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 .
Continued Examination Under 37 CFR 1.114
A request for continued examination under 37 CFR 1.114, including the fee set forth in 37 CFR 1.17(e), was filed in this application after final rejection. Since this application is eligible for continued examination under 37 CFR 1.114, and the fee set forth in 37 CFR 1.17(e) has been timely paid, the finality of the previous Office action has been withdrawn pursuant to 37 CFR 1.114. Applicant's submission filed on 5/5/2025 has been entered.
Priority
The priority date for this application is the date of the provisional application: 03/22/2021.
Election/Restrictions
Claims 32-33 were withdrawn from further consideration pursuant to 37 CFR 1.142(b) as being drawn to a nonelected groups, there being no allowable generic or linking claim. Election was made without traverse in the reply filed on 8/13/2024.
Therefore claims remain withdrawn.
Status of the Claims
This action is in response to papers filed 5/5/2025 in which no claims were canceled or added and claim 1 was amended.
Claims 1-4,6,8,11,13-15,17-18,20,23,25, and 29 are under prosecution.
Amendments & Response to Arguments
Applicant has amended claim 1 to overcome the 103 rejections; in view of claim amendments, a new 103 rejection has been presented in this office action.
The NSDP rejection of copending Application No. 17/320,965 has been withdrawn in view of the abandonment of referenced application.
Arguments applicable to newly applied rejections to amended or newly presented claims are addressed below. Arguments that are no longer relevant are not addressed.
Rejections not reiterated here are withdrawn.
Claim Interpretation
The phrase, “promoter operably linked” in claim 1 is being interpreted as per specification to mean a promoter whose activity controls a gene’s expression and not to mean a promoter located directly upstream of the gene whose activity it controls (A promoter is said to be operably linked to a gene if the promoter controls the degree to which the gene is expressed, Pg. 8, 2nd paragraph).
The limitation, wherein the repressor is an endoribonuclease, an RNAi molecule, or a ribozyme, recites optional limitations (or). Therefore, if any one alternative is known in the prior art, then the limitation is known in the prior art.
Wherein clause:
It is noted that the subject matter of a properly construed claim is defined by the terms that limit its scope. It is this subject matter that must be examined. As a general matter, the grammar and intended meaning of terms used in a claim will dictate whether the language limits the claim scope. Language that suggests or makes optional but does not require steps to be performed or does not limit a claim to a particular structure does not limit the scope of a claim or claim limitation. “Wherein” clauses are examples of language that may raise a question as to the limiting effect of the language in a claim. See MPEP 2103 I.C. and MPEP § 2111.04.
It is also noted that a “wherein” clause, such as that in (claim 1), must give “meaning and purpose to the manipulative steps.” See, MPEP § 2111.04.
In the instant claims, the wherein clauses are followed by functional language: reduction or absence of the repressor results in increased expression of the output molecule (claim 1), rather than a structural limitation. Thus, the wherein clauses recite inherent functions which will flow from the structural limitations of the claims they depend from. See, MPEP § 2112.01: II. COMPOSITION CLAIMS — IF THE COMPOSITION IS PHYSICALLY THE SAME, IT MUST HAVE THE SAME PROPERTIES.
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.
The factual inquiries for establishing a background for determining obviousness under 35 U.S.C. 103 are summarized as follows:
1. Determining the scope and contents of the prior art.
2. Ascertaining the differences between the prior art and the claims at issue.
3. Resolving the level of ordinary skill in the pertinent art.
4. Considering objective evidence present in the application indicating obviousness or nonobviousness.
This application currently names joint inventors. In considering patentability of the claims the examiner presumes that the subject matter of the various claims was commonly owned as of the effective filing date of the claimed invention(s) absent any evidence to the contrary. Applicant is advised of the obligation under 37 CFR 1.56 to point out the inventor and effective filing dates of each claim that was not commonly owned as of the effective filing date of the later invention in order for the examiner to consider the applicability of 35 U.S.C. 102(b)(2)(C) for any potential 35 U.S.C. 102(a)(2) prior art against the later invention.
Claims 1-4, 6, 8, 11, 13-15, 17-18, 20, 23, 25, and 29 are rejected under 35 U.S.C. 103 as being unpatentable over Benenson (US 2017 /0159135, Jun. 8, 2017) in view of Borchardt et al. (2015, RNA, 21: 1921-1930).
