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 .
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and the fee set forth in 37 CFR 1.17(e) has been timely paid, the finality of the previous Office action has been withdrawn pursuant to 37 CFR 1.114.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 10-20-2025 has been entered.
Applicant's amendments to the claims and arguments filed on 10-20-2025 have been received and entered. Claims 1 and 5 have been amended. Claims 2, 11-12, 14-15, 24 have been canceled. Claim 25 has been added. Claims 1, 3-10, 13, 16-23, 25 are pending in the instant application.
Election/Restrictions
Applicant’s election without traverse of Group I, Claims 1-20, in the reply filed on 09-25-2024 is acknowledged.
Claims 21-23 are withdrawn from further consideration pursuant to 37 CFR 1.142(b) as being drawn to a nonelected subject matter, there being no allowable generic or linking claim. Election was made without traverse in the reply filed on 09-25-2024.
Claims 1, 3-10, 13, 16-20, 25 are under consideration
Priority
This application is a 371 of PCT/US2020/032688 filed on 05/13/2020 which claims priority from US provisional application no. 62/847,032 filed on 05/13/2019.
Withdrawn- Claim Rejections - 35 USC § 112
Claims 1, 3-10, 13, 16-20, 24 were 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. In view of applicant argument, the previous rejections of claims are hereby withdrawn.
Withdrawn- Claim Rejections - 35 USC § 112
Claim 5 was rejected under 35 U.S.C. 112(a) or 35 U.S.C. 112 (pre-AIA ), first paragraph, as failing to comply with the written description requirement. Applicant's amendments to claim 5 obviates the basis of the rejection. Applicants' arguments with respect to the withdrawn rejections are thereby rendered moot.
New-Claim Rejections - 35 USC § 112-necessitated by amendments
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.
Claim 5 is 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 5 recites the phrase “one or more mutations are selected from the group consisting of N497A R661 A Q695A, K810A, K848A, K855A, Q926A, K1003A, R1060A, and/or D1135E with reference to the numbering system of SpyCas9”. However, there is no SEQID number recited in the claim for system of SpyCas9. Given that different lab may have different variants of SpyCas9 with different sequences including various variant of amino acids, a person of ordinary skill in the art would not know where the sequence of system of SpyCas9starts or ends to map the recited mutation.
Maintained in modified form and New -Claim Rejections - 35 USC § 103-necessitated by amendments
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.
Claims 1, 3-8, 10, 13, 16-20, and newly added claim 25 are rejected under 35 U.S.C. 103 as being unpatentable over Lindbo (WO 2018/226972 A2, 13 December 2018) in view of Khan et al (Pub. No.: US 2017/0079916 A1, Pub. Date: Mar. 23, 2017) and Alt et al (Pub. No .: US 2020/0399609 A1, Provisional application No. 62/333,845 , filed on May 10, 2016) and Sahin et al (Pub. No.: US 2015/0314018 A1, Pub. Date: Nov. 5, 2015) and/or Simplicon ( Data Sheet, Applicant own work, Plasmid DNA Cat. # SCR727, Date: 2018-04-20, B18R-E3L Plasmid, https://www.sigmaaldrich.com/deepweb/assets/sigmaaldrich/product/documents/333/182/scr727ds.pdf?srsltid=AfmBOooVKFtMAtKi4Joo7zIPs8qUBHP5sLYEt9YXRQLVX1KppVx16uZ0).
Regarding to claim 1 and claim 16, Lindbo teaches expression of a functional CRISPR complex derived from an RNA virus vector ([0008], page 2). Lindbo teaches a recombinant self-replicating RNA, wherein said recombinant self-replicating RNA encodes at least one or more genes selected from the group consisting of i) a replicase capable of transcribing the recombinant self-replicating RNA, ii) a movement protein facilitating intercellular movement of the RNA, iii) a Clustered regularly interspaced short palindromic repeats (CRISPR) endonudease, and iv) at least one guide RNA; wherein said at least one guide RNA is capable of directing sequence-specific binding of the CRISPR endonuclease to target DNA ([0009], page 2). Lindbo teaches Cas9 Type II CRISPR systems ([0123], page 24).
Lindbo does not teach a plurality of non-structural replication complex proteins from an alphavirus. However, Khan et al cure the deficiency.
