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 .
Claim Status
Claims 1-3, 5, 6, and 8-20 are pending. Claims 4 and 7 are canceled. Claims 1-3, 5, 6, and 8-20 are examined on the merits.
Response to Amendment
The objection to claim 9 is withdrawn because claim 9 has been amended.
The rejection of Claims 1, 2, 4, and 8-13 under 35 U.S.C. 112(b) is withdrawn in view of the amendment and cancellation of claim 4.
The rejection of claim 12 under 35 U.S.C. 112(a) for lack of written description is maintained but modified in view of the amendment.
The rejection of claims 1-4, 6, 8-13, 15, and 16 under 35 U.S.C. 112(a) for lack of enablement is maintained but modified in view of the amendment.
The rejection of claims 3, 6, and 14 under 35 U.S.C. 102 (a) (1) over Mullineaux is withdrawn in view of the amendment. However, Mullineaux remains relied upon as prior art in the rejection under 35 U.S.C. 103, as set forth below.
The rejection of claims 1, 2, 5, 8-11, 13, 15-17, and 20 under 35 U.S.C. 103 over Mullineaux in view of Li is maintained but modified in view of the amendment. Claims 4 and 7 are canceled.
The rejection of claims 12, 18, and 19 under 35 U.S.C. 103 over Mullineaux in view of Li and further in view of Crocco is maintained but modified in view of the amendment.
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.
Written Descriptions
Claim 12 is 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 application of 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.
Claim 12 regards a corn plant comprising an edit in an endogenous BBX gene and further requires the functional limitation that the corn plant has an “attenuated Shade Avoidance Response compared to a control corn plant that is devoid of the edit”. Claim 12 depends from claims 11 and 8, where claim 8 broadly defines the endogenous BBX gene as a BBX10(DBB4) gene or DBB6 gene comprising sequence having at least 80% sequence identity to SEQ ID NO:70 or SEQ ID NO:73, encoding polypeptides having at least 90% sequence identity to SEQ ID NO:71 or SEQ ID NO:74, and encoding a region having at least 90% sequence identity to SEQ ID NO: 83-85.
“shad avoidance response” (SRS) refers to a plant response to reduced light quality or quantity in which plants elongate and alter development to compete for light resources (instant specification, paragraph 0004). The claim therefore encompasses a genus of edited corn plants comprising edits within identity-defined BBX10(DBB4)/DBB6 genes, wherein the edited plants exhibit the recited attenuated shade avoidance phenotype.
The specification only provides phenotype measurements for a limited subset of embodiments. In particular, the disclosure describes a specific shade avoidance assay (Example 3) and reports results for particular edited maize alleles generated using the disclosed guide spacers PWsp2100 (SEQ ID NO:86) and PWsp2101 (SEQ ID NO:87), with sheath height measurements reported for those specific alleles/genotypes combinations under control and shade conditions (Example 4, Tables 5-6, paragraph 0344-0351). However, claim 12 is not limited to those particular guide spacers, edited alleles, mutation types, or genotype combinations. The specification therefore discloses only a limited number of representative species relative to the broader identity-defined genus now claimed.
The lack of possession is further underscored because BBX proteins are zinc-finger transcription factors in which B-box domain integrity can be determinative of biological function. For example, mutation of conserved residues within a B-box domain can abolish or materially alter BBX activity. Saura-Sánchez (Maite Saura-Sánchez, et. al., Plant Cell Physiol. 64(5): 474–485 (2023)) describes BBX24 as a transcription factor involved in shade avoidance response in Arabidopsis, where mutant line bbx24-1 exhibits altered SAR phenotypes (page 476, right column, paragraph 2). Likewise, Xu (Dongqing Xu, et. al., Plant Physiology , March 2018, Vol. 176, pp. 2365–2375) report that BBX21 mutant line bbx21-1 exhibits altered phenotypes associated with BBX functional disruption (fig 2, page 2368). These references demonstrate that relatively small sequence variations within BBX proteins can materially alter biological activity and phenotype. Accordingly, sequence identity alone does not establish that all edits within the claimed ≥80%/≥90% identity-defined BBX10(DBB4)/DBB6 genus will produce the claimed attenuated Shade Avoidance Response phenotype.
In addition, BBX family members exhibit divergent expression patterns and functional divergence even among closely related BBX genes. Wu (Zilin Wu, et. al., BMC Genomics (2023) 24:79) identify BBX duplication-related pairs sharing greater than 80% similarity (page 3, left column, paragraph 1; page 9, fig 5), yet report substantially different expression patterns and transcriptional responses among those BBX gene under low-nitrogen stress conditions (page 13, left column paragraph 2-3). Such evidence further demonstrates that BBX genes sharing high sequence similarity may nevertheless exhibit materially different regulation and biological function. Therefore, the specification does not provide sufficient representative species or identify structural features common to the full scope of edited BBX10(DBB4)/CB6 genes that correlate with the claimed attenuated Shade Avoidance Response phenotype.
Accordingly, the specification does not reasonably convey possession of the full scope of claim 12.
