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 22 January 2026. Claims 1-2, 6-7, 9-10, 12-14, 20, 22-23, 25-26, 28-29, 32, 34-35, and 37-38 are currently pending. Accordingly, claims 1-2, 6-7, 9-10, 12-14, 20, 22-23, 25-26, 28-29, 32, 34-35, and 37-38 are examined herein.
Any rejection or objection not reiterated herein has been overcome by amendment. Applicant' s arguments have been thoroughly reviewed, but are not persuasive to place the claims in condition for allowance for the reasons that follow.
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, 6-7, 9-10, 14, 20, 22-23, 25, 29, 34-35, and 37 is/are rejected under 35 U.S.C. 103 as being unpatentable over Jin (PG Pub No. WO 2017/011721 A1) in view of Basilla (PLoS One 12.11 (2017): e0188593). This rejection is maintained.
Regarding claim 1, Jin is drawn to an invention concerned with targeted gene editing (Abstract). Jin teaches the use of a system comprising: (i) a sequence-targeting protein, or a polynucleotide encoding the same, (ii) an RNA scaffold, or a DNA polynucleotide encoding the same, and (iii) a non-nuclease effector fusion protein, or a polynucleotide encoding the same (pg. 2). Jin teaches that the RNA scaffold comprises (a) a nucleic acid-targeting motif comprising a guide RNA sequence that is complementary to a target nucleic acid sequence (i.e., a crRNA), (b) a CRISPR/Cas9 motif capable of binding to the sequence-targeting protein (i.e., a tracrRNA), and (c) a recruiting RNA motif (pg. 2). Jin teaches that the non-nuclease effector fusion protein comprises (a) an RNA binding domain capable of binding to the recruiting RNA motif, (b) a linker sequence, and (c) an effector domain (pg. 2). Jin teaches that the non-nuclease effector can have the activity of cytosine deaminases and be selected from AID or APOBEC3G (i.e., the effector domain may have cytosine deamination activity) (pg. 15). Jin teaches that the system may be utilized in a method of site-specific modification of a target DNA in a eukaryotic cell (pg. 3). Jin teaches that the eukaryotic cell may be an induced pluripotent stem cell (pg. 31). Jin teaches that the cell may then be cultured under a suitable condition which allows for the expression of the RNA and proteins through the use of a vector (pg. 27). Jin teaches that the RNA scaffold may comprise multiple 2'-0-methyl analogs (pg. 19).
Jin does not teach or suggest that the RNA scaffold is chemically modified to comprise a 2'-0-methyl phosphorothioate modification on at least one 5’ nucleotide and at least one 3’ nucleotide (Claim 1).
Basilla is drawn towards a study concerned with how 2'-O-methyl phosphorothioate linkage modifications within synthetic guide RNAs, resulting in increased stability and efficient CRISPR-Cas9 gene editing (Abstract). Basilla teaches the use of synthetic guide RNAs that comprise multiple 2'-O-methyl phosphorothioate linkages at both the 3’ and 5’ ends of the guide RNA’s crRNA and tracrRNA (pg. 7-8; see Fig. 2). Basilla teaches that Cas9 guide RNAs comprising three different 2'-O-methyl phosphorothioate linkages at both the 3’ and 5’ ends of the guide RNA provided stabilization to nuclease degradation and facilitated significant gene editing, indicating the increased persistence of the guide RNA through a minimal chemical modification pattern that increased the stability of the guide RNA and avoided cellular toxicity observed with more highly modified gRNA (pg. 2-3, 6).
Therefore, it would have been obvious to one of ordinary skill in the art before the effective filing date of the claimed invention to modify the Cas9 RNA scaffold of Jin such that it comprised at least one 2'-O-methyl phosphorothioate linkage at both the 3’ and 5’ ends of the guide RNA scaffold, as taught by Basilla. A person of ordinary skill in the art would have been motivated to do so in order to increase the RNA scaffold stability and provide it protection against nuclease degradation. A person of ordinary skill in the art would have had a reasonable expectation of success because Jin teaches that the RNA scaffold may comprise 2'-O-methyl analogs and Basilla teaches that utilizing 2'-O-methyl phosphorothioate linkages at both the 3’ and 5’ ends of a guide RNA results in the increased stability of the guide RNA.
Regarding claims 6-7, Jin teaches that the sequence-targeting protein may be a dCas9 or an nCas9 (pg. 4-5; see FIG. 1A).
Regarding claim 9, Jin teaches that the non-nuclease effector can be an AID and be utilized to introduce site-specific conversion of target nucleotides (pg. 5; see FIG. 2).
Regarding claim 10, Jin teaches that the non-nuclease effector can be an ADA (pg. 19).
