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 .
Election/Restrictions
Applicant’s election without traverse of Group I, encompassing claims (1-2,8,11-13,15,17-20,22,24-25,27-28,30,32, and 36-38), in the reply filed on 12/18/2025 is acknowledged.
Claims 40-41 are withdrawn from further consideration pursuant to 37 CFR 1.142(b) as being drawn to a nonelected invention, there being no allowable generic or linking claim.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 12/18/2025. Therefore, claims 1-2,8,11-13,15,17-20,22,24-25,27-28,30,32, and 36-38 are under examination.
Priority
Receipt is acknowledged of certified copies of papers required by 37 CFR 1.55.
Information Disclosure Statement
The information disclosure statement (IDS) was filed before the mailing date of the non-final first action on the merits. The submission is in compliance with the provisions of 37 CFR 1.97. Accordingly, the information disclosure statement is being considered by the examiner.
Specification
The disclosure is objected to because it contains an embedded hyperlink and/or other form of browser-executable code ( See page 19- line 22, page 28- line 9 and 13, and page 60-line 2) . 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.
Claim Interpretation
It should be noted that the optional recitations in claims 13,15,20,22, 25, 28,30,32, and 38 are not given patentable weight as they are not required by the subject claim.
Claim Rejections - 35 USC § 112
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 2, 30, and 32 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.
The claims recite the term "Preferably" which renders the claim indefinite because it
is unclear whether the limitation(s) following the phrase are part of the claimed invention. The metes and bound of the claims are unclear.
Claim Rejections - 35 USC § 102
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.
Claims 1-2, 11-12, 18, 20, 30 and 32 are rejected under 35 U.S.C. 102(a)(1) as being anticipated by Robinson et al (Antimicrobial Agents and Chemotherapy, 2010), as evidenced by Shi et al (Horizon Bioscience; 2006. Chapter 2).
Regarding claim 1-2, 8, and 11-12, Robinson et al disclose an HCV subgenomic replicon comprising of a self-replicating, bicistronic viral RNA. The first cistron typically encodes a reporter gene and/or a selectable marker, and expression is driven by the HCV internal ribosome entry site (IRES). The second cistron encodes the HCV nonstructural proteins, and expression is driven by the encephalomyocarditis virus (EMCV) IRES. According to Robinson, the nonstructural proteins are translated as a polyprotein, proteolytically processed by the viral NS3/4A protease, and form a replication complex in which the NS5B RNA-dependent RNA polymerase replicates the entire replicon RNA. ( See Figure.1, and page 3099-1st column-2nd paragraph). It should be noted that EMCV-derived IRES is a viral IRES, and hence the expression of the functional nonstructural protein is independent of the cellular translation initiation factors, this reads on claims 2 and 8. It should also be noted that the RNA replicon of Robinson et al does not comprise a 5’ cap, this reads on claim 11.
Regarding claim 12 and 30, Robinson et al do not explicitly teach that the RNA replicon comprises a 5’ replication recognition sequence (RRS) or 3’RRS ( also known in the art as conserved sequence element (CSE)). However, Robinson et al explicitly state that once the nonstructural proteins are expressed they form a functional replication complex (i.e. NS5B-RNA-depnednet RNA polymerase) that replicates the entire RNA replicon. ( See page 3099-1st column-2nd paragraph). It is known in the art that for an RNA replicon to be amplified/replicated, the replicon must contain a 5’ RRS and 3’RRS, otherwise the RNA replicon would lose its replicative potential. Hence, the presence of 5’ RRS and 3’RRS in Robinson’s replicon is presumed to be inherent; otherwise the RNA replicon would not be entirely replicated as stated by Robinson, and as evidenced by Shi et al, 2006 ( See abstract).
Regarding claim 18, the RNA replicon of Robinson et al does not comprise an open reading frame encoding a truncated nonstructural protein. ( See Fig.1).
Regarding claim 20 and 24, Robinson et al teach an RNA replicon comprising an open reading frame encoding a protein of interest downstream from the 5' replication recognition sequence and upstream from the IRES, wherein the protein of interest is neomycin, this reads on claim 20. ( See Fig.1A). It should be noted that the expression of the neomycin is driven by the HCV internal ribosome entry site (IRES), and wherein the expression of the neomycin is initiated at its native initiation codon. ( See Fig.1A).
Regarding claim 32, Robinson et al teach that the second cistron encodes the HCV functional nonstructural protein, which upon translation form a replication complex comprising NS5B RNA-dependent RNA polymerase that replicates the entire replicon RNA. It should be noted that the nonstructural protein of Robinson’s replicon are from HCV which is a self-replicating virus.
