Ex Parte Russell et alDownload PDFPatent Trial and Appeal BoardFeb 13, 201713011666 (P.T.A.B. Feb. 13, 2017) Copy Citation United States Patent and Trademark Office UNITED STATES DEPARTMENT OF COMMERCE United States Patent and Trademark Office Address: COMMISSIONER FOR PATENTS P.O.Box 1450 Alexandria, Virginia 22313-1450 www.uspto.gov APPLICATION NO. FILING DATE FIRST NAMED INVENTOR ATTORNEY DOCKET NO. CONFIRMATION NO. 13/011,666 01/21/2011 Sean M. Russell 2971-9843US(67614-US-NP) 5120 7590 02/13/2017 Edgar R. Cataxinos TraskBritt, PC P. O. Box 2550 Salt Lake, UT 84110 EXAMINER KEOGH, MATTHEW R ART UNIT PAPER NUMBER 1663 MAIL DATE DELIVERY MODE 02/13/2017 PAPER Please find below and/or attached an Office communication concerning this application or proceeding. The time period for reply, if any, is set in the attached communication. PTOL-90A (Rev. 04/07) UNITED STATES PATENT AND TRADEMARK OFFICE BEFORE THE PATENT TRIAL AND APPEAL BOARD Ex parte SEAN M. RUSSELL and JOSEPH F. PETOLINO1 Appeal 2016-000945 Application 13/011,666 Technology Center 1600 Before ERIC B. GRIMES, TIMOTHY G. MAJORS, and DEVON ZASTROW NEWMAN, Administrative Patent Judges. NEWMAN, Administrative Patent Judge. DECISION ON APPEAL This appeal under 35 U.S.C. § 134 involves claims to methods of excising a segment of DNA from a plant genome by cleaving the DNA with a zinc finger nuclease and plants produced by these methods, which have been rejected as lacking adequate written description and as nonenabled. We have jurisdiction under 35 U.S.C. § 6(b). We reverse. 1 Appellants identify the Real Party in Interest as Dow AgroSciences. App. Br. 2. Appeal 2016-000945 Application 13/011,666 STATEMENT OF THE CASE Background Custom-designed zinc finger nucleases (ZFNs) are proteins designed to deliver a targeted site-specific double-strand break in DNA, with subsequent recombination of the cleaved ends. ZFNs combine the non-specific cleavage domain of FokI restriction endonuclease with zinc finger DNA-binding proteins. . . . Individual zinc finger motifs can be designed to target and bind to a large range of DNA sites. Spec. 1 8. Using such zinc finger nucleases, the Specification discloses: a method for deleting a region of DNA in a plant wherein a viable plant containing a genomic DNA, the genomic DNA comprising the region of DNA, is provided; and a zinc finger nuclease, engineered to cleave the genomic DNA at a recognition sequence, is expressed or introduced in the viable plant containing the genomic DNA; thereby resulting in cleavage of the genomic DNA at recognition sequences resulting in the excision of the genomic DNA, wherein the region of DNA is absent from the genomic DNA. Spec. 19. The Specification further discloses “transforming a plant cell or tissue comprising a gene of interest with an isolated nucleic acid molecule comprising a nucleic acid sequence encoding a zinc finger nuclease,” excising the native gene of interest, and regenerating the “whole plant” such that the plant no longer contains the excised gene. Spec. 116. 2 Appeal 2016-000945 Application 13/011,666 Claims 3—5, 11—13, 16—19, 21, 22, and 25 are on appeal. Claims 11 and 16 are the independent claims and read as follows: 11. An isolated nucleic acid molecule comprising: a promoter; and a nucleic acid sequence encoding a zinc finger nuclease, wherein the promoter is operably linked to the nucleic acid sequence encoding the zinc finger nuclease, wherein the nucleic acid sequence is flanked by zinc finger nuclease cleavage sites. 16. A method of excising a native gene of interest in a plant comprising: transforming a plant cell or tissue comprising a gene of interest with an isolated nucleic acid molecule encoding a zinc finger nuclease, wherein the zinc finger nuclease recognizes and cleaves at a first polynucleotide positioned 5 ’ with respect to the native gene of interest; and wherein the zinc finger nuclease recognizes and cleaves at a second polynucleotide positioned 3 ’ with respect to the native gene of interest; and regenerating a whole plant. App. Br. 10 and 11 (Claims Appendix). The claims stand rejected as follows: Claims 3—5, 11—13, 16—19, 21—22, and 25 are rejected under 35 U.S.C. § 112 (pre-AIA), first paragraph, as failing to comply with the written description requirement. Ans. 2. Claims 3—5, 11—13, 16—19, 21—22, and 25 are rejected under 35 U.S.C. § 112 (pre-AIA), first paragraph, because the specification fails to reasonably enable these claims. Ans. 4. 