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 .
Priority
Acknowledgement is made of applicant’s claim for benefit under 35 U.S.C. 119(e). As such, the effective filing date of Claims 1 and 3-29 is 07/20/2020.
Status of the Claims
Amendments dated 11/03/2025 have been entered.
Claims 1 and 3-29 are pending.
Claims 1 and 3-29 are examined herein.
The objections to the Drawings are withdrawn in view of Applicant’s amendments to the Drawings.
The objections to the Nucleotide and/or Amino Acid Sequence Disclosures are withdrawn in view of Applicant’s amendments to the Drawings and instant specification.
The objections to the specification are withdrawn in view of Applicant’s amendments to the specification.
The rejections of Claims 1 and 3-28 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or a joint inventor (or for applications subject to pre-AIA 35 U.S.C. 112, the applicant), regards as the invention are withdrawn in view of Applicant’s amendments to the claims.
The rejections of Claims 1 and 3-28 under 35 U.S.C. 103 as being unpatentable over Ren et al. (US 20160152994 A1; published 06/02/2016; IDS Document) in view of Daros et al. (WO 2015177100 A1; published 11/26/2015) and Daros (Molecular plant pathology 17.8 (2016): 1170-1177; IDS Document) are withdrawn in view of Applicant’s amendments to the claims.
Claim Rejections - 35 USC § 112
Written Description
The following is a quotation of the first paragraph of 35 U.S.C. 112(a):
(a) IN GENERAL.—The specification shall contain a written description of the invention, and of the manner and process of making and using it, in such full, clear, concise, and exact terms as to enable any person skilled in the art to which it pertains, or with which it is most nearly connected, to make and use the same, and shall set forth the best mode contemplated by the inventor or joint inventor of carrying out the invention.
The following is a quotation of the first paragraph of pre-AIA 35 U.S.C. 112:
The specification shall contain a written description of the invention, and of the manner and process of making and using it, in such full, clear, concise, and exact terms as to enable any person skilled in the art to which it pertains, or with which it is most nearly connected, to make and use the same, and shall set forth the best mode contemplated by the inventor of carrying out his invention.
---The following is a new rejection made in view of Applicant’s amendments to the claims and further inspection of the instant specification that re-opens prosecution. Applicant’s Remarks have been reviewed and are deemed inapposite to the new rejection.---
Claims 1 and 3-29 are 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. The claim(s) contains subject matter which was not described in the specification in such a way as to reasonably convey to one skilled in the relevant art that the inventor or a joint inventor, or for applications subject to pre-AIA 35 U.S.C. 112, the inventor(s), at the time the application was filed, had possession of the claimed invention.
The Federal Circuit has clarified the written description requirement. The court stated that a
written description of an invention "requires a precise definition, such as by structure, formula, [or] chemical name, of the claimed subject matter sufficient to distinguish it from other materials". University of California v. Eli Lilly and Co., 119 F.3d 1559, 1568; 43 USPQ2d 1398, 1406 (Fed. Cir. 1997).
The court also concluded that "naming a type of material generally known to exist, in the absence of
knowledge as to what that material consists of, is not description of that material". Id. Further, the court
held that to adequately describe a claimed genus, Patent Owner must describe a representative number
of the species of the claimed genus, and that one of skill in the art should be able to "visualize or recognize the identity of the members of the genus". Id.
The claims are broadly directed to a method of delivering an effector to a eukaryote comprising providing to a plant, plant tissue, or plant cell a composition comprising a recombinant polynucleotide comprising: (i) a single-stranded RNA (ssRNA) viroid sequence of a viroid from the family Avsunviroidae and (ii) an RNA sequence comprising or encoding an effector, wherein the RNA sequence is inserted into the ssRNA viroid sequence and is heterologous to the ssRNA viroid sequence, wherein the recombinant polynucleotide replicates in the plant, plant tissue, or plant cell; and wherein the eukaryote is; the plant, plant, plant tissue, or plant cell; or (b) is a fungus, an insect, a nematode, or an animal which consumes or contacts the plant, plant tissue, or plant cell, or a processed product thereof; whereby the effector comprised by or encoded by the RNA sequence is delivered to the eukaryote. The claims are drawn to any plant, plant tissue, or plant cell from any diverse source known in the art. The claims are drawn to any viroid from the family Avsunviroidae known in the art, wherein the composition comprising the viroid can replicate in any plant known in the art.