Regarding claim 14, Jin teaches that the method may be utilized to correct a genetic mutation or inactivate the expression of a target gene (pg. 4).
Regarding claim 20, Jin teaches that the RNA scaffold can be comprised of multiple RNA molecules (i.e., the RNA scaffold can comprise two separate components) (pg. 18). Jin teaches that the RNA scaffold can be synthesized via chemical synthesis (pg. 18).
Regarding claim 22, Jin teaches that the RNA scaffold can be created via the synthetic fusion of phage RNA scaffolds and CRISPR RNA scaffolds (i.e., the scaffold is a synthetic scaffold) (pg. 46).
Regarding claim 23, Jin teaches that the RNA motif is located at the 3’ end of the RNA scaffold (pg. 4-5; see FIG. 1A).
Regarding claim 25, Jin teaches that the RNA motif may be an MS2 aptamer (pg. 6-7; see FIG. 6).
Regarding claim 29, Jin teaches that the system can be multiplexed to target sequences upstream and downstream of a target site simultaneously (pg. 27-28).
Regarding claim 34, Jin teaches that the system may be utilized in a method of site-specific modification of a target DNA in a eukaryotic cell (pg. 3). Jin teaches that the eukaryotic cell may be an induced pluripotent stem cell (pg. 31).
Regarding claim 35, Jin teaches that when the system was introduced into target cells to induce a C1592C>T conversion (i.e., a genetic modification), 100% of the clones comprised the genetic modification (pg. 5). Therefore, because Jin teaches that the edited cell may be an induced pluripotent stem cell (pg. 31), at least 10% of the edited induced pluripotent stem cells would comprise the genetic modification.
Regarding claim 37, Basilla teaches that the modified nucleotides were located at the first three nucleotides at the 5’ end and the last three nucleotides at the 3’ end of the crRNA and tracrRNA (pg. 7; see Figure 2).
Claim(s) 2 and 26 is/are rejected under 35 U.S.C. 103 as being unpatentable over Jin (PG Pub No. WO 2017/011721 A1) in view of Basilla (PLoS One 12.11 (2017): e0188593) as applied to claims 1, 6-7, 9-10, 14, 20, 22-23, 25, 29, 34-35, and 37 above, and further in view of Wang (Cell research 27.10 (2017): 1289-1292). This is a new rejection necessitated by amendment.
Regarding claims 2 and 26, Jin in view of Basilla renders obvious claims 1, 6-7, 9-10, 14, 20, 22-23, 25, 29, 34-35, and 37 as described above.
Jin further teaches that the RNA motif is a single MS2 located at the 3’ end of the RNA scaffold (pg. 4-5; see FIG. 1A).
Jin in view of Basilla does not teach or suggest that the sequence-targeting component comprises a sequence-targeting protein fused to one or more UGI peptides (Claim 2). Jin in view of Basilla does not teach or suggest that the sequence-targeting fusion protein comprises nCas9 fused with one or two UGIs (Claim 26).
Wang is drawn towards a study concerned with enhanced base editing by co-expression of a uracil DNA glycosylase inhibitor (Abstract). Wang teaches that once an nCas9 nicks a target nucleic acid, uracil DNA glycosylases and other DNA repair pathways are triggered, leading to unwanted indels and substitutions at the target nucleic acid (pg. 1289). Wang teaches that utilizing a UGI to inhibit uracil DNA glycosylase activity alongside the Cas9 resulted in less indels and that the UGI is pivotal for efficient and high-fidelity base editing (pg. 1289). Wang teaches the use of an nCas9 fused to a singular, or multiple, UGIs (pg. 1290-1291; see Figure 1). Wang teaches that fusing multiple UGIs to an nCas9 displayed the most robust and significant effect (pg. 1291).
Therefore, it would have been obvious to one of ordinary skill in the art before the effective filing date of the claimed invention to have arrived at the claimed requirements of an nCas9 fused to one or more UGIs because it would have merely amounted to a simple combination of known elements according to known methods to yield predictable results. Because Jin in view of Basilla teaches using Cas9 for a similar purpose as Wang, namely the editing of target nucleic acids in cells with an nCas9, then one would have had a reasonable expectation of success in modifying the nCas9 to include one or more UGIs a be functional when used in the method of Jin and Basilla. And because Wang teaches that fusing multiple UGIs to an nCas9 displayed the most robust and significant editing effect, one would have been motivated to do so.
Claim(s) 12-13, 28, and 32 is/are rejected under 35 U.S.C. 103 as being unpatentable over Jin (PG Pub No. WO 2017/011721 A1) in view of Basilla (PLoS One 12.11 (2017): e0188593) as applied to claims 1, 6-7, 9-10, 14, 20, 22-23, 25, 29, 34-35, and 37 above, and further in view of Galetto (PG Pub No. WO 2014/184744 A1). This is a new rejection necessitated by amendment.
