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 .
Response to Amendment
The amendment filed 10/23/2024 has been entered. Claims 35-37 and 39 have been amended, and claims 40-43 and 50-52 have been canceled.
Election/Restrictions
Applicant elected Group I (claims 35-49) without traverse in the reply filed on 04/07/2024 and previously withdrawn claims 50-52 have been canceled.
Applicant elected the species Pseudomonas syringae pathovars in claim 37 in the reply filed on 04/07/2024.
Claims 38,39 and the other Gram-negative bacterial species (other than Pseudomonas syringae pathovars) recited in claim 37, remain withdrawn from further consideration pursuant to 37 CFR 1.142(b) as being drawn to a nonelected species, there being no allowable generic or linking claim.
Applicant elected species “said siRNA or miRNA inhibits at least one gene encoding a virulence factor or an essential gene or an antibacterial resistance gene if said bacterium is pathogenic” in claim 44 in the reply filed on 04/07/2024.
The species of siRNA or miRNA that inhibits at least one gene encoding a repressor of growth or a negative regulator of a pathway that is useful for the host if said bacterium is beneficial for the host in claim 44 remain withdrawn from further consideration pursuant to 37 CFR 1.142(b) as being drawn to a nonelected species, there being no allowable generic or linking claim.
Claims 35-37 and 44-49 are under examination.
Information Disclosure Statement
The non-patent literature document (Cardin et al.) on the IDS filed on 10/23/24 only appears to go to page 53 and pager 56.
Specification
The abstract of the disclosure is objected to because the amended abstract is not on a separate sheet. See MPEP 714(II)(B) A corrected abstract of the disclosure is required and must be presented on a separate sheet, apart from any other text. See MPEP § 608.01(b).
Response to Arguments
Applicant’s arguments, see page 7, filed 10/23/2024, with respect to the objection to the abstract and the objection to the specification have been fully considered and are persuasive. The objection to the abstract has been withdrawn due to the amendment to the abstract to reduce the number of words to less than 150 words.
Applicant’s arguments, see page 7, filed 10/23/2024, with respect to the objection to the specification have been fully considered and are partially persuasive. The objection to the specification regarding the embedded hyperlink on page 76 has been withdrawn due to the amendment to the specification removing the embedded hyperlink on page 76. However, there is also another embedded hyperlink on page 80, line 17 and therefore the objection to the specification remains.
Applicant’s arguments, see page 18, filed 10/23/2024, with respect to claims 36 and 37 have been fully considered and are persuasive. The 112(b) indefiniteness rejection of claims 36 and 37 has been withdrawn due to the amendments to claims 36-37 reciting “target Gram-negative bacterium” which corrects the antecedent basis issues.
Applicant’s arguments, see pages 19-20, filed 10/23/2024, with respect to claims 35,40,41 and 44 have been fully considered and are persuasive. The 35 U.S.C. 102(a)(1) rejection of claims 35,40,41 and 44 as anticipated by Gong et al. has been withdrawn due to the amendment to claim 35 to recite that the target Gram-negative bacterium is contacted directly extracellularly with said siRNA or miRNA”. Therefore Gong et al. which teaches that the siRNA is transformed into the Pseudomonas aeruginosa strain by electroporation rather than directly extracellularly contacted with siRNA does not anticipated the current amended claims.
Claim Rejections - 35 USC § 112
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.
Claims 35-37 and 44-49 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.
Claims 35-37 and 44-49 encompass a large genera of siRNAs and miRNAs of 15-30 base pairs, inhibiting specifically the expression of a target Gram-negative bacterium bacterial gene, wherein said siRNA or miRNA inhibits at least one gene encoding a virulence factor, essential gene, or antibacterial resistance gene if said bacterium is pathogenic. Any siRNA or miRNA of 15-30 base pairs that inhibits the expression of at least one gene encoding a virulence factor, essential gene, or antibacterial resistance gene if said bacterium is pathogenic in a target Gram-negative bacterium are encompassed by claim 35. Claim 36 limits the target Gram-negative bacterium to phytopathogenic bacterium, and claim 37 limits to the recited elected species, Pseudomonas syringae pathovars.
When claims 35-37 and 44-49 are analyzed in light of the specification, the instant invention encompasses a large genera of siRNAs and miRNAs of 15-30 base pairs, inhibiting specifically the expression of a target Gram-negative bacterium bacterial gene, wherein said siRNA or miRNA inhibits at least one gene encoding a virulence factor, essential gene, or antibacterial resistance gene. Page 11 contemplates that the method allows the targeting of one or multiple bacterial gene(s) by expressing iRNA molecules (precursors of siRNAs and miRNAs) in plant cells or delivering small RNAs on plant tissues prior to and/or after bacterial infection. The functional iRNAs of the invention are long single-stranded RNA molecules converted into long dsRNA molecules by plant RNA-dependent RNA polymerases and further processed into siRNAs by plant DCL proteins, or are long double-stranded RNA molecules that act as siRNA precursors and can be processed into siRNAs, in planta by DCL proteins and other small RNA biogenesis factors encoded by plant genomes (page 14).