Scope of Enablement
Claims 1, 3, 8, 11-12, 14-16, and 18-19 are rejected under 35 U.S.C. 112(a) or 35 U.S.C. 112 (pre-AIA ), first paragraph, because the specifications, while being enabling for editing the corn BBX10(DBB4) and DBB6 gene targets suing the disclosed CRISPR-Cas guide spacers PWsp2100 (SEQ ID NO:86) and PWsp2101 (SEQ ID NO:87) does not reasonably provide enablement for the full scope of the claimed invention, which encompasses guide nucleic acids and editing systems targeting endogenous BBX10(DBB4) or DBB6 genes defined by at least 80% nucleotide sequence identity to SEQ IN NO: 70 or SEQ ID NO:73, at least 90% amino acid sequence identity to SEQ ID NO:71 or SEQ ID NO: 74 and target regions having at least 90% amino acid sequence identity to SEQ ID NO: 83-85. The specification does not enable any person skilled in the art to which it pertains, or with which it is most nearly connected, to make and/or use the invention commensurate in scope with these claims.
An “analysis of whether a particular claim is supported by the disclosure in an application requires a determination of whether that disclosure, when filed, contained sufficient information regarding the subject matter of the claims as to enable one skilled in the pertinent art to make and use the claimed invention.” MPEP 2164.01. “A conclusion of lack of enablement means that. . . the specification, at the time the application was filed, would not have taught one skilled in the art how to make and/or use the full scope of the claimed invention [i.e. commensurate scope] without undue experimentation.” In re Wright, 999 F.2d 1557,1562, 27 USPQ2d 1510, 1513 (Fed. Cir. 1993); MPEP 2164.01.
In In re Wands, 858 F.2d 731,8 USPQ2d 1400 (Fed. Cir. 1988), several factors implicated in determination of whether a disclosure satisfies the enablement requirement and whether any necessary experimentation is “undue” are identified. These factors include, but are not limited to:
(A) The breadth of the claims;
(B) The nature of the invention;
(C) The state of the prior art;
(D) The level of one of ordinary skill;
(E) The level of predictability in the art;
(F) The amount of direction provided by the inventor;
(G) The existence of working examples; and
(H) The quantity of experimentation needed to make or use the invention based on the content of the disclosure. In re Wands, 858 F.2d 731,737, 8 USPQ2d 1400, 1404 (Fed. Cir. 1988). No single factor is independently determinative of enablement; rather “[i]t is improper to conclude that a disclosure is not enabling based on an analysis of only one of the above factors while ignoring one or more of the others.” MPEP 2164.01. Likewise, all factors may not be relevant to the enablement analysis of any individual claim.
Claims 1, 3, 8, and 14-16 recites guide nucleic acids, a gene editing systems, and editing methods directed to an endogenous BBX gene, wherein the BBX gene is a BBX10(DBB4) gene or a DBB6 gene and is further defined by sequence identity to SEQ ID NO:70 or SEQ ID NO: 73, SEQ ID NO: 71 or SEQ ID NO: 74, and/or SEQ ID NO: 83-85. Dependent claims 11, 12, 18, and 19 further require regenerated plants, progeny plants, or selection based on reduced /attenuated shade avoidance response.
The specification provides working examples for particular maize BBX10(DBB4) and DBB6 targets using the disclosed guide spacers PWsp2100 (SEQ ID NO:86) and PWsp2101 (SEQ ID NO:87). Those examples may enable the specific disclosed guide-target combinations and the particular edited maize alleles tested in the specification. However, the independent claims are not limited to those exact guide-target combinations, edited alleles, mutation types, or genotype backgrounds. Rather, the claims continue to encompass guide nucleic acids and editing systems that bind to target sites within identity-defined BBX10(DBB4)/DBB6 genes and regions.
For embodiments outside the specific disclosed guide-target combinations, a person of ordinary skill in the art would need to identify candidate BBX10(DBB4)/DBB6 sequence variants withing the claimed identity scope, locate suitable PAM-adjacent target sites, design guide spacers, evaluate guide binding and cleavage efficiency, confirm locus specificity, recover edited plant cells or plants, and validate the resulting edited genotype and phenotype. For claims requiring reduced or attenuated shade avoidance response, the artisan would also need to test whether ethe particular edit actually produces the claimed shade avoidance phenotype.
The need for this experimentation is not merely routine confirmation. Guide-target performance depends on the exact target sequence, PAM presence, mismatch position and tolerance, chromosomal context, and plant transformation/editing conditions. Small sequence differences within the claimed identity-defined BBX10(DBB4).DBB6 scope may materially affect guide binding, cleavage efficiency, specificity, and editing outcome. The specification does not provide a predictive roadmap for selecting target sites across the full identity-defined scope or for determining which edits within BBX10(DBB4)/DBB6 will produce the claimed reduced or attenuated shade avoidance response.
Accordingly, although the specification provide examples of particular maize BBX10(DBB4)/DBB6 edits, the number and diversity of working examples are not commensurate with the breadth of the claims. Practicing the full scope of the claimed invention would require extensive iterative guide design, target-site testing, editing validation, plant regeneration, and phenotype screening.
Applicant’s major 112(a) written description arguments and response:
Argument 1: the amendments narrow claim 12 to corn and to BBX10(DBB4)/DBB6, so the WD rejection should be withdrawn.
