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 .
Claim Status
Claims 1, 3, 9-12 and 14-18, 21 and 22 are pending and examined. Claims 2, 4-8, 13, 19, 20 and 23-26 have been cancelled.
The rejection of claims 1, 3, 9-12, 14-18, 21 and 22 on the ground of nonstatutory double patenting as being unpatentable over claims 1, 2, 9, 11, 12, 13 and 14 of copending Application No. 17/297,527 (referred to herein as ‘527; published as Pub. No. US 2022/0010322 A1) is withdrawn as ‘527 has been abandoned.
Claim Rejections - 35 USC § 103
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.
Claim(s) 1, 3, 9-12 and 14-18, 21 and 22 REMAIN rejected under 35 U.S.C. 103 as being unpatentable over Senis et al (2016, Nucleic Acids Research, 45:1-17) in view of Maori et al (Patent No. US 11,555,199 B2) and Gurumurthy et al (Pub. No. US 2018/0127787 A1) and Zhao et al (2016, Scientific Reports, 6:1-11), and in further view of Mitter et al (2015, Virus Research, 211:151-158) and Thomas et al (2004, Australasian Plant Pathology, 33:597-599).
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.
Instant claims 1, 3, 9-12 and 14-18, 21 and 22 are drawn to a method of reducing expression of a viral target gene in a tomato plant cell by introducing a ZFN, TALEN or nuclease that cleaves a native tomato pre-miRNA and making at least two double stranded DNA breaks at said site and selecting for a cell where the breaks have been repaired with intervening DNA encoding an amiRNA comprising a core sequence complementary to the target viral gene resulting in a tomato plant cell comprising the amiRNA comprising the core sequence and wherein the plant is heterozygous, wherein the target is a Bunyavirales gene or a tomato spotted wilt virus gene, wherein the genomic site comprises SEQ ID NO: 6 or 7 and the intervening DNA comprises SEQ ID NO: 2 and a method of producing tomato plant seeds by crossing a plant comprising said cell with another plant.
The specification teaches that SEQ ID NO: 2 is the TSWV sequence of amiTSWV and is embedded within the tomato sequence of miR156b scaffold SEQ ID NO: 6 and is encompassed by SEQ ID NO: 9 (p. 5).
Senis et al teach introducing an amiRNA into a miRNA gene using a sequence specific nuclease such as Cas9 or TALEN to reduce expression of a target gene without perturbing endogenous gene expression (e.g. see Abstract; see also p. 2; see p. 13). The amiRNA is embedded in a miRNA scaffold that is also the scaffold of the native pre-miRNA (see Abstract; see also p. 5, ¶ 1 and 2).
Senis et al teach the importance of keeping at least one allele intact when introducing intervening DNA as the miRNA being altered may play an essential physiological role (p. 13, col. 2, last ¶ bridging p. 14). Therefore, Senis et al reasonably provides motivation for cells being heterozygous for modified pre-miRNAs.
Senis et al teach that this method of linking exogenous to endogenous RNAi triggers to precisely engineer and harness miRNA loci for expression of detectable foreign RNA sequences should prove valuable and can include replacement of a target miRNA with another artificial or natural miRNA (p. 14, col. 2, ¶ 2). Thus, Senis et al reasonably teach replacing rather than inserting intervening DNA into a native pre-miRNA.
However, because Senis et al does not teach practicing this method in plants, the issue is whether one of ordinary skill in the art would have found it obvious to do so while making at least two double strand DNA breaks, and whether one would target a Bunyavirales gene or SEQ ID NO: 2.
To this point, Maori et al teach one of ordinary skill in the art was aware of introducing modified miRNAs/amiRNAs into a plant genome in order to silence a target gene of interest using TALENs or CRISPR (see claims 1, 2, 9 and 10, see also col. 3 and 4; see col. 10; see also col. 16; col. 24 and 26). The method is applicable to any plant, and includes targeting genes of pathogens/exogenous targeting genes affecting tomato or biotic stresses (col. 11 and 12; see col. 49 and 54).
Similarly, Gurumurthy et al teach modifying gene expression in a cell using nucleases wherein an amiRNA replaces an endogenous target sequence (see Abstract; see also claims 1, 7-9, 14; see Figures 2-5; see also ¶ 0255). The method is applicable to plants (¶ 0041). These amiRNAs are inserted into intronic regions where endogenous miRNAs are present and thus would not affect the expression of the host gene (¶ 0220-0221).
Zhao et al teach the deletion of endogenous miRNAs and their replacement with an intervening DNA corresponding to the TFL1 gene by making two double stranded DNA breaks (see Abstract; see also Figure 1 and 2). This allows for targeted gene replacement intervening DNA in plants such as maize that are transgene free as opposed to inserting intervening DNA (p. 6, ¶ 4).
Mitter et al teach that TSWV is an economically important viral pathogen of a wide range of field and horticultural crops and that amiRNA can be used for broad spectrum resistance to tospoviruses and other viruses (e.g., see Abstract).
