Ex Parte Zernicka-Goetz et alDownload PDFPatent Trial and Appeal BoardAug 28, 201411933153 (P.T.A.B. Aug. 28, 2014) 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. 11/933,153 10/31/2007 Magdalena Zernicka-Goetz KILBURN1100-5 3318 7590 08/28/2014 Lisa A. Haile, J.D., Ph.D. DLA PIPER US LLP Suite 1100 4365 Executive Drive San Diego, CA 92121-2133 EXAMINER GIBBS, TERRA C ART UNIT PAPER NUMBER 1674 MAIL DATE DELIVERY MODE 08/28/2014 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 MAGDALENA ZERNICKA-GOETZ, FLORENCE WIANNY, MARTIN JOHN EVANS, and DAVID MOORE GLOVER __________ Appeal 2012-010432 Application 11/933,153 Technology Center 1600 __________ Before DEMETRA J. MILLS, ERIC B. GRIMES, and ROBERT A. POLLOCK, Administrative Patent Judges. MILLS, Administrative Patent Judge. DECISION ON APPEAL This is an appeal under 35 U.S.C. § 134. The Examiner has rejected the claims for obviousness. We have jurisdiction under 35 U.S.C. § 6(b). STATEMENT OF CASE According to the Specification, page 1 ¶ [0002], “[t]he present invention relates to inhibiting gene expression. In particular, it relates to inhibiting gene expression in mammals using double stranded RNA (dsRNA).” Appeal 2012-010432 Application 11/933,153 2 The following claim is representative. 1. An in vivo RNA interference method for inhibiting the expression of a target gene in a mammalian cell, the method comprising: introducing into the cell an RNA interference molecule comprising a double stranded structure having a nucleotide sequence which is substantially identical to at least a part of the target gene and which is derived from an endogenous template, wherein the cell is an oocyte, or a cell of an early embryo, and verifying inhibition of expression of the target gene in the cells to which the RNA interference molecule was introduced, wherein inhibition can be observed at least four days after introduction of the RNA interference molecule. Examiner Cited References (“Fire PCT”) WO 99/32619 July 1, 1999 Barlow et al., Interferon synthesis in the early post-implantation mouse embryo, 27 DIFFERENTIATION 229-235 (1984). Haggarty et al., An embryonic DNA-binding protein specific for a region of the human IFNβ1 promoter, 16 NUCLEIC ACIDS RESEARCH 10575-10592 (1988). Mary Kay Francis & John M. Lehman, Control of β-Interferon Expression in Murine Embryonal Carcinoma F9 Cells, 9 MOL. CELL. BIOL. 3553-3556 (1989). Harada et al., Absence of the Type I IFN System in EC Cells: Transcriptional Activator (IRF-1) and Repressor (IRF-2) Genes Are Developmentally Regulated, 63 CELL 303-312 (1990). Asangla Ao & Robert P. Erickson, Injection of Antisense RNA Specific for E-Cadherin Demonstrates That E-Cadherin Facilitates Compaction, the First Differentiative Step of the Mammalian Embryo, 2 ANTISENSE RESEARCH AND DEVELOPMENT 153-163 (1992). Appeal 2012-010432 Application 11/933,153 3 Fire, RNA-triggered gene silencing, 15 TRENDS IN GENETICS 358-363 (1999). Appellants’ Cited Art Sharp, RNAi and double-strand RNA, 13 GENES & DEVELOPMENT 139-141 (1999). Caplen et al., dsRNA-mediated gene silencing in cultured Drosophila cells: a tissue culture model for the analysis of RNA interference, 252 GENE 95- 105 (2000). Silva et al., RNA interference: a promising approach to antiviral therapy? 8 TRENDS IN MOLEC. MED. 505-508 (2002). Grounds of Rejection Claims 1–11, 13, 14, 18–20, 22, and 23 are rejected under 35 U.S.C. § 103(a) as being unpatentable over WO 99/32619 (Fire PCT) in view of Fire and Ao. FINDINGS OF FACT The Examiner’s findings of fact are set forth in the Answer at pages 3–14. The following facts are highlighted. 1. The Examiner finds that With regard to claim 1, WO 99/32619 teaches the use of dsRNA to inhibit expression of a target gene in a cell. It exemplifies RNA-mediated inhibition of target genes in C. elegans. It further discloses the use of dsRNA to inhibit expression of a target gene in a mammalian cell such as a mouse, rat and human (page 12, lines 3-8 and 20). (Ans. 5.) Appeal 2012-010432 Application 11/933,153 4 2. The Examiner finds that Fire explicitly teaches: “Even if the underlying mechanisms are absent in mammals, it is possible that RNA-triggered silencing will have clinical applications”. “Any gene-specific dsRNA response in mammals would need to exist in cells or conditions where PKR is less effective, or would need to work in the shadow of the PKR-induced global response” (Ans. 6.) 