DETAILED ACTION
The present application, filed on or after March 16, 2013, is being examined under the first inventor to file provisions of the AIA .
This application is the national stage of PCT/US2022/018754, filed 03 March 2022, claiming priority to US provisional application 63/157,088, filed 05 March 2021. This International Search Report and Written Opinion issued in the PCT application have been received and reviewed.
Election/Restrictions
Applicant’s election of Group I, and of the species of (1) a Prevotella dCas13 nuclease, (2) a Pumilio aptamer sequence, and (3) an RNA splicing factor, in the reply filed on 29 May 2026 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Claims 15 and 21-22 are withdrawn from further consideration pursuant to 37 CFR 1.142(b) as being drawn to a nonelected invention, there being no allowable generic or linking claim. Election was made without traverse in the reply filed on 29 May 2026.
Claims 3, 6-8, and 11-12 are withdrawn from further consideration pursuant to 37 CFR 1.142(b) as being drawn to a nonelected species, there being no allowable generic or linking claim. Election was made without traverse in the reply filed on 29 May 2026.
Claims 1-2, 4-5, 9-10, 13-14, and 17-19 correspond to the election invention and species and are under consideration herein.
Drawings
The drawings filed 01 September 2023 are objected to because Figure 1C is blurry and Figures 3A-3B include shading that is overly dark (such that depicted sequences are not plainly legible) (see also below regarding the need to provide sequence identifiers for sequences set forth in these figures). Corrected drawing sheets in compliance with 37 CFR 1.121(d) are required in reply to the Office action to avoid abandonment of the application. Any amended replacement drawing sheet should include all of the figures appearing on the immediate prior version of the sheet, even if only one figure is being amended. The figure or figure number of an amended drawing should not be labeled as “amended.” If a drawing figure is to be canceled, the appropriate figure must be removed from the replacement sheet, and where necessary, the remaining figures must be renumbered and appropriate changes made to the brief description of the several views of the drawings for consistency. Additional replacement sheets may be necessary to show the renumbering of the remaining figures. Each drawing sheet submitted after the filing date of an application must be labeled in the top margin as either “Replacement Sheet” or “New Sheet” pursuant to 37 CFR 1.121(d). If the changes are not accepted by the examiner, the applicant will be notified and informed of any required corrective action in the next Office action. The objection to the drawings will not be held in abeyance.
Specification
The disclosure is objected to because it contains an embedded hyperlink and/or other form of browser-executable code (see page 4 at line 32). Applicant is required to delete the embedded hyperlink and/or other form of browser-executable code; references to websites should be limited to the top-level domain name without any prefix such as http:// or other browser-executable code. See MPEP § 608.01. It is noted that this objection may be overcome by simply deleting the recitation of “http://”).
Nucleotide and/or Amino Acid Sequence Disclosures
REQUIREMENTS FOR PATENT APPLICATIONS CONTAINING NUCLEOTIDE AND/OR AMINO ACID SEQUENCE DISCLOSURES
Items 1) and 2) provide general guidance related to requirements for sequence disclosures.
37 CFR 1.821(c) requires that patent applications which contain disclosures of nucleotide and/or amino acid sequences that fall within the definitions of 37 CFR 1.821(a) must contain a "Sequence Listing," as a separate part of the disclosure, which presents the nucleotide and/or amino acid sequences and associated information using the symbols and format in accordance with the requirements of 37 CFR 1.821 - 1.825. This "Sequence Listing" part of the disclosure may be submitted:
In accordance with 37 CFR 1.821(c)(1) via the USPTO patent electronic filing system (see Section I.1 of the Legal Framework for Patent Electronic System (https://www.uspto.gov/PatentLegalFramework), hereinafter "Legal Framework") as an ASCII text file, together with an incorporation-by-reference of the material in the ASCII text file in a separate paragraph of the specification as required by 37 CFR 1.823(b)(1) identifying:
the name of the ASCII text file;
ii) the date of creation; and
iii) the size of the ASCII text file in bytes;
In accordance with 37 CFR 1.821(c)(1) on read-only optical disc(s) as permitted by 37 CFR 1.52(e)(1)(ii), labeled according to 37 CFR 1.52(e)(5), with an incorporation-by-reference of the material in the ASCII text file according to 37 CFR 1.52(e)(8) and 37 CFR 1.823(b)(1) in a separate paragraph of the specification identifying:
the name of the ASCII text file;
the date of creation; and
the size of the ASCII text file in bytes;
In accordance with 37 CFR 1.821(c)(2) via the USPTO patent electronic filing system as a PDF file (not recommended); or
In accordance with 37 CFR 1.821(c)(3) on physical sheets of paper (not recommended).