The dsRNAs and sRNAs of the invention can also be produced by in vitro synthesis, in which the synthesized dsRNAs were digested with RNase III to produce the siRNAs (Example 1, pages 80 and 81). Pages 22-32 disclose possible bacterial genes that the iRNA of the invention may inhibit expression of. Table 1 on pages 59-62 includes SEQ ID NOs of the dsRNA that target specific genes of specific bacteria, and in some cases the sequences are used to target multiple genes (SEQ ID NO: 1 is the sequence of the first arm of the CFA6/HRPL dsRNA used to concomitantly target HrpL and Cfa6 genes of Pto DC3000). Example 1, pages 71-73 discloses chimeric hairpins that produce artificial siRNAs targeting a specific region of specific genes and includes SEQ ID NOs of the sequences of the first and second arms of the dsRNA used to target the specific genes of the specific species of bacteria. However, these specific sequences disclosed in the specification are not the siRNAs or miRNAs that are claimed, but are the sequences of the first and second arms of dsRNA that will be processed into siRNAs by digestion with RNase III (pages 79,80). While the specification provides written support for the large dsRNA sequences that are the precursors of the siRNAs, the specification does not describe the siRNA from the processed dsRNA. The specification also does not describe any miRNAs from processed dsRNA.
Good et al. (Frontiers in Microbiology, Vol. 2, Published 12 Sept 2011, pages 1-9) teach natural RNA silencing in bacteria, and that antisense mechanisms are abundant and involved in core cellular processes and adaptive responses (page 1, right column) and have the ability to work alone as gene regulators through RNA/RNA interactions (page 2, left column). Good et al. teach that the silencing sequence must be sufficiently abundant in cells to sequester the bulk of transcript mRNA to repress translation initiation, and that it is difficult to design silencers that specifically recognize and inhibit the target mRNA without unintended effects (page 3, right column), however no specific sequences of siRNAs or miRNAs that inhibit the expression of a bacterial target gene are taught by Good et al.
Caswell et al. (Frontiers in Cellular and Infection Microbiology, Vol. 4 Published 28 October 2014, pages 1-10) teach small RNA molecules as key regulators controlling bacterial gene expression and that there may be more than one highly related sRNA produced by a given bacterium, termed sibling sRNAs, which are highly similar at the nucleotide level but that the sibling sRNAs may not necessarily exert identical regulatory functions (Abstract page 1). Caswell et al. teach that while some sibling sRNAs exert overlapping regulatory functions, some sibling sRNAs perform unique, non-redundant functions within the bacterium in which they are produced, which may be the result of differential regulation of the sibling sRNA-encoding genes, varying mRNA targets between the siblings, and/or mechanisms of regulating gene expression that are unique to each sibling sRNA (pages 1-2,10 and Figure 1). Caswell et al. summarizes the known sibling sRNAs to date in Table 1 page 2, including sibling RNAs from Yersinia sp., S. enterica, P. aeruginosa, Pseudomonas sp., E. coli, A. tumefaciens, B. abortus, S. meliloti, Vibrio sp. Streptococcus sp., B. subtilis, and L. pneumophila. This demonstrates that even sRNAs having nucleotide similarity are capable of regulating the expression of unique sets of genes compared to their sibling (non-redundant regulation).
Gong et al. (BMB Reports, Korean Society for Biochemistry and Molecular Biology. 47, 1. 1 April 2014. 203-208), cited on an IDS, teach the in-vitro siRNA-mediated gene silencing of MexB in the Pseudomonas aeruginosa strain PAO1 (page 205 left column), in which the siRNA was 21 base pairs and teaches the specific sequence, and was transformed into the PAO1 strain (siRNA design and construction page 206) and that one of the siRNAs targeting MexB was effective in reducing MexB expression and affecting antimicrobial sensitivity (page 205, right column). Therefore, Gong et al. shows the in-vitro reduction in expression of a Pseudomonas aeruginosa gene using the specific siRNA of 21 bp.
Huang et al. (eds.) (Bioinformatics in MicroRNA Research, Methods in Molecular Biology, Vol. 1617, Chapter 3, Published 25 May 2017, pages 39-52) teach that due to their small size, miRNAs are the ideal mechanism for bacteria and viruses that have limited room in their genomes, and a single miRNA can target up to ~ 30 genes, but that a limited number of miRNAs and miRNA-like RNAs have been found in bacteria (Abstract, page 39). Huang et al. teach that bacteria do not possess miRNAs per se, but many species produce small RNAs that are similar to miRNAs in their ability to regulate gene expression through antisense base-pairing, and that the sRNAs behave similarly to miRNAs in that they bind to mRNA targets to regulate gene expression, however are generally longer than miRNAs (page 48, first paragraph). Huang et al. demonstrates the variability in the genes that an miRNA can target, and that a limited number of miRNA-like RNAs have been found in bacteria.
Borges et al. (Nat Rev Mol Cell Biol., Vol. 16, Published Dec 2015, pages 727-739), teach that most plant small RNAs are produced as 21-24 nu molecules as a result of activity of Dicer-like proteins, and the process forms dsRNA intermediates from hairpin precursors or from the synthesis of dsRNA from ssRNAs (page 727, left column). Borges et al. teach plant small RNAs are divided into miRNAs, hairpin-derived siRNAs, natural antisense siRNAs, secondary siRNAs and heterochromatic siRNAs (page 727, right column). While Borges et al. teach that plant small RNAs, including siRNAs and miRNAs, function in plant development, reproduction and genome reprogramming (page 727, left column), Borges et al. does not teach plant siRNAs or miRNAs as having a function of inhibiting genes in bacteria.