3. Table 1 of Barlow is reproduced below. “Table 1 shows both constitutive and induced interferon synthesis in separate tissues of the embryo and the maternal tissues enclosing the developing embryo at the early 7th, late 7th and 8th day of development.” (Page 231, col. 2.) Appeal 2012-010432 Application 11/933,153 5 4. According to Barlow, 1. Induced synthesis [of interferon] is initially absent in most tissues of the early 7th-day embryo, with the exception of the trophoblast, which shows a low level (33%) of inducible synthesis. It should also be noted that control virus-induced maternal tissues early in the 7th day showed a reduced level of induced synthesis [of interferon] compared to the late 7th and early 8th day of development (approximately 35%, compared to greater than 70% at later stages.) These results were seen in two separate assays of early 7th-day material obtained from different matings. 2. Induced synthesis is developmentally regulated, reaching high levels in late 7th-day and early 8th day embryos in tissues which initially showed nil or low levels of induction . . . . By the early 8th day, all tissues, with the exception of the visceral extra-embryonic endoderm . . . and the embryonic ectoderm . . ., could be induced to produce interferon. (Page 231, col. 2.) 5. According to the Specification, page 3 ¶ [0006], “[p]art of the interferon response is the activation of a dsRNA responsive protein kinase (PKR) (Clemens, Int J Biochem Cell Biol 29, 945-949 (1997)).” 6. According to the Specification, page 15 ¶ [0038], “[t]he cell may be any individual cell of the early embryo, and may be a blastocyte. Alternatively, it may be an oocyte.” 7. Example 4 of the Specification, page 30 ¶ [0083], states that, “dsRNA to E-cadherin was microinjected into one cell of a two cell stage mouse embryo . . . .” Appeal 2012-010432 Application 11/933,153 6 Discussion ISSUE The Examiner concludes from the cited evidence that It would have been prima facie obvious to one of ordinary skill in the art, at the time the invention was made to devise an in vivo RNA interference method for inhibiting the expression of a target gene in a mammalian cell using the teachings of WO 99/32619. It would have been prima facie obvious to one of ordinary skill in the art, at the time the invention was made to have the mammalian cell be an oocyte or cells of an early embryo using the teachings and motivation of WO 99/32619 and Fire. One of ordinary skill in the art would have been motivated to devise an in vivo RNA interference method for inhibiting the expression of a target gene in a mammalian cell since WO 99/32619 and Fire taught that such a method could have clinical applications. One of ordinary skill in the art would have been motivated to have the mammalian cell be an oocyte or cells of an early embryo since Fire taught that in cells void of the interferon response, RNAi would be successful, and at the time of invention, these two cell types were known to be incapable of the PKR response. See the evidence of Haggarty et al., Harada et al., Barlow et al., and/or Francis and Lehman. One of ordinary skill in the art would have had a reasonable expectation of success of devising an in vivo RNA interference method for inhibiting the expression of a target gene in a mammalian cell since WO 99/32619 generally taught such a method and Fire taught that RNAi would successfully work in cells where the interferon response is less effective. One of ordinary skill in the art would have been well aware that oocytes and cells of the early embryo are examples of such cells since it was known that these cells are void of the interferon or PKR response. One of ordinary skill in the art would have had a reasonable expectation of success of observing inhibition of the expression of the target gene at least four days after introduction of the dsRNA since Ao et al. taught inhibition of Appeal 2012-010432 Application 11/933,153 7 the expression of the target gene at least four days after introduction of an antisense RNA and KSR forecloses that the simple substitution of one known element for another would have yielded predictable results at the time of the invention. (Ans. 8–9.) Appellants assert that the perception at the time of the filing of the present application was that RNAi cannot be made to work in mammals. As such, one of ordinary skill in the art would have no reasonable expectation of success in practicing