When a “Sequence Listing” has been submitted as a PDF file as in 1(c) above (37 CFR 1.821(c)(2)) or on physical sheets of paper as in 1(d) above (37 CFR 1.821(c)(3)), 37 CFR 1.821(e)(1) requires a computer readable form (CRF) of the “Sequence Listing” in accordance with the requirements of 37 CFR 1.824.
If the "Sequence Listing" required by 37 CFR 1.821(c) is filed via the USPTO patent electronic filing system as a PDF, then 37 CFR 1.821(e)(1)(ii) or 1.821(e)(2)(ii) requires submission of a statement that the "Sequence Listing" content of the PDF copy and the CRF copy (the ASCII text file copy) are identical.
If the "Sequence Listing" required by 37 CFR 1.821(c) is filed on paper or read-only optical disc, then 37 CFR 1.821(e)(1)(ii) or 1.821(e)(2)(ii) requires submission of a statement that the "Sequence Listing" content of the paper or read-only optical disc copy and the CRF are identical.
Specific deficiencies and the required response to this Office Action are as follows:
Specific deficiency – Nucleotide and/or amino acid sequences appearing in the drawings are not identified by sequence identifiers in accordance with 37 CFR 1.821(d). Sequence identifiers for nucleotide and/or amino acid sequences must appear either in the drawings or in the Brief Description of the Drawings. In particular, see Figures 1C and 3A-B.
Required response – Applicant must provide:
Replacement and annotated drawings in accordance with 37 CFR 1.121(d) inserting the required sequence identifiers;
AND/OR
A substitute specification in compliance with 37 CFR 1.52, 1.121(b)(3) and 1.125 inserting the required sequence identifiers into the Brief Description of the Drawings, consisting of:
A copy of the previously-submitted specification, with deletions shown with strikethrough or brackets and insertions shown with underlining (marked-up version);
A copy of the amended specification without markings (clean version); and
A statement that the substitute specification contains no new matter.
It is reiterated that new Drawings are also required for other reasons, as indicated above.
Claim Interpretation
Regarding the recitation “(PspdCas13)” in claim 4, it is noted that this is interpreted as an abbreviation corresponding to the entire prior recitation “Prevotella P5-125 dCas13 nuclease” (as this is consistent with the usage of this abbreviation throughout the application as filed).
Regarding the term “RNA effector molecule” (which appears in independent claim 14 and 17), it is noted that the specification discusses such molecules at pages 15-17, providing numerous and varied examples thereof, and broadly defining the term as referring to “a molecule (e.g., a protein or peptide) that can be detected (e.g., imaged) and/or that acts on a target RNA” (see page 15, lines 19-20). Thus, this term encompasses any molecule that “can be detected”, and/or any molecule “that acts on a target RNA”; with regard to the embodiment of “detectable molecules”, it is further noted that the specification teaches that such molecules “may be tracked in a cell” via various methods, and include such molecules as fluorescent proteins and dyes (see page 15 bridging to page 16).
Regarding claim 14, as the claim requires delivering “an RNA-editing complex that comprises” multiple listed components, the limitation “an RNA effector molecule linked to a detectable molecule and an RNA-binding domain (RBD) sequence that specifically binds to the RNA aptamer sequence” is interpreted as requiring that the “RNA molecule” is linked to both “a detectable molecule” and “an RNA-binding domain (RBD) sequence” as specified in the claim.
Claim Rejections - 35 USC § 112(b)/second paragraph
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 13 and 17-19 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.
Claim 13 is indefinite over the recitation of the limitation “wherein the Cas13 gRNA binds to a nonrepetitive RNA sequence”, because it is unclear how this language is further limiting of the method of claim 1 (from which claim 13 depends). More particularly, it is unclear whether the claim is simply reciting a property/characteristic of the Cas 13 gRNA, or whether this claim is referring to an activity (binding) that must actually occur during the performance of the method. As there are multiple reasonable interpretations of the claim language that impart different types of boundaries on what is claimed, further clarification is required.
