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 .
This action is in response to the amendment filed 02/13/2026, in which claims 1, 4, 7 and 18 were amended, claims 21-32 were previously withdrawn due to a restriction requirement mailed 08/28/2025. Claims 1-20, 33 and 34 are currently pending.
Applicant’s arguments have been thoroughly reviewed, but are not persuasive for the
reasons that follow. Any rejection and objections not reiterated in this action have been
withdrawn. This action is FINAL.
Claim Objections
Claim 19 is objected to because of the following informalities:
Claim 19 relies on claim 18 where claim 18 recites “An isolated host cell, isolated cell line or isolated progeny thereof comprising the system of claim 1”. Claim 19 should comprise the same amendments which would recite “The isolated host cell, isolated cell line or isolated progeny thereof of claim 18”.
Appropriate correction is required.
Response to Amendments - Claim Objections
The previous objection of claim 4 has been withdrawn in view of Applicant’s amendments to the claims filed on 02/13/2026.
Claim Rejections - 35 USC § 112
The previous rejection of claim 4 under 35 U.S.C. 112(a), first paragraph, has been withdrawn in view of Applicant’s amendments to the claims filed on 02/13/2026.
Claim Rejections - 35 USC § 101
The previous rejection of claim 18 under 35 U.S.C. 101 has been withdrawn in view of Applicant’s amendments to the claims filed on 02/13/2026.
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 text of those sections of Title 35, U.S. Code not included in this action can be found in a prior Office action.
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.
Claims 1-3, 5, 6, 8-20, 33 and 34 are rejected under 35 U.S.C. 103 as being unpatentable over Zhang et (WO 2017/106657 A1) as evidenced by Meister et al (Molecular Cell, Vol 15, 185-193; 2004).
Regarding claims 1, 2. 5, 6 and 8, Zhang teaches one or more nucleic acid vectors encoding elements of a nucleic acid-targeting system (e.g., page 7, paragraphs [0023] and [0029]; paragraph bridging pages 50-52). Zhang teaches the nucleic acid vector(s) encoding a Cpf1 effector protein and a nucleic acid-targeting guide RNA (targeting sequence of the claims) (e.g., paragraph [0023]; paragraph bridging pages 50-52). Zhang teaches that Cpf1 has DNA cleavage and RNA cleavage activity (e.g., paragraph bridging pages 46-47). Zhang teaches the nucleic-acid targeting guide RNA for Cpf1 can be an escorted guide (e.g., paragraph bridging pages 214-215). Zhang teaches the escorted guide RNA (egRNA or esgRNA) comprises a direct repeat 5’ to an RNA guide sequence capable of hybridizing to a target sequence in a genomic locus of interest in a cell, for example where the sequence comprises 19 nts of partial direct repeat followed by 23-25 nt of guide sequence or spacer sequence (5’ to 3’ of a direct repeat and a guide sequence comprising a crRNA of the claim), and an escort RNA aptamer sequence, wherein the escort aptamer is complementary to a target miRNA (microRNA target site of the claims), which results in cleavage of the egRNA by an RNA-induced silencing complex (RISC) within the cell (e.g., page 216, 1st full paragraph; page 217, 3rd full paragraph; paragraph bridging pages 217-218; page 233, last full paragraph; paragraph bridging pages 233-234).
Zhang does not explicitly teach that the miRNA target site is 3’ to the guide nucleotide sequence capable of hybridizing with a target sequence.
However, Zhang suggests 3’ modification of the egRNA (e.g., page 235, 1st full paragraph). Zhang teaches that guide RNA can include addition of nucleotides to the 3' end of a guide RNA which do not match a target sequence downstream of the CRISPR motif, where the addition is 12 nt, 13 nt, 14 nt, 15 nt, 16 nt, 17 nt, 18 nt, 19 nt, 20 nt, or longer (e.g., page 210, 3rd full paragraph). Zhang teaches that the efficiency of functionalized Cpf1 can be increased by the addition of these nucleotides to the 3’ end of the guide RNA (e.g., page 210, 3rd full paragraph).
It would have been obvious to one of ordinary skill in the art before the effective filing date of the claimed invention to impose a specific 5’ to 3’ order of direct repeat, guide nucleotide sequence and miRNA target site on the elements of the egRNA taught by Zhang, because Zhang teaches that the egRNA has a direct repeat 5’ to the guide nucleotide sequence, and suggests that the 3’ end of the egRNA can be modified. One would have added the miRNA target site to the 3’ end of the egRNA in order to achieve the predictable result of providing the egRNA with a miRNA target site capable of being cleaved by RISC.
One would have been motivated to make such a modification in order to receive the expected benefit of providing a 3’ addition of the guide RNA that does not hybridize to the target sequence to improve efficiency of functionalized Cpf1 as taught by Zhang et al.
