Ex Parte McGonigleDownload PDFPatent Trial and Appeal BoardDec 14, 201612747606 (P.T.A.B. Dec. 14, 2016) 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. 12/747,606 10/21/2010 Brian McGonigle 7616 7616 23906 7590 12/16/2016 E I DU PONT DE NEMOURS AND COMPANY LEGAL PATENT RECORDS CENTER CHESTNUT RUN PLAZA 721/2340 974 CENTRE ROAD, P.O. BOX 2915 WILMINGTON, DE 19805 EXAMINER ZHOU, SHUBO ART UNIT PAPER NUMBER 1662 NOTIFICATION DATE DELIVERY MODE 12/16/2016 ELECTRONIC 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. Notice of the Office communication was sent electronically on above-indicated "Notification Date" to the following e-mail address(es): PTO-Legal.PRC@dupont.com PTOL-90A (Rev. 04/07) UNITED STATES PATENT AND TRADEMARK OFFICE BEFORE THE PATENT TRIAL AND APPEAL BOARD Ex parte BRIAN McGONIGLE1 Appeal 2015-006369 Application 12/747,606 Technology Center 1600 Before RICHARD J. SMITH, JOHN E. SCHNEIDER, and TIMOTHY G. MAJORS, Administrative Patent Judges. MAJORS, Administrative Patent Judge. DECISION ON APPEAL This is an appeal under 35 U.S.C. § 134 involving claims to modified nucleic acid fragments, and to methods of reducing expression of a target sequence in plant cells transformed with such nucleic acid fragments. The claims have been rejected as obvious. We have jurisdiction under 35 U.S.C. § 6(b). We affirm. 1 Appellant identifies the Real Party in Interest as E.I. du Pont de Nemours and Company. (App. Br. 3.) Appeal 2015-006369 Application 12/747,606 STATEMENT OF THE CASE Appellant’s invention “relates to constructs and methods to down- regulate expression of targeted sequences” in plant cells. (Spec. 1:11—13.) According to the Specification, [mJicroRNAs (miRNAs). . . play an important role in regulating gene activity. These 20-22 nucleotide noncoding RNAs have the ability to hybridize via base-pairing with specific target mRNAs and downregulate the expression of these transcripts, by mediating either RNA cleavage or translational repression. (Id. at 1:15—19.) The Specification discloses “[ajrtificial miRNAs replace the microRNA and its complementary star sequence[2] in a precursor miRNA and substitute sequences that target an mRNA to be silenced.” (Id. at 2:12-13.) Claims 1—6 are on appeal. Claim 1 is illustrative: 1. An isolated nucleic acid fragment comprising the deoxyribonucleotide sequence set forth in SEQ ID NO: 11 wherein (i) nucleotides 430 to 450 of SEQ ID NO: 11 are replaced by a first variable nucleotide subsequence ranging in size from 19 to 24 nucleotides depending upon the target sequence whose expression is to be reduced, (ii) nucleotides 244 to 264 of SEQ ID NO: 11 are replaced by a second variable nucleotide subsequence ranging in size from 19 to 24 nucleotides, said second variable nucleotide subsequence being capable of hybridizing to the first variable subsequence of the precursor miRNA, and (iii) a precursor miRNA produced by said isolated nucleic acid fragment which has the same stem structure as a precursor miRNA produced by endogenous SEQ ID NO: 11. 2 “Star sequences are largely the complementary sequences within the miRNA precursor that form a duplex with the miRNA.” (Spec. 3:9—10); see also Ans. 2—3 (background technical discussion by Examiner).) 2 Appeal 2015-006369 Application 12/747,606 (App. Br. 16 (Claims App’x).) Claims 1—6 stand rejected as obvious under 35 U.S.C. § 103(a) over Zhang,3 Lutfiyya,4 and Kim.5 DISCUSSION Issue Has the Examiner established by a preponderance of the evidence that claims 1—6 would have been obvious over Zhang, Lutfiyya, and Kim? Findings of Fact FF 1. The Examiner’s findings of fact and statement of the rejection may be found at pages 2—9 of the Examiner’s Answer. We adopt those findings and provide the following for emphasis. FF 2. Zhang teaches “MicroRNAs (miRNAs) represent a newly identified class of non-protein-coding ~ 20 nt small RNAs which play important roles in multiple biological processes by degrading targeted mRNAs or repressing mRNA translation.” (Zhang Abstract.) Zhang teaches “we found 188 maize miRNAs belonging to 29 miRNA families . . . A total of 115 potential targets were identified for 26 of the miRNA families based on the fact that miRNAs exhibit perfect or nearly perfect complementarity with their target sequences.” (Id.) Zhang discloses the “[predicted hairpin secondary structures of identified miRNAs,” including 3 Zhang et al., Identification of 188 conserved maize microRNAs and their targets, 580 FEBS Letters 3753—62 (2006). 