Applicant’s argument has been considered but is not persuasive. Although the claims have been narrowed to corn and BBX10(DBB4)/DBB6 genes, claim 12 still broadly recites a corn plant comprising an edit in its endogenous BBX gene and having an attenuated Shade Avoidance Response. The claim is not limited to the specific guide spacers, edited alleles, mutation types, or genotype combinations actually tested in the specification. Therefore, the amended claim remains broader than the disclosed embodiments.
Argument 2: The claims provide sufficient structure because BBX10(DBB$) and DBB6 are defined by SEQ ID NOs and sequence identity.
This argument is not persuasive because sequence identity alone does not establish possession of the full functional genus. The specification does not identify structural features common to the claimed BBX10(DBB4)/DBB6 edits that distinguish edits producing attenuated Shade Avoidance Response from edits that would not. Thus, the claims recite a structural genus plus a functional results, but the specification does not provide a sufficient structure-function correlation across the full scope.
Argument 3: Example 4 shows that mutation of BBX10(DBB4)/DBB6 in corn results in attenuated SAR.
Example 4 supports the specific tested embodiments, but it does not support the full scope of claim 12. The example reports results for particular edited maize alleles generated using specific guide spacers and tested in specific genotype combinations. Claim 12 is not limited to those embodiments and therefore still lacks representative species across the full claimed genus.
Argument 4: Enzo supports written description because structure plus function can show possession.
Applicant’s reliance on Enzo is not persuasive. Enzo requires sufficiently detailed identifying characteristics showing possession. Here, the specification does not provide enough representative examples or a disclosed correlation between the claimed sequence-identity-defined BBX edits and the functional phenotype of attenuated Shade Avoidance Response. Therefore, the disclosure does not reasonably convey possession of the full scope of claim 12.
Applicant’s major 112(a) enablement arguments and response:
Argument 1: The claims are now narrowed to BBX10(DBB4)/DBB6 in corn, so the enablement rejection should be withdrawn.
Applicant’s argument has been considered but is not persuasive. The amendments narrow the claims, but the claims still encompass guide nucleic acids and editing systems targeting identity-defined BBX10(DBB4)/DBB6 gene and regions beyond the specific disclosed guide-target combinations. The specification may enable the specific examples, but not the full amended claim scope.
Argument 2: example is shows PWsp2100 and PWsp2101 successfully edited both BBX10(DBB4) and DBB6.
Example 1 demonstrates successful editing for the disclosed guide spacers and target sites. However, independent claims 1, 3, 8, and 14 are not limited to PWsp2100 and PWsp2101. For other guide-target combinations within the claimed identity-defined scope, a skilled artisan would still need to identity target sites, confirm PAM compatibility, design guides, test cleavage, and validate edits.
Argument 3: CRISPR methods were known and routine.
General knowledge of CRISPR does not enable the full scope of these claims. The issue is not whether CRSIPR editing was generally known, but whether the specification enables the full claimed genus of BBX10(DBB4)/DBB6 guide-target/edit combinations and the resulting phenotypes. Guide performance depends on exact target sequence, PAM availability, mismatch tolerance, genomic context, and editing outcome.
Argument 4: Working examples plus high skill in the art are enough under Wands.
The working examples are not commensurate with the claim breadth. The specification provides limited examples using specific guides and specific maize target sequences, but the claims cover broader identity-defined BBX10(DBB4)/DBB6 genes and regions. Practicing the full scope would require iterative guide design, screening, editing validation, plant regeneration, and phenotype testing. Under the Wands factors, the breadth of the claims, limited guidance, limited representative examples, and unpredictability support lack of enablement.
Argument 5: The amended claims define the genes by sequence identity, so a POSITA could identify covered genes.
Identifying a sequence within the claimed identity range is not the same as practicing the claimed invention. The skilled artisan must also select a workable target site, design and effective guide, achieve site-specific editing, recover edited plants, and, for phenotype claims, confirm reduced or attenuated Shade Avoidance Response the specification does not provide predictive guidance sufficient to do this across the full scope without undue experimentation.
Claim Rejections - 35 USC § 103
The following is a quotation of 35 U.S.C. 103 which forms the basis for all obviousness rejections set forth in this Office action:
A patent for a claimed invention may not be obtained, notwithstanding that the claimed invention is not identically disclosed as set forth in section 102, if the differences between the claimed invention and the prior art are such that the claimed invention as a whole would have been obvious before the effective filing date of the claimed invention to a person having ordinary skill in the art to which the claimed invention pertains. Patentability shall not be negated by the manner in which the invention was made.
Claims 1-3, 5-6, 8-11, 13-17 and 20 are rejected under 35 U.S.C. §103 as being unpatentable over Mullineaux (WO2022129856A1, filed 2021-11-18, published 2022-06-23) as applied claim 3 and 14, in view of Li (Li, Wenlan et al. Functional & integrative genomics 17.6, pp: 653-666, 2017).
The rejection is applied to the claimed BBX10(DBB4) alternative. The DBB6 alternative is not relied upon for this rejection.
