Cold Spring Harbor Laboratory (CSHL) is a storied institution in molecular biology, being the site of annual meetings related to this view of life since Schrodinger proposed to use quantitative methods to examine biology in the wake of the despair in physics occasioned by the use of nuclear weapons to end World War II. Last month the Patent Trial and Appeals Board of the U.S. Patent and Trademark Office denied four petitions for inter partes review brought by Benitec Biopharma Limited against four CSHL patents directed to gene silencing methods using short hairpin RNA (shRNA).
The four petitions were directed to related patents (U.S. Patent Nos. 8,153,776; 8,202,846; 8,383,599; and 8,829,264), wherein "[t]he ʼ599 patent issued from a continuation of application No. 10/055,797, filed Jan. 22, 2002 [and t]he '846, '776, and '264 patents derive from a continuation-in-part of Application No. 10/055,797 (Application No. 10/997,086, filed Nov. 23, 2004) and share substantially the same specification."
The IPRs are identified by the following case numbers and illustrated by the following representative claims for each petition:
Case IPR2016-00014 (Patent 8,202,846)
Claim 1:
1. A method for attenuating expression of a target gene in a mammalian cell, the method comprising:
introducing into a mammalian cell an expression vector comprising:
(i) an RNA polymerase promoter, and
(ii) a sequence encoding a short hairpin RNA molecule comprising a double-stranded region, wherein the double-stranded region consists of at least 20 nucleotides but not more than 29 nucleotides,
wherein the short hairpin RNA molecule is a substrate for Dicer-dependent cleavage and does not trigger a protein kinase RNA-activated (PK) response in the mammalian cell,
wherein the double-stranded region of the short hairpin RNA molecule comprises a sequence that is complementary to a portion of the target gene, and
wherein the short hairpin RNA molecule is stably expressed in the mammalian cell in an amount sufficient to attenuate expression of the target gene in a sequence specific manner, and is expressed in the cell without use of a PK inhibitor, whereby expression of the target gene is inhibited.
Case IPR2016-00015 (Patent 8,383,599)
Claim 1:
1. A population of mammalian cells stably transfected or stably transduced with a library of expression constructs, wherein each expression construct encodes a short hairpin RNA, each expression construct comprising:
(i) an RNA polymerase promoter, and
(ii) a sequence encoding a short hairpin RNA molecule comprising a double-stranded region, wherein the double-stranded region consists of at least 20 nucleotides but not more than 29 nucleotides,
wherein the short hairpin RNA molecule is a substrate for Dicer-dependent cleavage and does not trigger a protein kinase RNA-activated (PKR) response in the mammalian cells,
wherein the double-stranded region of the short hairpin RNA molecule comprises a sequence that is complementary to a portion of the target gene in the mammalian cells, wherein the target gene is an endogenous gene of the mammalian cells, and
wherein said population of mammalian cells comprises cells in which the short hairpin RNA molecule is stably expressed in the mammalian cell in an amount sufficient to attenuate expression of the target gene in a sequence specific manner without use of a PK inhibitor.
Case IPR2016-00016 (Patent 8,153,776)
Claim 1:
1. A method for attenuating expression of a target gene in a mammalian cell, the method comprising
introducing into mammalian cells a library of RNA expression constructs, each expression construct comprising:
(i) an RNA polymerase promoter, and
(ii) a sequence encoding a short hairpin RNA molecule comprising a double-stranded region wherein the double-stranded region consists of at least 20 nucleotides but not more than 29 nucleotides,
wherein the short hairpin RNA molecule is a substrate for Dicer-dependent cleavage and does not trigger a protein kinase RNA-activated (PKR) response in the mammalian cell,
wherein the double-stranded region of the short hairpin RNA molecule comprises a sequence that is complementary to a portion of the target gene, and
wherein the short hairpin RNA molecule is stably expressed in the mammalian cell in an amount sufficient to attenuate expression of the target gene in a sequence specific manner, and is expressed in the cell without use of a PK inhibitor, whereby expression of the target gene is inhibited.
Case IPR2016-00017 (Patent 8,829,264)
Claim 1:
1. A transgenic mouse comprising a germline or somatic cell, wherein the germline or somatic cell comprises a transgene, wherein the transgene comprises a sequence encoding a short hairpin RNA (shRNA) molecule,
wherein the shRNA molecule comprises a double-stranded region, wherein the double-stranded region consists of at least 20 nucleotides but not more than 29 nucleotides,
wherein the shRNA molecule is a substrate for Dicer-dependent cleavage and dose not trigger a protein kinase RNA-activated (PK) response in the mammalian cell,
wherein the double-stranded region of the shRNA molecule comprises a sequence that is complementary to a portion of a target gene, and
wherein the shRNA molecule is stably expressed in said germline or somatic cell without use of a PK inhibitor and in an amount sufficient to attenuate expression of the target gene in a sequence specific manner.
