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and the fee set forth in 37 CFR 1.17(e) has been timely paid, the finality of the previous Office action has been withdrawn pursuant to 37 CFR 1.114.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 May 12, 2025 has been entered.
Applicant's Amendment to the Claims filed on May 12, 2025 has been entered.
Claim status
Claims 1-42, 44-46, and 48-283 are canceled.
Claims 287-299 are new.
Claims 43, 47, and 284-299 are pending.
Election/Restrictions
Applicant’s election without traverse of Invention Group IV (drawn to a synthetic RNA circuit comprising a first and second RNA molecule each comprising a sequence recognized by a protein) in the reply filed on 01/29/2024 is as previously acknowledged.
Priority
This US17/735,627 is a DIV of 15/509,258 filed on 03/07/2017 (now US Patent 11,351,271) which is a 371 of PCT/US15/49045 filed on 09/08/2015 which claims priority benefit of US Provisional 62/195,747 filed on 07/22/2015 and 62/047,137 filed on 09/08/2014.
Response to Amendment
All rejections made in the previous Office Action mailed on 12/12/2024 and not repeated in this Office Action are withdrawn in light of the Applicants’ Amendment to the Claims filed on May 12, 2025.
Claim Objections
Newly added claim 295 is objected to because of the following informalities: In line 2, the misspelled word “untraslated” should recite untranslated. Appropriate correction is required.
Claim Rejections - 35 USC § 103 – new grounds of rejection
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.
Currently amended claims 43, 47, and 284-299 are rejected under 35 U.S.C. 103 as being unpatentable over Endo et al in “A versatile cis-acting inverter module for synthetic translational switches” (Nature Communications 4:2393, published September 3, 2013, pages 1-9; of record), in view of Chen et al (PNAS May 2010 Vol 107, No.19, pages 8531-8536; of record), in view of the Bloom Dissertation titled “Design And Characterization of Synthetic MicroRNA-Based Genetic Circuits” (Stanford University, May 2014; of record), in view of Pasotti et al (PloS One Published July 20 2012), in further view of Sztuba-Solinska et al (“Subgenomic messenger RNAs: Mastering regulation of (+)-strand RNA virus life cycle” Virology Vol 412, No.2, April 10, 2011; pages 245-255 of record), in further view of Nilsen et al (“In Vitro Transcription of Labeled RNA: Synthesis, Capping, and Substitution” (Cold Spring Harbor Protocols, 2012: pages 1181-1186).
Regarding claims 43, 47, and 295, each of the references of Endo et al, Chen et al, and Bloom disclose functional synthetic RNA circuits. Endo et al discloses a synthetic RNA circuit that comprises an RNA molecule comprising an RNA motif configured to bind to a protein and sequence encoding an output molecule, protein that specifically binds to an RNA motif, that is capable of inhibiting protein production. Further, Endo et al disclose that the RNA circuit comprises an RNA molecule comprising an RNA motif configured to bind to a protein, and a sequence encoding a protein, wherein binding of the protein to the RNA motif inhibits production of the protein.
Further, regarding claims 43, 47, and 295, Endo et al discloses that the output molecule is a BimEL protein, which is a type of immunomodulatory protein because it plays a role in controlling immune cell apoptosis.
Further, regarding claims 292-295 Endo et al disclose that RNA elements in synthetic RNA circuits comprise a 5' untranslated region (UTR) and 3' UTR. (See Introduction: “This switch binds to an input protein at a specific site in the 5′-untranslated region (UTR) to block translation.” ). For example, an RNA circuit is shown in Endo et al in FIG1a & legend just below. Endo et al states “Our module could be employed to develop new ON switches from available translational OFF switches in which the 5′-UTRs of the mRNAs respond to a variety of input molecules, including small molecules, RNA and proteins, in eukaryotic cells. In addition, Endo et al explicitly suggest that it “should also be possible for our module to invert ON switches8 to OFF switches, because the IRES-driven production of an output protein from the inverted switches is inversely related to the activity of the cap-dependent translation of the bait ORF that corresponds to the output of the parental switches.”