Applicant describes methods using a singular Avsunviroidae viroid denoted as Eggplant Latent Viroid (ELVd). Applicant does not describe the use of any other Avsunviroidae viroid in the methods of the invention.
Applicant describes in Example 3 (pgs. 86-87) the production of circular RNA using E. coli transfected with a eggplant tRNA ligase, ELVd RNA (one species of the family Avsunviridae viroid), and a Spinach RNA aptamer. The results of this working example show the accumulation of circular ELVd RNA in RNA mixtures derived from bacterial cells comprising the eggplant tRNA ligase. Applicant does not describe any results regarding the replication of the ELVd viroid in the bacteria cells.
Applicant describes in Example 9 (pgs. 91-94) the delivery of circular RNA containing an ELVd sequence to Arabidopsis and Zea mays protoplasts using PEG-mediated transfection, wherein the totality of the experiment was to determine if the protoplasts were positive for transfection of the circular RNA. Applicant does not describe any results regarding the replication of the ELVd viroid in the plant protoplast cells.
Applicant describes in Example 10 (pgs. 94-95) the delivery of circular RNA containing an ELVd sequence to Arabidopsis, Zea mays, and Nicotiana benthamiana plants using a leaf rubbing method. In one aspect of the working example, circular RNA delivery to Arabidopsis and Zea mays was quantified using RT-qPCR. In another aspect of the working example the circular RNA also comprised a mature miRNA designed to silence the NbPDS gene, wherein suppression of the target gene was used to quantify circular RNA delivery. Applicant does not describe any results regarding the replication of the ELVd viroid in the plants that underwent circular RNA delivery.
Applicant describes in Example 11 (pgs. 95-96) the delivery of circular RNA containing an ELVd sequence to Arabidopsis, Zea mays, and Nicotiana benthamiana plants using a leaf infiltration method. Circular RNA delivery to Arabidopsis, Zea mays, and Nicotiana benthamiana plants was quantified using RT-qPCR. Applicant does not describe any results regarding the replication of the ELVd viroid in the plants that underwent circular RNA delivery.
Applicant describes in Example 12 (pgs. 96-97) the modification of an ELVd viroid vector to include a hairpin RNA that targets the tomato PDS gene for virus-induced gene silencing when the viroid is transfected into tomato mesophyll protoplast cells. Effective delivery of the modified viroid vector into the tomato protoplast was measured by the suppression of the target gene was used to quantify RNA delivery. Applicant does not describe any results regarding the replication of the ELVd viroid in the tomato protoplasts that underwent suppression of the native PDS gene.
Applicant describes in Example 13 (pgs. 97-99) the modification of an ELVd viroid to produce and deliver an guide RNA molecule, that includes an effector targeting a Zea mays endogenous gene (Zmgl2; Zea mays glossy2), to a maize B73 plant cell for the purpose of editing the genome of the maize plant cell. Circularized ELVd-gRNA was co-transfected with ASCAS12a into maize B73 protoplasts, wherein gene editing was confirmed 24 hours later to determine if modified viroid including CRISPR guide RNAs were effective in editing a target gene. Applicant does not describe any results regarding the replication of the ELVd viroid in the maize protoplasts that underwent gene editing.
Applicant describes in Example 19 (pgs. 105-106) describes the use of an RNA targeting motif comprising an ELVd viroid designed using the sequence of the complete eggplant latent viroid genome and the repetition of the plus-strand hammerhead ribozyme domain for the longer-than-unit ELVd to traffic a Spinach RNA aptamer to the chloroplast of a tomato mesophyll protoplast cell. After confirming the RNA vector was traffic the chloroplasts of tomato protoplasts, the RNA vector was transfected into tomato plant leaves. The delivery of the RNA vector into the tomato plant leaves was quantified using RT-qPCR. Applicant does not describe any results regarding the replication of the ELVd viroid (comprised within the RNA vector) in the tomato plant leaves.