3 Appeal 2016-000945 Application 13/011,666 WRITTEN DESCRIPTION The Examiner has rejected all of the claims on appeal for lack of adequate written description. The Examiner finds that the Specification does not adequately describe the recited target genes because the instant specification failed to describe the structures of a representative number of potential target sites which would be targeted to delete or excise any segment of DNA from any plant genome. The single set of target sites described in the working examples fails to represent the immense breadth of any potential target site in any plant cell genome. Ans. 3. The Examiner reasons that because the claims “are broadly drawn to methods of deleting or excising any segment of DNA from a plant genome by cleaving the DNA with any zinc finger nuclease,” and further because “[tjhere is variability as to the zinc finger nucleases used and how the zinc finger nuclease was introduced into the plant,” the Specification should contain a “representative number of potential target sites which would be targeted to delete or excise any segment of DNA from any plant genome.” Id. Appellants argue: Zinc finger nucleases are a well-known and extensively studied class of proteins and, for those known zinc finger proteins, their cleavage sites are similarly well known and extensively studied. Consequently, requiring the appellants to describe these proteins and cleavage sites in detail or with numerous examples in order to satisfy the written description requirement moves beyond the requirement for written description. App. Br. 5 4 Appeal 2016-000945 Application 13/011,666 Appellants further argue the Examiner’s rejection is improper because it interprets the claims to include “‘putative’ zinc finger nucleases or ‘putative’ cleavage sites.” Id. at 6. Appellants argue “the claims do not encompass any zinc finger containing protein or any nucleic acid sequence” but rather specifically recite “‘zinc finger nuclease’ (a specific well known class of proteins which recognize and cleave specific sequences of nucleotides) and ‘zinc finger nuclease cleavage site’ (a specific well known class of nucleic acids which are recognized and cleaved by zinc finger nucleases).” Id. The Examiner responds that “despite the large body of art regarding zinc finger nucleases, . . . the structure/fimction relationship of zinc finger nucleases was not understood in the prior art.” Ans. 7. The Examiner cites Isalan,2 published two years after Appellants’ priority date, as evidence that although “a multitude of methods exist for engineering zinc fingers, one could be forgiven for thinking that making ZFNs ... is a solved problem . . . there are still many issues that need to be considered on a case-bv-case basis. ” Id. (emphasis original). In addition, the Examiner argues that Ramirez,3 submitted by Appellants as evidence that the “structure/fimction relationship of zinc finger nucleases was [] well understood,” (see, e.g., App. Br. 6), is in fact evidence supportive of Appellants’ failure to describe. Ans. 8. The Examiner notes “Ramirez et al were only able to engineer functional 2 Mark Isalan, Zinc-finger nucleases: how to play two good hands, 9(1): NATURE METHODS 32-4 (January 2012). 3 Cherie L. Ramirez, et al., Unexpected failure rates for modular assembly of engineered zinc fingers 5(5): NATURE METHODS 374—5 (May 2008). 5 Appeal 2016-000945 Application 13/011,666 ZNFs [sic] for a given target site 24% of the time.” Id. The Examiner argues “a success rate higher than 24% would be expected” if the zinc finger structure/function relationship was “truly understood.” Id. The Examiner also states “functional recitation alone is not sufficient to provide written description of a claimed genus of chemical structures or methods that require functional chemical structures.” Id. at 9. We agree with Appellants that the Examiner has not shown that the Specification fails to adequately describe the claimed method. A description adequate to satisfy 35 U.S.C. § 112, first paragraph, must “clearly allow persons of ordinary skill in the art to recognize that [the inventor] invented what is claimed.” In other words, the test for sufficiency is whether the disclosure of the application relied upon reasonably conveys to those skilled in the art that the inventor had possession of the claimed subject matter as of the filing date. AriadPharms., Inc. v. EliLilly & Co., 598 F.3d 1336, 1351 (Fed. Cir. 2010) (citation omitted, alteration in original). “The descriptive text needed to meet these requirements varies with the nature and scope of the invention at issue, and with the scientific and technologic knowledge already in existence.” Capon v. Eshhar, 418 F.3d 1349, 1357 (Fed. Cir. 2005). Here, the claims are directed to methods of excising a segment of DNA from a plant genome by cleaving the genomic DNA with a zinc finger nuclease and plants produced by said methods. The Examiner has identified the zinc finger nuclease cleavage sites as not sufficiently described commensurate with the broad scope of the claims. Ans. 3^4. The Specification describes the methods of excising a segment of DNA in several ways. For example, the Specification provides: 6 Appeal 2016-000945 Application 13/011,666 the method comprises contacting a plant with a vector, wherein the vector includes one or more zinc finger nuclease(s) (ZFNs). . . . The ZFN(s) may be designed or engineered to recognize a cleavage sequence that flanks a nucleic acid sequence, the excision of which is desired. Production of the ZFN(s), then, . . . results in excision of the nucleic acid sequence between the cleavage sequences recognized by