Thomas et al teach sequencing and analysis of TSWV within the Bunyaviridae family, and in particular GenBank Accession No. AY611529 having 100% sequence identity to SEQ ID NO: 2 of the instant invention (see Attachment A in the Office action dated 17 August 2023; see also p. 599, col. 1). Viruses are a significant production problem in chickpeas, and TSWV is known to infect them (p. 597).
Therefore, prior to the effective filing date of the instant invention it would have been prima facie obvious to one of ordinary skill in the art to apply the method as taught by Senis et al to silence expression of a target gene of interest, for example, as taught by Maori et al and Zhao et al.
One would have found it obvious to do so because the methods are functionally equivalent to one another in so far as each method is used to silence a gene of interest by insertion or replacement without the need for implementing classical molecular genetics and transgenic tools comprising expression cassettes that have a promoter, terminator and selection markers to produce improved crops or novel non-GMO plants with increased crop yield having protection against stress, pathogens and pests (e.g., see Maori et al, col. 11; see also Zhao et al, Abstract).
Moreover, one would be motivated to do this because when the amiRNAs are inserted into intronic regions where endogenous miRNAs are present the expression of the host genes will not be disturbed (Senis et al, see Abstract; see also p. 2; see p. 13; see also Gurumurthy et al, ¶ 0220-0221).
One would have a reasonable expectation of success in doing so because each of Senis et al and Maori et al and Gurumurthy et al teach the successful inhibition of a gene of interest whereas Zhao et al demonstrate the successful replacement of endogenous miRNA with intervening DNA that functional and expressed.
One would have used the method to target SEQ ID NO: 2 because it is a design choice: TSWV sequences were known in the art (e.g., see Thomas et al), and the specific sequence targeted is inconsequential so long as gene silencing occurs and TSWV resistance is increased, the importance of which is noted above. The same is true for the placement of the intervening DNA: so long as it does not interfere with endogenous gene expression its location is inconsequential.
As this target sequence would be replacing native pre-miRNA in the plant genome, it is necessarily follows that the genomic site would comprise SEQ ID NO: 6 or 7 or that the cell would comprise SEQ ID NO: 2.
Response to Arguments
Applicant traverses the rejection of the claims because Senis teaches the importance of keeping one allele intact when introducing intervening DNA as the miRNA being altered may play an essential physiological role, including tumor suppression and is silent on replacing a native pre-miRNA with a modified pre- miRNA, let alone in plant cells. (Applicant reply dated 12 May 2026, p. 6, penultimate ¶).
Applicant’s argument appears to depend on Senis teaching that intervening DNA is introduced/added into the miRNA as opposed to replacing a segment of the miRNA. This argument is not persuasive because Senis suggests, in fact, replacement of miRNA with artificial or natural miRNA (p. 14, col. 2, ¶ 2).
Applicant asserts Senis teaches the integration of a shmiRNA into the liver-specific miR-122/hcr locus in hepatoma cells and was integrated upstream of the miR-122 hairpin and thus does not replace, but is integrated in addition to, a native pre-miRNA (Applicant reply dated 12 May 2026, p. 6, last ¶ and p. 7).
This argument is not persuasive as Senis suggests replacement of a target miRNA with another artificial miRNA (p. 14, col. 2, ¶ 2), while Maori specifically claims modifying the endogenous miRNA with an amiRNA. In fact, Senis teaches the expression strategy inserts shmiRNA into a cellular miRNA gene (e.g., see Figure 1).
Applicant asserts the term "heterozygous" in the context of Senis refers to one copy of the integrated allele, but both the wild-type and integrated allele still contain the native miR-122 hairpin. As the shmiRNA does not replace the native miR-122, the liver cells of Senis process both copies of the native miRNA as well as at least one copy of the shmiRNA and cautions against replacing the native miRNA (Applicant reply dated 12 May 2026, p. 7, last ¶ bridging p. 8; see also p. 9, ¶ 1).
This argument is not persuasive because Senis does not, in fact, caution against replacing native miR-122 but stands for the proposition that if an endogenous miRNA is to be modified then one allele should remain unaffected as failing to do so could have adverse consequences.
In any event, Applicant’s argument is not commensurate is scope with what is claimed as (1) there is no requirement that the “entire” miR-122 is replaced; (2) claim 1 is not directed to any particular pre-miRNA; and (3) Applicant seemingly reiterates the position of the Office by writing “Senis teaches the importance of keeping one allele intact when introducing intervening DNA as the miRNA being altered may play an essential physiological role” (Applicant reply dated 12 May 2026, p. 6, ¶ 1).