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FIG1 just above is explained in the following legend:
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Specifically, Endo et al disclose an cis-acting RNA module to invert the function of a synthetic translational OFF switch to an ON switch in mammalian cells (Abstract). See Fig 5a below from Endo et al. The BimEL is an immunomodulatory protein being a cell death output protein. The L7Ae is an RNA binding protein that specifically binds an RNA motif shown in the figure as a stem-loop structure.
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Regarding base claim 295, Endo et al discloses a synthetic RNA circuit comprising: a first RNA molecule comprising a 5' cap, a 5' untranslated region (UTR), a first RNA motif configured to bind to a first protein, a sequence encoding an immunomodulatory protein, 3' UTR, and a poly(A) tail, wherein binding of the first protein to the first RNA motif inhibits production of the immunomodulatory protein.
Further, regarding claims 289-291 and 295, Endo et al does not explicitly show a poly A tail on the RNA constructs of the RNA circuit. Chen et al disclose that RNA elements in synthetic RNA circuits comprise a poly(A) tail (e.g., Fig1B). Chen et al teach a synthetic RNA circuit comprising: an RNA molecule comprising a first RNA motif configured to bind to a first protein and a sequence encoding an output molecule, where binding of the first protein to the first RNA motif inhibits production of the output molecule; and a second RNA molecule comprising a second RNA motif configured to bind a second protein, and a sequence encoding the first protein, where binding of the second protein to the second RNA motif inhibits production of the first protein; and
at least one sequence recognized by a first protein that specifically binds to a RNA motif and inhibits protein production, and a sequence encoding an output molecule. See Fig 1B, just below.
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Chen et al discloses that the output molecule is a cytokine protein, which is a type of an immunomodulatory protein. For example, Chen et al teach a method of inducing an immune response in a mouse comprising administering to a mammal a synthetic RNA circuit comprising a first RNA molecule comprising at least one sequence recognized by a first protein that specifically binds to a RNA motif and inhibits protein production, and a sequence encoding an output molecule. See Fig 4 and legend; page 8536, under heading “Materials and Methods”: “In vivo T-Cell Proliferation Studies in NOD/SCID-IL2(ko) Mice”.
Also, regarding claims 286-288, and 295, the cited references disclose expression constructs for RNA transcripts but do not explicitly show the 5’cap usually present on mRNA transcripts within a cell. Nilsen et al disclose that 5’-capping of RNAs in a cell serves important functions including “preventing 5’ to 3’ nuclease activity. (See page 1185, Discussion: para 2). One of ordinary skill in the art would have been motivated to include a 5’-cap for RNAs of an RNA circuit because 5’-caps are known to be used on the 5’-end of RNA transcripts for adding stability. (See Nilsen et al page 1185, Discussion: para 2). In view of the high skill level in the art it would have been obvious to include a 5’-cap structure to protect RNAs of an RNA circuit from degradation in the cell.
Further, regarding claim 284-285, and 296-299, Endo et al disclose using an IRES to facilitate expression of two different genes of interest but do not explicitly recite using a subgenomic promoter for such purpose. Sztuba-Solinska et al disclose the use of subgenomic promoters for bicistronic expression constructs for the rationale of expressing multiple genes of interest.(See Fig2 & legend). Sztuba-Solinska et al disclose that RNAs expressed from SG promoters are translated in large amounts, “producing proteins which can be used in vaccines or as therapeutics”. (page 253, right col, para 3).
The level of skill in the art was high before the effective filing date of the presently claimed invention. One of ordinary skill in the art would have been motivated to use a subgenomic promoter in place of an IRES for use in a synthetic RNA circuit for the rationale of Sztuba-Solinska et al to express two separate genes independently from the same operon rather than using an IRES for such purpose.