4 Lutfiyya et al., US 2006/0200878 Al, published Sept. 7, 2006. 5 Kim et al., GenBank Accession No. DR963981 (2005). 3 Appeal 2015-006369 Application 12/747,606 for miRNA 159. (Id. at Fig. 4; see, in particular, underlined portion of structure for nucleotide sequence of the mature miRNA); Ans. 4—5.) Zhang further teaches the EST (expressed sequence tag) database corresponding to miRNA 159c is provided in DR963981 (Kim). (Zhang Table 1; Ans. 4—5.) FF 3. Kim teaches a sequence of nucleotides 1 through 875, including nucleotides 244—264 and 430-450 of SEQ ID NO: 11 for Zea mays. (Kim passim', Ans. 4—5 and 7—9.) FF 4. Lutfiyya teaches “novel mature miRNA sequences and MIR gene sequences from crop plants, including maize and soybean.” (Lutfiyya 125.) Lutfiyya further teaches “These MIR genes and their encoded mature miRNAs . . . serve as sequence sources for engineered (non-naturally occurring) miRNAs that are designed to target sequences other than the transcripts targeted by the naturally occurring miRNA sequence.” (Id.; see also id. at Abstract and Tflf 200 and 218.) FF 5. Lutfiyya discloses “[t]he gene suppression element can be transcribable DNA of any suitable length, and will generally include at least 19 to about 27 nucleotides (for example 19, 20, 21, 23, or 24 nucleotides) for every target gene that the recombinant DNA construct is intended to suppress.” (Id. at 1122.) Lutfiyya teaches nucleotides derived from a miRNA can include DNA derived from a miRNA precursor sequence, such as a native pri-miRNA or pre-miRNA sequence, or nucleotides corresponding to regions of a native miRNA and nucleotides that are selected from a target gene sequence number such that the overall structure (e.g., the placement of mismatches in the stem structure of the pre- miRNA) is preserved to permit the pre-miRNA to be processed into mature miRNA. . . . [T]he DNA that includes nucleotides derived from a miRNA can include [a] sequence naturally 4 Appeal 2015-006369 Application 12/747,606 occurring in a miRNA or a miRNA precursor molecule, synthetic sequence, or both. {Id. at 1145.) FF 6. The Specification discloses “SEQ ID Nos: 11-15 correspond to miRNA precursor sequences for 159c, 164h, 168a, 169r, and 396h, respectively.” (Spec. 2:35:36 and 25 (Table 2).) Principles of Law “[OJbviousness cannot be avoided simply by a showing of some degree of unpredictability in the art so long as there was a reasonable probability of success. . . . Indeed, a rule of law equating unpredictability to patentability . . . would mean that any new salt—including those specifically listed in the [prior art patent] itself—would be separately patentable, simply because the formation and properties of each salt must be verified through testing. This cannot be the proper standard since the expectation of success need only be reasonable, not absolute.” Pfizer, Inc. v. Apotex, Inc., 480 F.3d 1348, 1364 (Fed. Cir. 2007). Analysis Appellant does not separately argue the patentability of the claims on appeal. We select claim 1 as representative. The Examiner finds Zhang teaches “sequences of miRNAs isolated from maize including miRl59c, which Zhang [] indicate [s] is encoded by EST taught in GenBank Accession No. DR963981 [Kim]. . . and an miRl 59 miRNA hairpin structure with corresponding 21 nt miRNA and miRNA* sequences (Abstract, Table 1, Figure 4.).” (Ans. 4.) According to 5 Appeal 2015-006369 Application 12/747,606 the Examiner, “[g]iven that the alignment of [Kim] is an identical match with SEQ ID NO: 11, it is clear that the polynucleotide of instantly claimed SEQ ID NO: 11 is the same as the miRNA 159c taught in Zhang [].” (Id.) The Examiner further finds that given that the underlined miRNA sequence of Zhang [] exactly correlates with instantly claimed nucleotides 430-450 of SEQ ID NO: 11, one of ordinary skill would have understood that this region, along with the complementary region of the hairpin as depicted in Figure 4 [of Zhang] would be the miRNA and miRNA* sequences of miR159. Given this information, one would have also been motivated and enabled to find the corresponding miRNA* region of the miRl 59c pre-miRNA from [Kim], which corresponds to nucleotides 244-264 of instantly claimed SEQ ID NO: 11. (Id. at 5 (showing