Claims 17-19 are indefinite over the recitation in independent claim 17 of the limitation “a first Cas13 guide RNA (gRNA) lined to a first RNA aptamer sequence and a first detectable molecule linked to a first RNA-binding domain (RBD) sequence...” because it is unclear whether this language is referring to two separate components (the first Cas13 gRNA and the first detectable molecule), or to a single first Cas13 gRNA linked to both the “first RNA aptamer sequence” and the “first detectable molecule”. As there are multiple reasonable interpretations imparting different boundaries on what is claimed, further clarification is required.
Claims 17-19 are similarly indefinite over the recitation of the limitation “a second gRNA linked toa second RNA aptamer sequence and an RNA effector molecule, optionally a second detectable molecule, linked to a second RBD sequence….”. While it is noted that the language “optionally a second detectable molecule” clearly sets forth an optional further limitation that applies to the “RNA effector molecule”, it is unclear whether this claim language is referring to two separate components (the second Cas13 gRNA and the RNA effector molecule), or to a single second Cas13 gRNA linked to both “a second RNA aptamer sequence” and “an RNA effector molecule”. As there are multiple reasonable interpretations imparting different boundaries on what is claimed, further clarification is required.
Claim Rejections - 35 USC § 102
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 the appropriate paragraphs of 35 U.S.C. 102 that form the basis for the rejections under this section made in this Office action:
A person shall be entitled to a patent unless –
(a)(1) the claimed invention was patented, described in a printed publication, or in public use, on sale, or otherwise available to the public before the effective filing date of the claimed invention.
(a)(2) the claimed invention was described in a patent issued under section 151, or in an application for patent published or deemed published under section 122(b), in which the patent or application, as the case may be, names another inventor and was effectively filed before the effective filing date of the claimed invention.
Claim(s) 1-2, 13-14, and 17-19 are rejected under 35 U.S.C. 102(a)(1) and 35 U.S.C. 102(a)(2) as being anticipated by Hsu et al (US 10,476,825 [12 Nov 2019]; cited herein).
Regarding all of independent claims 1, 14, and 17, Hsu et al teach “CRISPR/Cas methods and compositions for targeting RNA molecules, which can be used to detect, edit, or modify a target RNA” (see entire reference, particularly the Abstract). Among the methods taught by Hsu et al are methods of live cell labeling and imaging/visualizing that may target multiple different RNAs, which methods may employ one or more non-naturally occurring or engineered CRISPR-Cas systems that comprise a Cas13 protein that may be a catalytically inactive Cas13d (i.e., a type of dCas13), a Cas13 guide RNA (gRNA) that comprises an aptamer sequence, and a detectable molecule linked to an RNA-binding domain (RBD) sequence that specifically binds the RNA aptamer sequence; see entire reference, particularly e.g., col 29, line 25-col 30, line 34; col 37, line 37-col 38, line 49; col 49, lines 7-58; and col 51, lines 16-42, noting in particular the embodiment discussed at col 51, lines 35-42, in which an fluorescently labeled MS2 phage coat protein specifically binds to an MS2 RNA aptamer sequence within the gRNA, as well as the more general disclosure of different effector domains and aptamer binding partners at col 38, lines 29-49. It is also particularly noted that the methods discussed at col 51, lines 16-42 are disclosed as being methods of targeting an RNA that result in “detecting, visualizing, or labeling a target RNA”, i.e., the methods achieve visualizing/“imaging” a detectable molecule (e.g., the above noted fluorescently label) to achieve detection of the target RNA. With further regard to the limitation “delivering to a” cell/live cell in independent claims 1 and 14, Hsu et al also clearly teach “introducing into a cell (such as a eukaryotic or prokaryotic cell) containing the one or more target RNA molecules” their CRISPR-Cas system(s) via a variety of different known techniques that meet the requirement of “delivering to a live cell” the disclosed complex(es); see again, e.g., col 30, lines 2-27). Thus, Hsu et al also disclose methods meeting all requirements of claims 1 and 14. (With further regard to the recitation of the elected species of “an RNA splicing factor” in claim 14, it is noted that this is clearly identified in the claim as optional, such that all limitations of the claim are disclosed as discussed above; however, Hsu et al do teach effectors that include RNA splicing activity [see, e.g., col. 56, lines 1-12]). With further regard to (indefinite) independent claim 17, Hsu et al also clearly teach the use together of, e.g., 2-20 different gRNAs as disclosed (see again, e.g., col 30, lines 28-34, as see also the teaching “multiplexing, e.g., the delivery of multiple gRNAs to a cell….to target multiple target RNAs” at col 46, lines 40-43), and teach transfection as a method of introduction of their CRISPR-Cas systems (see again, e.g., lines 3-27); it is also reiterated that Hsu et al disclosed multiple different aptamers and corresponding effectors and binding partners that function in their methods (see again col 38, lines 29-49, and col 51, lines 35-42). Thus, “multiplex live cell imaging” as set forth in claim 17 (to the extent that it is presently understood) is also among the embodiments disclosed by Hsu et al.