Khan et al teaches Large, replicating RNAs (repRNAs) have been developed for delivery of vaccine antigens to cells ([0006], page 1), and due to the availability of self-replicating mRNAs (repRNAs) based on alphavirus or flavivirus genomes, very low doses can be employed to achieve maximal immunogenicity and antigen production levels ([0130], page 11-12). repRNAs are derived from a modified alphavirus species, including, but not limited to, a Venezuelan equine encephalitis virus (VEEV) ([0142], page 12). Alphaviral self-amplifying repRNA typically includes a 5' Cap; 5' untranslated region (5'UTR), non-structural genes (e.g., NSP1-4) encoded within a first open reading frame a genomic promoter region (e.g., 26S Sub genomic promoter), a second open reading frame, a 3' untranslated region (3'UTR) and a 3' poly-adenylated tail. repRNA molecules are typically between 9,000 and 20,000 nucleotides in length, depending upon the size of the encoded genic sequence (See FIGS. 1A-1C) ([0132], page 12). Khan et al also teaches system for induces a single or a double strand break in the target cells genome is a CRISPR/Cas system ([0298], page 25).
PNG
media_image1.png
708
643
media_image1.png
Greyscale
Therefore, it would have been prima facie obvious for a person of ordinary skill in the art before the effective filing date of the rejected claims to combine the teachings of prior art to modify the method of Lindbo by using Aphaviral self-amplifying repRNA with non-structural genes as taught by Khan et al as instantly claimed, with a reasonable expectation of success. Said modification amounting to combining prior art elements according to known methods to yield predictable results. One of ordinary skill in the art would have been motivated to do so because Khan et al teaches advantages of gene-based approaches to vaccines over conventional methods, as they are fully synthetic, rapidly customizable, and can be produced in adjuvant-free preparations ([0452], page 34), and due to the availability of self-replicating mRNAs (repRNAs) based on alphavirus or flavivirus genomes, very low doses can be employed to achieve maximal immunogenicity and antigen production levels ([0130], page 11-12). One of ordinary skill in the art would have had a reasonable expectation of success in doing so because Khan et al provides proof of principle with detailed instructions, materials and working examples for preparing RNA vectors for use as vaccines (Example 1, [0325]-[0334]).
Lindbo and Khan et al do not teach a sequence encoding vaccinia virus B18R-E3L proteins. However, Alt et al cures the deficiency.
Alt et al teaches a self-replicating RNA for inducing somatic differentiation of unmodified adult stem cells (Abstract), and FIG. 5. Multi-step construction of self-replicating RNAs ( srRNAs) expression vector of this disclosure ([0070], page 5, and see below). Alt et al teaches that to prepare the self-replicating RNAs ( srRNAs), the original srRNA production vector Simplicon-E3L contained the promoter for T7 RNA polymerase followed by coding sequences for four non-structural proteins, cloning sites for transgenes, and coding sequences for E3L (a Vaccinia virus protein affecting interferon signaling pathways) and puromycin -resistance gene Puro (for positive selection of treated cells) . To reduce the cellular immune response and stabilize srRNA after its transduction into cells , the E3L protein generated from the same RNA and the separately applied B18R protein are used ([0088], page 6). Also, The B18R-E3L vector is transfected into human foreskin fibroblasts and cultured for 24 hours ([0096], page 7).
PNG
media_image2.png
618
1068
media_image2.png
Greyscale
Therefore, it would have been prima facie obvious for a person of ordinary skill in the art before the effective filing date of the rejected claims to combine the teachings of prior art to modify the method of Lindbo and Khan et al by using a sequence encoding vaccinia virus B18R-E3L proteins as taught by Alt et al as instantly claimed, with a reasonable expectation of success. Said modification amounting to combining prior art elements according to known methods to yield predictable results. One of ordinary skill in the art would have been motivated to do so because Alt et al teaches advantages of reducing the cellular immune response and stabilizing srRNA after its transduction into cells by using the E3L protein generated from the same RNA and the separately applied B18R protein are used ([0088], page 6). One of ordinary skill in the art would have had a reasonable expectation of success in doing so because Alt et al provides working examples and data for generating self-replicating RNA with the use of a sequence encoding B18R and E3L proteins.
Lindbo and Khan et al and Alt et al do not teach the vector further comprises a sequence encoding vaccinia virus B18R-E3L proteins. However, Sahin et al cures the deficiency.