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 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 1-2,11-12,20,24-25,27-28,30, and 32 are rejected under 35 U.S.C. 103 as being unpatentable over Kim et al ( PNAS, 2014), in view of Spuul et al ( Journal of Virology, 2011), Robinson et al (Antimicrobial Agents and Chemotherapy, 2010), and Mizuguchi et al ( Molecular Therapy, 2000).
Regarding claim 1, Kim et al teach an Alphavirus genome-based, self-replicating RNA replicon that can be used for the delivery and expression of heterologous genes, such as those derived from the Venezuelan Equine Encephalitis Virus (VEEV), hence the name VEEV-based replicon. The replicon of Kim et al comprises two open reading frames (ORFs). The first ORF comprises of the viral genome RNA encoding for four nonstructural protein (i.e. nsP1-4), wherein the nsPs are from a self-replicating virus. The second ORFs comprises of the subgenomic RNA (SG) encoding the heterologous gene of interest. ( See Fig. 1C). It is noted that the expression of the functional nonstructural protein in Kim et al’s replicon is driven by a promoter found in the 5’ end of the positive-sense genomic RNA. This differs from the replicon in the instant claim, wherein the expression of the functional nonstructural protein is driven by an IRES.
Spuul et al teach an Alphavirus derived trans-replication systems comprising of two nucleic acid molecules (i.e. trans replicon), wherein one nucleic acid molecule encodes a viral replicase and the other nucleic acid molecule can be replicated by said replicase in trans.( See abstract). Spuul et al teach that the first nucleic acid is an RNA construct encoding for four nonstructural protein from a self-replicating virus, wherein the expression of these proteins is controlled by an upstream IRES. Spuul et al teach that the RNA construct can be prepared in vitro in the absence of the cap structure m7G(5')ppp(5')G. ( See page 4741, 2nd column, lines 4-6). The second nucleic acid is an RNA template that is provided in trans, wherein the template contains the known conserved sequence elements including those located at the 5’ UTR and at the end of the 3’UTR , which are required for a full alphavirus replication cycle (i.e. 5’RRS and 3’RRS). The RNA template may also contains florescent marker proteins inserted either under the control of the subgenomic promoter (termed Stluc) or directly at the 5’ end of the genome (Nsluc). ( See abstract, and Fig.1, and section “ Replication of RNA template on page 4742). To achieve high-level of expression, Spuul et al teach that the nonstructural protein in the RNA construct is inserted after the internal ribosome entry site (IRES) element of encephalomyocarditis virus (EMCV). Taken together, Spuul et al teach an advantage for placing the nonstructural protein under the control of an IRES element, wherein the advantage being to enhance the expression level of these protein, as these protein once expressed they assemble into a replicase that replicate the RNA replicon provided in trans in Spuul system. ( See 2nd column on page 4741 lines 4-6).
The teachings of Robinson et al are set forth above
Therefore, claim 1 would have been obvious to one of ordinary skill in the art, as there was some teaching, suggestion, or motivation in the prior art that would have led one of ordinary skill to modify the prior art reference or to combine prior art reference teachings to arrive at the claimed invention. Kim et al teach a cis-RNA replicon comprising an ORF encoding for functional nonstructural protein from a self-replicating virus, but fail to teach a replicon comprising an IRES element driving the expression of the functional nonstructural protein. According to Spuul et al, inserting an IRES element into RNA template encoding for nonstructural protein has the advantage of increasing the expression of these proteins, and hence enhancing the amplification of the replicon. Robinson et al teach a cis- RNA replicon comprising ORF encoding for functional nonstructural protein, wherein the expression of these proteins is under the control of IRES element. Therefore, one with ordinary skill in the art who had reviewed Kim et al could have come across Spuul and Robinson and immediately noticed the strong possibility of using the IRES element, taught by Spuul and Robinson, to drive the expression of functional nonstructural protein. There is a reasonable expectation of success, when producing viral RNA replicon, that taking the IRES element taught by Robinson and Spuul, and using it to drive the expression of the nonstructural protein in a cis- or trans-replicon, that the RNA replicon of claim 1 could be successfully produced.
Regarding claim 2, following the discussion of claim 1 above, both Spuul and Robinson teach using a viral IRES element that is derived from EMCV.
Regarding claim 11, the expression of the nonstructural protein in the RNA construct of Spuul et al does not does not contain a 5’ cap. ( See page 4741, 2nd column, lines 4-6).
Regarding claim 12, following the discussion of claim 1 above, the combined teachings of Kim et al in view of Robinson and Spuul render obvious the RNA replicon of claim 1. The RNA replicon of Kim et al also comprises a 5' replication recognition sequence ( also known as CSE). ( See Fig.1, and section “ Design of More Efficient VEEV-Based Expression System.” On page 10709).