the claimed method of inhibiting the expression of a target gene in a mammalian cell using a double stranded RNAi molecule. (Br. 6.) Appellants contend that, “Exhibits A-C[1], as well as the Fire Article itself, clearly show that it is unequivocal that … skepticism existed in the art for some years after its publication and such skepticism pervaded the art.” (Br. 7.) Appellants conclude that Based on the art-accepted skepticism as to the workability of RNAi in mammals both at the time of the Fire references and in recollections of Fire himself, clearly there could be no reasonable expectation for one ordinarily skilled in the art of successfully practicing RNA interference in mammalian cells as claimed. (Br. 9.) Finally, Appellants argue that the claimed subject matter is the product of unexpected results and that the Examiner has engaged in hindsight reconstruction of Appellants’ invention. (Br. 12.) 1 The references by Silva, Sharp, and Caplen, cited previously. Appeal 2012-010432 Application 11/933,153 8 The issue is: Does the Examiner’s cited evidence establish a prima facie case of obviousness? If so, have Appellants rebutted the Examiner’s prima facie case of obviousness by a preponderance of the evidence? PRINCIPLES OF LAW In making our determination, we apply the preponderance of the evidence standard. See, e.g., Ethicon, Inc. v. Quigg, 849 F.2d 1422, 1427 (Fed. Cir. 1988) (explaining the general evidentiary standard for proceedings before the Office). The Board “determines the scope of claims in patent applications not solely on the basis of the claim language, but upon giving claims their broadest reasonable construction ‘in light of the specification as it would be interpreted by one of ordinary skill in the art.’” Phillips v. AWH Corp., 415 F.3d 1303, 1316 (Fed. Cir. 2005) (quoting In re Am. Acad. of Sci. Tech. Ctr., 367 F.3d 1359, 1364 (Fed. Cir. 2004). “In rejecting claims under 35 U.S.C. § 103, the examiner bears the initial burden of presenting a prima facie case of obviousness. Only if that burden is met, does the burden of coming forward with evidence or argument shift to the applicant.” In re Rijckaert, 9 F.3d 1531, 1532 (Fed. Cir. 1993) (citations omitted). In order to determine whether a prima facie case of obviousness has been established, we consider the factors set forth in Graham v. John Deere Co., 383 U.S. 1, 17 (1966): (1) the scope and content of the prior art; (2) the differences between the prior art and the claims at issue; (3) the level of ordinary skill in the relevant art; and (4) objective evidence of nonobviousness, if present. Appeal 2012-010432 Application 11/933,153 9 “The combination of familiar elements according to known methods is likely to be obvious when it does no more than yield predictable results.” KSR Int’l Co. v. Teleflex Inc., 550 U.S. 398, 416 (2007). ANALYSIS We find that the Examiner has provided evidence to support a prima facie case of obviousness. In particular, Fire PCT generally teaches “the use of dsRNA to inhibit expression of a target gene in a cell. It exemplifies RNA-mediated inhibition of target genes in C. elegans. It further discloses the use of dsRNA to inhibit expression of a target gene in a mammalian cell such as a mouse, rat and human (page 12, lines 3-8 and 20).” (Ans. 5.) Fire suggests that due to the vehement response of mammals to dsRNA “[a]ny gene-specific dsRNA response in mammals would need to exist in cells or conditions where PKR is less effective, or would need to work in the shadow of the PKR-induced global response.” (Fire, page 363, col. 1.) According to the Specification, page 3, it is known that “[p]art of the interferon response is the activation of a dsRNA responsive protein kinase (PKR) (Clemens, Int J Biochem Cell Biol 29, 945-949 (1997)).” Thus, Fire would reasonably appear to suggest that to avoid the vehement response of mammals to dsRNA one of ordinary skill in the art should select a cell where the PKR response and interferon response is less effective. The Examiner asserts that, “the lack of a PKR response in undifferentiated cells was known well before the priority date of the instant application,” citing Haggarty, Harada, Barlow, and Francis to support this position. (Ans. 6.) Appeal 2012-010432 Application 11/933,153 10 Barlow, in particular, “tested the competence of early embryonic and associated maternal tissues to synthesise interferon” (page 229, col. 1) and