The art does not teach at the time of the effective filing date, a representative number of complete structures of siRNAs or miRNAs inhibiting specifically the expression of a target bacterial gene encompassed by the broad genus as claimed.
In analyzing whether the written description requirement is met for genus claims, it is first determined whether a representative number of species have been described by their complete structure. In the instant case there are no siRNAs or miRNAs for inhibiting the expression of a gene in a target bacterium whose complete structure is disclosed. The genus encompasses a large number of siRNAs and miRNAs of 15-30 bp that inhibit specifically the expression of a gene encoding a virulence factor, essential gene, or antibacterial resistance gene in a target Gram-negative bacterium and siRNAs and miRNAs in kind and the genus encompass a large number of species of siRNAs and miRNAs that have a different structure, as each siRNA or miRNA would have a different sequence dependent on the target bacterial gene that it is inhibiting expression of, and the specification does not describe the complete structure of a representative number of species of the large genus of siRNAs and miRNAs of 15-30 bp that inhibit the expression of a gene encoding a virulence factor, essential gene, or antibacterial resistance gene in a target Gram-negative bacterium, or functional equivalents thereof.
While the specification discloses numerous sequences of first and second strands of dsRNA’s that will be used to produce the siRNAs, the specification and examples do not provide support for the entire genera of siRNAs or miRNAs of 15-30 base pairs with the function of inhibiting specifically the expression of a gene encoding a virulence factor, essential gene, or antibacterial resistance gene in a target Gram-negative bacterium as in claims 35-37 and 44-49. One would need to further determine what sequence was produced and if a produced sequence is an siRNA or miRNA having the desired activity of inhibiting the expression of a gene encoding a virulence factor, essential gene, or antibacterial resistance gene in a target Gram-negative bacterium. Next, then it is determined whether a representative number of species have been sufficiently described by other relevant identifying characteristics (i.e., other than nucleotide sequence), specific features and functional attributes that would distinguish different members of the claimed genus. In the instant case, the functional characteristic in claims 35-37 and 44-49 (inhibiting specifically the expression of a gene encoding a virulence factor, essential gene, or antibacterial resistance gene in a target Gram-negative bacterium) is not coupled with a known structure. The specification fails to identify a core structure necessary for inhibiting specifically the expression of a gene encoding a virulence factor, essential gene, or antibacterial resistance gene in a target Gram-negative bacterium, as well as a partial structure, physical or chemical property, or functional characteristic coupled with a structure/function relationship responsible for inhibiting the expression of a gene encoding a virulence factor, essential gene, or antibacterial resistance gene in a target Gram-negative bacterium to demonstrate possession of the full invention as claimed at the time of filing.
Applicant’s attention is directed to the Guidelines for the Examination of Patent Applications Under the 35 U.S.C. 112(a) or Pre-AIA 35 U.S.C. 112, first paragraph, "Written Description" Requirement (MPEP2163).
In conclusion, the instant disclosure embracing sequences of dsRNA’s for producing siRNAs of the claimed broad genus of siRNAs and miRNAs of 15-30 base pairs for inhibiting specifically the expression of a gene encoding a virulence factor, essential gene, or antibacterial resistance gene in a target Gram-negative bacterium is not deemed sufficient to reasonably convey to one skilled in the art that the instant disclosure was in possession of the claimed broad genus at the time the application was filed. Thus, it is concluded that the written description requirement is not satisfied for the claimed genus.
Response to Arguments
Applicant's arguments filed 10/23/2024 have been fully considered but they are not persuasive.
Applicant cites case law In re Barker and Reagents of the Univ. of Cal. V. Eli Lilly on pages 8-9 of response, and Capon v. Eshhar and MPEP 2163 on page 9 of response and states that the inventor’s contribution to the public is that the inventors’ discoveries demonstrate that it is in fact possible to direct silencing of any bacterial gene by contacting bacterial cells with small RNAs bearing sequence homologies to one or multiple bacterial target genes, and the small RNAs can be stably expressed by said plant cells to protect them against one or multiple bacterial pathogens, or can be exogenously administered to plant tissues that will encounter phytopathogenic bacterium, thereby dampening its pathogenicity and growth.
With respect to the arguments on page 9 that the inventor’s contribution is that they discovered that it is in fact possible to direct silencing of any bacterial gene by contacting bacterial cells with small RNAs bearing sequence homologies to one or more bacterial target genes (See page 5 of the specification), the arguments are not found persuasive because observing that bacterial cells are sensitive to exogenously derived siRNA and the siRNA can be used in antibacterial applications does not provide written description for the siRNA or miRNA inhibiting specifically the expression of a target Gram-negative bacterial gene. Furthermore, the prior art of record (Gong et al. BMB Reports, Korean Society for Biochemistry and Molecular Biology, 47:203-208, 2014) teach siRNA targeting MexB was effective in reducing MexB expression and affecting antimicrobial sensitivity.