Claim 1 is drawn to a guide nucleic acid that binds to a target site within an endogenous B-BOX(BBX) gene, comprising a sequence having at least 80% sequence identity to SEQ ID NO: 70 or SEQ ID NO:73; at least 90% sequence identity to the amino acid sequence of SEQ ID NO:71 or SEQ ID NO:74; and the target site least 90% sequence identity to any one of SEQ ID NOs:83-85, wherein the BBX gene is a BBXl0 (DBB4) gene or a DBB6 gene.
Mullineaux teaches guide nucleic acids used in CRISPR-Cas editing systems, wherein the guide nucleic acid comprises a spacer sequence that binds to at target site within an endogenous BBX gene encoding a BBX transcription factor (claim 9, and 11, and p29, line 15-30). Mullineaux further teaches using the guide nucleic acid to target and modify an endogenous BBX gene in a plant (claim 21 and 22, p29, line 15-30).
Mullineaux does not expressly teach that the endogenous BBX gene is a corn BBX10(DBB4) gene having the claimed sequence identity to SEQ ID NO: 70 and encoding a polypeptide having the claimed sequence identity to SEQ ID NO:71.
Li teaches ZmDBB4 gene as GRM2M2G019335 (Chr4: 137141449-137142700 (-)). The instant application identifies DBB4/BBX10 as Zm00001d051018 (Zm00001d051018 Chr4: 137141449-137142700 (-)) (paragraph 0344), with SEQ ID NO: 69, 70, and 71 as genomic sequence, cDNA sequence and polypeptide sequence. Therefore, Li teaches the same gene as claimed DBB4/BBX10 (alignment below).
It would have been obvious to one of ordinary skill in the art to apply the CRISPR-Cas BBX editing system of Mullineaux to the maize BBX10(DBB4) gene taught by Li, because Mullineaux teaches targeted genome editing of BBX transcription factor genes, and Li identifies maize BBX10(DBB4) as maize BBX/DBB transcription factor genes. A person of ordinary skill would have had a reasonable expectation of success because CRISPR-Cas guide nucleic acids are designed based on sequence complementarity to a selected genomic target site.
Accordingly, claim 1 is prima facie obvious over Mullineaux in view of Li.
Claim 2 is drawn to the guide nucleic acid of claim 1, , wherein the guide nucleic acid comprises a spacer having the nucleotide sequence of SEQ ID NO:86 or SEQ ID NO:87.
Regarding claim 2, Mullineaux in view of Li teaches the limitations of claim 2 for the same reasons set forth with respect to claim1. It would have been obvious to one of ordinary skill in the art to selecta a spacer sequence complementary to a target site within the maize BBX10(DBB4) gene taught by Li, including the spacer sequences recited in claim 2, in order to direct site-specific CRISPR-Cas cleavage of the selected BBX10(DBB4) target site. SEQ ID NO:86 matching a segment within the cDNA of ZmDBB4 (GRMZM2G019335) (below). Therefore, claim 2 is prima facie obvious.
Claim 3 recites a gene editing system comprising a CRISPR-Cas effector protein in association with a guide nucleic acid, wherein the guide nucleic acid comprises a spacer sequence that binds to a B-BOX (BBX) gene, wherein the BBX gene is a BBX10 (DBB4) gene or a DBB6gene and wherein the BBX gene comprises a sequence having at least 80% sequence identity to the nucleotide sequence of SEQ ID NO:70 or SEQ ID NO:73 and encodes a polypeptide comprising a sequence having at least 90% sequence identity to the amino acid sequence of SEQ ID NO:71 or SEQ ID NO:74.
Regarding claim 3, Mullineaux in view of Li teaches the limitations of claim 3 for the same reasons set forth with respect to claim 1. Claim 3 further recites a gene editing system comprising a CRISPR-Cas effector protein in association with the guide nucleic acid. Mullineaux teaches a CRISPR-Cas effector protein in association with a guide nucleic acid comprising a spacer sequence that binds to a BBX gene (p29, line 15-30). Therefore, claim 3 is prima facie obvious.
Claim 5 is drawn to the gene editing system of claim 3, wherein the guide nucleic acid comprises a spacer having SEQ ID NO:86 or SEQ ID NO:87.
Claim 5 is rejected for the same reasons set forth above with respect to claim 2 because claim 5 recites the same spacer sequence limitation, SEQ ID NO: 86 in the gene editing system of claim 3.
Claim 6 recites the gene editing system of claim 3, further comprising a tracr nucleic acid that associates with the guide nucleic acid and a CRISPR-Cas effector protein, optionally wherein the tracr nucleic acid and the guide nucleic acid are covalently linked.
Mullineaux discloses tracrRNA, CRISPR-Cas effector protein and sgRNA concepts directly (page 29, line 15-30). Accordingly claim 6 is obvious over Mullineaux and Li.
Under BRI, claim 8 can be interpreted broadly as a method of editing a site within a corn plant cell genome using a CRISPR-Cas system directed to an endogenous BBX10(DBB4) gene, where the guide nucleic acid binds a target site within the BBX gene and the CRISPR-Cas effector protein performs site-specific cleavage, thereby generating any edit int eh endogenous BBX gene.