Regarding claim 20 and 24, the combined teachings of Kim, Spuul, and Robinson render obvious the RNA replicon comprising an open reading frame encoding a functional nonstructural protein and an IRES element driving the expression of the functional nonstructural proteins. Kim et al do not teach that RNA replicon, that further comprises another open reading frame encoding a protein of interest downstream from the 5' replication recognition sequence and upstream from the IRES.
Robinson et al’s teach RNA replicon comprising an open reading frame encoding a protein of interest downstream from the 5' replication recognition sequence and upstream from the IRES, wherein the protein of interest is neomycin, this reads on claim 20. ( See Fig.1A). However, because the expression of protein of interest using Robinson replicon is controlled by a viral IRES, it will not generate a fusion protein comprising of the protein of interest and a fragment of nonstructural protein. In other words, Robinson et al do not teach the limitation recited in claim 24.
Mizuguchi et al teach a bicistronic construct comprising of two ORFs. The first ORF encodes for a protein of interest, which is expressed in a cap-dependent manner. The second ORF encodes for a second protein of interest, whose expression is driven by an IRES element. ( See abstract). Mizuguchi et al demonstrate, when a vector comprising the two ORFs is expressed in an eukaryotic cell such as Hela, L, and CHO cells, the expression of the protein driven by the IRES element is less efficient compared to the level of protein driven by the cap-dependent pathway. It is noted that Mizuguchi do not teach an RNA replicon, however Mizuguchi et al teach a favorable design that can be incorporated in an RNA replicon. For example, an ORF encoding for a protein of interest could be inserted alongside the ORF encoding the nonstructural protein. In addition, one with ordinary skill in the art, upon reviewing Mizuguchi et al, would also be motivated to incorporate such design, in an RNA replicon where the expression level of a protein of interest is preferable over the expression of the nonstructural protein.
Therefore, claim 24 is combining prior art elements according to known methods to yield predictable results, namely the predictable result being the insertion of an ORF encoding for a protein of interest between the 5’ replication recognition sequence and the IRES sequence, and wherein the protein of interest is expressed in a cap-dependent manner, whereas the expression of the nonstructural protein is driven by the IRES element. One with ordinary skill in the art upon reviewing Kim et al and Robinson et al, could have come across Mizuguchi et al and immediately noticed the strong possibility of modifying the replicon of Kim et al to include another ORF encoding a protein of interest downstream of the 5’ replication recognition sequence and upstream of the ORFs encoding the nonstructural protein, wherein the protein of interest in Kim replicon would be expressed in cap-dependent manner, generating a fusion protein comprising a fragment of the a nonstructural protein (i.e. the N-terminal portion of nsp1). This is because the 5’RRS required for RNA replication in the replicon of Kim et al comprises an AUG start codon for nsP1 and thus overlaps with the coding sequence for the N-terminal fragment of the alphavirus nsP1, resulting in the production of a protein of interest containing a fragment of nsp1. ( See Fig.1, and section “Design of More Efficient VEEV-Based Expression System" on page 10709). Therefore, an ordinary skill in the art, upon reviewing Robinson, would be motivated to modify the replicon of Kim to include an IRES element to drive the expression of a functional nonstructural protein, as discussed above. An ordinary skill in the art ,upon reviewing Mizuguchi et al, would also be motivated to generate RNA replicon comprising of two ORFs, wherein one OFR would encode for a protein of interest upstream of the IRES, and a second ORF encoding for functional nonstructural protein under the control of the IRES element. In other words, one with ordinary skill in the art who had reviewed Kim and Robinson, could have come across Mizuguchi et al and immediately noticed the strong possibility of modifying the RNA replicon of Kim et al , as taught by Mizuguchi, would have the predictable result of generating an effective RNA replicon comprising of two ORFs that enables efficient expression of a protein of interest in a cell or organism.
Regarding claim 25, 27-28, 30, and 32, the replicon of Kim et al further contains a subgenomic RNA comprising a subgenomic promoter (i.e. SG promoter) driving the expression of a protein of interest (i.e. Het.gene), wherein the gene of interest is inserted in the subgenomic RNA template, and wherein the subgenomic promotor is located downstream from the open reading frame encoding a functional nonstructural protein from a self-replicating virus, this reads on claims 25, and 27-28. (See abstract, and Fig.1B-C). The RNA replicon of Kim et al also comprises a 5' and 3' replication recognition sequences, as well as subgenomic promotor that are derived from a self-replicating virus, this reads on claim 30. ( See Fig.1 and section “ Design of More Efficient VEEV-Based Expression System” on page 10709). The RNA replicon of Kim et al can be replicated by an RNA-dependent RNA polymerase (also known as replication enzyme) derived from a functional nonstructural protein from a self-replicating virus, this reads on claim 32. (See abstract).