This is also not found persuasive because MPEP 2163(II)(A)(3(a)) states:
Conversely, describing a composition by its function alone typically will not suffice to sufficiently describe the composition. See Eli Lilly, 119 F.3 at 1568, 43 USPQ2d at 1406 (Holding that description of a gene’s function will not enable claims to the gene "because it is only an indication of what the gene does, rather than what it is."); see also Fiers, 984 F.2d at 1169-71, 25 USPQ2d at 1605-06 (discussing Amgen Inc. v. Chugai Pharm. Co., 927 F.2d 1200, 18 USPQ2d 1016 (Fed. Cir. 1991)).
Therefore, while the function of silencing any bacterial gene by contacting bacterial cells with small RNAs may be adequately described, this does not provide written support for the corresponding structure of the small RNAs (siRNA or miRNA) that have the claimed function (inhibiting specifically the expression of a target Gram-negative bacterial gene), as there is no structure-function correlation. The specification does not provide adequate written description for the claimed genus of siRNA and miRNA having 15-30 base pairs, as a representative number of species of siRNA and miRNA having 15-30 base pairs have not been described. The specification discloses bacterial genes that may be targeted as well as working examples disclosing making dsRNA targeting genes from sub-species of bacteria. Example 1 describes an IR-CFA6/HRPL chimeric hairpin to produce artificial siRNAs targeting a 250 bp region of Cfa6 (from nucleotide 1-250) and a 250 bp region of HrpL from nucleotides 99-348 (SEQ ID NO: 1,2 and 3) under control of the constitutive 35S promoter (See Example 1, pages 71-72). The dsRNA precursors, IR-CYP51 or IR-CFA6/HRPL produce small RNAs with unknown sequences (See Figure 1 and working examples). As CFA6 and HRPL are different proteins, the nucleotide sequences for CFA6 and HRPL are different. In addition, Figure 2 shows the 250 bp regions of LuxA (1-250 nt) and LuxB (1-250nt) genes were used to generate the chimeric hairpin construct (Figure 2, and spec. pages 63-64).
The issue at hand, as shown above, is that the sequences of the long dsRNA that are used to generate the chimeric hairpin constructs do not share a common nucleotide sequence (one sequence of a siRNA or a miRNA having 15 to 30 nucleotides in length) with a genus of Gram-negative bacterial genes. The sequences of the long dsRNA or the names of genes that may be the basis for the dsRNA do not provide an adequate description and representation of the structure of the genus of siRNA and miRNA. No siRNA sequences produced by the dsRNA constructs are disclosed in the specification, and the skilled artisan would have to further experiment with the RNA produced by the dsRNA in the bacterial cell and determine which RNA is considered siRNA or miRNA having a size from 15 to 30 base pairs and then would have to sequence these sequences and determine if they have the desired biological activity.
The claimed genus of siRNA and miRNA encompasses substantial variation and the specification does not describe a sufficient variety of species to reflect the variation within the genus. There is no essential nucleotide sequence(s) to represent the genus of siRNA or miRNA molecules because each siRNA or miRNA targeting a Gram-negative bacterial gene would have a different nucleotide sequence because each small RNA would target a nucleotide sequence of a different gene having a different nucleotide sequence. There are millions of possible siRNA or miRNA sequences embraced by the genus. While the specification contemplates the method and working examples show small RNAs are produced by dsRNA constructs, the specification does not describe the sequences for the small RNAs produced in the bacterial cells for inhibiting specifically the expression of a target Gram-negative bacterial gene.
Applicant argues on page 10 of response that the disclosure provides sufficient information describing the claimed method to one of ordinary skill in the art and to show one of ordinary skill in the art that the patentee was in possession of the claimed invention as one of ordinary skill understands what the term “small RNA” means and can visualize small RNA having a length of 15-30 bp as claimed. Applicant argues there is plenty of information to easily design small RNAs specific for any target bacterial gene, and complete genomes of numerous bacterial species are available on the internet and cites case law Hybritech, Inc. v. Monoclonal Antibodies, Inc.. Applicant argues on page 10 of response that the office has inappropriately concluded that the art does not teach a representative number of complete structures of siRNAs or miRNAs inhibiting specifically the expression of a target bacterial gene encompassed by the broad genus as claimed, and that the Applicant does not concede. Applicant argues the art teaches all that is needed to design a small RNA within the scope of the disclosure, which is sufficient, because no one of ordinary skill in the art would have expected to have found all possible small RNAs against bacterial genes in the prior art, and the discovery that directly extracellular contact of bacterial cells with small RNAs is sufficient to control gene expression inside the bacteria is new and unexpected, but the technology supporting the functioning of the claimed method is not new. Applicant argues on page 11, that Nobel Prizes awarded to Andrew Fire and Craig Mello in 2006 for the discovery of RNA interference in 1998, and the discovery of miRNA is even older and was found and characterized in 1993. Applicant argues that numerous journal articles describe studies to control gene expression and can be used for customized design of small RNAs for gene inactivation and therefor, design of the dsRNA or small RNAs is trivial and routine aspect of the claimed method, and all that is needed is the genome sequence of the specific target bacteria, and designing the specific dsRNA or small RNA to silence a specific target gene would be routine. Applicant provided a list of well-known essential genes or virulence factors on pages 22-31 of the instant specification, therefore, one of ordinary skill in the art would have believed the Applicants were in possession of the entire scope of the claimed invention.