The state of the art regarding ELVd viroid sequences being co-expressing in a plant with tRNA ligase, teaches the production of recombinant RNA in host cells through the co-expression of a tRNA ligase and a chimeric RNA molecule that comprises a target RNA within a plant viroid scaffold [Daros et al. (WO 2015177100 A1; published 11/26/2015); pg. 11, lines 15-23], more specifically the overproduction of recombinant RNAs using the eggplant latent viroid (part of the family Avsunviroidae) delivery (ELVd) system of an RNA of interest into E. coli cells, wherein the recombinant RNAs using ELVd as a viroid scaffold can be overproduced in plant tissues (See, title of Example 2.5). Daros et al. teaches that in plant tissues, the ELVd RNA and tRNA ligase are expressed using Agrobacterium tumefaciens. Once cloned in binary plasmids that replicate in E. coli and A. tumefaciens under the control of the appropriate promoters (for example Cauliflower mosaic virus 35S promoter), both constructs are delivered into the plant tissue through agroinfiltration (pg. 37, lines 15-23). Daros also teaches viral vectors are used to express ELVd RNA and tRNA ligase in plant tissues. Daros also teaches that co-expression of a tRNA ligase and a chimeric RNA molecule that comprises a target RNA within an ELVd scaffold would inherently circularize (pg. 29, lines 6-10).
At the time of filing, it is not even clear if the Applicant has theorized that replication of the ELVd viroid sequences used in the working examples would occur, but rather, merely measures their ability to circularize with the use of tRNA ligase in the methods of the invention and their ability to be transfecting into plant cells. Applicant has disparaged the disclosure of Daros et al. (WO 2015177100 A1; published 11/26/2015) by explicitly reciting in the Applicant’s Remarks dated 11/03/2025 (pg. 13) that the circularization of the viroid described by Daros is not synonymous with replication of the viroid sequence in the plant tissues. In fact, Applicant has explicitly stated for the record that the ELVd RNA and tRNA ligase that are expressed in plant tissues using Agrobacterium tumefaciens would not be able to replicate in plant tissues (Applicant’s Remarks, pg. 13). In the Declaration submitted on 11/03/2025 after the time of filing, Applicant has only provided evidence of viroid replication in a plant by introducing ELVd RNA and genes of interest into ELVd’s native host plant (eggplant), wherein Applicant does not describe the use of tRNA ligase for circularization of the viroid sequence in the plant or any other method steps taking place (Declaration, pgs. 2-5). In light of the Applicant’s Remarks and Declaration, it appears that for replication of the viroid sequence, the method only works in the viroid’s native host plant—or there is some other structure-function relationship within the viroid sequence or between the viroid and the host plant that allows for viral replication that has not been adequately described by Applicant. Applicant has not described how to “engineer” the ELVd sequence carrying the gene of interest (see the term “engineered ELVd” in Experiments A-E in the Declaration filed on 11/03/2025). Applicant has not described the necessary structure required for the ELVd viroid sequence to be able to replicate in any host plant known in the art, such as RNA transporters, RNA polymerases, RNases, and RNA ligases. Applicant has not described the necessary structure for any viroid from the family Avsunviroidae to be able to replicate in any host plant known in the art, such as RNA transporters, RNA polymerases, RNases, and RNA ligases. The instant claims only require a composition comprising an ssRNA viroid sequence from the family Avsunviroidae and an RNA sequence comprising or encoding an effector to perform the recited function of replication in the plant; however, Applicant does not describe any other required structures to perform the method steps, and Applicant does not describe which viroid sequences would work in which host plants in such a way that one of ordinary skill in the art would be able to recognize viroid sequence and host plants that could perform the recited method steps and have viroid replication in the host plant. The only evidence the Applicant provides at the time of filing is working examples that identify the presence of the ELVd viroid sequence in a host plant or bacteria or the circularization of the viroid sequence in a host plant or bacteria, without any evidence disclosing replication of the ELVd viroid.