Claims 13,15, 17-19, and 36-38 are rejected under 35 U.S.C. 103 as being unpatentable over Kim et al ( PNAS, 2014), in view of Spuul et al, Robinson et al, and Mizuguchi et al, as applied to claims 1-2,11-12,20,24-25,27-28,30, and 32 above, and further in view of Beissert et al ( WO 2017/162460 A1).
The teachings of Kim, Spuul, and Robinson are set forth above.
Regarding claim 13, 15 Kim in view of Spuul, and Robinson render obvious claim1. Kim et al teach RNA replicon containing a 5’ RRS comprising a 51-nt conserved sequence element (51-nt CSE), wherein the 51-nt CSE ,is located in the nsP1-coding sequence, and functions as an enhancer of alphavirus genome replication. It should be noted that the 51-nt CSE reads on an open reading frame that is homologous to a fragment of a nonstructural protein, as it contains an AUG start codon for nsP1 ( e.g. nsp1). ( See Fig.1, and section “ Design of More Efficient VEEV-Based Expression System” on page 10709). Neither Kim et al nor Spuul or Robinson teach the removal of at least one initiation codon form the 51-nt CSE.
Beissert et al teach a RNA replicon that can be replicated by a replicase of alphavirus origin. In particular, the RNA replicon of Beissert comprises a 5' replication recognition sequence, wherein the 5' replication recognition sequence is characterized in that it comprises the removal of at least one initiation codon compared to a native alphavirus 5' replication recognition sequence, this reads on claim 13. Beissert et al state that “ The fact that the replication recognition sequence required for RNA replication comprises an AUG start codon for nsP1 and thus overlaps with the coding sequence for the N-terminal fragment of the alphavirus nonstructural protein represents a serious bottle-neck for the engineering of alphavirus-based vectors because a replicon comprising the 5' replication recognition sequence will typically encode (at least) a part of alphavirus nonstructural protein, typically the N-terminal fragment of nsP1”. Therefore, Beissert et al teach that the removal of at least one initiation codon from the 5’replication recognition sequence prevents the undesired production of fragments of alphavirus nonstructural protein, and therefore enables efficient and safe expression of a protein of interest in a cell or organism. ( See abstract, claim 5, and page 6 lines 10-25).
Therefore, claim 13 is combining prior art elements according to known methods to yield
predictable results, namely the predictable result being the removal of at least one initiation codon from the ORF of a nonstructural protein or a fragment thereof to produce the replicon of claim1. Beissert et al teach RNA replicon that is modified by the removal of at least one initiation codon from the 5’ RRS, and strongly suggest that such removal would be advantageous, as it would prevent the undesired production of a fusion protein comprising a fragment of alphavirus nonstructural protein. The combined teachings of Kim, Robinson and Spuul render obvious the replicon of claim 1. Therefore, one with ordinary skill in the art who had reviewed Kim, Robinson, and Spuul, as discussed above, could have come across Beissert et al and immediately noticed the strong possibility of modifying the 5’ replication recognition sequence in the RNA replicon of Kim et al, as taught by Beissert et al, would have the predictable result of generating an effective RNA replicon that enables efficient and safe expression of a protein of interest in a cell or organism.
Regarding claim 15, following the discussion of claim 13 above. Beissert et al also state that “ In a preferred embodiment, the sequence homologous to an open reading frame of a non-structural protein or a fragment thereof from an alphavirus is characterized in that it comprises the removal of one or more initiation codons other than the native start codon of the open reading frame of a nonstructural protein”. ( See page 9, lines 19-25)
Regarding claim 17, Beissert et al also teach that the RNA replicon comprises one or more nucleotide changes compensating for nucleotide pairing disruptions within one or more stem loops introduced by the removal of at least one initiation codon. ( See page 10 lines 1-3).
Regarding claim 18, Beissert et al further teach that the RNA replicon does not comprise an open reading frame encoding a truncated alphavirus nonstructural protein.( See page 10 lines 5-6).
Regarding claim 19, Beissert et al RNA replicon comprising an open reading frame encoding functional Alphavirus nonstructural protein that does not overlap with the 5' replication recognition sequence. ( See page 11 lines 11-12).
Regarding claims 36-38, Beissert et al also teach a DNA comprising the nucleic acid encoding RNA replicon and a composition comprising RNA replicon and a pharmaceutically acceptable carrier. ( See page 103 lines 17-20, and page 105 lines 3-12).
Conclusion
No claim is allowed.
Any inquiry concerning this communication or earlier communications from the examiner should be directed to FATIMAH KHALAF MATALKAH whose telephone number is (703)756-5652. The examiner can normally be reached Monday-Friday,7:30 am-4:30 pm EST.
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/FATIMAH KHALAF MATALKAH/Examiner, Art Unit 1638
/Tracy Vivlemore/Supervisory Primary Examiner, Art Unit 1638