This is not found persuasive because Hybritech, Inc. V. Monoclonal Antibodies, Inc. pertains to antibodies rather than small RNAs, and therefore does not correlate to the present invention. It is acknowledged that bacterial genes are known in the prior art and methods of making siRNA are also known in the prior art. However, knowledge of bacterial gene(s) and methods of making siRNA does not put the applicant in possession of siRNA or miRNA having the desired biological activity. As evidenced by Huang et al. (Nature Biotechnology, Vol. 31 No. 4, Published 10 March 2013, pages 350-356), siRNA design algorithms are imperfect, and identifying potent siRNAs often requires testing several sequences, which can be time consuming and costly (page 352). Huang et al. was cited to address applicant’s arguments that methods of making siRNA provides written support for the claimed invention. See also Amgen Inc. v. Sanofi, 872 F.3d 1367, 1378, 124 USPQ2d 1354, 1361 (Fed. Cir. 2017) recited in MPEP 2163(II)(3)(a). In addition, applicant appears to be making an enablement argument in that there is information available to design and make small RNAs specific for any target bacterial gene, however this rejection is under 112 Written Description and not enablement.
In addition, MPEP 2163(II)(A)3(a) states:
An adequate written description of a chemical invention also requires a precise definition, such as by structure, formula, chemical name, or physical properties, and not merely a wish or plan for obtaining the chemical invention claimed. See, e.g., Univ. of Rochester v. G.D. Searle & Co., 358 F.3d 916, 927, 69 USPQ2d 1886, 1894-95 (Fed. Cir. 2004) (The patent at issue claimed a method of selectively inhibiting PGHS-2 activity by administering a non-steroidal compound that selectively inhibits activity of the PGHS-2 gene product, however the patent did not disclose any compounds that can be used in the claimed methods. While there was a description of assays for screening compounds to identify those that inhibit the expression or activity of the PGHS-2 gene product, there was no disclosure of which peptides, polynucleotides, and small organic molecules selectively inhibit PGHS-2. The court held that "[w]ithout such disclosure, the claimed methods cannot be said to have been described."…
Without disclosure of which siRNAs and miRNAs perform the claimed function, the claimed methods do not have adequate written description. The sequences of the long dsRNA or the names of genes that may be the basis for the dsRNA do not provide an adequate description and representation of the structure of the genus of siRNA and miRNA. With the lack of the siRNA sequences produced by the dsRNA constructs disclosed in the specification, the skilled artisan would have to further experiment with the RNA produced by the dsRNA in the bacterial cell and determine which RNA is considered siRNA or miRNA having a size from 15 to 30 base pairs and then would have to sequence these sequences and determine if they have the desired biological activity.
Regarding applicant’s argument about the discovery of Andrew Fire and Craig Mello, the discovery was to dsRNA comprising a sequence that is complementary to a target gene having several hundred nucleotides rather than siRNA or miRNA having 15-30 nucleotides in length.
MPEP 2163 IIA3(a) states:
For example, disclosure of an antigen fully characterized by its structure, formula, chemical name, physical properties, or deposit in a public depository does not, without more, provide an adequate written description of an antibody claimed by its binding affinity to that antigen, even when preparation of such an antibody is routine and conventional. See Amgen Inc. v. Sanofi, 872 F.3d 1367, 1378, 124 USPQ2d 1354, 1361 (Fed. Cir. 2017)("knowledge of the chemical structure of an antigen [does not give] the required kind of structure-identifying information about the corresponding antibodies"); see also Centocor Ortho Biotech, Inc. v. Abbott Labs., 636 F.3d 1341, 1351-52, 97 USPQ2d 1870, 1877 (Fed. Cir. 2011)(patent disclosed the antigen the claimed antibody was supposed to bind, but did not disclose any antibodies with the specific claimed properties).
Therefore, the disclosure of the well-known gene sequences is likened to the disclosure of a fully-characterized antigen, which does not provide adequate written description of an antibody claimed by its binding affinity to that antigen, even when preparation of such an antibody is routine and conventional. The disclosure of nucleotide sequences or known virulence genes or an essential gene or an antibacterial resistance gene in said bacterium in the prior art or methods of making siRNA known in the prior art does not provide written description of the siRNAs and miRNAs that may be prepared from the dsRNA constructs, even if such preparation of siRNA is known in the art and routine and conventional. With respect to miRNA inhibiting expression of a target Gram-negative bacterial gene, a search of the prior art indicates that there are no known miRNA that have structure and function embraced by the claimed invention. The specification does not describe any miRNA which inhibit specifically the expression of the target bacterial gene. The fact that the discovery of RNA interference, miRNA and amiRNA technology occurred long ago does not necessarily support that the specification or state of the art provides adequate written description for the structure of the siRNA or miRNAs that perform the recited function. The prior art and the instant disclosure do not appear to teach miRNA inhibiting specifically the expression of a target Gram-negative bacterial gene were well known in the prior art. “Though bacteria do not possess miRNAs per se, many species do produce small RNAs (sRNAs) that are similar to miRNAs in their ability to regulate gene expression through antisense basepairing.” See page 48 of Cardin et al. (Bioinformatics in MicroRNA Research, Methods in Molecular Biology, Vol. 1617:39-53, 2017) cited on an IDS filed on 10/23/24 (after the mailing of the non-final rejection). “SRNAs also differ from miRNAs in that their size varies from -50 to 450 nucleotides (nts), whereas miRNAs are roughly 22-25 nts long (page 48).”