Based on the experimental data provided post-filing in the Declaration dated 11/03/2025, Applicant does not appear to have adequately considered these factors in the instant application at the time of filing. Even if the factors recited above had been considered by Applicant at the time of filing, Applicant has still not provided adequate disclosure as to the range of host organisms that could actually perform replication of an ELVd viroid sequence and a gene of interest, other than the native host of the viroid sequence, much less any Avsunviroidae viroid known in the art. In fact, the state of the prior art regarding replication of Avsunviroidae viroid sequences in plants explicitly teaches that Avsunviroidae viroids are restricted to their natural hosts [Beltran and Daros (2023); pg. 11, paragraph bridging pgs. 11-12].
The number of species described by Applicant are insufficient to describe the recited genus by virtue of example, given the vast size of the recited genus and the lack of written description in the instant specification with regard to the structural and functional characteristics of the claimed compositions.
Hence, Applicant has not, in fact, described the claimed compositions used in the methods of the invention within the full scope of the claims, and the specification fails to provide an adequate written description of the claimed invention.
Closest Prior Art
Claims 1 and 3-29 appear to be free of the prior art. The closest prior art regarding Claims 1 and 3-29 can be found in the combination of Ren et al. (US 20160152994 A1; published 06/02/2016; IDS Document) in view of Daros et al. (WO 2015177100 A1; published 11/26/2015) and Daros (Molecular plant pathology 17.8 (2016): 1170-1177; IDS Document).
Ren et al. (herein referred to as Ren) teaches a method for transgenic expression with enhanced specificity in an eukaryotic organism said method comprising the steps of (paragraph 0026): a) providing an expression construct comprising a promoter sequence functional in said eukaryotic organism and functionally linked thereto a nucleotide sequence to be expressed into a chimeric RNA sequence (paragraph 0027), said nucleotide sequence comprising i) at least one sequence capable to confer a preferred phenotype or beneficial effect to said eukaryotic organism (0028) and ii) at least one sequence (microRNA tag) substantially complementary to a microRNA sequence naturally expressed in said eukaryotic organism (paragraph 0029), wherein at least one of sequence i) and sequence ii) are heterologous to each other, and b) introducing said expression construct into an eukaryotic organism (paragraph 0030). Based on Applicant’s definition of effector (Specification, pg. 2, line 15 “the effector modifies a trait, phenotype, or genotype of a target cell”, pg. 8, lines 23-25 “the term "effector" refers to a moiety that can be integrated into a recombinant polynucleotide (e.g., viroid-derived vector) and that is capable of modulating (e.g., modifying) a state of a plant or plant cell”), the at least one sequence capable of conferring a preferred phenotype or beneficial effect to said eukaryotic organism taught by Ren encompasses sequences that would be defined as effectors. Additionally, the miRNA sequences (microRNA tag) recited in the chimeric RNA of Ren would also be considered effectors based on the Applicant’s definition of the term effector and the function disclosed by Ren which teaches that the microRNA tags can be designed to modulate the expression of an endogenous target sequence in the eukaryotic organism (paragraphs 0276 and 0647-48). Ren teaches that the cells and organism (e.g., plant, animal, protozoan, virus, bacterium, or fungus) of the present invention comprise at least one chimeric RNA of the invention, or an RNA agent (e.g., an expression construct or expression vectors encoding said chimeric RNA molecule). In certain embodiments, the cell is suspended in culture; while in other embodiments the cell is in (or part of) a whole organism (e.g., a microorganism, plant or an animal, such as a non-human mammal) (paragraph 0248).
Regarding the ssRNA viroid sequence that comprises the inserted heterologous RNA sequence recited in Claim 1, Ren teaches that the chimeric RNA is produced in the cell by an expression construct or expression vector, wherein suitable vectors (or delivery agents) for introducing a chimeric RNA of the invention into a target cell include any known viroid (paragraph 0221), further wherein an exemplary vector is a single or double-stranded RNA or DNA viral vector (paragraph 0166).