Meister is only cited to show RISC contains Ago2 which is a miRNA-associated protein (Page 189, Column 2, RISC Activity Requires Ago2 but Not Ago1, Ago3 or Ago4).
Regarding claim 3, Zhang teaches RNA(s) of the nucleic acid targeting system (e.g., paragraph bridging pages 50-52).
Regarding claim 9, Zhang teaches mature crRNA comprises a direct repeat sequence and a guide sequence [0045] and when the crRNA forms a complex with the Cpf1 and hybridizes to the target sequence, the Cpf1 induces distal cleavage of the target sequence [0063 and 00114].
Regarding claims 10-14, Zhang teaches the system wherein the CRISPR-Cas complex comprises Cpf1 as the CRISPR-Cas protein and the Cpf1 protein is derived from Lachnospiraceae bacterium ND2006 (LbCpf1) (Page 58 and Page 62, Paragraph 1). Zhang teaches 86.6% identity of the Lachnospiraceae bacterium ND2006 sequence, identified as SEQ ID NO: 109, compared to the instant SEQ ID NO: 1 (See Appendix II).
Regarding claim 15, Zhang teaches the crRNA sequence is 23-25 nucleotides in length [0045].
Regarding claims 16-20, Zhang teaches the sequence associated with the target locus of interest is linear or supercoiled DNA [0013]. Zhang teaches the target sequence is a genomic locus of interest within a hematopoietic stem cell (Page 88, Paragraphs 3 and 4; Page 90, Paragraph 2).
Regarding claims 33 and 34, Zhang teaches the cell is a eukaryotic cell from an animal or human (Page 90, Paragraph 2).
Claim 4 is rejected under 35 U.S.C. 103 as being unpatentable over Zhang et (WO 2017/106657 A1) as evidenced by Meister et al (Molecular Cell, Vol 15, 185-193; 2004) and in view of Moore et al (Cancer Metastasis Rev 30:419-435, 2011).
The teachings of Zhang are described above and applied as before. Further, Zhang teaches the inclusion of the miRNA target site in the egRNA for the purpose of providing a mechanism to control the activity of the egRNA, where cleavage by RISC results in activation of the guide (e.g., paragraph bridging pages 234-235; page 235, 1st and 2nd full paragraphs).
Regarding claim 4, Zhang does not teach the use of an AU-rich element downstream of the microRNA target site.
Moore teaches AU-rich elements within the 3’UTR are important for providing target sequences for select miRNA-meditated regulation indicating the potential for crosstalk between miRNAs with AU-rich elements within the 3’UTR (Page 420, Column 1). Moore teaches AU-rich elements mediate stability of the mRNA transcript and microRNAs, such as miR-12-1, have shown to contain sequence homology to AREs (AU-rich elements) (Page 425, Column 2). Moore teaches that due to miR-16-1′s unique sequence complementarity to AREs, it has been shown to functionally interact with various RNA binding proteins involved with mediating ARE-containing mRNA decay such as the fact that miR-16-1 has been shown to work in conjunction with the mRNA-destabilizing factor tristetraprolin (TTP) to promote rapid decay of ARE-containing mRNAs through interaction with components of the RISC complex (Page 425, Column 2).
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 teachings of Zhang to include the AU-rich element as taught by Moore in the targeting sequence, because Zhang teaches it is within the ordinary skill in the art to modify the activity of a guide RNA with the addition of exogenous sequence and Moore teaches AU-rich elements within the 3’UTR are important for providing degradation signal for mRNA.
One would have been motivated to make such a modification in order to receive the expected benefit of promoting rapid decay of ARE-containing mRNAs through interaction with components of the RISC complex as taught by Moore.
Claim 7 is rejected under 35 U.S.C. 103 as being unpatentable over Zhang et (WO 2017/106657 A1) as evidenced by Meister et al (Molecular Cell, Vol 15, 185-193; 2004) and in view of Latham et al (US 7,993,831 B2).
The teachings of Zhang are described above and applied as before.
Regarding claim 7, Zhang does not teach the specific sequence of SEQ ID NO: 205.
Latham teaches target mRNAs contain multiple miRNA binding sites which allows very fine tuning of gene expression at the mRNA level (Column 1, Lines 14-16). Latham teaches human miRNA sequences which are differentially expressed in cancer and therefore targets such as SEQ ID NOs: 1-114 which are mature miRNAs (Column 3, lines 64-67). Latham teaches SEQ ID NO: 11 is 100% identical to instant SEQ ID NO: 205 (See Appendix I).
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 target miRNA of Zhang for the specific sequence of SEQ ID NO: 11 as taught by Latham because Zhang teaches it is within the ordinary skill in the art to use a CRISPR cas system for microRNA-enabled gene editing and Latham teaches the microRNA-target site comprising SEQ ID NO: 11.