Applicant cites MPEP 2163.02 on page 12, and that the term small RNA is self-explanatory, and one of ordinary skill in the art knows what this means and what their structure is, and that the definition provided in the specification is consistent with the meaning of the term in the art (Specification p. 15) and that the claims are limited to small RNAs of 15-30 base pairs and therefore there is no need for applicants to provide any additional structure in the specification.
This is not found persuasive, because while the term small RNA may be known in the art, and the claims are directed to having a size of from 15-30 base pairs, the siRNAs and miRNAs recited in the claims encompass millions of possible siRNA and miRNA sequences that target different regions of any Gram-negative bacterial gene which is a virulence factor, essential gene, or antibacterial resistance gene.
Applicant argues possession by reduction to practice on pages 12-13, and that the specification provides examples whereby exogenously provided small RNAs were shown to cause reduction in expression of several target bacterial cell genes (Figure 10), as well as a proof-of-concept experiment demonstrating in vitro synthesized anti-Cfa6 and anti-HrpL siRNAs triggered bacterial gene silencing and suppression of Pto DC3000-induced stomatal reopening (Figure 10B/C, Figure 6A), as well as in vitro synthesized anti-fusA and anti-gyrB siRNAs possess a strong bactericidal effect (Figure 10D/E and specification page 57). Applicant argues on page 13 that the nucleic acids used to generate the synthetic siRNAs were clearly described, and applicants provide the sequences for a variety of dsRNAs used to prepare the siRNA. Applicant argues that one of ordinary skill in the art is well familiarized with multiple other methods of easily preparing siRNA against any number of genes and does not need further instruction from the specification on how to do so.
This is not found persuasive based on MPEP 2163 IIA3(a) and case law Eli Lilly and Amgen Inc. v. Sanofi, previously cited above. There is no correlation between the structure or common nucleotides and the function of the recited siRNA or miRNA. As previously stated, the claimed genus of siRNA and miRNA encompasses substantial variation and millions of possible siRNA or miRNA sequences and the specification does not describe a sufficient variety of species to reflect the variation within the genus. The sequences of the long dsRNA or the names of genes that may be the basis for the dsRNA do not provide an adequate description and representation of the structure of the genus of siRNA and miRNA.
Applicant argues on page 14 that the written description support for the dsRNA sequences is enough because siRNAs can be easily obtained by RNAase III digestion of dsRNAs and is of routine skill for ordinary artisans without isolating the resulting siRNAs to obtain their sequence, and that the product will be a small RNA duplex of the claimed size that will work to interfere with expression of the sequence-complementary mRNA targets against which the dsRNA was designed. Applicant argues it is not reasonable to conclude that the disclosure’s dsRNA sequences for producing siRNAs is not sufficient to provide written description. Applicant cites case law Ariad Pharms., Inc. v. Eli Lilly and Co. on page 14 and that functional claim language can meet the written description requirement when the art has established a correlation between structure and function. Applicant argues the art has established correlation between structure and function, and numerous publications and cites a review article by Rana, TM. Applicant argues on page 15 that the numerous examples of species of nucleic acids that easily produce small RNAs of the claimed length of 15-30 bases is clearly sufficient written description support for the claims, and one cannot reasonable expect the applicants to provide sequences of all 5000 or so genes of P. aeruginosa genome in the specification, or the sequences of other bacterial genes and the sequences of all small RNA capable of targeting those genes. Applicant argues those genome sequences are well-described in the art and easily accessible, and the invention is not the individual sequences but the use of the direct extracellular small RNA to change gene expression in bacteria. Applicant cites MPEP 2163(II)(A)(2). Applicant argues that one does not need to envision the sequence to know it is a small RNA of 15-30 bp and the structure is most relevant which has been provided by the applicant which is that the RNA sequences are 15-30 base pairs in length and easily designed based on the known sequences of the target gene.
This is not found persuasive based on MPEP 2163 IIA3(a) and case law Eli Lilly and Amgen Inc. v. Sanofi, previously cited above. Therefore, while function may have adequate written support, there is no correlation between the structure or common nucleotides and the function of the recited siRNA or miRNA, and therefore lack of written description. As stated previously, the sequences of the long dsRNA that is used to generate the chimeric hairpin constructs do not share a common nucleotide sequence (one sequence of a siRNA or a miRNA having 15 to 30 nucleotides in length) with a genus of Gram-negative bacterial genes and do not provide an adequate description and representation of the structure of the genus of siRNA and miRNA. As no siRNA sequences produced by the dsRNA constructs are disclosed in the specification, the skilled artisan would have to further experiment with the RNA produced by the dsRNA in the bacterial cell and determine which RNA is considered siRNA or miRNA having a size from 15 to 30 base pairs and then would have to sequence these sequences and determine if they have the desired biological activity.