Sahin et al teach method for cellular RNA expression (title). The invention relates to expressing RNA in cells and, in particular, enhancing viability of cells in which RNA is to be expressed (Abstract). Sahin et al teach Example 9: use of viral interferon inhibitors to enhance self-replicating RNA-expression (Example 9, page 30). Sahin et al teach self-replicating RNA is alphaviral genomic RNA or is derived from alpha-viral genomic RNA ([0123], page 9), and the vaccinia virus B18R, vaccinia virus E3 and/or vaccinia virus K3 are provided to the cell in the form of nucleic acid encoding the vaccinia virus B18R, vaccinia virus E3 and/or vaccinia virus K3, either on the same or on two or more different nucleic acid molecules ([0021], page 2). Sahin et al stated that “We improved replicon expression by co-expressing proteins from Vaccinia virus (VacV), namely E3L, B18R and K3L (EKB) ([0375], page 31).
Thus, cloning nucleic acid encoding the vaccinia virus B18R, vaccinia virus E3 on the same or on two or more different nucleic acid molecules for cellular RNA expression of self-replicating RNA was recognized in the prior art to be a result-effective variable. A person of ordinary skill in the art would have been motivated to perform the cloning and expressing E3L, B18R alone or together on a single replicon out of the course of routine optimization. Given that cloning techniques are also routine performed in the art, and Sahin et al teach vaccinia virus B18R, vaccinia virus E3 can be on the same or on two or more different nucleic acid molecules ([0021], page 2), a person of ordinary skill in the art would be able to clone nucleic acid encoding E3L and B18R genes together in a self-replicating RNA vector derived from alpha-viral genomic RNA.
Therefore, it would have been prima facie obvious for a person of ordinary skill in the art before the effective filing date of the rejected claims to combine the teachings of prior art to modify the method of Lindbo and Khan et al and Alt et al by co-expressing proteins from Vaccinia virus (VacV), namely E3L, B18R with RNA to be expressed in a cell as taught by Sahin et al instantly claimed, with a reasonable expectation of success. Said modification amounting to combining prior art elements according to known methods to yield predictable results. One of ordinary skill in the art would have been motivated to do so because Sahin et al teaches advantages of enhancing viability of cells in which RNA is to be expressed (Abstract), improved replicon expression by co-expressing proteins from Vaccinia virus (VacV), such as E3L, B18R ([0375], page 31). Also, co-transfer of IFN-inhibitors is a promising tool to enhance the efficacy of replicon-based vectors for therapeutic gene delivery or vaccination. Thereby the overall amount of RNA needed to treat patients can be reduced which would increase effectiveness and profitability of RNA vaccines.” ([0376], page 32). One of ordinary skill in the art would have had a reasonable expectation of success in doing so because Sahin et al provide proof of principle for co-transfer of IFN-inhibitors to enhance the efficacy of replicon-based vectors for therapeutic gene delivery or vaccination with detailed instruction, working examples and data.
Even though Sahin et al reference alone satisfies the requirements of the claims, Simplicon is added to show the availability of additional prior art.
Simplicon (Applicant own work) teaches commercially available B18R-E3L Plasmid (Title). Simplicon teaches that “Simplicon is a novel system to effect immediate high sustained
protein expression of multiple genes into transfected cells without the risk of genome integration. The technology employs a single, synthetic, polycistronic, self-replicating RNA based on the Venezuelan equine encephalitis (VEE) genome” (Page 1, left column, 1st para.), “To suppress the IFN responses, a Vaccinia virus protein, B18R, is used for the original Simplicon technology. Recently, we found that another Vaccinia virus protein5, E3L, also suppresses the IFN responses in Simplicon RNA expression.” (Page 1, left column, 2nd para.), and “in the Simplicon Expression System, B18R and E3L are provided as a B18R-E3L RNA (Cat. No. SCR722) for the suppression of IFN responses at RNA transfection. For sustained transgene expression, recombinant B18R protein (Cat. No. SCR156 and SCR197) or B18R conditioned medium (B18R-CM) can be used” (Page 1, left column, 4th para.).