Regarding claims 12-13, 28, and 32, Jin in view of Basilla renders obvious claims 1, 6-7, 9-10, 14, 20, 22-23, 25, 29, 34-35, and 37 as described above.
Jin in view of Basilla does not teach or suggest that the immune cell is a T cell (Claim 12). Jin in view of Basilla does not teach or suggest that the immune cell comprises a TCR (Claim 13). Jin in view of Basilla does not teach or suggest that the genetic modification results in reduced expression of TRAC and CD52 (Claim 26). Jin in view of Basilla does not teach or suggest that an exogenous nucleic acid sequence is introduced into the genome of the immune cell (Claim 32).
However, one of ordinary skill in the art would have considered the teachings of Galetto as both references are common fields of endeavor pertaining to the use of CRISPR nucleases for targeted editing of nucleic acids in target cells.
Galetto is drawn towards an invention concerned with methods for developing engineered T-cells for immunotherapy and more specifically to methods for modifying T-cells by inactivating at immune checkpoint genes, preferably at least two selected from different pathways, to increase T-cell immune activity (Abstract). Galetto teaches that, following the introduction of at least one rare-cutting endonuclease that can target a sequence of interest in a target genome, an exogenous nucleic acid can be integrated at the target genomic sequence via homologous recombination (pg. 34). Galetto teaches that the rare-cutting endonuclease can be a CRISPR/Cas9 nuclease (i.e., a sequence-targeting protein) and that guide RNAs can be designed to target a gene encoding a TCR component such that the Cas9 can induce cleavage within a TCR gene (pg. 26, 60). Galetto teaches that teaches that exogenous nucleic acids can be used to modify a targeted existing gene in order to up- or down-regulate the expression of the targeted gene via a promoter swap (i.e. the exogenous nucleic acid may be inserted in a genomic region of interest to downregulate target genes of interest) (pg. 28). Galetto teaches the use of nucleotide sequences that could be utilized to target a TALE nuclease to TRAC and CD52 genes (pg. 72; see Table 6). Galetto teaches that the goal of TRAC gene inactivation is to render T lymphocytes unresponsive to T-cell receptor stimulation (pg. 76). Galetto teaches that the goal of CD52 gene inactivation is to render T lymphocytes resistant to anti-CD52 antibody mediated immunosuppression (pg. 76).
Therefore, it would have been obvious to one of ordinary skill in the art before the effective filing date of the claimed invention to arrive at the claimed invention because it would have amounted to a simple combination of prior art elements according to known methods to yield predictable results. Because Jin and Basilla teaches using a Cas9 and guide RNA for a similar purpose as Galetto, namely editing target nucleic acids in eukaryotic cells, then one would have had a reasonable expectation of success in using the targeting sequence of Galetto in order to edit a target nucleic acid present within a T-cell with a CRISPR/Cas9 nuclease and insert an exogenous nucleic acid that resulted in TRAC gene inactivation. And because Galetto teaches that editing a T-cell with a CRISPR/Cas9 system can be used to increase T-cell immune activity, one would have been motivated to do so.
Claim(s) 38 is/are rejected under 35 U.S.C. 103 as being unpatentable over Jin (PG Pub No. WO 2017/011721 A1) in view of Basilla (PLoS One 12.11 (2017): e0188593) as applied to claims 1, 6-7, 9-10, 14, 20, 22-23, 25, 29, 34-35, and 37 above, and further in view of Hendel ("Chemically modified guide RNAs enhance CRISPR-Cas genome editing in human primary cells." Nature biotechnology 33.9 (2015): 985-989). This is a new rejection necessitated by amendment.
Regarding claims 12-13, 28, and 32, Jin in view of Basilla renders obvious claims 1, 6-7, 9-10, 14, 20, 22-23, 25, 29, 34-35, and 37 as described above.
Jin in view of Basilla does not teach or suggest that the last 3’ end is unmodified (Claim 38).
However, one of ordinary skill in the art would have considered the teachings of Hendel as both references are common fields of endeavor pertaining to the use of 2′-O-methyl phosphorothioate modified sgRNAs.