Regarding claims 1 and 11, Benenson teach a cellular biosensor system comprising: (i) a sensor circuit comprising a first constitutive promoter (CMV), operably linked to a nucleic acid sequence encoding: (a) a repressor (LacI); and (b) one or more target sequences for a first set of one or more miRNAs (miR-21 binding region); and (ii) a signal circuit comprising a second constitutive promoter (CAG) operably linked to a nucleic acid sequence encoding: (a) a repressor recognition sequence that is capable of being bound by the repressor of (i)(a); and (b) a nucleic acid sequence encoding an output molecule (DSRed) (Benenson, Fig. [AltContent: rect]10 (rtTA-Standard Sensor). See Examiner-annotated Fig. 10 from Benenson reproduced below from previous office action dated 8/21/24.
Examiner has interpreted Benenson’s biosensor system as a sequestron as it meets all the structural requirements as instantly claimed. Benenson do not specifically teach wherein the repressor is an endoribonuclease (claim 11), an RNAi molecule, or a ribozyme (claim 1) nor teach the amended limitation wherein reduction or absence of the repressor results in increased expression of the output molecule (claim 1).
However, at the time of the effective filing date, Borchardt teach making and using endoribonucleases in genetic circuits (abstract). Borchardt teach the bacterial CRISPR endoribonuclease Cys4 cleaves an RNA hairpin stem. Borchardt disclose this about the mechanism of action of the repressor: endoribonuclease Csy4 binds its substrate RNA through a specific 28-nt hairpin sequence and rescues the target mRNA substrate from degradation, resulting in protein expression (abstract). Non-binding mutants were unable to exert any of these effects. Thus, binding of the repressor (resulting in the absence of a free repressor) increased expression of the output.
Borchardt discloses the study providing the ability of CRISPR endoribonuclease Csy4 to control the mRNA stability and translation by transfecting two plasmid vectors in HEK293 cells; one vector containing a reporter transcript of a GFP or Gaussia Luciferase (GLuc) reporter genes with a Csy4 target hairpin (HP) inserted within the 5’ UTR and second vector containing a Csy4 encoding transcript (pg. 1922). Both the vectors were under the control of the constitutive promoter, chicken-beta actin (CBA) promoter (pg. 1927-1928).
Thus Borchardt’s first vector with Csy4 encoding transcript and second vector with reporter transcripts (i.e. the output with endoribonuclease target site within the 5’UTR) reads on sensor and signal circuit, respectively, with identical CBA promoter in each vector. When the repressor binds to its cognate sequence on the signal circuit it is sequestered, resulting in an absent repressor, the output molecule is expressed.
It would have been prima facie obvious to a person of ordinary skill in the art before the effective filing date to combine the teachings of Benenson taken with Borchardt to use as endoribonuclease as a repressor in place of LacI in Benenson’s biosensor system.
A person of ordinary skill in the art would have been motivated to combine the teachings for the advantage of creating a sequestron capable of increased control of post-transcriptional expression of intended targets, specifically binding of an RNA repressor (e.g., endoribonuclease) by its cognate sequence to result in high output expression to arrive at the instant claim 1. It would be a simple substitution for one of ordinary skill in the art to replace generic repressor or recombinase in the biosensor system of Benenson with the endoribonuclease taught by Borchardt. See MPEP 2143 I.(B) and 2144 II. One of ordinary skill in the art and would be able to make such a substitution with reasonable expectation of success because both references are in the field of genetic circuits designed to effectuate modulation of a target gene.
Of the alternative limitations wherein the repressor is an endoribonuclease, an RNAi molecule, or a ribozyme; an RNAi molecule, or a ribozyme have not been considered because they are recited as being optional.
Thus, Benenson in view of Borchardt make obvious instant claims 1 and 11.
Regarding claim 2, Benenson teach the biosensor system of claim 1, wherein the one or more target sequences for the first set of one or more miRNAs of (i)(b) are downstream from the nucleic acid sequence encoding the repressor (Fig. 10).
Regarding claim 3, Benenson teach the biosensor system of claim 1, wherein the nucleic acid sequence encoded by the signal circuit of (ii) further comprises one or more target sequences for a second set of one or more miRNAs (Fig. 10).