PNG
media_image3.png
1003
1151
media_image3.png
Greyscale
Therefore, it would have been prima facie obvious for a person of ordinary skill in the art before the effective filing date of the rejected claims to combine the teachings of prior art to modify the method of Lindbo and Khan et al and Alt et al by cloning a sequence encoding vaccinia virus B18R-E3L proteins into the alphavirus vector as taught by Simplicon as instantly claimed, with a reasonable expectation of success. Said modification amounting to combining prior art elements according to known methods to yield predictable results. One of ordinary skill in the art would have been motivated to do so because Simplicon stated that “B18R neutralizes type I interferons by direct binding, while E3L inhibits the cytoplasmic signaling pathways of IFN responses. Therefore, B18R and E3L are both employed in the Simplicon Expression System and work collaboratively to suppress IFN responses. As a result, there is increased cell viability during RNA transfection and increased expression of the transgenes” (Page 1, left column, 2nd para.). One of ordinary skill in the art would have had a reasonable expectation of success in doing so because Simplicon stated that “The B18R-E3L Plasmid (human codon optimized for B18R and E3L (Cat. No. SCR727) is used as a DNA template for the synthesis of B18R-E3L RNA (Cat. No. SCR722). The B18R-E3L RNA is a synthetic polycistronic mRNA and is used for co-transfected with the Simplicon RNA to suppress the IFN responses.” (Page 1, right column, 2nd para.) with detailed instruction.
Regarding to claim 3, 4, Lindbo teaches Cas9 molecules include, but are not limited to, a Cas9 molecule of: S. pyogenes ([0127], page 26).
Regarding to claim 6, Lindbo teaches that a Cas9 molecule or Cas9 polypeptide can differ from naturally occurring Cas9 molecules, e.g., a non-complementary strand of a nucleic acid molecule or a complementary strand of a nucleic acid molecule (nickase activity), or the ability to cleave a nucleic acid molecule, e.g., a double stranded or single stranded nucleic acid molecule, can be eliminated ([0128], page 26-27). Also, Cas9 mutants can act as single stranded nickases, or other mutants with modified nuclease activity ([0194], page 44).
Regarding to claim 7, Lindbo teaches that in some embodiments, the CRISPR endonucleases of the present disclosure encompass a Nuclear Localization Sequence (NLS) ([0194], page 44).
Regarding to claim 8, Lindbo teaches Figure 10: Depicts Cas9-2a-GFP fusions expressed from T-DNA (pJL 124) or viral vector (pJL 126). Several days post infiltration of Agro with these plasmids, infiltrated leaf tissue was examined under UV light to trigger GFP ([0062], page 9).
Regarding to claim 10, Lindbo teaches that in some embodiments, the present disclosure teaches the codon optimization of one or more genes selected from the group consisting of the replicase, the movement protein, the CRISPR endonuclease and the coat protein ([0219], page 50). Optimized coding sequences containing codons preferred by a particular eukaryotic host can be prepared, for example, to increase the rate of translation or to produce recombinant RNA transcripts having desirable properties, such as a longer half-life, as compared with transcripts produced from a non-optimized sequence ([0222], page 51).
Regarding to claim 13, Lindbo teaches that desired traits also include selectable marker genes (e.g., genes encoding herbicide or antibiotic resistance used only to facilitate detection or selection of transformed cells) ([0339], page 81).
Regarding to claim 17, Lindbo teaches the term ''host cell" refers to any eukaryotic cell capable of being infected by the recombinant self-replicating RNAs or DNA vectors of the present disclosure ([0103], page 18).
Regarding to claim 18, Lindbo teaches the recombinant self-replicating RNAs direct the expression of both a CRISPR endonuclease and a guide RNA capable of directing sequence-specific binding of the CRISPR endonuclease to a target DNA (Abstract). The CRISPR endonuclease to which the guide RNA sequence in the recombinant self-replicating RNA capable of binding is Cas9 ([0014], page 3).
Regarding to claim 19, Lindbo teaches vectors encoding recombinant self-replicating RNAs: Necessary parts can be included in order to ensure that the plasmids/vectors of the present disclosure can be amplified and expressed in various cells. In some embodiments for example, the vectors of the present disclosure will comprise one or more of the parts including, but not limited to, at least one origin of replication, one functional resistance marker, and one or more promoter for synthesizing the recombinant self-replicating RNA ([0237], page 55).
Regarding to claim 20, Lindbo teaches that in some embodiments, the present disclosure teaches a DNA vector, wherein the promoter in the DNA vector is a T7 promoter ([0028], page 4). Functional self-replicating RNA can be produced by in vitro transcription via a T7 promoter ([0059], page 9).