Hendel is directed towards a study concerned with chemically modified Cas9 guide RNAs (Abstract). Hendel teaches the use of a Cas9 sgRNA that comprises 3 chemically modified nucleotides at the 5’ end of the guide RNA and 3 chemically modified nucleotides at the 3’ end of the sgRNA (pg. 986; see Figure 1). Hendel teaches that when the chemically modified nucleotides were 2′-O-methyl 3′phosphorothioate groups (i.e., termed “MS”: a 2′-O-methyl phosphorothioate modification), the resulting chemically modified guide RNA had higher on-target editing efficiency compared to an unmodified Cas9 guide RNA (pg. 986; see Figure 1). Hendel teaches that at all three targeted loci, the MS-modified sgRNAs stimulated higher levels of homologous repair than the unmodified sgRNAs (pg. 987). Hendel teaches that the last nucleotide of the 3’ end of the sgRNA is a uracil that does not comprise a 2’-O-methyl modification (i.e., the last nucleotide of the 3’ end of the sgRNA is unmodified) (see Supplementary Table 1).
Therefore, it would have been obvious to one of ordinary skill in the art before the effective filing date of the claimed invention to have arrived at the claimed invention because it would have amounted to a simple substitution of one known phosphorothioate modified sgRNA for another. Because each of the two ′-O-methyl phosphorothioate modified sgRNAs of Jin in view of Basilla, and Hendel, were used in a similar way, namely the modification of a target nucleic acid with a Cas9, then it would have been predictable to have used the 2′-O-methyl phosphorothioate modified sgRNA that does not have its last nucleotide on the 3’ end modified as the Cas9 sgRNA in order to edit a target nucleic acid. And one would have been motivated to do so because Hendel teaches that the sgRNA stimulated high levels of homologous repair.
Response to Arguments
Applicant's arguments filed 22 January 2026 have been fully considered but they are not persuasive.
Applicant alleges that the teachings of Basilla would not be applicable to the teachings of Jin because Basilla is directed towards assessing indel formation and/or phenotypic gene knockout while the instant invention is directed towards a base editing system that comprises an effector domain having cytidine or adenosine deamination activity (Remarks; pg. 4). Applicant alleges that the noticeable absence in Basilla of reference to base editing systems would suggest to persons of ordinary skill in the art that it was not applicable to base editing systems (Remarks; pg. 4).
MPEP 716.01(c) makes clear that arguments of counsel cannot take the place of evidence in the record. There is no teaching in Basilla that states that the teachings are not applicable to base editing systems.
Further, these arguments are not found persuasive because it is piecemeal analysis of the rejection which is based on a combination of references. 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).
Applicant alleges that a person of ordinary skill in the art would not, upon reading Basilla, ignore its disclosure about the limited benefits of the chemical modifications and that the chemical modifications of Basilla were identified as not being a universal benefit and that the increased stability is necessary for only some applications (Remarks; pg. 4). Applicant alleges that, therefore, one of ordinary skill in the art would not have been motivated to apply the modification of Basilla to base editing systems (Remarks; pg. 4).
These arguments are not found persuasive because the relied upon quote of Basilla specifically recites that “when using a Cas9-stable cell line and lipid transfection, modifications were not required for stability and did not enhance gene editing for three gene targets (Fig 4A), suggesting that increased stability is necessary for only some applications” (pg. 14). Thus Basilla only teaches specific two transfection methods in which the 2'-0-methyl phosphorothioate modifications would not be “required” for stability of the Cas9 guide RNA.
MPEP 716.01(c) makes clear that arguments of counsel cannot take the place of evidence in the record. There is no teaching in Basilla that states that the modifications are not applicable to base editing systems in general, nor that the modifications would impair the stability of the base editing systems, outside of two specific transfection methods.
Further, these arguments are not found persuasive because it is piecemeal analysis of the rejection which is based on a combination of references. 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).
Applicant alleges that Basilla only discloses the use of the 2'-0-methyl phosphorothioate modifications in K-562, U2OS, and HeLa cells (Remarks; pg. 5). Applicant alleges that none of the cell lines are immune cells or iPSCs and a person of ordinary skill in the art would not assume that the teachings of Basilla would be applicable in immune cells or iPSCs.
These arguments are not found persuasive because it is piecemeal analysis of the rejection which is based on a combination of references. 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).
Further, MPEP 716.01(c) makes clear that arguments of counsel cannot take the place of evidence in the record. There is no teaching in Basilla that states that the teachings are not applicable to iPSCs nor that as that degradation of RNA occurs only in Basilla’s specific disclosed cells. Houseley ( "The many pathways of RNA degradation." Cell 136.4 (2009): 763-776) is drawn towards a review study concerned with DNA degradation and teaches that there are substantial similarities in the basics of RNA degradation between bacteria, archaea, and eukaryotes (pg. 763). Houseley teaches that there are many known RNA degradation pathways, each facilitated by known proteins, that exist within eukaryotic cells and promote the degradation of RNA (pg. 764-756’ see Table 1).
Thus, the prior art provides evidence that the stabilizing modifications of Basilla would be considered useful in more cells than the three cell types disclosed in Basilla because it was known in the art that eukaryotic cells comprise well-known RNA degradation pathways.
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
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