the ZFN(s), thereby producing a nucleic acid sequence that contains a cleavage junction that is free of a residual recognition sequence. Spec. 172. Spec. Tflf 73—75 provide three additional embodiments of the method for excising a segment of DNA, including providing promotors and/or regulatory regions used in the method. With regard to the use of zinc finger nucleases, the Specification at 76—82 provides significant detail on the use of zinc finger nucleases: a) 176 teaches “ZFNs may be used that target a recognition sequence engineered to flank a particular nucleic acid sequence ... or ZFNs may be designed to target a naturally occurring nucleic acid sequence flanking a particular nucleic acid sequence to be excised;” b) 177 provides ways in which the recognition specificities of zinc finger nucleases may be manipulated by experimentation; c) 178 teaches that “[t]he requirement for dimerization of cleavage domains of chimeric zinc finger nucleases imparts a high level of sequence specificity” and that “two chimeric nucleases effectively demand an 18 bp target because each set of three zinc fingers binds nine consecutive pairs;” and d) 179 teaches “[k]ey amino acids in ZFNs, at position -1, 2, 3, and 6 relative to the start of the a-helix, contribute most of the specific interactions by the zinc finger motifs” and can be changed while maintaining the backbone amino acids. 7 Appeal 2016-000945 Application 13/011,666 The Specification cites multiple prior art references in support of its statements regarding the manipulation of ZFN binding sites. Spec. Tflf 77— 79. In addition the Specification at || 80-81 provides multiple references that describe the design and selection of zinc finger proteases, zinc finger design modules and 1 82 cites references to an existing zinc finger nuclease with known specificity. The working examples 1—5 detail Appellants’ use of a zinc finger nuclease and nuclease binding sites to excise DNA from a plant genome and reproduce and cultivate plants without the excised DNA, including techniques performed to confirm excision. See Spec 95—176. Accordingly, we find the preponderance of the evidence favors Appellants’ argument that the Specification allow persons of ordinary skill in the art to recognize that the inventors had possession of the claimed method of employing zinc finger nucleases to excise a segment of DNA from a plant genome by cleaving the DNA with a zinc finger nuclease and to produce plants using this method. Ariad, 598 F.3d at 1351. The Specification cites numerous references that describe the relationship between the amino acid sequence of zinc finger DNA-binding motifs and the DNA sequence to which they bind, and the manipulation of zinc fingers to bind to a desired DNA target sequence. The fact that the structure and function of some zinc finger nucleases and zinc finger cleavage sites is not fully understood does not mean that Appellants were not in possession of the claimed method as of the filing date, as the claims would have been understood at that time, and with the information provided in the Specification to assist the skilled artisan in performing the method. The Examiner has not shown that a person of ordinary skill in the art would not 8 Appeal 2016-000945 Application 13/011,666 have recognized possession of the claimed method, based on the knowledge in the art at the time of filing, from the Specification's written description. We therefore reverse the rejection under 35 U.S.C. § 112, first paragraph, for lack of adequate written description. ENABLEMENT The Examiner rejects claims 3—5, 11—13, 16—19, 21—22, and 25 as failing to comply with the enablement requirement of 35 U.S.C. 112, first paragraph, because “the specification, while being enabling for deleting or excising some specific regions of DNA from a plant cell genome such as the working example set forth in the specification, does not reasonably provide enablement for deleting or excising any region of DNA from a plant cell genome with a zinc finger nuclease.” Ans. 4. “Applicants do not teach deleting a naturally occurring endogenous region of DNA. Nor do they teach which target sites could be successfully modified using zinc finger nucleases.” Id. at 5. The Examiner cites a review by Carroll4 that “highlights the challenges of genomic modification using custom zinc finger nucleases” and “teach[es] that off-target cleavage, sites in the genome that simply cannot be cut by zinc finger nucleases (likely due to chromatin structure), and zinc finger nucleases which do not work are all challenges that need to be addressed when trying to modify a locus of interest in a genome.” Id. 4 Dana Carroll, Genome Engineering With Zinc-Finger Nucleases, 188 GENETICS 773-782 (August 2011). 