Regarding to claim 25, Lindbo teaches “the Cas9 endonuclease of the present disclosure can include, but is not limited to, one or more of SEQ ID Nos …. or is identical to any Cas9 molecule sequence described herein, or a naturally occurring Cas9 molecule sequence.” ([0126], page 25)
Claim 5 is rejected under 35 U.S.C. 103 as being unpatentable over Lindbo (WO 2018/226972 A2, 13 December 2018) in view of Khan et al (Pub. No.: US 2017/0079916 A1, Pub. Date: Mar. 23, 2017) and Alt et al (Pub. No .: US 2020/0399609 A1, Provisional application No. 62/333,845 , filed on May 10, 2016) and Sahin et al (Pub. No.: US 2015/0314018 A1, Pub. Date: Nov. 5, 2015) and/or Simplicon (Data Sheet, Applicant own work, Plasmid DNA Cat. # SCR727, Date: 2018-04-20, https://www.sigmaaldrich.com/deepweb/assets/sigmaaldrich/product/documents/333/182/scr727ds.pdf?srsltid=AfmBOooVKFtMAtKi4Joo7zIPs8qUBHP5sLYEt9YXRQLVX1KppVx16uZ0) as applied to claims 1, 3-8, 10, 13, 16-20, and newly added claim 25 above, and further in view of Kleinstiver et al (Nature 529, 490–495 (2016), doi: 10.1038/nature16526).
The teachings of Lindbo and Khan et al and Alt et al and Sahin et al and/or Simplicon above are incorporated herein in their entirety.
The above references do not teach mutations are selected from the group consisting of N497A, R661A, Q695A, K81 0A, K848A, K855A, Q926A, K1003A, R1060A, and/or D1135E, with reference to the numbering system of SpyCas9. Kleinstiver et al cure the deficiency.
Regarding to claim 5, Kleinstiver et al teach “High-fidelity CRISPR–Cas9 nucleases with no detectable genome-wide off-target effects” (Title). Kleinstiver et al teach “SpCas9-HF1, a high-fidelity variant harbouring alterations designed to reduce non-specific DNA contacts. SpCas9-HF1 retains on-target activities comparable to wild-type SpCas9 with >85% of single-guide RNAs (sgRNAs) tested in human cells” (Abstract). Kleinstiver et al constructed 15 different SpCas9 variants bearing all possible single, double, triple, and quadruple combinations of N497A, R661A, Q695A, and Q926A substitutions (Page 490, right column, 2nd para.).
It is note that Lindbo teaches that a naturally occurring Cas9 molecule can be altered, e.g., to alter PAM recognition, e.g., to alter the PAM sequence that the Cas9 molecule or Cas9 polypeptide recognizes to decrease off-target sites and/or improve specificity ([0129], page 27). Since Kleinstiver et al teach “High-fidelity CRISPR–Cas9 nucleases with no detectable genome-wide off-target effects” (Title), a person of ordinary skill in the art would combine the references and generate Cas9 nucleases with no detectable genome-wide off-target effects by constructing different SpCas9 variants bearing one or more mutations N497A, R661A, Q695A, and Q926A.
Therefore, it would have been prima facie obvious for a person of ordinary skill in the art before the effective filing date of the rejected claims to combine the teachings of prior art to modify the method of the above references by generating Cas9 nucleases with no detectable genome-wide off-target effects with constructing different SpCas9 variants bearing one or more mutations N497A, R661A, Q695A, and Q926A as taught by Kleinstiver et al as instantly claimed, with a reasonable expectation of success. Said modification amounting to combining prior art elements according to known methods to yield predictable results. One of ordinary skill in the art would have been motivated to do so because Kleinstiver et al stated that “Overall, our results demonstrate that the approach of mutating non-specific DNA contacts is highly effective at increasing SpCas9 specificity and suggest it might be extended to other naturally occurring and engineered Cas9 orthologues, as well as other CRISPR-associated nucleases” (Page 494, right column, 1st para.) and “SpCas9-HF1 rendered all or nearly all off-target events undetectable by genome-wide break capture and targeted sequencing methods. Even for atypical, repetitive target sites, the vast majority of off-target mutations induced by wild-type SpCas9 were not detected with SpCas9-HF1. With its exceptional precision, SpCas9-HF1 provides an alternative to wild-type SpCas9 for research and therapeutic applications. More broadly, our results suggest a general strategy for optimizing genome-wide specificities of other CRISPR-RNA-guided nucleases” (Abstract). One of ordinary skill in the art would have had a reasonable expectation of success in doing so because Kleinstiver et al were successful in generation of high-fidelity CRISPR–Cas9 nucleases with no detectable genome-wide off-target effects.