Regarding the heterologous RNA sequence, whereby the effector comprised by or encoded by the heterologous RNA sequence is delivered to the eukaryote recited in Claim 1, Ren teaches a) providing an expression construct comprising a promoter sequence functional in said eukaryotic organism and functionally linked thereto a nucleotide sequence to be expressed into a chimeric RNA sequence (paragraph 0027), said nucleotide sequence comprising i) at least one sequence capable to confer a preferred phenotype or beneficial effect to said eukaryotic organism (paragraph 0028), and ii) at least one sequence substantially complementary to a microRNA sequence naturally expressed in said eukaryotic organism (paragraph 0029), wherein at least one of sequence i) and sequence ii) are heterologous to each other, and b) introducing said expression construct into an eukaryotic organism (paragraph 0030). Based on Applicant’s definition of effector (Specification, pg. 2, line 15 “the effector modifies a trait, phenotype, or genotype of a target cell”, pg. 8, lines 23-25 “the term "effector" refers to a moiety that can be integrated into a recombinant polynucleotide (e.g., viroid-derived vector) and that is capable of modulating (e.g., modifying) a state of a plant or plant cell”), the at least one sequence capable of conferring a preferred phenotype or beneficial effect to said eukaryotic organism taught by Ren et al. encompasses sequences that would be defined as effectors. Additionally, the miRNA tag sequences recited in the chimeric RNA of Ren would also be considered effectors based on the Applicant’s definition and the function disclosed by Ren which teaches that the microRNA tag can be designed to modulate the expression of an endogenous target sequence in the eukaryotic organism (paragraphs 0276 and 0647-48). Ren et al. further teaches that the expression construct is heterologous with respect to the host, and must have been introduced into the host cell or an ancestor of the host cell by a transformation event (paragraph 0112).
However, Ren et al. does not explicitly teach the claim limitations, wherein this ssRNA viroid sequence is from the family Avsunviroidae and wherein the recombinant polynucleotide replicates in the plant.
Daros et al. (herein referred to as Daros) teaches the production of recombinant RNA in host cells through the co-expression of a tRNA ligase and a chimeric RNA molecule that comprises a target RNA within a plant viroid scaffold (pg. 11, lines 15-23), more specifically the overproduction of recombinant RNAs using the eggplant latent viroid (part of the family Avsunviroidae) delivery (ELVd) system of an RNA of interest into E. coli cells, wherein the recombinant RNAs using ELVd as a viroid scaffold can be overproduced in plant tissues (replicated) (See, title of Example 2.5). Daros et al. teaches that in plant tissues, the ELVd RNA and tRNA ligase are expressed using Agrobacterium tumefaciens. Once cloned in binary plasmids that replicate in E. coli and A. tumefaciens under the control of the appropriate promoters (for example Cauliflower mosaic virus 35S promoter), both constructs are delivered into the plant tissue through agroinfiltration (pg. 37, lines 15-23).
Daros (Molecular plant pathology 17.8 (2016): 1170-1177) teaches when compared to different viroids (ASBVd, CChMVd, and CEVd), ELVd was the viroid whose transcripts processed more efficiently in the plant chloroplast with an excellent yield of circular molecules (pg. 1174, right column, bottom of first full paragraph).
However, the combination of Ren, Daros et al., and Daros does not teach or suggest an embodiment of the invention wherein the recombinant polynucleotides comprising the ELVd RNA and effector sequences replicate in plant tissues. Despite the fact that Daros et al. teaches that co-expression of a tRNA ligase and a chimeric RNA molecule that comprises a target RNA within an ELVd scaffold would inherently circularize (pg. 29, lines 6-10), Applicant’s Remarks dated 11/03/2025 (pg. 13) recite that the circularization of the viroid described by Daros et al. is not synonymous with replication of the viroid sequence in the plant tissues. In fact, Applicant has explicitly stated for the record that the ELVd RNA and tRNA ligase that are expressed in plant tissues using Agrobacterium tumefaciens would not be able to replicate in plant tissues (Applicant’s Remarks, pg. 13).
Conclusion
No claims are allowed.
This action is NON-FINAL.
Any inquiry concerning this communication or earlier communications from the examiner should be directed to KELSEY L. MCWILLIAMS whose telephone number is (703)756-4704. The examiner can normally be reached M-F 08:00-17:30.
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/KELSEY L MCWILLIAMS/Examiner, Art Unit 1663
/Amjad Abraham/SPE, Art Unit 1663