Regarding claim 8, Mullineaux in view of Li teaches the limitations of claim 8 for the same reasons set forth with respect to claim 3. Claim 8 further recites introducing the gene editing system into a corn plant cell and site -specific cleavage of the endogenous BBX10(DBB4) gene, thereby generating an edit in the endogenous BBX gene of the corn plant cell. Mullineaux teaches CRISPR-Cas mediated site-specific cleavage and editing of endogenous BBX genes in plant cells (p29, line15-30). It would have been obvious to apply the BBX-targeted CRISPR-Cas editing system of Mullineaux to the maize BBX10(DBB4) gene taught by Li in a corn plant cell to generate and edit in the endogenous BBX gene. Therefore, claim 8 is prima facie obvious.
Claims 9, 10, 11, and 13 are drawn to a method depend on claim 8, wherein a spacer sequence comprises a nucleotide sequence of SEQ ID NO:86 or SEQ ID NO:87 (claim 9), wherein the edit results in a mutation in the B-BOX domain of the BBX transcription factor (claim 10), wherein the edit is located in a region of a B-BOX domain encoded by the endogenous BBX gene (claim 13), the method further comprising regenerating a corn plant from the plant cell comprising the edit in the endogenous BBX gene to produce a corn plant comprising the edit in its endogenous BBX gene (claim 11).
Mullineaux teaches “In certain embodiments, one or more mutations are introduced into a least one plant cell and the plant is regenerated from the at least one mutated plant cell” (page 35, line 4-5). Mullineaux further teaches that B-BOX DOMAIN CONTAINING PROTEIN32 (BBX32) is a negative regulator of photosynthetic capacity (page 2, line 20-35), abolishing the expression of at least one nucleic acid sequence encoding a B-Box Domain containing protein 32 (BBX32) polypeptide reducing or abolishing the activity of a BBX32 polypeptide in the plant (page 19, lime 19-36, page 20, line 1-8). Mullineaux teaches “plants comprise one or more mutations in BBX32” (claim 21 and 22).
Li teaches the two B-BOX domains in DBB4 gene (GRMZM2G019335), and teaches the important function of B-Box domain (page 653, introduction).
It would have been obvious to one of ordinary skill in the art to apply the BBX-targeted CRISPR-Cas editing system of Mullineaux to the maize DBB4 gene taught by Li and to target/mutate the B-BOX domain because Mullineaux teaches introducing mutations into BBX genes and regenerating plants from mutated plant cells, while Li teaches that the DBB4 gene contains two B-BOX domains and that B-BOX domains are important functional domains. A person of ordinary skill would have been motivated to target the B-BOX domain to reduced or alter BBX transcription factor activity. Therefore, claims 9, 10, 11, and 13 are prima facie obvious.
Claim 14 recites a method of generating variation in a plant BBX transcription factor, comprising contacting an endogenous BBX gene within a plant cell with a CRISPR-Cas editing system, wherein the system is targeted to a region of the gene that encodes the transcription factor, wherein the BBX gene is a BBX10(DBB4) or a DBB6 gene.
Mullineaux discloses a gene editing system(claim 9, 11, 12-14, 16, 18, 22, and page 29, line 15-30) to modify Arabidopsis BBX32 gene (a B-BOX transcription factor) through plant cell ( plant cell is plant part as claim 16 in Mullineaux). Accordingly claim 14 is anticipated with Mullineaux. Li teaches ZmDBB4 gene as GRM2M2G019335 (Chr4: 137141449-137142700 (-)). The instant application identifies DBB4/BBX10 as Zm00001d051018 (Zm00001d051018 Chr4: 137141449-137142700 (-)) (paragraph 0344), with SEQ ID NO: 69, 70, and 71 as genomic sequence, cDNA sequence and polypeptide sequence. Therefore, Li teaches the same gene as claimed DBB4/BBX10 (alignment below).
Therefore, claim 14 is rejected as being unpatentable over Mullineaux in view of Li for the same reasons set forth above with respect to claim 1.
Claims 15-17 are drawn to the method of claim 14, wherein the endogenous BBX gene comprises a nucleotide sequence having at least 80% identity to SEQ ID NO: 70 or SE ID NO: 73 and encodes an amino acid sequence having at least 90% sequence identity of SEQ ID NO: 71 or SEQ ID NO:74 (claim 15), wherein the targeted region encodes an amino acid sequence having at least 90% sequence identity to any one of SEQ ID NOs:83-85 (claim16), and wherein the variation is generated in a region of the BBX transcription factor comprising a B-BOX domain (claim 17).
The sequence-identity limitations recited in claims 15 and 16 correspond to the BBX10(DBB4) gene and target-region limitations addressed above with respect to claims 1, 8, and 14. The B-BOX domain limitations recited in claim 17 corresponds to the B-BOX domain limitations addressed above respect to claim 10 and 13. Therefore, claims 15-17 are prima facie obvious for the same reasons set forth above.
Claim 20 recites a plant transformed with a recombinant DNA construct comprising a guide nucleic acid, wherein the guide nucleic acid comprises a spacer sequence that binds to a B- BOX (BBX) gene that comprises a region of homology of at least 98% sequence identity with at least 20 contiguous nucleotides with SEQ ID NO:86or SEQ ID NO:87.