Applicant argues that Senis relates to juxtaposing exogenous miRNA next to the existing endogenous one and is described as something of great potential requiring further research and that direct replacement of a target miRNA with another artificial or natural miRNA is nothing more than pure speculation ("This could include a direct replacement of a target miRNA with another artificial or natural miRNA, to study effects on physiology, differentiation or other basic cellular parameters.") and limits this statement to the study of endogenous genes linked to physiology or other cellular mechanisms. It is completely silent about the use of such methods to redirect intracellular miRNA mechanisms against exogenous target pest genes. Not only Senis does not disclose the claimed method that comprises replacing an miRNA core sequence, but it also does not disclose any use in the context of biotic stresses and the defense against pathogens (Applicant reply dated 12 May 2026, p. 9, ¶ 3 and 4).
This argument is unpersuasive and has been previously addressed as the purported deficiency of Senis is remedied by Maori et al, which teaches one of ordinary skill in the art was aware of introducing modified miRNAs/amiRNAs into a plant genome in order to silence a target gene of interest using TALENs or CRISPR (see claims 1, 2, 9 and 10, see also col. 3 and 4; see col. 10; see also col. 16; col. 24 and 26), and that the method is applicable to any plant, and includes targeting genes of pathogens/exogenous targeting genes affecting tomato or biotic stresses (col. 11 and 12; see col. 49 and 54).
Moreover, when viewed in light of Mitter et al, which teaches that TSWV is an economically important viral pathogen of a wide range of field and horticultural crops and that amiRNA can be used for broad spectrum resistance to tospoviruses and other viruses (e.g., see Abstract), one would have found it obvious to modify the methods as taught by Senis and Maori for use in the context of biotic stresses and the defense against pathogens.
Applicant argues Maori does not teach an enabling method, and does not reduce to practice, the replacement of the native core miRNA by an artificial core miRNA while retaining the original miRNA scaffold, together with the selection of a cell heterozygous for one copy of the full native miRNA and one copy of the modified miRNA (artificial core within native scaffold), so that the resulting cell can continue with its essential cellular activity and target a new pest (viral) gene with the maximum cellular efficiency, and that most of the Example section of Maori is written in the present tense and discloses hypothetical, prophetic results (Applicant reply dated 12 May 2026, p. 10, ¶ 3).
Applicant’s argument is not persuasive the arguments of counsel cannot take the place of evidence in the record. In re Schulze, 346 F.2d 600, 602, 145 USPQ 716, 718 (CCPA 1965). See MPEP 716.01(c)(II). Namely, Applicant fails to explain why the examples of Maori would not work.
Here, evidence is critical since every patent is presumed valid (35 U.S.C. 282 ), and since that presumption includes the presumption of operability (Metropolitan Eng. Co. v. Coe, 78 F.2d 199, 25 USPQ 216 (D.C. Cir. 1935), examiners should not express any opinion on the operability of a patent. Affidavits or declarations attacking the operability of a patent cited as a reference must rebut the presumption of operability by a preponderance of the evidence. In re Sasse, 629 F.2d 675, 207 USPQ 107 (CCPA 1980). See MPEP 716.07.
Applicant argues Gurumurthy does not teach the replacement of the native core miRNA by an artificial core miRNA within the original miRNA scaffold. This is because the ssDNA use in Gurumurthy is introduced (added) to an existing genome region. In other words, the cell still needs to process the native gene as well as the introduced amiRNA (Applicant reply dated 12 May 2026, p. 10, ¶ 4).
This argument is not found to be persuasive because Gurumurthy need not teach the replacement of the native core miRNA by an artificial core miRNA within the original miRNA scaffold as this is within the purview of a rejection of claims under 35 U.S.C. 102.
Here, Gurumurthy et al teaches that one of ordinary skill in the art appreciates that gene expression can be modified in a cell using nucleases wherein an amiRNA replaces an endogenous target sequence, that the method is applicable to plants and that one is motivated to do so because these amiRNAs are inserted into intronic regions where endogenous miRNAs are present and thus would not affect the expression of the host gene.
Furthermore, the latter teaching of Gurumurthy reinforces what is taught by Senis: if an endogenous miRNA is to be modified then one allele should remain unaffected as failing to do so could have adverse consequences.
Applicant argues Zhao teaches the replacement of an entire gene region, in this case, two miRNA genes, with a new construct (TFL1) and does not teach the replacement of the native core miRNA by an artificial core miRNA while retaining the original miRNA scaffold and therefore fails to complement any of the previously cited references to arrive at the present invention (Applicant reply dated 12 May 2026, p. 10, ¶ 5).
This argument is not persuasive because as noted with Gurumurthy, Zhao need not teach the replacement of the native core miRNA by an artificial core miRNA while retaining the original miRNA scaffold. Rather, Zhao is referenced to demonstrate one’s reasonable expectation of success in expressing a gene or amiRNA of interest when endogenous miRNAs are replaced as opposed to not replacing the endogenous miRNA.
Conclusion
No claim is allowed.
THIS ACTION IS MADE FINAL. Applicant is reminded of the extension of time
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/JASON DEVEAU ROSEN/Primary Examiner, Art Unit 1662
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