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 .
Claims 1-4, 6, 7, 10, 12, 13, 15, 17, 19, 20, 23, 26, 27, 29, 30, 34, and 36 are pending.
Election/Restrictions
Applicant’s election of group I in the reply filed on 07/13/2026 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)).
Upon further consideration, the restriction requirement of 05/12/2026 has been modified as follows:
Group I. Claims 1-4, 6, 7, 10, 12, 13, 15, 17, and 19, drawn to a nucleic acid, classified in C40B40/00.
Group II. Claims 20, 23, 26, 27, 29, and 36, drawn to a genetic circuit, classified in G16B15/30.
Group III. Claim 30, drawn to a method of treating a disease, disorder, or conditions in a subject, classified in C12N15/1086.
Group IV. Claim 34, drawn to a method of detecting an RNA molecule in a sample, classified in C12Q1/68.
Since groups I-IV have been combined into new group I, the new group I will be examined.
Claims 20, 23, 26, 27, 29, 30, 34, and 36 are withdrawn claims from further consideration pursuant to 37 CFR 1.142(b) as being drawn to a nonelected invention, there being no allowable generic or linking claim.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 07/13/2026.
Claims 1-4, 6, 7, 10, 12, 13, 15, 17, and 19 are examined.
Claim interpretation
Claim limitations preceded by “optionally” are interpreted that a limitation is not required, and therefore, the claim limitations preceded by “optionally” have not been examined.
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, 7, 10, and 12 are rejected under 35 U.S.C. 103 as being unpatentable over Qian (Qian et al., BioRxiv, posted on May 26, 2022), in view of Kaseniit (Kaseniit et al., BioRxiv, posted on January 29, 2022).
Qian teaches Cell access through RNA sensing by Endogenous ADAR (CellREADR), an RNA sensing technology that leverages RNA editing mediated by adenosine deaminase acting on RNA (ADAR). The sensor RNA (sesRNA) is complementary to a target cellular RNA, and when the target RNA is present, the two RNA hybridize and form dsRNA. ADAR is recruited to this dsRNA and converts the adenine in the UAG stop codon to inosine, which is interpreted as G. After the action of ADAR, the translation proceeds into the downstream effector. Furthermore, Qian teaches that CellREADER has the potential for RNA-based editing of animal cells which is specific, versatile, easy, and applicable to many organisms with broad application in programmable RNA medicine (abstract).
Regarding claim 1, Qian teaches readrRNA which contains a translation initiation sequence AUG at the 5’ end and sensor domain which is complementary to a specific cellular RNA through sequence-specific base pairing (see fig. 1a and first paragraph of page 4). The sensor domain contains one or more ADAR-editable STOP codons that act as a translation switch. Downstream to the sesRNA, and in-frame with the STOP codon, there is a sequence coding for self-cleaving peptide, T2A, followed in-frame by an effector RNA (efRNA). Qian teaches that the entire readrRNA is deliverable to cells through viral vectors and inside the cells, the sesRNA form a dsRNA by sequence complementary with target RNA, which recruits ADARs which converts UAG STOP codon to UIG codon, switching on the translation of the efRNA (Abstract, page 4 first paragraph, and figure 1a).
Furthermore, Qian teaches CAG promoter drives expression of BFP followed by sequence coding for sesRNA, Cas9, and eGFP effectors. This teaches the limitation of claim 1 sequence encoding for an output (see figure legend of extended data Fig. 2).
Qian teaches ADAR2 and a CellREADR sensor/output construct in Extended data fig. 10c. where ADAR2 is placed upstream of senRNA. See below extended fig. 10c from Qian.
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Thus, Qian teaches a nucleic acid comprising, from 5' to 3': (i) a translation initiation sequence (see figure 1a for AUG; start codon); (ii) a sensor RNA comprising a premature stop codon; (iii) an enzyme, ADAR, that acts on the dsRNA formed between sensor RNA and target RNA and sequence coding for an output.