Regarding claim 4, Benenson teach the biosensor system of claim 1, wherein the nucleic acid sequence encoded by the signal circuit of (ii) further comprises one or more target sequences for a second set of one or more miRNAs and wherein these sequences are downstream from the nucleic acid sequence encoding the output molecule (Fig. 10).
Regarding claim 6, Benenson teach various embodiments of their circuits. Benenson Fig. 1b shows a repressor module comprising genes in their cumulative gene action exert repressing and/or inhibitory effect(s) on an output module (Benenson Abstract, Fig. 1b). Thus, Benenson teach a cellular biosensor system comprising (i) a sensor circuit, made up of two expression cassettes, that cumulatively exert repressing and/or inhibitory effect(s) on a (ii) a signal circuit, that read on components of instantly claimed sequestron. As evidenced by Benenson, Pg. 4, lines bridging 1st and 2nd columns: CMV and CAG are constitutive promoters. See Examiner-annotated Fig. 1b from Benenson showing the discussed embodiment of a biosensor system
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[AltContent: textbox (Output module (Signal circuit as per instant claim))][AltContent: textbox (A Repressor module (Sensor circuit as per instant claim))][AltContent: oval][AltContent: oval][AltContent: textbox (Components of Repressor module (Claim 1(i)(a) and (b) of Sensor circuit as per instant claim))][AltContent: textbox (Repressor)][AltContent: textbox (Repressor Recognition Sequence)][AltContent: arrow][AltContent: textbox (First constitutive promoter)][AltContent: textbox (Second constitutive promoter)][AltContent: textbox (Output Molecule)][AltContent: textbox (Target Sequence for first set of miRNAs)][AltContent: textbox (Target Sequence for second set of miRNAs)][AltContent: arrow][AltContent: arrow][AltContent: textbox (Fig.1b)][AltContent: rect]reproduced below from previous office action dated 8/21/24.
Specifically, with respect to claim 6, Benenson further teach wherein the biosensor system comprises a plurality of the signal circuit (Fig. 4), wherein the individual circuit was shown in Fig. 1b . The optional limitations following the wherein clause are not considered because they are recited as optional; i.e., not required.
Regarding claim 8, the biosensor system of claim 1 is taught above. Benenson further teach wherein the biosensor system comprises a plurality of the sensor circuit (Fig. 4). The optional limitations following the wherein clause are not considered because they are recited as optional; i.e., not required.
Regarding claim 13, the biosensor system of claim 1 is taught above. Benenson further teach wherein the first and/or second constitutive promoter is an hEF1-alpha promoter (Pg.18, column 6, line 10; and Pg.19, column 7, line 56).
Regarding claim 14, the biosensor system of claim 1 is taught above. Benenson further teach a plurality of biosensor systems of claim 1 (Fig. 4), wherein (A) the biosensor system encodes a combination of different repressors (Pg.19, column 7, line 21; and Fig.4: Gene1 depicting Activator, and Gene2 depicting Recombinase 1), (C) the repressor encoded by the sensor circuit of each of the plurality of biosensor systems is capable of binding or cleaving the repressor recognition sequence of the signal circuit of the same biosensor system (Fig.4: Activator binds to Gene2, and Recombinase 1 acts on Gene3).
Benenson do not teach (B) the repressor recognition sequence of (ii)(a) of each of the plurality of biosensor systems comprises a different nucleic acid sequence, and (D) the repressor encoded by the sensor circuit of each biosensor system is not capable of binding or cleaving the repressor recognition sequence of a different biosensor system, in the above described embodiment.
However, Benenson does describe embodiments wherein the sensor circuit comprises (B) the repressor recognition sequence of (ii)(a) of each of the plurality of biosensor systems comprises a different nucleic acid sequence (the repressor encoded by the transcriptional repressor sequence (TR) of gene (2) is selected from the group consisting of a (poly)peptide repressor, a non-coding RNA repressor, preferably a small or long non-coding RNA repressor, a combination of different repressors, paragraph [0055]); Further, Benenson teaches (D) the repressor encoded by the sensor circuit of each biosensor system is not capable of binding or cleaving the repressor recognition sequence of a different biosensor system (Negative interference with repressor components, Fig. 13).