It would have been obvious for one of ordinary skill in the art to replace the IRES such as used in the construct of Endo et al for a subgenomic promoter because Sztuba-Solinska et al disclose they are used for a similar purpose in RNA expression constructs, to express different codons from the same transcript.
In view of the high skill in the art it is considered that one of ordinary skill in the art having the cited references would have had a reasonable expectation of success to replace an IRES with a subgenomic promoter in a synthetic RNA circuit to achieve gene regulatory mechanism.
Further, Endo et al does not disclose an RNA target site configured to bind to an siRNA molecule or a microRNA molecule, and a sequence encoding a protein “B”, wherein binding of the siRNA molecule or the microRNA molecule to the RNA target site inhibits production of the protein “B”.
Bloom teaches design of synthetic miRNA-based generic circuits. Bloom teach an RNA genetic circuit comprising an RNA molecule comprising an RNA target site configured to bind to an miRNA molecule, and a sequence encoding a protein B, wherein binding of the miRNA molecule to the RNA target site inhibits production of the protein B. Bloom discloses an miRNA genetic circuit comprising an RNA molecule comprising at least one sequence recognized by a microRNA molecule, and a sequence encoding a protein that specifically binds to an RNA motif and inhibits protein production. Further, Bloom discloses that the synthetic RNA circuit further comprises the microRNA molecule that binds to the RNA molecule. (See Figs 1-2, below). (See Fig 1-2 & legends, on pages 30 & 32 just below).
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Bloom discloses a genetic circuit for performing OFF logic in response to levels of endogenous proteins within cells. Bloom created the circuit by combining two different synthetic RNA-based regulators, a ligand-responsive ribozyme and a miRNA. Specifically, Bloom combined an MS2-responsive ribozyme with a miRNA that targeting an MS2-dsRed fusion protein into the circuit architecture such that the system exerted negative feedback over MS2 levels within the cell. (See page vi, entire document).
Further, Bloom disclose that RNAi “is a well-characterized pathway in which noncoding RNA is processed into approximately 21 nt fragments that silence genes by binding to sequences which are often located in the 3’ UTR of the target transcript”. Bloom disclose that successful design of RNA circuits is achieved by combining known modular components of gene regulation. (See para bridging pages 7-8). Further, Bloom discloses that such modular design of RNA circuits is known for mammalian cells (para bridging pages 10-11).
In addition, Bloom teaches design of a protein-responsive miRNA circuit which comprises at least three RNA molecules involved in feedback regulation and expression of an output molecule and multiple RNA motifs configured to bind proteins. (See especially Figure 6 & legend).
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Pasotti et al disclose that functional genetic circuits can be constructed using the concept of combining regulatory modules. Pasotti et al disclose three-input genetic circuits.
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The level of skill in the art was high before the effective filing date of the presently claimed invention.
One of ordinary skill in the art would have been motivated to combine the elements of the known RNA circuits shown in the cited references for the rationale of regulating expression of genes/output immunomodulatory proteins of interest for rationale of potential therapeutics. Specifically such as for cell death proteins for killing unwanted cells such as cancer cells as suggested in Endo et al or for cytokine production such as shown in Chen et al.
It would have been obvious to one of ordinary skill in the art to combine the regulatory elements of the cited references used in the RNA circuits of the cited references because these references show successful RNA circuits in cells using RNA binding motifs, aptamers, miRNA binding motifs, to regulate output protein expression.
In view of the high skill level before the effective filing date of the presently claimed invention it is considered that one of ordinary skill in the art having the cited references would have had a reasonable expectation of success to combine the elements of the RNA circuits to arrive at the presently claimed invention.