Regarding claim 2, Qian teaches that ADARs are recruited by stretches of base-paired dsRNA wherein ADAR converts A of STOP codon into I (page 3-4, under section “cellREADER design and implementation in mammalian cells”).
Regarding claim 3, specification of the instant application discloses that the therapeutic protein includes a protein capable of binding and processing gRNA into a mature component of a ribonucleoprotein (RNP) and may include Cas9.
Qian teaches that the output/effector sequence comprise an effector protein. Specifically, Qian descries the effector RNA (efRNA) region as encoding various effector proteins and demonstrates cellREADR constructs encoding Cas9 (see extended figure 2a). Furthermore, Qian teaches that CellREADR will facilitate diagnosis and therapeutics, such as detecting cancer cells by RNA markers and eliminating them by inducing programmed cell death or recruiting immune killer cells (second paragraph of discussion).
Regarding claim 4, Qian teaches that cellREADR construct comprising Cas9 as an effector protein (Extended fig. 2a). Qian further teaches that Cas9 is used together with a guide RNA (gRNA), demonstrating that Cas9 effector is capable of binding RNA.
Regarding claim 7, Qian teaches that the sensor domain contains ADAR-editable STOP codon positioned within the sensor sequence and expressly describe conversion of a UAG STOP codon to UIG following ADAR-mediated A-to-I editing, wherein Inosine is recognized and interpreted as guanosine (G) by cellular machinery (fig. 1a).
Regarding claim 10, Qian teaches a translation initiation sequence comprising an AUG start codon positioned at 5’ end, upstream of the sensor sequence and UAG STOP codon, as shown in figure 1a. Thus, Qian does not disclose an ATG start codon that is positioned 3’ end (downstream) of the premature stop codon and in frame with the translation initiation sequence.
Regarding claim 12, Qian teaches the sensor region with STOP codon (see fig. 1a and 2d). However, the sensor sequence taught by Qian does not comprise TAA which is listed as an option of claim 12, and other options have not been considered because they have been listed as an alternative.
Regarding claim 15, Qian teaches viral delivery of CellREADR in mouse and rat brain and ex vivo human brain tissue (see abstract). Particularly, Qian teaches use of AAV for the delivery of CellREADR (see extended fig. 9g).
Regarding claim 19, Qian teaches producing a recombinant viral preparation comprising the CellREADR construct, wherein the viral preparation is resuspended in cell lysis buffer and subsequently washed with PBS (see “virus production” section of methods). Since the construct was mixed in buffer, this meets the requirement of pharmaceutical composition as recited in claim 19.
Although Qian teaches an RNA-based enzyme (ADAR) that acts on dsRNA to recognize stretches of base-paired dsRNA and function as a sequence-guided base-editing mechanism, it does not explicitly teach a sequence encoding a base editor that acts on double stranded ribonucleic acid (dsRNA) as recited in claim 1.Furthermore, Qian does not teach ADAR to be located downstream of sensor sequence comprising premature stop codon as recited in claim 1.
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 nucleic acid of Qian by including, downstream of sensor sequence, a sequence encoding base editor, such as ADAR, so that expression of the base editor would be activated following edition of the stop codon. Qian teaches that overexpression of ADAR2 increases the CellREADR efficiency (fig. 1h, i and 3rd paragraph of page 5). Similarly, Kaseniit also teaches that sensor output was enhanced by the overexpression of ADAR and increases with increasing level of ADAR overexpression (Figure 1c and 1d). Therefore, an artisan would have been motivated to modify Qian’s nucleic acid construct and include sequence encoding base editor downstream of stop codon to increase ADAR mediated editing and to improve the efficiency of the RNA editing system.
In view of the foregoing, claims 1-4, 7, 10, 12, 15, and 19 taken as a whole would have been prima facie obvious before the effective filing date.
Claim 6 is rejected under 35 U.S.C. 103 as being unpatentable over Qian (Qian et al., BioRxiv, posted on May 26, 2022), in view of Kaseniit (Kaseniit et al., BioRxiv, posted on January 29, 2022) as applied to claims 1-4, 7, 10, and 12 above, and further in view of Katrekar (Katrekar et al., Nature Methods, (2019), 239:242, cited in IDS).