Similarly, the asserted prior art was the same:
• Zamore et al., US 7,691,995, for anticipation under § 102(e);
• Graham et al., US 6,573,099, for anticipation under § 102(b);
and varying combinations of:
Graham and/or Zamore, Tuschl et al., US 2002/0085356 A1; Fire et al., US 6,506,559; Harborth et al., 2001, Identification of essential genes in cultured mammalian cells using small interfering RNAs, 114 J. CELL SCI. 4557–4565; Parrish et al., 2000, Functional Anatomy of a dsRNA Trigger: Differential Requirement for the Two Trigger Strands in RNA Interference, 6 MOLECULAR CELL 1077–1087; Sijen et al., 2001, On the Role of RNA Amplification in dsRNA-Triggered Gene Silencing, 107 CELL 465–476; Green & Mathews, 1992, Two RNA-binding motifs in the double-stranded RNA-activated protein kinase, DAI, 6 GENES & DEVELOPMENT 2478–2490; Waterhouse et al., 2001, Gene Silencing As an Adaptive Defense Against Viruses, 411 NATURE 834; Symonds et al., US 7,345,025; Tian et al., 2000, Expanded CUG repeat RNAs form hairpins that activate the double-stranded RNA-dependent protein kinase PKR, 6 RNA 79–87; Svoboda et al., 2001, RNAi in Mouse Oocytes and Preimplantation Embryos: Effectiveness of Hairpin dsRNA, 287 BIOCHEM & BIOPHYS. RES. COMM. 1009–1104; Zernicka-Goetz et al., US 2003/0027783 A1; and/or Wianny & Zernicka-Goetz, 2000, Specific interference with gene function by double-stranded RNA in early mouse development, 2 NATURE CELL BIO. 70–75.
In each case, the Board's decision begins with an express statement regarding claim construction:
In an inter partes review, the Board interprets a claim term in an unexpired patent according to its broadest reasonable construction in light of the specification of the patent in which it appears. 37 C.F.R. § 42.100(b); In re Cuozzo Speed Techs., LLC, 793 F.3d 1268, 1275–79 (Fed. Cir. 2015), cert. granted sub nom. Cuozzo Speed Techs., LLC v. Lee, 136 S. Ct. 890 (mem.) (2016). Under that standard, and absent any special definitions, we assign claim terms their ordinary and customary meaning, as would be understood by one of ordinary skill in the art at the time of the invention,16 in the context of the entire patent disclosure. In re Translogic Tech., Inc., 504 F.3d 1249, 1257 (Fed. Cir. 2007). Only terms which are in controversy need to be construed, however, and then only to the extent necessary to resolve the controversy. Vivid Techs., Inc. v. Am. Sci. & Eng'g, Inc., 200 F.3d 795, 803 (Fed. Cir. 1999).
In the present matter, the parties do not dispute the meaning of any claim term nor, for the purposes of our decision, do we find that any term requires express construction.
And in each case, the Zamore reference is defeated as prior art, because the Board agreed with the patentee that the reference was not supported by its priority document, and thus whatever was disclosed did not qualify as invention before the filing date (and constructive earliest invention date) of the patents at issue. The Board notes that the Petitioner did not present testimonial evidence from an expert to support its position that the person having ordinary skill in the art would have appreciated that the Zamore inventors had possession of the invention claimed in the '995 patent at their earliest priority date based on the disclosure of provisional application 60/305,185.
The grounds for rejecting Petitioner's arguments with regard to anticipation based on the Graham reference are specifically tailored to each claim set (e.g., the absence of any teachings in the reference of a transgenic mouse in the IPR directed towards the '264 patent). In common in all these decisions is the disclosure in Graham of hairpin structures in the disclosed constructs as being a problem to be avoided rather than a feature to be exploited for regulating gene expression. (And again, the Board notes the absence of expert testimony to support Petitioner's arguments regarding anticipation by the Graham reference.)
Turning to the obviousness grounds, the Board notes that "Patent Owner contends that Petitioner's 'kitchen sink' approach obscures the bases for the underlying obviousness challenge and, thus, requests that we deny the Petition as violating the particularity provisions of 35 U.S.C. § 312(a)(3) and 37 C.F.R. § 42.22(a)(2)," which argument is "not without merit" according to the Board. However, in each case the opinions set forth the limitations of the cited art as applied to the claims in each of the petitions, finding that in none of them had Petitioner carried its burden of establishing obviousness by a preponderance of the evidence. Of note in this regard is the Board's treatment of the combination of the Svoboda, Zernicka-Goetz, and Wianny references for teaching gene silencing using shRNAs, and separately the combination of the Tuschl, Fire, and Parrish references for teaching the length of gene silencing shRNAs. Regarding the first combination, the Board finds in each reference the deficiency that the reference does not teach a hairpin structure as required by the claims in any of the patents challenged in any of the IPRs. With regard to the second set of combined references, the Board found similar deficiencies, but was also persuaded by the testimony (unchallenged, according to the Board) of CHSL's expert based on "the leading literature in the field [, which] would have taught away from using an expressed short hairpin molecule, which to have gene silencing activity, must first be processed in the cell."
Finally, the Board found that Petitioner had not shown why the skilled worker would turn to the Tian or Green references, which are not directed "to the design of constructs for RNA interference", and that the Sijen reference (relating to C. elegans) are inapposite because these organisms do not possess the innate anti-viral response involving a double-stranded RNA activated protein kinase that the shRNA molecules and uses thereof are intended to avoid.
These decisions illustrate what many believed would be the case: the original high instance of patent claim invalidation by the Board was in large part an artifact of the selection process whereby the most egregious patents (having any commercial value) would be challenged first, and that biotech and pharma patents would be harder to invalidate due to the complexity of the technology and the generally thorough prosecution scrutiny to which patents in this area are subjected. IPR proceedings against commercially important patents on inventions in the biotechnology and pharmaceutical space are sure to continue to increase in number, and these decisions contain lessons that both petitioners and patent owners would to well to learn.