Response to Arguments
The Applicants’ Remarks filed on May 12, 2025 have been fully considered but are unpersuasive regarding this new grounds of rejection under 35 U.S.C. 103. The applicants argue that claims 46, 80, 81, 123, 206, 241, and 242 have been cancelled, and that claim 43 has been amended:
to specify that the “output molecule is an antigen, an adjuvant, or an immunomodulatory protein’ and to delete reference to “an RNA molecule comprising a sequence encoding a TetR protein and a sequence encoding an output protein, and an aptamer sequence that is bound by the TetR protein in the absence of tetracycline; wherein the aptamer sequence is positioned relative to the sequence encoding the output protein so that it suppresses translation of the output protein in the absence of tetracycline.” Insofar as the rejection applies to the amended claims and new claims, Applicant contends that the instant claims are not obvious over the prior art at least because the cited references fail to disclose or suggest every element of the claims in the specific combination described therein.
However, this argument is unpersuasive for reasons provided in the body of the rejection and specifically because regarding the added limitation to base claims 43 and 295 regarding an immunomodulatory molecule as the type of output molecule, the references of Chen et al discloses that the output molecule is a cytokine protein, which is a type of an immunomodulatory protein. Also, Endo et al discloses that the output molecule is BimEL which is an immunomodulatory protein. The present rejection is updated regarding the present claim amendments and discloses or suggests the elements of the present claims as shown in the body of the rejection above. Further, the applicants argue regarding the previous rejection:
An obviousness determination requires the consideration of all claim limitations when determining patentability of an invention over the prior art'’. Further, courts have found that the asserted prior art combination does not render a claim obvious where the combination did not teach or suggest all of the limitations of the claim'*. Similarly, the mere fact that references can be combined or modified does not render the combination obvious unless the results would have been predictable to one of ordinary skill in the art.!° Moreover, while obviousness does not require absolute predictability, at least some degree of predictability is required; mere speculation or hope is not sufficient to create a reasonable expectation of success.
As acknowledged by the Examiner, Chen does not teach or suggest a synthetic circuit comprising three RNA molecules in which each RNA molecule regulates or modulates the others. Instead, Chen discloses a simple single-switch system in which the presence of a drug activates a ribozyme switch located in the 3' UTR of a target transgene. Upon activation, the ribozyme degrades the transgene. In contrast, the present invention involves three distinct RNA molecules: a first RNA motif, a second RNA motif, and an RNA target site, each of which inhibits the production of the output molecule, the first protein, and the second protein, respectively. Chen neither discloses nor suggests the use of a multi-component RNA system comprising multiple RNA molecules that regulate or modulate the expression of each other, much less the synthetic RNA circuit of the instant claims. None of Bloom, Endo, or Sztuba-Solinska, alone or in combination, remedy this deficiency. Accordingly, one of ordinary skill in the art would not have had any reason to arrive at a multi-component RNA system, where each RNA molecule modulates the expression of others, based on the cited references.
However, this argument is unpersuasive as it may pertain to this new grounds of rejection. The present references of Endo, Bloom, and Chen show that synthetic RNA circuits were known in the art. Bloom teaches design of synthetic miRNA-based generic circuits. Bloom teach an RNA genetic circuit comprising an RNA molecule comprising an RNA target site configured to bind to an miRNA molecule, and a sequence encoding a protein B, wherein binding of the miRNA molecule to the RNA target site inhibits production of the protein B. The reference of Pasotti et al disclose that functional genetic circuits can be constructed using the concept of combining regulatory modules. Pasotti et al disclose three-input genetic circuits. The rejection is for the combination of references.
Conclusion
No claim is allowed.
Related prior art which may be applied in a future office action if appropriate:
Marchisio et al (Bioinformatics 2008 Vol 24, No 17: pages 1903-1910; of record).
Kamrud et al (Virology April 2007, Vol 360, No.2, pages 376-387; of record).
Any inquiry concerning this communication or earlier communications from the examiner should be directed to CATHERINE S HIBBERT whose telephone number is (571)270-3053. The examiner can normally be reached M-F 8:00-5:00.
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/CATHERINE S HIBBERT/Primary Examiner, Art Unit 1658