With further regard to dependent claim 2, Hsu et al describe the normal function of Cas13d in processing pre-crRNA units into individual crRNAs (see, e.g., col 20, lines 55-66), and disclose the use of “catalytically inactive” Cas13d proteins, include proteins that may or may not have the ability to process pre-crRNA (which constitutes an inherent disclosure of dCas13 nucleases meeting the requirements of claim 2) (see, e.g., col 33, line 17-col 37, line 65). Regarding (indefinite) dependent claim 13, Hsu et al teach that gRNAs include both repeats (i.e., repetitive sequences) and spacers, with the spacers being variable and specifically binding to target RNA (see, e.g., col 45, lines 15-45); Hsu et al thus teach at least one embodiment embraced by the language of claim 13. With further regard to dependent claim 18, the limitations of transfection and use of a catalytically inactive Cas13 nuclease are addressed above. Regarding dependent claim 19, the use of multiple gRNAs targeting multiple target RNAs is also addressed above.
Accordingly, Hsu et al anticipate claims 1-2, 13-14, and 17-19.
Claim Rejections - 35 USC § 103
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.
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) 4-5 are is/are rejected under 35 U.S.C. 103 as being unpatentable over Hsu et al (US 10,476,825 [12 Nov 2019]; cited herein) in view of Yang et al (Molecular Cell 76:981-997 [Dec 2019]; cited in IDS).
Regarding independent claim 1 (from which the rejected claims depend), Hsu et al teach “CRISPR/Cas methods and compositions for targeting RNA molecules, which can be used to detect, edit, or modify a target RNA” (see entire reference, particularly the Abstract). Among the methods taught by Hsu et al are methods of live cell labeling and imaging/visualizing that may target multiple different RNAs, which methods may employ one or more non-naturally occurring or engineered CRISPR-Cas systems that comprise a Cas13 protein that may be a catalytically inactive Cas13d (i.e., a type of dCas13), a Cas13 guide RNA (gRNA) that comprises an aptamer sequence, and a detectable molecule linked to an RNA-binding domain (RBD) sequence that specifically binds the RNA aptamer sequence; see entire reference, particularly e.g., col 29, line 25-col 30, line 34; col 37, line 37-col 38, line 49; col 49, lines 7-58; and col 51, lines 16-42, noting in particular the embodiment discussed at col 51, lines 35-42, in which an fluorescently labeled MS2 phage coat protein specifically binds to an MS2 RNA aptamer sequence within the gRNA, as well as the more general disclosure of different effector domains and aptamer binding partners at col 38, lines 29-49. It is also particularly noted that the methods discussed at col 51, lines 16-42 are disclosed as being methods of targeting an RNA that result in “detecting, visualizing, or labeling a target RNA”, i.e., the methods achieve visualizing/“imaging” a detectable molecule (e.g., the above noted fluorescently label) to achieve detection of the target RNA. With further regard to the limitation “delivering to a” cell, Hsu et al also clearly teach “introducing into a cell (such as a eukaryotic or prokaryotic cell) containing the one or more target RNA molecules” their CRISPR-Cas system(s) via a variety of different known techniques that meet the requirement of “delivering to a live cell” the disclosed complex(es); see again, e.g., col 30, lines 2-27). Thus, Hsu et al also disclose methods meeting all requirements of claim 1.
While Hsu et al clearly teach the use of a dCas13 nuclease, as described above, Hsu et al do not teach the use in their methods of a Prevotella dCas13 nuclease (as required by claims 4-5), including the particular such nuclease set forth in dependent claim 5.
Yang et al teach use of the dCas13 system in labeling RNAs (i.e., the same application described by Hsu et al) (see entire reference). With particular regard to dependent claims 4-5, Yang et al disclose screening for and identifying Prevotella sp. P5-125 (Psp)Cas13b for use in such methods, and identifying dPspCas13b (which meets the requirements of claims 4-5 for “a Prevotella dCas13 nuclease” and “a Prevotella P5-125 dCas13 nuclease (PspdCas13)”, respectively) as being “the most efficient cCas13 protein to label RNA” based on their analysis (see entire reference, in particular page 983 ( particularly at the second line of the right column and the bottom of the right column), as well as pages 985 and 987). Yang et al state that their dPspCas13 “achieved…robust….rapid…and efficient…RNA tracking in live cells” (page 993, bottom of left column).