Mullineaux teaches plant transformation with a recombinant DNA construct/vector comprising a guide nucleic acid for CRISPR-Cas editing of an endogenous BBX gene in a plant cell (claim 9, and 11, 12, and p29, line 15-30). Mullineaux further teaches that the guide nucleic acid includes a spacer sequence complementary to a target site in the BBX gene and is used to introduce mutations into the endogenous BBX gene (claim 21 and 22, p29, line 15-30) .
Mullineaux does not expressly teach a guide nucleic acid that binds a BBX gene comprising a region having at least 98% sequence identity with at least 20 contiguous nucleotides of SEQ ID NO:86 or SEQ ID NO:87.
Li teaches maize BBX10/DBB4, the same maize DBB4 gene identified in the instant application, and the SEQ ID NO:86 matches a segment within the cDNA of ZmDBB4 /GRMZM2G019335.(below)
It would have been obvious to one of ordinary skill in the art to use the CRISPR guide/vector system of Mullineaux to target the maize DBB4/BBX10 gene sequence taught by Li, including a spacer sequence corresponding to a 20-nucleotide target region within the known DBB4 sequence, because selecting a guide spacer complementary to a known endogenous gene sequence is a routine CRISPR design step based on sequence complementarity and PAM compatibility.
Therefore, the recombinant DNA construct of claim 20 would have been obvious over Mullineaux in view of Li
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Claims 12, 18, and 19 are rejected under 35 U.S.C. §103 as being unpatentable over WO2022129856A1 (Mullineaux 2022), in view of Li (2017) as applied on claims 8 and 14, and further in view of Crocco (Carlos D. Crocco et. al., Nature communications 6:6202, pp1-10, 2015).
Claims 8 and 14 as the teachings of Mullineaux and Li are discussed above.
Claim 12 is interpreted as dependent of claim 8.
Claim 18 is interpreted as dependent of claim 14.
The rejection is applied to the claimed BBX10(DBB4) alternative. The DBB6 alternative is not relied upon for this rejection.
Claim 12 depends from claim 8 and is drawn to the corn plant comprising the edit in its endogenous BBX gene has an attenuated Shade Avoidance Response.
18 and 19 drawn to the method of producing edit plant and subsequent regenerating a plant from the edited cell, selfing the plant to obtain E1 progeny, and selecting progeny with reduced shade avoidance response relative to a control plant (claim 18), further comprising selfing the selected progeny to produce E2, and selecting progeny with reduced SAR relative to a control (claim 19).
Mullineaux teaches modifying an endogenous BBX transcription factor gene in a plant using targeted genome editing (e. g., CRISPR/Cas with a guide nucleic acid) to generate mutations in the endogenous BBX gene and to obtain plants having the resulting increasing photosynthesis and improving yield genotype (claim 24). Mullineaux further teaches a workflow of regeneration, comprising: (1) producing an edited BBX gene in a plant part (cell); (2) regenerating a plant from the edited plant part (cell); (3) advancing to progeny generations (T1) via selfing/propagation; (4) phenotyping/screening and selecting progeny exhibiting the desired phenotype relative to a control (page 35-37); (5) and advancing edited /regenerated plants through successive progeny generations (e. g., T2 and later generations) by repeated selfing, coupled with phenotyping/assaying and selecting progeny having the desired phenotype (page 35). “T1/T2” (Mullineaux) is alternative conventional label of “E1/E2” for instant claims.
Mullineaux does not explicitly teach the particular maize BBX/DBB gene sequence set recited in claim12 (e. g., the specific SEQ ID NO selections and/or the “≥80% identity” framing as applied to the particular claimed maize BBX gene region/polypeptide).
Li teaches the identification/characterization of maize BBX/DBB genes, provides maize DBB/BBX genes sequence and structural (such as double B-box, without CCT domain)(fig 4, page 658), and points out BBX/DBB genes (DBB4/DBB6) “play an essential role in the light signaling pathway”(page 663), Li also teaches in BBX family “similar gene structures may share the similar gene functions”(page 663).
Crocco teaches that BBX24 in Arabidopsis sharing the same structure as maize DBB4/6 (two B-Box)(page 2), and participating in light-response/photomorphogenesis networks (including shade avoidance response) (abstract). Crocco further teaches mutating BBX24 results “shade-response defect”(abstract).
A person of ordinary skill in the art would have been motivated to apply Mullineaux’s CRISPR-based editing approach for endogenous BBX genes to the specific maize BBX/DBB family members identified/characterized by Li, because Li provides concrete maize BBX/DBB targets within the same gene family addressed by Mullineaux. Further, Crocco and the BBX family domain-structure framework (Sreeramaiah N. Gangappa et al., Trends in Plant Science, July 2014, Vol. 19, No. 7) support that BBX genes sharing the relevant conserved domain architecture are credible regulators of light/shade response outputs, mutate BBX gene causes avoid SAR. Accordingly, the skilled artisan would have been motivated to apply Mullineaux’s CRISPR-Cas spacer-guided targeting/editing approach to Li’s identified maize DBB/BBX genes, then regenerate a plant and self across generations (E1/E2) with assaying /selection for reduced shade avoidance, in order to generate targeted edits and assess BBX/DBB function in light signaling/photosynthesis-related pathways, with a reasonable expectation of success, because Li links ZmDBB genes to light-responsive regulation/expression and Crocco supports BBX involvement in shade/light-regulated development.