Claim 9 is rejected under 35 U.S.C. 103 as being unpatentable over Lindbo (WO 2018/226972 A2, 13 December 2018) in view of Khan et al (Pub. No.: US 2017/0079916 A1, Pub. Date: Mar. 23, 2017) and Alt et al (Pub. No .: US 2020/0399609 A1, Provisional application No. 62/333,845 , filed on May 10, 2016) and Sahin et al (Pub. No.: US 2015/0314018 A1, Pub. Date: Nov. 5, 2015) and/or Simplicon (Data Sheet, Applicant own work, Plasmid DNA Cat. # SCR727, Date: 2018-04-20, https://www.sigmaaldrich.com/deepweb/assets/sigmaaldrich/product/documents/333/182/scr727ds.pdf?srsltid=AfmBOooVKFtMAtKi4Joo7zIPs8qUBHP5sLYEt9YXRQLVX1KppVx16uZ0) as applied to claims 1, 3-8, 10, 13, 16-20, and newly added claim 25 above, and further in view of Meyers et al (Pub. No .: US 2020/0392517 A1, Provisional application No. 62/598,831 , filed on Dec. 14 , 2017).
The teachings of Lindbo and Khan et al and Alt et al and Sahin et al and/or Simplicon above are incorporated herein in their entirety.
The above references do not teach one functional domain is an epigenetic modification domain, a transcriptional activation domain, or a transcriptional repressor domain. However, Meyers et al cures the deficiency.
Regarding to claim 9, Meyers et al teaches self -replicating RNA may be derived from a noninfectious, self-replicating Venezuelan equine encephalitis (VEE) virus RNA replicon ([0105]), and programmable nucleic acid modification system may be an RNA -guided CRISPR nuclease system ([0038], page 4). A programmable nucleic acid modification protein may be a fusion protein comprising a non -nuclease domain and a programmable nucleic acid -binding domain. Examples of suitable non -nuclease domains include epigenetic modification domains. In general, epigenetic modification domains alter gene expression by modifying the histone structure and/or nucleic acid structure , histone acetylase domains , repressor domains , activator domains ([0102], page 10).
Therefore, it would have been prima facie obvious for a person of ordinary skill in the art before the effective filing date of the rejected claims to combine the teachings of prior art to modify the method of the above references by using programmable nucleic acid modification protein that is a fusion protein comprising a non -nuclease domain and a programmable nucleic acid -binding domain as taught by Meyers et al as instantly claimed, with a reasonable expectation of success. Said modification amounting to combining prior art elements according to known methods to yield predictable results. One of ordinary skill in the art would have been motivated to do so because Meyers et al teaches advantages of improved and effective means of genome editing, especially in organisms where the frequency of homologous recombination (HR) is low ([0004], page 1), and the use of self -replicating RNA derived from a noninfectious, self-replicating Venezuelan equine encephalitis ( VEE) virus as nucleic acid constructs ([0105], page 11). One of ordinary skill in the art would have had a reasonable expectation of success in doing so because Meyers et al provides proof of principle for genome editing by using programmable nucleic acid modification system with detailed instructions for the materials, constructs, working examples and data.
Response to Arguments
Applicant's arguments filed 10-20-2025 have been fully considered but they are not persuasive.
Applicant argue that “Claim 1 has been amended to require "... and wherein the vector further comprises a sequence encoding vaccinia virus B18R-E3L proteins." In other words, the sequences encoding both the E3L and B18R proteins are part of the "self-replicating RNA vector." …… Sahin is cited for teaching that the vaccinia virus is co-transfected. The presently claimed invention does not claim this element therefore Sahin is of no moment. Thus, Lindbo in view of Khan, Alt and Sahin does not teach, fairly suggest nor render predictable at least the element of" ... and wherein the vector further comprises a sequence encoding vaccinia virus B18R-E3L proteins" of the presently pending invention” (Remarks, page 7-8).