alignment between Zhang and SEQ ID NO: 11 in Kim).) The Examiner finds that Zhang does not teach “replacing the miRNA and miRNA* sequences with a variable sequence to down regulate expression of a target gene” and so turns to Lutfiyya. (Id. at 5.) According to the Examiner, Lutfiyya teaches “using miRNA sequences of maize ... for engineered (non-naturally occurring) miRNAs that are designed to target heterologous sequences other than the transcripts targeted by the naturally occurring miRNA sequence.” (Id.) The Examiner finds “Lutfiyya [] also teach[es] that ‘the native miRNA sequence can be replaced with a region of the target sequence, preferably a region that meets structural and thermodynamic criteria believed to be important for miRNA function’” and “that the gene suppression element will generally include about 19 to 27 nucleotides.” (Id. at 6 (emphasis and citations omitted).) 6 Appeal 2015-006369 Application 12/747,606 The Examiner concludes “it would have been obvious ... to modify the miR159c of Zhang [] to substitute the miRNA and miRNA* sequences [of Zhang in view of Kim] ... for an artificial miRNA and miRNA* sequence as taught by Lutfiyya.” (Id.) The Examiner reasons the skilled person “would have been motivated by the teaching of Lutfiyya [] that miRNA transcript sequences from maize can be used to target other genes of interest in a transgenic plant. . . and the knowledge common in the art that maize is [a] valuable crop plant which has a highly profitable market for biotechnology research and development.” (Id. at 6—7.) The Examiner further reasons the skilled artisan “would have had a reasonable expectation of success . . . given the success of Lutfiyya . . . [and] given that there is a high level of skill in the art.” (Id. at 7.) Appellant argues the skilled person “would not have had a reasonable expectation of success to select miR159c (SEQ ID NO:l 1) as an artificial miRNA (‘amiRNA’) backbone.” (App. Br. 9.) More specifically, Appellant argues, given the number of miRNAs and structural diversity disclosed in Zhang, “a person of skill in the art would not have a reasonable expectation of success to identify miR159c as useful [as] the basis of an amiRNA of the 188 [] maize miRNAs reported by Zhang.” (Id. at 9-10.) Appellant contends “the procedure for producing an artificial miRNA that maintains the original structure of the native miRNA is not nearly as simple as implied by Lutfiyya.” (Id. at 10.) Because Kim is “simply a GenBank database entry,” Appellant argues, “the skilled person would not know which SEQ ID NO: 11 sequences to replace in order to produce a functional miRNA.” (Id. at 11.) Moreover, according to Appellant, “[different miRNA backbones 7 Appeal 2015-006369 Application 12/747,606 can display variability in their ability to silence target genes” as discussed in the art and the Specification’s Examples. {Id. at 11—13.) Thus, Appellant argues, “the skilled artisan would understand that various miRNAs would have different silencing abilities” and “without recognizing the usefulness of miR159c as the basis of an amiRNA, a person of ordinary skill in the art would not have had a reasonable expectation of success to arrive at Applicant’s invention as claimed.” {Id. at 12.) The Examiner has the better position. On the present evidentiary record, we agree with the Examiner that claim 1 would have been obvious over Zhang, Kim, and Lutfiyya. The combination of Zhang and Kim discloses the miRNA precursor sequence and mature miRNA nucleotide sequence for 159c. (FF 2—3 and 6; Ans. 2—9.) As the Examiner determined, from these teachings, the skilled person would have known the miRNA sequence and complementary miRNA star sequence for 159c, which corresponds to nucleotides 430-450 and 244—264 respectively of Kim — precisely as in claim 1. (Ans. 5 and 8; FF 2—3.) Consistent with Lutfiyya’s teachings, it was known in the art to design artificial miRNAs by replacing the native miRNA and miRNA* sequence with substitute sequences aimed at silencing a target mRNA of interest. (FF 4—5; see also Ans. 3 (discussing Schwab6) and 5—6.) We are persuaded that the skilled artisan would have predictably modified the prior art in the manner proposed by the Examiner to produce a nucleic acid fragment as claimed. 6 Schwab et al., Highly Specific Gene Silencing by Artificial MicroRNAs in Arabidopsis, 18 The Plant Cell 1121—1133 (2006). 