evidences that Induced synthesis [of interferon] is initially absent in most tissues of the early 7th-day embryo, with the exception of the trophoblast, which shows a low level (33%) of inducible synthesis. It should be also noted that control virus-induced maternal tissues in the 7th day showed a reduced level of induced synthesis [of interferon] compared to the late 7th and early 8th day of development . . . . (Page 231, col. 2.) For a dsRNA introduced at day 1 or day 2 of development, four days after introduction of the dsRNA (as claimed) would be approximately day 6 of embryonic development. Barlow suggests that induced synthesis of interferon is initially absent in most tissues of the early 7th day mouse embryo and that induced synthesis of interferon is developmentally regulated. (Page 231, col. 2.) From this, one of ordinary skill in the art would understand that on day 6 of embryonic development, the induced synthesis of interferon would be at least reduced compared to older embryos, if not completely absent. One of ordinary skill in the art would also have understood that because the interferon response is reduced or absent there would be little or no PKR response (FF5), and no vehement response to dsRNA, and therefore an introduced dsRNA would not be prevented from inhibiting a target gene. Thus, consistent with the suggestion in Fire and Barlow, a day six embryo would have been recognized by those of ordinary skill in the art as a cell “or conditions where PKR is less effective.” (FF2.) Therefore, we find that the Examiner has presented a prima facie case of obviousness. Appeal 2012-010432 Application 11/933,153 11 “[W]hen a prima facie case is made, the burden shifts to the applicant to come forward with evidence and/or argument supporting patentability.” In re Glaug, 283 F.3d 1335, 1338 (Fed. Cir. 2002). Rebuttal evidence is “merely ‘a showing of facts supporting the opposite conclusion.’” In re Piasecki, 745 F.2d 1468, 1472 (Fed. Cir. 1984). In rebuttal, Appellants assert that the perception at the time of the filing of the present application was that RNAi cannot be made to work in mammals. As such, one of ordinary skill in the art would have no reasonable expectation of success in practicing the claimed method of inhibiting the expression of a target gene in a mammalian cell using a double stranded RNAi molecule. (Br. 6.) Appellants contend that “Exhibits A-C[2], as well as the Fire Article itself, clearly show that it is unequivocal that this skepticism existed in the art for some years after its publication and such skepticism pervaded the art.” (Br. 7.) We are not persuaded. Appellants have requested consideration of three references as evidence that skepticism existed for several years after the Fire publication. (Br. 7.) Appellants characterize the references as follows: 1) Silva et al. . . . state that “[T]he use of RNAi as an experimental or therapeutic tool in mammalian systems was initially problematic owing, ironically, to the presence of an endogenous antiviral response”. See column 1, page 506. 2) Sharp . . . state that “[I]n vertebrate systems, dsRNA was long ago recognized as a potent signaling molecule in the 2 The references by Silva, Sharp and Caplen, cited previously. Appeal 2012-010432 Application 11/933,153 12 induction of interferons and execution of the antiviral state.” See column 1, page 141. 3) Caplen et al. . . . introduced dsRNA molecules into mammalian tissue culture cells from three different species: human, hamster, and mouse but failed to produce any evidence for RNAi. Instead, they found that the dsRNAs produced either no effect, or a non-specific decrease in gene expression. See id at 102, section 3.6 and Fig. 7. (Br. 7.) While Silva agrees with Fire that “dsRNA activates Protein Kinase R (PKR) and RNase L pathways, leading to . . . apoptosis” (Silva, page 506, col. 1), for the reasons discussed above, a skilled artisan would not expect an early (pre-day 7) embryo to synthesize interferon or produce a PKR reaponse. Sharp further acknowledges the teachings of Fire that “[i]n vertebrate systems, dsRNA was long ago recognized as a potent signaling molecule in the induction of interferons and execution of the antiviral state.” (Sharp 141, col. 1) Caplen also recognizes a response to dsRNA in mammalian cells is mediated by PKR. (Page 96, col. 1.) However, none of the cited references evidences that there would be a dsRNA