In view of the teachings of Yang et al, it would have been prima facie obvious to one of ordinary skill in the art before the effective filing date of the claimed invention to have modified the methods of Hsu et al so as to have employed dPspCas13b as taught by Yang et al instead of any of the various dCas13d alternatives taught by Hsu et al, particularly for method involving the imaging/tracking/visualizing of RNA in live cells. An ordinary artisan would have been motivated to have made such a modification for the benefits of efficient, robust, and rapid RNA tracking, as taught by Yang et al. Further, given the detailed guidance provided by both Hsu et al and Yang et al, an ordinary artisan would have had a reasonable expectation in so modifying the methods of Hsu et al.
Claim(s) 9-10 and 13 are rejected under 35 U.S.C. 103 as being unpatentable over Hsu et al in view of Higashikuni et al (ACS Synth. Biol. 8:2607-2619 [Nov 2019]; cited herein).
While claim 13 is also rejected under 35 USC 102 as discussed above, this rejection applies to the claim to the extent that it may be directed to “nonrepetitive” targets as discussed by Higashikuni et al.
The teaching of Hsu et al as they apply to claim 1 (from which the rejected claim depend) are set forth above. While Hsu et al teach use in their dCas13 system-based methods of MS2 and PP7 aptamers and their corresponding binding sequences, and state that “other aptamers” may also be used – see again col 38 lines 29-49 and col 51, lines 35-42 - Hsu et al do not teach the elected species of “a Pumilio aptamer sequence” (as set forth in claims 9-10).
Higashikuni et al teach “CRISPR-based programmable platforms” for applications other than genome editing, including CRISPR-based imaging platforms (see entire reference, particularly page 2611, right column-page 2612). Higashikuni et al teach modified gRNAs having integrated aptamers (i.e., the same general type of modified gRNAs taught by Hsu et al), and provide as an example a Pumilio binding sequence (taught as being used “in combination with fusions of aptamer-binding proteins and fluorescent proteins”, and applied to labeling both repetitive and nonrepetitive regions (see page 2612, left column).
In view of the teachings of Hsu et al and Higashikuni et al, it would have prima facie obvious to one of ordinary skill in the art before the effective filing date of the claimed invention to have modified the methods of Hsu et al so as to have substituted a gRNA including a Pumilio aptamer sequence (and a corresponding detectable molecule/protein containing a Pumilio binding domain) for the aptamer embodiments specifically referenced by Hsu et al (such as PP7, MS2, etc.). As Hsu et al teach that “other aptamers” may be used, and Higashikuni et al provide Pumilio sequences as alternative aptamers usable in the same type of CRISPR-Cas based system, such a modification constitutes the simple substitution of one aptamer type for another to achieve a predictable result. Additionally or alternatively, as Higashikuni et al teach a possible advantage of such aptamers in targeting “nonrepetitive elements”, an ordinary artisan would have been motivated to have made such a modification for the benefit of detecting such nonrepetitive elements (and thus Higashikuni et al also render obvious an alternative embodiment embraced by claim 13). Furthermore, given the detailed guidance provided by Hsu et al and Higashikuni et al, an ordinary artisan would have had a reasonable expectation of success in performing such methods.
Conclusion
Braselmann et al (Cell Chemical Biology 27:891 [Aug 2020]; cited herein) provide an overview of known methods for imaging RNA in live mammalian cells, which methods include dCas13-based imaging systems (see entire reference, particularly page 894 under the heading “dCas13”; see also Figures 1-2).
Any inquiry concerning this communication or earlier communications from the examiner should be directed to DIANA B JOHANNSEN whose telephone number is (571)272-0744. The examiner can normally be reached Monday-Friday, 7:30 am-3:30 pm EST.
Examiner interviews are available via telephone, in-person, and video conferencing using a USPTO supplied web-based collaboration tool. To schedule an interview, applicant is encouraged to use the USPTO Automated Interview Request (AIR) at http://www.uspto.gov/interviewpractice.
If attempts to reach the examiner by telephone are unsuccessful, the examiner’s supervisor, Wu-Cheng Winston Shen can be reached at (571) 272-3157. The fax phone number for the organization where this application or proceeding is assigned is 571-273-8300.
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/DIANA B JOHANNSEN/Primary Examiner, Art Unit 1682
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