Regarding claim 6, the nucleic acid of claim 1 is discussed above. Qian does not teach sensor sequence which comprise MS2 hairpin sequence.
However, Katrekar teaches RNA base editing via adenosine deaminases acting on RNA (ADAR) enzymes (abstract). Katrekar teaches RNA-editing architecture where an antisense RNA region is flanked by MS2 hairpins (see figure 1C). The antisense domain is complementary to the target and create the RNA duplex recognized by ADAR.
See figure 1c from the Katrekar.
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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 modified the sensor sequence of Qian and incorporate the MS2 hairpin sequence as taught by Katrekar because Katrekar teaches that the construct that has MS2 hairpin flanking an antisense region provide robust targeted RNA editing.
In view of the foregoing, claim 6 taken as a whole would have been prima facie obvious before the effective filing date.
Claim 13 is rejected under 35 U.S.C. 103 as being unpatentable over Qian (Qian et al., BioRxiv, posted on May 26, 2022), in view of Kaseniit (Kaseniit et al., BioRxiv, posted on January 29, 2022) as applied to claims 1-4, 7, 10, and 12 above, and further in view of Verkhusha (US20180044383A1, published 15 February 2018).
Regarding claim 13, the nucleic acid of claim 1 is discussed above. Qian does not teach the sequence of nucleic acid as recited in claim 13.
However, Verkhusha teaches a nucleic acid sequence corresponding to SEQ ID NO: 33. The sequence alignment between SEQ ID NO: 21 of instant application and SEQ ID NO: 33 of Verkhusha shows that the sequences are 95.7 identical. Thus, Verkhusha teaches nucleic acid sequence having at least 95% identity to SEQ ID NO: 21 as required by claim 13. See sequence alignment is shown below-
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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 substituted the target gene sequence of Qian with the sequence of miRFP720 (SEQ ID NO: 33) of Verkhusha because Verkhusha teaches that iRFP720 fully rely on endogenous biliverdin (see paragraph 0009), thereby permitting fluorescence without requiring external viliberdin supplementation or co-expression of heme oxygenase. Furthermore, Verkhusha teaches that these proteins can be used as easy as GFP-like fluorescence protein, providing an alternative reporter for the encoded reporter or output of Qian.
In view of the foregoing, claim 13 taken as a whole would have been prima facie obvious before the effective filing date.
Regarding claim 17, Qian teaches recombinant AAVs comprising nucleic acids encoding RNA-responsive CellREADR construct. For example, extended fig. 10c of Qian teaches an AAV READR vector comprising hSyn, ADAR2, senRAN, and tTA2 effector. Qian further teaches that READR AAV is delivered to and expressed in mouse cortical neurons (see extended fig. 10d).
Qian does not teach RNA-responsive sensors that is flanked by first and second AAV inverted terminal repeat (ITR).
However, Li (Li and Samulski 2020, Nature Reviews Genetics 21: 255-272) teaches engineering an AAV vector cassette in which a therapeutic transgene is positioned between a 5’ ITR and 3’ ITR (see fig. 2).
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 modified CellREADR AAV construct of Qian with the AAV vector cassette as taught by Li, including positioning the nucleic acid construct between the 5’ and 3’ AAV ITRs, because ITRs are known cis-acting elements of AAV vectors and are required for replication and packaging of the recombinant AAV vector.
In view of the foregoing, claim 17 taken as a whole would have been prima facie obvious before the effective filing date.
Conclusion
No claims are allowed.
Any inquiry concerning this communication or earlier communications from the examiner should be directed to SURAJ SAPKOTA whose telephone number is (571)270-0842. The examiner can normally be reached Monday-Thursday 7am-5pm.
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If attempts to reach the examiner by telephone are unsuccessful, the examiner’s supervisor, Ram R Shukla can be reached at (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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Suraj Sapkota
Patent Examiner
AU 1635
/RAM R SHUKLA/Supervisory Patent Examiner, Art Unit 1635
Prosecution Insights