8 Appeal 2015-006369 Application 12/747,606 Appellant argues the person of ordinary skill in the art would have lacked a reasonable expectation of success in making this combination, but this argument is unpersuasive. (App. Br. 8—14; Reply Br. 5—10.) The expectation of success corresponds to the scope of the claims. Intelligent Bio-Systems, Inc. v. Illumina Cambridge Ltd., 821 F.3d 1359, 1367 (Fed. Cir. 2016) (“The reasonable expectation of success requirement refers to the likelihood of success in combining references to meet the limitations of the claimed invention.”) And here, the scope of claim 1 is broad. As pointed out by the Examiner, “the appealed claims are broadly drawn to allow for substitution of any subsequence, targeting any gene.” (Ans. 16.) Claim 1 does not, for example, specify any particular replacement sequence, such as one targeted to phytoene desaturase (as in Appellant’s Examples); nor does claim 1 indicate any level or range of reduced expression provided with the nucleic acid fragment claimed. Thus, the skilled person needed only a reasonable expectation of success in making the nucleic acid fragment that is claimed — and, at most, an expectation that it would provide some reduction of expression of some target sequence. See Intelligent Bio-Systems, 821 F.3d at 1367; Pfizer 480 F.3d at 1364. The teachings of the cited art and reasoning provided by the Examiner persuade us the skilled artisan would have had sufficient motivation and a reasonable expectation of success in making the nucleic acid fragment as claimed. Appellant’s argument that the skilled person would not have predictably chosen miR159c for modification from among the 188 maize miRNAs reported in Zhang is also unpersuasive. (App. Br. 9-10; Reply Br. 8—9.) Zhang discloses 159c as part of a much shorter list of miRNAs for 9 Appeal 2015-006369 Application 12/747,606 which the precursor and miRNA nucleotide sequence and predicted structure are provided. (FF 2.) As the Examiner noted, “miR159C is one of only 28 miRNAs for which Zhang [] include[d] in Table 1, which identifies the known sequence accessions submitted in GenBank for the listed miRNA backbones.” (Ans. 13.) We agree with the Examiner that this comprises “a reasonable and finite number of miRNA backbones” that the skilled person would have predictably modified to create artificial miRNAs, particularly given the breadth of claim 1. Merck & Co., Inc. v. Biocraft Labs., Inc., 874 F.2d 804, 807 (Fed. Cir. 1989) (“[D]isclos[ing] a multitude of effective combinations does not render any particular formulation less obvious.”) In the Reply Brief, Appellant argues the skilled person would not have selected miRNA 159 because it is longer than several other disclosed miRNA sequences in Zhang, and longer RNA sequences are “more complicated to manipulate.” (Reply Br. 8 (citing Moore7).) This is new argument and evidence, and Appellant has offered no explanation why it was not provided earlier. 37 C.F.R. § 41.41(b) & (c). The argument is, in any event, unpersuasive. Moore’s teachings are general in nature and relate to the potential for RNAs to undergo conformational changes. Appellant has cited no persuasive evidence that would have taught away from using any particular miRNA, much less miRNA 159. Also, notwithstanding Appellant’s contention that the skilled person would not use respectively 7 Peter B. Moore, The RNA World, 383—84 (Raymond F. Gestleland et al. eds., 2nd ed. 1999). 10 Appeal 2015-006369 Application 12/747,606 longer miRNA precursors, we observe that at least Schwab and Ossowski8 suggest otherwise. Those references disclose that miRNA precursors having a variety of different lengths (e.g., MIR319a, MIR172a MIR164b, MIR159a, and MIR171) have been used successfully for engineering artificial miRNAs. (Schwab 1126; Ossowski 684.) Appellant contends the process for producing artificial miRNA as claimed is not as simple as implied in Lutfiyya. (App. Br. 10.) We are unpersuaded. Appellant does not provide factual evidence sufficient to support its contention such as, for example, a declaration of a skilled person explaining why Lutfiyya’s teachings are incomplete or incorrect, and detailing what other knowledge would have been required (but unknown to the artisan at the time of invention) in order to make the nucleic acid fragment recited in claim 