One would have been motivated to make such a modification in order to receive the expected benefit of specific targeting of miRNA for human cancer targets as taught by Latham.
Response to Arguments - Claim Rejections - 35 USC § 103
The previous rejection of claims 1-3, 5, 6, 8-20, 33 and 34 under 35 U.S.C. 103 as being unpatentable over Zhang et (WO 2017/106657 A1) as evidenced by Meister et al (Molecular Cell, Vol 15, 185-193; 2004) has been maintained in view of Applicant’s Amendments filed on 02/13/2026. Applicant’s arguments have been fully considered but have not been found persuasive.
The previous rejection of claim 4 under 35 U.S.C. 103 as being unpatentable over Zhang et (WO 2017/106657 A1) as evidenced by Meister et al (Molecular Cell, Vol 15, 185-193; 2004) and in view of Moore et al (Cancer Metastasis Rev 30:419-435, 2011) has been maintained in view of Applicant’s Amendments filed on 02/13/2026. Applicant’s arguments have been fully considered but have not been found persuasive.
The previous rejection of claim 7 under 35 U.S.C. 103 as being unpatentable over Zhang et (WO 2017/106657 A1) as evidenced by Meister et al (Molecular Cell, Vol 15, 185-193; 2004) and in view of Latham et al (US 7,993,831 B2) has been maintained in view of Applicant’s Amendments filed on 02/13/2026. Applicant’s arguments have been fully considered but have not been found persuasive.
Applicant argues independent claim 1 is not obvious over Zhang and Meister at least because neither Zhang nor Meister provide any specific teaching or motivation to generate a targeting sequence that incorporates a microRNA target site 3’ of a guide nucleotide sequence as required by the instant claims. Applicant continues to argue that this broad generalized teaching in Zhang does not provide the specific combination of structural element claimed by the Applicant, particularly a microRNA target site positioned 3’ to a guide nucleotide sequence.
However, the specific motivation was provided for the modification of the 3’ end of the guide RNA as provided above and re-iterated herein. Zhang suggests 3’ modification of the egRNA (e.g., page 235, 1st full paragraph). Zhang teaches that guide RNA can include addition of nucleotides to the 3' end of a guide RNA which do not match a target sequence downstream of the CRISPR motif, where the addition is 12 nt, 13 nt, 14 nt, 15 nt, 16 nt, 17 nt, 18 nt, 19 nt, 20 nt, or longer (e.g., page 210, 3rd full paragraph). Zhang teaches that the efficiency of functionalized Cpf1 can be increased by the addition of these nucleotides to the 3’ end of the guide RNA (e.g., page 210, 3rd full paragraph). It would have been obvious to one of ordinary skill in the art before the effective filing date of the claimed invention to impose a specific 5’ to 3’ order of direct repeat, guide nucleotide sequence and miRNA target site on the elements of the egRNA taught by Zhang, because Zhang teaches that the egRNA has a direct repeat 5’ to the guide nucleotide sequence, and suggests that the 3’ end of the egRNA can be modified. One would have added the miRNA target site to the 3’ end of the egRNA in order to achieve the predictable result of providing the egRNA with a miRNA target site capable of being cleaved by RISC. One would have been motivated to make such a modification in order to receive the expected benefit of providing a 3’ addition of the guide RNA that does not hybridize to the target sequence to improve efficiency of functionalized Cpf1 as taught by Zhang et al. Meister is only cited to show RISC contains Ago2 which is a miRNA-associated protein (Page 189, Column 2, RISC Activity Requires Ago2 but Not Ago1, Ago3 or Ago4).
Applicant argues unexpected results that certain structures located 3’ to a guide nucleotide sequence result in significantly improved editing efficiency as compared to other, specifically, Applicant points to example 6. Applicant continues to argue the "direct repeat - crRNA -microRNA target site" construct was significantly more effective than the "direct repeat - crRNA- direct repeat" construct in reducing expression of beta-2-microglobulin (as determined by detecting loss of MHC Class I) in fibroblasts and specifically point to the specification as originally filed at Fig. 5B and page 55, line 28 to page 56, line 4 (showing that the "direct repeat - crRNA - microRNA target site" construct led to a 31.8 % decrease in MHC expression as compared to the "direct repeat - crRNA - direct repeat" construct, which only led to a 14.2% reduction). Applicant points to MPEP § 2145 ("A showing of unexpected results must be based on evidence, not argument or speculation." (citing in re Mayne, 104 F.3d 1339, 1343-44 (Fed. Cir. 1997)) and continues to argue that the specification provides concrete experimental evidence demonstrating the unexpected superiority of the claimed invention.
MPEP § 716.02(d)(I) recites “Evidence of nonobviousness consisted of comparing a single composition within the broad scope of the claims with the prior art. The court did not find the evidence sufficient to rebut the prima facie case of obviousness because there was "no adequate basis for reasonably concluding that the great number and variety of compositions included in the claims would behave in the same manner as the tested composition”.