The claimed invention in claims 12, 18 and 19 as a whole is prima facie obvious over the combined teachings of the prior arts above.
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Arabidopsis BBX gene structure (Gangappa et al.,)
Response to Applicant’s Arguments Regarding 103 rejection
Applicant’s arguments have been fully considerate but are not persuasive for the following reasons.
Argument 1: Mullineaux does not teach the amended BBX10(DBB4) or DBBX10 genes.
Applicant argues that Mullineaux only teaches Arabidopsis BBX32 and does not teach corn BBX10(DBB4) or DBB6. This argument is not persuasive because the rejection is based on the combination of Mullineaux and Li, not Mullineaux alone. Mullineaux is replied upon for teaching CRISPR-Cas editing of an endogenous BBX transcription factor gene in a plant cell. Li is relied upon for teaching the maize DBB/BBX family, including ZmDBB4 and ZmDBB6, thus, the combination provides both the CRISPR-Cas BBX editing method and the specific maize BBX/DBB target genes now recited in the amended claims.
Argument 2: Li does not teach the claimed target sites or spacer sequences.
Applicant argues that Li does not disclose suitable CRISPR target sites, PAM requirements, or the exact spacer sequence recited in the claims. This argument is not persuasive. Once the endogenous DBB4/DBB6 gene sequence is known, selecting a PAM-adjacent target site and designing a complementary guide spacer is a routine CRISPR design step. The claimed guide/spacer limitations do not require an unexpected property, special editing efficiency, or non-routine design feature. Mullineaux teaches the CRISPR-Cas/guide system for BBX gene editing, and Li provides the maize DBB/BBX gene targets. Therefore, selecting a spacer sequence complementary to the known target gene would have been routine optimization.
Argument 3: There is no motivation to choose DBB4 or DBB6 from the maize DBB family.
This argument is not persuasive because Li expressly identities DBB4 as maize DBB/BBX gene involved in light-regulated pathways. The claims do not require that DBB4 or DBB6 be the only or best target. Obviousness does not require the prior art to identify the claimed target as uniquely preferred. It is sufficient that the prior art provides a reason to select the claimed genes from a finite group of known BBX/DBB genes, including DBB4 and DBB6, as light-responsive BBX transcription factors.
Argument 4: The art does not teach reduced Shade Avoidance Response for DBB4/DBB6.
Applicant argues that Li does not teach DBB4 or DBB6 as controlling shade avoidance response. This argument is not persuasive at least for claims where reduced SAR is not recited. Claims 1, 3, 14-17 and 20 broadly recite guide nucleic acids, editing systems, or methods of generating/editing BBX variation, and do not require an attenuated SAR phenotype. For claims 12, 18, and 19, Crocco is additionally relied upon for teaching BBX involvement in Shade/light-response pathways and that mutation of a BBX gene can result in shad-response defects. Thus, Crocco supplies the additional shade-response rationale for the SAR-related claims.
Argument 5: The rejection improper “obvious to try”.
Applicant argues that the rejection is based on impermissible hindsight and obvious-to-try reasoning in the dark. This argument is not persuasive. The cited art does not merely invite the skilled artisan to explore a broad, undefined field. Instead, the art identifies a known gene family, known maize DBB4/DBB6 target genes, known CRISPR-Cas BBX editing methods, and known BBX involvement in light/shade-responsive pathways. Therefore, the rejection is based on applying a known genome-editing method to known light-responsive BBX/DBB genes, not on varying all parameters without guidance.
Argument 6: There is no reasonable expectation of success.
Applicant argues that the cited references do not provide a reasonable expectation of successfully obtaining the claimed invention. This argument is not persuasive because reasonable expectations of success does not require absolute predictability or guaranteed phenotype. Mullineaux teaches that BBX genes can be targeted and edited in plant cells using CRISPR-Cas system, and Li identities the maize DBB4/Dbb6 sequences/loci. Therefore, a skilled artisan would have reasonably expected success in designing guide RBAs to target those known maize BBX genes, and generating edited plant cells/plants. For the SAR-related claims, Crocco provides additional expectation the BBX mutations may affect shade/light-response phenotypes.
Accordingly, Applicant’s arguments do not overcome the prima facie case of obviousness. The 103 rejection is maintained.
Double Patenting
The nonstatutory double patenting rejection is based on a judicially created doctrine grounded in public policy (a policy reflected in the statute) so as to prevent the unjustified or improper timewise extension of the “right to exclude” granted by a patent and to prevent possible harassment by multiple assignees. A nonstatutory double patenting rejection is appropriate where the conflicting claims are not identical, but at least one examined application claim is not patentably distinct from the reference claim(s) because the examined application claim is either anticipated by, or would have been obvious over, the reference claim(s). See, e.g., In re Berg, 140 F.3d 1428, 46 USPQ2d 1226 (Fed. Cir. 1998); In re Goodman, 11 F.3d 1046, 29 USPQ2d 2010 (Fed. Cir. 1993); In re Longi, 759 F.2d 887, 225 USPQ 645 (Fed. Cir. 1985); In re Van Ornum, 686 F.2d 937, 214 USPQ 761 (CCPA 1982); In re Vogel, 422 F.2d 438, 164 USPQ 619 (CCPA 1970); In re Thorington, 418 F.2d 528, 163 USPQ 644 (CCPA 1969).