1. See In re Geisler, 116 F.3d 1465, 1471 (Fed. Cir. 1997) (argument by counsel cannot take the place of evidence). Appellant argues the skilled person would not know, based on Kim, which subsequences of SEQ ID NO: 11 to replace to make a functional miRNA. (App. Br. 11.) This argument is not persuasive because it neglects the combined teachings of the art. In re Merck & Co., 800 F.2d 1091, 1097 (Fed. Cir. 1986) (“Non-obviousness cannot be established by attacking references individually where the rejection is based upon the teachings of a combination of references [].”) Based on Kim, in combination with Zhang and Lutfiyya, the skilled person would know to replace the subsequences at 244—264 and 430-450 of SEQ ID NO: 11, which would correspond to the 8 Ossowski et al., Gene silencing in plants using artificial microRNAs and other small RNAs, 53 The Plant Journal 674-690 (2008). 11 Appeal 2015-006369 Application 12/747,606 respective miRNA and miRNA* sequences of the precursor miRNA. (FF 2— 5; Ans. 4—7; Schwab Fig. 1.) Indeed, Appellant acknowledges in the “Background” of the Specification that replacing miRNA and miRNA* sequences was a known approach to designing artificial miRNAs. (Spec. 2:12-13.) Citing publications, and Examples in the Specification, Appellant argues different miRNAs have different silencing abilities and, thus, this variability means the art is unpredictable and claim 1 nonobvious. (App. Br. 11—14; Reply Br. 6—10.) This argument is unpersuasive. Once again, claim 1 is broad and does not require any specific subsequence be used, or that any particular mRNA transcript or gene be silenced. Moreover, contrary to Appellant’s argument, the fact that certain art recognized variability between different miRNAs shows that the variability allegedly illustrated in Example 7 and 10 of the Specification would not have been unexpected. Schwab, for example, teaches that different miRNA backbones (MIR319a and MIR172a precursors) “can be used for amiRNA expression” yet “they were not always equally effective.” (Schwab 1126.) In some instances, and for some targets, one backbone worked better than the other. (Id.) This is what Appellant’s Examples show. (See Spec. 31—32 (Table 5) and 35 (Table 9); see also Ans. 10 and 15-17.) Appellant’s arguments and the cited data in the Specification fail to persuade us there was anything sufficiently advantageous or unexpected through use of artificial miRNA 159c that overcomes the Examiner’s prima facie case. Example 7 reports that 159c-PDS provided 14% silencing, whereas several other artificial miRNA constructs were more effective (e.g., 12 Appeal 2015-006369 Application 12/747,606 58—90% silencing); and, in Example 10, the 159c-FAD miRNA precursor provided no silencing for fad2-l. Appellant argues these examples show that 159c has “targeted efficiency” and is “tissue-specific” in a manner that is unexpected and advantageous. (Reply Br. 7.) Yet the broad claims are not limited to any tissue-specific activity as allegedly provided in the much narrower Examples. In re Lindner, 457 F.2d 506, 508 (CCPA 1972) (“It is well established that the objective evidence of nonobviousness must be commensurate in scope with the claims.”). Nor does Appellant provide persuasive factual evidence that supports Appellant’s effort to now characterize this data as “surprising,” “unexpected,” or “advantageous.” In re De Blauwe, 736 F.2d 699, 705 (Fed. Cir. 1984) (“[I]t is well settled that unexpected results must be established by factual evidence. Mere argument or conclusory statements in the specification does not suffice.”).9 Conclusion of Law We conclude the Examiner established by a preponderance of the evidence that claim 1 would have been obvious over Zhang, Futfiyya, and Kim. Claims 2—6 have not been argued separately and so fall with claim 1. 37C.F.R. §41.37(c)(l)(iv). SUMMARY We affirm the rejection of claims 1—6 under 35 U.S.C. § 103(a) over Zhang, Futfiyya, and Kim. 9 Furthermore, as pointed out by the Examiner, the data cited in the Specification does not sufficiently demonstrate a tissue-specific nature of the miRNA. (Ans. 12—13.) 13 Appeal 2015-006369 Application 12/747,606 TIME PERIOD FOR RESPONSE No time period for taking any subsequent action in connection with this appeal may be extended under 37 C.F.R. § 1.136(a). AFFIRMED 14 Copy with citationCopy as parenthetical citation