The office agrees it is not reasonable to expect applicants to provide sequences for all of the genes of P. aeruginosa and sequences of other bacterial genes and the sequences of all small RNAs capable of targeting those genes, however, there are no sequences of any small RNAs provided at all to support that the claimed invention has adequate written description or to show the core sequence of nucleotides that performs the recited function.
Applicant cites case law In Re Rasmussen on page 15-16, and that this case is the same situation in that one would not need to be provided the exact sequence of each siRNA in the specification to understand the inventor was in possession of the claimed invention. Applicant cites the applicant would need only do so with “reasonably clarity” per MPEP 2163.02.
This is not found persuasive, because In Re Rasmussen is cited in MPEP 2163.05 regarding changes to the scope of claims, and is mentioned under I. B. Addition of Generic Claim, and as a situation where one species adequately supports a genus. In Re Rasmussen pertains to “a single method of adheringly applying one layer to another was sufficient to support a generic claim to adheringly applying because one skilled in the art reading the specification would understand that it is unimportant how the layers are adhered, so long as they are adhered”. This case law does not pertain to any chemical subject matter and therefore does not correlate to the present subject matter.
Applicant cites case law Capon v. Eshhar which is cited in MPEP, on pages 16-17, and provides claim 1 from Capon. Applicant argues in Capon, it was not necessary for the Applicant to describe the nucleic acid sequences of either components A or B in the claims or specification because numerous examples of nucleic acid sequences for the components A and B were known in the art, albeit separately, and therefore it has been interpreted that known nucleotide sequences need not be disclosed in the specification to support written description. Applicant cites the acknowledgement of this principle in Juno Therapeutics, Inc. V. Kite Pharma, Inc.
This is not found persuasive because the claim referenced in Capon is a chimeric gene encoding an scFv of an antibody and a gene encoding another protein, and does not pertain to small RNAs and therefore they do not correlate in subject matter.
Applicant concludes and summarizes their arguments on pages 17-18 that given the state of the art and common knowledge of nucleic acid sequence of the genome of a large number of bacterial species, applicant does not need to provide the sequences of the small RNAs within the scope of the claims to satisfy the written description requirement and the claimed invention is not the small RNAs themselves, but rather the discovery of the direct expression of bacterial cells to extracellular small RNAs, or embedded plant EVs, against a specific target gene in the bacterial cell is sufficient to modify function/expression of that gene in bacterial cells. Applicant agues the specification provides numerous examples that this methods works and one of ordinary skill would conclude the patentee was in possession of the invention.
For all of the reasons stated previously that are supported by MPEP 2163IIA3(a) and the case law cited by the office above, the examiner maintains the written description rejection of claims 35-37 and 44-49. The claimed genus of siRNA and miRNA encompasses substantial variation and millions of possible siRNA or miRNA sequences, and the specification does not describe a sufficient variety of species to reflect the variation within the genus. There is no essential nucleotide sequence(s) to represent the genus of siRNA or miRNA molecules and no structure-function correlation has been provided by the instant specification to show applicant was in possession of the claimed invention. The specification has provided no structure or sequences of the siRNAs and miRNAs having a size of from 15-30 base pairs in length that perform the function of inhibiting a gene encoding a virulence factor, essential gene or antibacterial resistance gene.
Improper Markush Rejection
Claims 35 is and claims 44 and 47 remain rejected on the basis that it contains an improper Markush grouping of alternatives. See In re Harnisch, 631 F.2d 716, 721-22 (CCPA 1980) and Ex parte Hozumi, 3 USPQ2d 1059, 1060 (Bd. Pat. App. & Int. 1984). A Markush grouping is proper if the alternatives defined by the Markush group (i.e., alternatives from which a selection is to be made in the context of a combination or process, or alternative chemical compounds as a whole) share a “single structural similarity” and a common use. A Markush grouping meets these requirements in two situations. First, a Markush grouping is proper if the alternatives are all members of the same recognized physical or chemical class or the same art-recognized class, and are disclosed in the specification or known in the art to be functionally equivalent and have a common use. Second, where a Markush grouping describes alternative chemical compounds, whether by words or chemical formulas, and the alternatives do not belong to a recognized class as set forth above, the members of the Markush grouping may be considered to share a “single structural similarity” and common use where the alternatives share both a substantial structural feature and a common use that flows from the substantial structural feature. See MPEP § 2117.
The Markush grouping of “wherein said siRNA or miRNA inhibits at least one gene encoding a virulence factor or an essential gene or an antibacterial resistance gene if said bacterium is pathogenic” in claims 35 and 44, and “a long dsRNA molecule targeting specifically at least one virulence bacterial gene or at least one essential bacterial gene or at least one antibacterial resistance gene” in claim 47 is improper because the alternatives defined by the Markush grouping do not share both a single structural similarity and a common use for the following reasons: each siRNA, miRNA or long dsRNA molecule targeting at least one virulence bacterial gene or at least one essential bacterial gene or at least one antibacterial resistance gene, does not share a single structural similarity or a common use because each would have a different nucleotide sequence because each would target a different nucleotide sequence encoding a protein having a different function.