Response to Arguments:
It appears that Applicant is arguing that the cited references do not expressly suggest the claimed invention. However, it is well established in case law that a reference must be considered not only for what it expressly teaches, but also for what it fairly suggests. In re Burkel, 201 USPQ 67 (CCPA 1979). Furthermore, in the determination of obviousness, the state of the art as well as the level of skill of those in the art are important factors to be considered. The teaching of the cited references must be viewed in light of these factors. In the instant case, Sahin et al teach method for cellular RNA expression (title) such as self-replicating RNA which is alphaviral genomic RNA or is derived from alpha-viral genomic RNA ([0123], page 9), and the vaccinia virus B18R, vaccinia virus E3 and/or vaccinia virus K3 are provided to the cell in the form of nucleic acid encoding the vaccinia virus B18R, vaccinia virus E3 and/or vaccinia virus K3, either on the same or on two or more different nucleic acid molecules ([0021], page 2). Sahin et al stated that “We improved replicon expression by co-expressing proteins from Vaccinia virus (VacV), namely E3L, B18R and K3L (EKB) ([0375], page 31). Thus, cloning nucleic acid encoding the vaccinia virus B18R, vaccinia virus E3 on the same or on two or more different nucleic acid molecules for cellular RNA expression of self-replicating RNA was recognized in the prior art to be a result-effective variable. A person of ordinary skill in the art would have been motivated to perform the cloning and expressing E3L, B18R alone or together on a single replicon expression out of the course of routine optimization. Given that cloning techniques are routine performed in the art, and Sahin et al teach vaccinia virus B18R, vaccinia virus E3 can be on the same or on two or more different nucleic acid molecules ([0021], page 2), a person of ordinary skill in the art would be able to clone nucleic acid encoding E3L and B18R genes together in a self-replicating RNA vector derived from alpha-viral genomic RNA.
As per MPEP 716.02, Any differences between the claimed invention and the prior art may be expected to result in some differences in properties. The issue is whether the properties differ to such an extent that the difference is really unexpected. In re Merck & Co., 800 F.2d 1091, 231 USPQ 375 (Fed. Cir. 1986). In the instant case, there is no evidence in record that cloning a sequence encoding vaccinia virus B18R-E3L proteins together in the same self-replicating RNA vector would result in unexpected/ superior results over prior arts.
Even though Sahin et al reference alone satisfies the requirements of the claims, Simplicon is added to show the availability of additional prior art.
Simplicon (Applicant own work) teaches commercially available B18R-E3L Plasmid (Title). Simplicon teaches that “a single, synthetic, polycistronic, self-replicating RNA based on the Venezuelan equine encephalitis (VEE) genome” (Page 1, left column, 1st para.), and “To suppress the IFN responses, a Vaccinia virus protein, B18R, is used for the original Simplicon technology. Recently, we found that another Vaccinia virus protein5, E3L, also suppresses the IFN responses in Simplicon RNA expression.” (Page 1, left column, 2nd para.), and “in the Simplicon Expression System, B18R and E3L are provided as a B18R-E3L RNA (Cat. No. SCR722) for the suppression of IFN responses at RNA transfection. For sustained transgene expression, recombinant B18R protein (Cat. No. SCR156 and SCR197) or B18R conditioned medium (B18R-CM) can be used” (Page 1, left column, 4th para.). One of ordinary skill in the art would have been motivated combine the references because Simplicon stated that “B18R neutralizes type I interferons by direct binding, while E3L inhibits the cytoplasmic signaling pathways of IFN responses. Therefore, B18R and E3L are both employed in the Simplicon Expression System and work collaboratively to suppress IFN responses. As a result, there is increased cell viability during RNA transfection and increased expression of the transgenes” (Page 1, left column, 2nd para.).
Conclusion
No claim is allowed.
Any inquiry concerning this communication or earlier communications from the examiner should be directed to KHOA NHAT TRAN whose telephone number is (571)270-0201. The examiner can normally be reached M-F (9-5).
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, PETER PARAS can be reached at (571)272-4517. The fax phone number for the organization where this application or proceeding is assigned is 571-273-8300.
Information regarding the status of published or unpublished applications may be obtained from Patent Center. Unpublished application information in Patent Center is available to registered users. To file and manage patent submissions in Patent Center, visit: https://patentcenter.uspto.gov. Visit https://www.uspto.gov/patents/apply/patent-center for more information about Patent Center and https://www.uspto.gov/patents/docx for information about filing in DOCX format. For additional questions, contact the Electronic Business Center (EBC) at 866-217-9197 (toll-free). If you would like assistance from a USPTO Customer Service Representative, call 800-786-9199 (IN USA OR CANADA) or 571-272-1000.
/KHOA NHAT TRAN/Examiner, Art Unit 1632
/PETER PARAS JR/Supervisory Patent Examiner, Art Unit 1632