9 Appeal 2016-000945 Application 13/011,666 The Examiner analyzes the invention using the Wands5 factors, and concludes that “given the breadth of the claims; the lack of guidance and working examples; the unpredictability in the art; and the state-of-the-art as discussed above, undue experimentation would have been required to practice the claimed invention, and therefore the invention is not enabled throughout the broad scope of the claims.” Id. at 6. Appellants argue: the presently pending claims are not directed to attempts to engineer or design zinc finger nucleases with altered specificity. Instead, the present claims recite a “zinc finger nuclease,” a “zinc finger nuclease cleavage site,” or a “cleavage site for a zinc finger nuclease.” Requiring the appellants to either provide a large number of examples or enable a breakthrough in the engineering of zinc finger nucleases with altered specificity to enable the pending claims is beyond the scope of the claims and the enablement requirement. App. Br. 8. Appellants have the better position. Appellants contend that “zinc finger nucleases are a well-known and extensively studied class of proteins . . . their cleavage sites are similarly well known and extensively studied.” Id. “The enablement requirement is often more indulgent than the written description requirement. The Specification need not explicitly teach those in the art to make and use the invention; the requirement is satisfied if, given what they already know, the Specification teaches those in the art enough that they can make and use the invention without ‘undue experimentation.’” Amgen, Inc. v. Hoechst Marion Roussel, Inc., 314 F.3d 1313, 1334 (Fed. 5 In re Wands, 858 F.2d 731, (Fed. Cir. 1988). 10 Appeal 2016-000945 Application 13/011,666 Cir. 2003). Here, the art establishes that the structure and function of zinc finger nucleases is quite well understood, as shown in Figure 1 of the Isalan reference cited by the Examiner (Ans. 7), which details how a zinc finger nuclease binds to DNA in the orientation and the exact number of base pair gaps required to obtain cleavage, identifies areas for engineering to improve binding specificity, and recommends a “G-rich target”6: IPiPs iuncfexat ss & pair DMA Issgsl in gsmsis, m re&ssah site, sssess&te stemslss FSptrs 11 SvsssBSfisrif the dkdtaifBS. fsr ■sfKpneenng fectioast snc'-fiiigs' ausitaes* Ti:« sdKHtaftfc shass two faBi-feges palfs fciadsag ts 08$ m a onssicst ssd highlights the win mpseerisg csastatRts and ccrskferalksns* Zinc-Sager binding sites are shaded ia bfee (darker far the ssisfe contacted D8A heses). In addition, Carroll references a Zinc Finger Consortium and a “group at ToolGen” that provides information regarding “individual [zinc] fingers in their collection that are best behaved in modular assembly.” Carroll 778. In view of these resources, in addition to the references described above regarding the study of zinc finger nucleases and their cleavage sites, we are not persuaded that undue experimentation would be required to practice the full scope of the claimed invention. See Spec. ^fl[ 76—176. 6 G represents guanine. 11 Appeal 2016-000945 Application 13/011,666 With regard to the Examiner’s concern that the Specification does not teach deleting a naturally occurring endogenous region of DNA or which target sites could be successfully modified using zinc finger nucleases, we find that the claims can be practiced by introducing a nucleic acid encoding both the zinc finger nuclease and the zinc finger cleavage sites. For example, the method for deleting a polynucleotide in a plant (claim 12) or excising a native gene of interest in a plant (claim 16) can be practiced by introducing the nucleotide of claim 11 such that the naturally occurring endogenous region of DNA is flanked by the zinc finger nuclease cleavage sites and the plant polynucleotide or native gene would be cut out after the zinc finger nuclease is expressed. While this method would require knowledge of the location of the plant polynucleotide or native gene for excision and its surrounding nucleotides, tools for identifying and mapping those are within the skill of the ordinary artisan or provided by the Specification. See, e.g., Spec. 83—87. We agree with Appellants’ position that, based on the combination of what is known in the art with respect to zinc finger nucleases and zinc finger nuclease cleavage sites in conjunction with what is disclosed in the Specification, one of skill in the art would know how to practice the method to accomplish excision. “That some experimentation may be required is not fatal; the issue is whether the amount of experimentation required is ‘undue.’” In re Vaeck, 947 F.2d 488, 495 (Fed. Cir. 1991) (emphasis in original). In sum, we are not persuaded, for the reasons discussed, that the Examiner has adequately established that the claims are not enabled for the steps of deleting a naturally occurring endogenous region of DNA or 12 Appeal 2016-000945 Application 13/011,666 modifying target sites to permit use of zinc finger nucleases and zinc finger nuclease cleavage sites steps as claimed. Accordingly we reverse the rejection of claims 3—5, 11—13, 16—19, 21—22, and 25 under 35 U.S.C. §112, first paragraph, as not being enabled. SUMMARY We reverse the rejection of all claims. REVERSED 13 Copy with citationCopy as parenthetical citation