Applicant argues that variants of the "direct repeat - crRNA - microRNA target site" construct that were tissue-specific: the 31.8% decrease in MHC expression was observed only when a microRNA target site for a miRNA expressed in fibroblasts (i.e., miR-106) was used, but not when a microRNA target site for a miRNA absent in fibroblasts (i.e., miR-142- 3p) was used and points to the specification as originally filed at Fig. 5B; page 55 lines 4-6; page 56 lines 2-4. Applicant continues to argue that this tissue-specific control represents a significant and unexpected advantage that is neither taught nor suggested by Zhang, Moore, or any other prior art of record.
However, Zhang teaches induction of esgRNA targeting using miR-122 as part of a gRNA in a HEK293 cell system showing that in the absence of the miR-122 did not meditate targeting EMX1.3 nuclease activity whereas when exogenous miR-122 was added resulting in targeted EMX1.3 cutting (Page 235, 2nd full paragraph). Zhang continues to teach that this demonstrates that highly expressed endogenous miRNAs can be utilized in systems that provide genetically inducible sgRNAs (Page 235, 3rd full paragraph). Therefore, the claim of unexpected results is not persuasive as it was known in the cited art to have improved sgRNA activity when using a guide RNA comprising a miRNA target site in the presence of that specific miRNA compared to without. Thus, the results provided in the specification are not unexpected based on the teachings of the prior art.
Applicant argues Latham provides no teaching, suggestion, or motivation to incorporate specific miRNA target sites into a CRISPR-Cas targeting sequence for purposes of cell-specific gene editing. Applicant continues to argue that while Latham deals with miRNA, its teaching relates to detection and quantification methods-not gene editing systems and the mere fact that both references mention miRNAs does not establish that a person of ordinary skill would combine them for the purpose claimed. Applicant also argues that Moore teaches that AU-rich elements (AREs) within the 3'UTR of mRNAs are important for mRNA stability and degradation, and that miR-16-1 can work with destabilizing factors to promote ARE-containing mRNA decay; However, Moore provides no teaching related to CRISPR-Cas systems or incorporating AREs into guide RNA constructs.
However, Moore is cited and explained above because Zhang does not teach the use of an AU-rich element downstream of the microRNA target site. Moore teaches AU-rich elements within the 3’UTR are important for providing target sequences for select miRNA-meditated regulation indicating the potential for crosstalk between miRNAs with AU-rich elements within the 3’UTR (Page 420, Column 1). Moore teaches AU-rich elements mediate stability of the mRNA transcript and microRNAs, such as miR-12-1, have shown to contain sequence homology to AREs (AU-rich elements) (Page 425, Column 2). Moore teaches that due to miR-16-1′s unique sequence complementarity to AREs, it has been shown to functionally interact with various RNA binding proteins involved with mediating ARE-containing mRNA decay such as the fact that miR-16-1 has been shown to work in conjunction with the mRNA-destabilizing factor tristetraprolin (TTP) to promote rapid decay of ARE-containing mRNAs through interaction with components of the RISC complex (Page 425, Column 2). 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 teachings of Zhang to include the AU-rich element as taught by Moore in the targeting sequence, because Zhang teaches it is within the ordinary skill in the art to modify the activity of a guide RNA with the addition of exogenous sequence and Moore teaches AU-rich elements within the 3’UTR are important for providing degradation signal for mRNA. One would have been motivated to make such a modification in order to receive the expected benefit of promoting rapid decay of ARE-containing mRNAs through interaction with components of the RISC complex as taught by Moore.
Latham is cited and explained above Zhang does not teach the specific sequence of SEQ ID NO: 205. Latham teaches target mRNAs contain multiple miRNA binding sites which allows very fine tuning of gene expression at the mRNA level (Column 1, Lines 14-16). Latham teaches human miRNA sequences which are differentially expressed in cancer and therefore targets such as SEQ ID NOs: 1-114 which are mature miRNAs (Column 3, lines 64-67). Latham teaches SEQ ID NO: 11 is 100% identical to instant SEQ ID NO: 205 (See Appendix I). 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 target miRNA of Zhang for the specific sequence of SEQ ID NO: 11 as taught by Latham because Zhang teaches it is within the ordinary skill in the art to use a CRISPR cas system for microRNA-enabled gene editing and Latham teaches the microRNA-target site comprising SEQ ID NO: 11. One would have been motivated to make such a modification in order to receive the expected benefit of specific targeting of miRNA for human cancer targets as taught by Latham.
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.
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/ALEXANDRA ROSE LIPPOLIS/Examiner, Art Unit 1637
/Jennifer Dunston/Supervisory Patent Examiner, Art Unit 1637
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