It would have been prima facie obvious to a person of ordinary skill in the art before the effective filing date to have tried to combine the various embodiments of Benenson and obvious variations of the same into a biosensor system, to arrive at the limitations in the claimed invention. A person of ordinary skill in the art would be motivated by looking at various embodiments of Benenson and make such a combination because such a combination would be within the scope of one of ordinary skill in the art given that Benenson explicitly disclose that standard molecular biology techniques were used in the construction of plasmid DNA constructs (Benenson Pg. 26, 1st column, 1st line of example 5). See MPEP 2143 I.(A, D, and G).
Regarding claims 15 and 29, the biosensor system of claim 1 is taught above. Benenson further teach the biosensor system of claim 1 is delivered using a suitable delivery method, e.g., liposomal vesicles Benenson, Pg.16, column 2, line 18 – 26, for intended use; and Pg.21, column 2, para [0138] for delivery). As evidenced by O'Driscoll, liposomes are an excipient for delivery of nucleic acids.
Regarding claim 17, the biosensor system of claim 1 is taught above. Benenson further teach wherein the biosensor system is in a cell (Benenson abstract, line 1: a cellular biosensor system).
Regarding claim 18, the biosensor system of claim 1 is taught above. Benenson further disclose that standard molecular biology techniques were used in the construction of plasmid DNA constructs (Benenson Pg. 26, 1st column, 1st line of example 5). As evidenced by Green & Sambrook, such techniques used in the construction of the biosensor system of claim 1 are performed in a bacterial cell. Thus, the biosensor system of claim 1 in a bacterial cell is rendered obvious by Benenson.
Regarding claim 20, the cell comprising the biosensor system of claim 17 is taught above. Benenson further teach wherein the cell is a eukaryotic cell (Benenson, Pg.17, 1st column, para [0042]).
Regarding claim 23, the cell comprising the biosensor system of claim 17 is taught above. Benenson further teach wherein the cell is a diseased cell (Benenson, Pg.20, 2nd column, para [0111]).
Regarding claim 25, the cell comprising the biosensor system of claim 17 is taught above. Benenson further teach wherein the cell expresses any one of the first set of microRNAs (Benenson, Claim 4 recitation, “The cellular biosensor system of claim 1, wherein the inputs are … selected from the group consisting of endogenously expressed microRNA molecules”).
Regarding claim 26, claim 26 is being interpreted as a cell comprising the biosensor system, i.e., a cell of claim 17. Regarding claim 26, the cell comprising the biosensor system of claim 17 is taught above. Benenson further teach a method comprising maintaining the cell comprising the biosensor system in culture (paragraph [0115]).
Thus, Benenson in view of Borchardt make obvious instant claims 2-4, 6, 8, 13-15, 17-18, 20, 23, 25, and 29.
Therefore the invention as a whole would have been prima facie obvious to one ordinary skill in the art before the effective filing date of the claimed invention to a person having ordinary skill in the art to which the claimed invention pertains.
Response to Arguments
Applicant's arguments filed 5/5/2025 to obviousness rejection of claims under 35 USC § 103 have been fully considered but are not found persuasive. Applicant's arguments are directed to the previous rejections of the previous claims.
The amendments made to the claims have overcome these previous rejections. However, the current rejections are applicable to the current claims. Applicant's remarks have been fully considered but are moot because they do not specifically address the current rejections of the current claims.
Double Patenting
Response to Applicant’s Remarks:
Applicant's arguments filed 5/5/2025 have been fully considered and are persuasive.
The NSDP rejection of instant invention in view of copending Application No. 17/153,276 and copending Application No. 17/320965 have been withdrawn because stated copending applications have been abandoned.
Conclusion
No claim is allowed.
Any inquiry concerning this communication or earlier communications from the examiner should be directed to SHABANA MEYERING, Ph.D. whose telephone number is (703)756-4603. The examiner can normally be reached M - F: 9am to 5pm EST.
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If attempts to reach the examiner by telephone are unsuccessful, the examiner’s supervisor, Ram Shukla can be reached on (571) 272-0735. The fax phone number for the organization where this application or proceeding is assigned is 571-273-8300.
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/SHABANA S MEYERING/Examiner, Art Unit 1635
/RAM R SHUKLA/Supervisory Patent Examiner, Art Unit 1635