interferon response in cells which do not present a PKR response. In other words, acknowledgement of the known PKR response to dsRNA in the cited references would not lead those skilled in the art to doubt the success of obtaining a dsRNA response in cells without a PKR response, as suggested by Fire. In KSR, the Supreme Court addressed the “obvious to try” issue: When there is a design need or market pressure to solve a problem and there are a finite number of identified, predictable solutions, a person of ordinary skill has good reason to pursue the known options within his or her technical grasp. If this Appeal 2012-010432 Application 11/933,153 13 leads to the anticipated success, it is likely the product not of innovation but of ordinary skill and common sense. In that instance the fact that a combination was obvious to try might show that it was obvious under § 103. KSR, 550 U.S. at 421. In the present case, the finite, predictable solution is that it is known that early embryo cells do not evidence a PKR/interferon response (Barlow). Since Fire suggests that a gene-specific dsRNA response in mammals would need to exist in cells or conditions where PKR is less effective, one of ordinary skill in the art would have had a good reason to pursue the known option of selecting an early embryo cell which exhibit a lessened (or absent) PKR response to obtain effective dsRNA gene silencing. In the present case, the use of early embryo cells with little or no PKR response, led to the anticipated success. For this reason, we do not agree that Appellants have presented evidence of an unexpected result (see Br. 12). Appellants further argue that the Examiner has engaged in hindsight and has used Appellants’ Specification as a blueprint to assemble the prior art publications to arrive at the claimed method. (Br. 12.) Again we are not persuaded. The suggestion to combine the cited references has come from the disclosure of Fire, which would reasonably appear to suggest that one of ordinary skill in the art select a cell where the PKR response and interferon response is less effective. We find no evidence of hindsight here. We acknowledge Appellants’ other arguments concerning Ao that antisense oligonucleotides and dsRNA are not functional equivalents (Br. 10) and that Haggarty used embryonic carcinoma cells which vary significantly from early embryo cells (Reply Br. 3–4) but do not find them Appeal 2012-010432 Application 11/933,153 14 convincing. We find that Haggarty is not necessary to support the rejection of the Examiner, notwithstanding its disclosure that both embryonic carcinoma cells and early embryos share the inability to produce interferon (Haggarty, page 10576). Ao discloses that antisense DNA, RNA, or oligonucleotides inhibit gene expression in mouse oocytes and preimplantation embryos. (Ao, page 159.) The Examiner primarily relied upon Ao et al. to teach that after administration of an antisense oligonucleotide in the preimplantation mouse embryo, expression of a target gene is inhibited after four days when compared to control embryos. This teaching provides one of skill in the art with a reasonable expectation of success of observing inhibition of target gene expression in a mammalian cell at least 4 days after introduction of a nucleic acid inhibitor of gene expression as instantly claimed. Therefore, all the functional elements of Appellant’s claimed method are accounted for in the prior art relied upon on the record. (Ans. 13.) The Examiner goes on to show that the induced interferon response is absent in most tissues of the early 7th day mouse embryo (Barlow) and by deduction, the embryo of Ao. While there are acknowledged differences between antisense DNA, RNA or oligonucleotides, Ao groups them together with respect to their ability to inhibit gene expression in mouse oocytes and preimplantation embryos (e.g., those with no PKR/interferon response). In view of the above, we conclude that Appellants have failed to rebut the Examiner’s prima facie case of obviousness by a preponderance of the evidence, and the obviousness rejection is affirmed. Appeal 2012-010432 Application 11/933,153 15 CONCLUSION OF LAW The cited references support the Examiner’s obviousness rejection which has not been rebutted by Appellants by a preponderance of the evidence. 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 cdc Copy with citationCopy as parenthetical citation