To overcome this rejection, Applicant may set forth each alternative (or grouping of patentably indistinct alternatives) within an improper Markush grouping in a series of independent or dependent claims and/or present convincing arguments that the group members recited in the alternative within a single claim in fact share a single structural similarity as well as a common use.
Response to Arguments
Applicant's arguments filed 10/23/2024 have been fully considered but they are not persuasive.
Applicant argues on page 19 that the office admits a Markush group is proper “where a Markush grouping describes alternative chemical compounds, whether by words or chemical formulas, and the alternatives do not belong to a recognized class as set above, the members of the Markush grouping may be considered to share a single structural similarity and common use where the alternatives share both a substantial structural feature and a common use that flows from the substantial structural feature. See MPEP 2117” and office action page 12. Applicant argues that this is the scenario here, but only provides an argument in regards to claim 47. Applicant argues that in claim 47, all members of the Markush group have in common that they are all targeted after processing of dsRNA into small RNA, and what is transfected is the dsRNA and that has the same structure and serves the same purpose regardless of the target.
This is not found persuasive, because small RNA target genes with different functions and each of the genes would have a different nucleotide sequence. Each small RNA would have a completely different nucleotide sequence and function based on the specific virulence bacterial gene, essential bacterial gene, or antibacterial resistance gene that it targets, and these genes have different functions. While the siRNA and miRNA have a size length of 15 to 30 nucleotides in length, this is not a “substantial structural feature and a common use that flows from the substantial structural feature” because each siRNA or miRNA has a different function and structure (nucleotide sequence). The siRNA or miRNA would have a different structure (nucleotide sequence) that would target a different gene with a different function. Therefore, the examiner maintains the improper Markush rejection of claim 47.
Applicant argues on page 19, that claim 44 has been canceled, rendering the rejection moot with respect to claim 44, however claim 44 is not listed as being canceled and is a currently pending claim. Applicant does not provide any specific arguments regarding the improper Markush rejection of claim 44 which is not canceled, and the same limitations of claim 44 are now in amended claim 35. Therefore, claim 35 is rejected and claim 44 remains rejected under Improper Markush.
Claim Rejections - 35 USC § 103
The text of those sections of Title 35, U.S. Code not included in this action can be found in a prior Office action.
Claims 35,36 and 44-49 are rejected under 35 U.S.C. 103 as being unpatentable over WO 2006/046148, hereinafter referred to as “‘148”, cited on an IDS.
Claim Interpretation: Claim 35 recites “the step of contacting said target Gram-negative bacterium extracellularly with at least one of an siRNA and a miRNA inhibiting specifically the expression of a target Gram-negative bacterial gene” in lines 2-4 and “wherein said target Gram-negative bacterium is contacted directly extracellularly with said siRNA or miRNA, wherein said siRNA or miRNA inhibits at least one gene…” in lines 5-7. Given the amendment reciting “said siRNA or miRNA” in lines 6 and 7, the examiner is interpreting “the step of contacting said target Gram-negative bacterium extracellularly with at least one of an siRNA and a miRNA” in lines 2-4 as either siRNA or miRNA and not requiring contacting with both siRNA and miRNA. Regarding that the target Gram-negative bacterium is contacted directly extracellularly, the specification discloses the small RNAs can be formulated in phytosanitary compositions, e.g., into sprayable liquid compositions (see below). In this case, the said compositions containing the said small RNAs can be administered directly to plant tissues or to bacteria (page 15, lines 23-25). Therefore, any direct contact on the extracellular surface of the Gram-negative bacterium with the said siRNA or miRNA would read on contacting directly extracellularly, such as the siRNA or miRNA being present on a surface and coming into contact with the bacterium directly, or being applied directly to the extracellular surface of the bacterium.
Regarding claims 35 and 36, the broadest reasonable interpretation of the siRNA or miRNA used in the method is exposing a bacterial cell to at least one siRNA or miRNA, wherein said siRNA or miRNA comprising a size of from 15-30 base pairs. The term ‘at least one of an siRNA’, the siRNA can be part of a larger dsRNA sequence. The prior art make obvious at least one siRNA or miRNA having a size of from 15-30 base pairs.
Regarding claim 35, ‘148 teaches double-stranded RNA mediated gene silencing, useful in dsRNA mediated plant pest control (Field of the Invention, page 1), including siRNA (pages 2-9) and that the target species may be bacteria (page 27, lines 33-35). Regarding the target Gram-negative bacterium in claims 35 and 36, ‘148 teaches that the bacteria that can be controlled with the constructs include Pseudomonas ssp. (pages 27-28), which are phytopathogenic bacterium. ‘148 teaches concatemer constructs with the length of each of the dsRNA fragments of at least 17-25 bp or more (page 6, lines 17-19). Regarding the step recited in claim 35 “wherein said target Gram-negative bacterium is contacted directly extracellular with said siRNA or miRNA”, ‘148 teaches that the pest cell or pest species may be contacted with the dsRNA (page 7, lines 13-14) and teaches a method o