance, with the mammalian cell-specific teachings of Choy, which concerns Ras protein localization via CAAX- box-mediated lipidation (Remarks; pg. 8). Applicant alleges that neither reference provides explicit or implicit suggestion in either reference to combine the teachings of Stirnweis and Choy (Remarks; pg. 9).
This argument is not found persuasive because, as noted at MPEP 2141, rationales that can support a conclusion of obviousness under 35 U.S.C. 103 can include simple substitution of one known element for another or [emphasis added] some teaching, suggestion, or motivation in the prior art that would have led one of ordinary skill to modify the prior art reference or to combine prior art reference teachings to arrive at the claimed invention. Accordingly, MPEP 2141 teaches that utilizing the simple substitution rationale does not require the recitation of an explicit motivation to combine references nor does the 35 U.S.C. 103 rejections of record recite a motivation statement with regard to pending claim 1 and the simple substitution of the heterologous amino acid sequence of Stirnweis that can direct the CRISPR/Cas protein to different subcellular regions for a CAAX motif (i.e., a heterologous amino acid sequence that can direct a protein of interest to a membrane of a replication subcellular organelle), as described by Choy. Further, as discussed above, a person of ordinary skill in the art would have had a reasonable expectation of success in substituting the heterologous amino acid sequence of Stirnweis that can direct the CRISPR/Cas protein to different subcellular regions for a CAAX motif, as described by Choy, because both references teach the fusing of amino acids to heterologous proteins of interest in order to target them to subcellular regions of interest. Therefore, one of ordinary skill in the art would have expected that the combination of Stirnweis and Choy would predictably result in arriving at the instantly claimed invention.
Applicant alleges that none of the references relied upon in the Office Action are directed to RNA targeting at a specified and targeted cellular location (Remarks; pg. 9). Applicant alleges that ([0096]) of Stirnweis merely points to general research into RNA knockdown, not “wherein administering the engineered Cas protein comprises administering a therapeutic that targets the target cellular location” let alone that the “therapeutic comprises an RNA-targeting nuclease for programmed cutting and ligation for targeted deletion of RNA” as claimed in instant claims 19-20 (Remarks; pg. 9).
This argument is not found persuasive because, as an initial matter, ([0096]) of Stirnweis states “In other embodiments, a CRISPR-Cas13 RNA editing complex may be used to alter the RNA coding potential in a programmable manner which allows a targeted knockdown of endogenous transcripts, preferably CPL3 transcripts, with comparable levels of knockdown as RNAi. […]”. Therefore, ([0096]) of Stirnweis teaches that CRISPR-Cas13 may be utilized therapeutically to knockdown target RNA of interest. Further, In response to applicant's arguments against the references individually, one cannot show nonobviousness by attacking references individually where the rejections are based on combinations of references. See In re Keller, 642 F.2d 413, 208 USPQ 871 (CCPA 1981); In re Merck & Co., 800 F.2d 1091, 231 USPQ 375 (Fed. Cir. 1986). It is the combination of Stirnweis and Choy that renders obvious the claimed method because Stirnweis teaches that CRISPR-Cas13 proteins may be fused to heterologous amino acids that target the protein to a subcellular region while Choy teaches that GFP may be fused to a heterologous CAAX motif in order to target the GFP to a target subcellular region of interest. Thus, the combination of Stirnweis and Choy render obvious the use of a Cas13 fused to a lipidation motif in order to therapeutically target RNA of interest in a subcellular region of interest in a subcellular region of interest.
Conclusion
THIS ACTION IS MADE FINAL. 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 KYLE T REGA whose telephone number is (571)272-2073. The examiner can normally be reached M-R 8:30-4:30, every other F 8:30-4:30 (EDT/EST).
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If attempts to reach the examiner by telephone are unsuccessful, the examiner’s supervisor, Neil Hammell can be reached at 571-270-5919. The fax phone number for the organization where this application or proceeding is assigned is 571-273-8300.
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/KYLE T REGA/Examiner, Art Unit 1636
/NEIL P HAMMELL/Supervisory Patent Examiner, Art Unit 1636