A timely filed terminal disclaimer in compliance with 37 CFR 1.321(c) or 1.321(d) may be used to overcome an actual or provisional rejection based on nonstatutory double patenting provided the reference application or patent either is shown to be commonly owned with the examined application, or claims an invention made as a result of activities undertaken within the scope of a joint research agreement. See MPEP § 717.02 for applications subject to examination under the first inventor to file provisions of the AIA as explained in MPEP § 2159. See MPEP § 2146 et seq. for applications not subject to examination under the first inventor to file provisions of the AIA . A terminal disclaimer must be signed in compliance with 37 CFR 1.321(b).
The filing of a terminal disclaimer by itself is not a complete reply to a nonstatutory double patenting (NSDP) rejection. A complete reply requires that the terminal disclaimer be accompanied by a reply requesting reconsideration of the prior Office action. Even where the NSDP rejection is provisional the reply must be complete. See MPEP § 804, subsection I.B.1. For a reply to a non-final Office action, see 37 CFR 1.111(a). For a reply to final Office action, see 37 CFR 1.113(c). A request for reconsideration while not provided for in 37 CFR 1.113(c) may be filed after final for consideration. See MPEP §§ 706.07(e) and 714.13.
The USPTO Internet website contains terminal disclaimer forms which may be used. Please visit www.uspto.gov/patent/patents-forms. The actual filing date of the application in which the form is filed determines what form (e.g., PTO/SB/25, PTO/SB/26, PTO/AIA /25, or PTO/AIA /26) should be used. A web-based eTerminal Disclaimer may be filled out completely online using web-screens. An eTerminal Disclaimer that meets all requirements is auto-processed and approved immediately upon submission. For more information about eTerminal Disclaimers, refer to www.uspto.gov/patents/apply/applying-online/eterminal-disclaimer.
Claims 1-20 are provisionally rejected on the ground of nonstatutory double patenting as being unpatentable over claims 1, 15, 24, 67, 89, 111, and 114 of copending Application No. US18593162 (reference application). Although the instant claims and the reference claims are not identical, they are not patentably distinct from each other because they do not add any non-obvious structural or procedural limitation beyond what is already claimed for editing the same endogenous BBX gene/target site.
This is a provisional nonstatutory double patenting rejection because the patentably indistinct claims have not in fact been patented.
Instant claims 8-17 recite introducing a targeted nuclease system (explicitly CRISPR-Cas) to cleave/edit the same endogenous BBX garget site defined by the same sequence identity limitations, thereby generating an edit/mutation, which is an obvious species/implementation of the reference’s claimed targeted nuclease editing of the same BBX loci (reference claim 67), including B-Box domain embodiments (reference claim 15) and reduced SAR embodiments (reference claims 24/89/114).
Instant claims 11, 18, and 19 add routine downstream steps (regenerating plants, selfing, assaying/sleeting progeny) that would have been obvious and conventional once the reference already claims producing plants having the BBX mutation and reduced SAR phenotype (reference claims 67, 89, 114). These steps do not render the claimed subject matter patentably distinct.
Instant claims 1-7 and 20 recite guides/CRISPR systems and transformed plants/constructs directed to binding /targeting the same BBX loci defined by the same sequence identity limitations. Such claims are obvious variants for practicing the reference’s claimed mutated plants and traits (reference claims 1, 24, 67, 89, 114), and therefore are not patentably distinct.
Accordingly, the claims 1-20 of application 18644352 are not patentably distinct from the claims of the reference application and a provisional obviousness-type double patenting rejection is appropriate.
Response to Double Patenting Argument
Applicant’s request to hold the provisional nonstatutory double patenting rejection in abeyance has been considered but is not persuasive. Provisional nonstatutory double patenting rejections are proper during prosecution where the claims are not patentably distinct from claims in a commonly owned copending application. Applicant has not traversed the merits of the rejection and has not filed a terminal disclaimer. Therefore, the provisional nonstatutory double patenting rejection is maintained.
Conclusion
No claims are allowed.
THIS ACTION IS MADE FINAL. Applicant is reminded of the extension of time policy as set forth in 37 CFR 1.136(a).
A shortened statutory period for reply to this final action is set to expire THREE MONTHS from the mailing date of this action. In the event a first reply is filed within TWO MONTHS of the mailing date of this final action and the advisory action is not mailed until after the end of the THREE-MONTH shortened statutory period, then the shortened statutory period will expire on the date the advisory action is mailed, and any nonprovisional extension fee (37 CFR 1.17(a)) pursuant to 37 CFR 1.136(a) will be calculated from the mailing date of the advisory action. In no event, however, will the statutory period for reply expire later than SIX MONTHS from the mailing date of this final action.
Any inquiry concerning this communication or earlier communications from the examiner should be directed to YANXIN SHEN whose telephone number is (571)272-7538. The examiner can normally be reached Monday-Friday.
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/YANXIN SHEN/Examiner, Art Unit 1663
/WEIHUA FAN/Primary Examiner, Art Unit 1663
Prosecution Insights