Broad Files Reply Brief in Interference No. 106,115 Cross-Appeal

McDonnell Boehnen Hulbert & Berghoff LLP

McDonnell Boehnen Hulbert & Berghoff LLP


In its contingent cross-appeal from the Patent Trial and Appeal Board's (PTAB) adverse decision on priority against Junior Party the University of California/Berkeley, the University of Vienna, and Emmanuelle Charpentier (collectively, "CVC") in Interference No. 106,115 (directed to CRISPR-mediated gene editing), Senior Party Broad Institute, Harvard University, and MIT (collectively, "Broad") argues that the PTAB erred in denying two Preliminary Motions in that interference.  The first, Broad's Motion No. 2 would have changed the Count to encompass double-guide RNA (dgRNA) species of the CRISPR-Cas9 complex, and the other (Motion No. 3) would have designated certain (a majority) of Broad's claims as not corresponding to the Count.  On July 24th, Broad filed its Reply brief to CVC's responsive brief against Broad's appeal.

The basis for Broad's appeal (which the brief acknowledges the Federal Circuit will not address unless the Court overturns the Board's decision in its favor on priority) is that the Board did not give the term "guide RNA" it broadest reasonable interpretation.  This argument relies on what Broad contends was the understanding of the term at the time the invention was conceived and reduced to practice (~late 2012), which would have included both dgRNA and single-guide RNA (sgRNA) species, the latter being the species the Board declared the Count to exclusively encompass.  Broad further argues that the Board's limited construction was not consistent with the definition of guide RNA in its specification(s), and also argues, counter to CVC's contentions, that the Court has discretion to address the claim construction issue regardless of whether that interpretation would affect the Board's decisions on these Motions.  The importance of the interpretive scope given the term "guide RNA" is that if the Count was broadened to include dgRNA Broad's evidence regarding its purported earlier reduction to practice of dgRNA embodiments of eukaryotic CRISPR could be used to establish their priority claim.  Regarding Motion No. 3, a decision in Broad's favor would have left Broad with dominating claims for CRISPR performed using either guide RNA species (similar to the position CVC was in at the conclusion of the earlier interference between these parties, No. 106,048, with regard to claims to eukaryotic cells versus claims not limited to biological species).  Broad also argues the ultimate issue, that the Board erred in not granting its motions.

On the specifics, the brief cites Microsoft Corp. v. Proxyconn, Inc., 789 F.3d 1292, 1301-02 (Fed. Cir. 2015), for the principle that "if there are different reasonable constructions of a claim term to the POSITA in light of all of the evidence, the Court must adopt the broadest of those constructions."  The brief also cites the Jinek 2012 reference (from CVC's Doudna lab; Jinek et al., 2012, "A Programmable Dual-RNA–Guided DNA Endonuclease in Adaptive Bacterial Immunity," Science 337(6096): 816-21))) that the term "guide RNA" would be understood by one of ordinary skill in the art to encompass both dgRNA and sgRNA CRISPR embodiments.  Broad argues than Jinek was the only reference prior to Broad's asserted conception that disclosed the sgRNA species, and that all other prior references disclosed the dgRNA form.  Moreover, Broad contends that Jinek disclosed this sgRNA as only an alternative to dgRNA-based CRISPR.  Further, the brief counters CVC's position in its responsive brief that Broad's specification provided an express definition that overcame the more generic meaning by arguing that "[where] a plain and ordinary meaning exists and the specifications as a whole do not clearly provide a different and narrower meaning, the plain meaning controls," citing Home Diagnostics, Inc. v. LifeScan, Inc., 381 F.3d 1352, 1356-58 (Fed. Cir. 2004), and  Thorner v. Sony, 669 F.3d 1362 (Fed. Cir. 2012).  Broad's specification, the brief maintains, provides no support for the CVC's contention (or the Board's conclusion) that "guide RNA" should be limited to the sgRNA form.  Under these circumstances and the cited precedent the Board erred in choosing the narrower sgRNA-only construction, according to Broad.

Broad appears to be on weaker rhetorical ground in challenging CVC's contention and the Board's conclusion that Broad's own specification equates "guide RNA" with "sgRNA," based on this sentence:

In aspects of the invention the terms "chimeric RNA," "chimeric guide RNA," "guide RNA," "single guide RNA," and "synthetic guide RNA" are used interchangeably and refer to the polynucleotide sequence comprising the guide sequence, the tracr sequence and the tracr mate sequence [emphasis in brief].

Broad's argument is that dgRNA and sgRNA fall within the scope of this definition because they both encompass "the guide sequence, the tracr sequence and the tracr mate sequence."  While this may be functionally true to the extent this disclosure was related to the structure of the guide RNA, it seems unsupported that sgRNA and dgRNA were used interchangeably.  And Broad's further arguments, that the sentence lacks such characteristics as reciting a phrase like "as used herein" to negate the disclosure's provision of a definition would not appear to negate the construction CVC asserts and the Board applied, even in the context of the Broad specifications using such definitional phrases elsewhere.  Broad's further contention that the word "interchangeably" can be reasonably interpreted to mean "that the concepts are used interchangeably only in certain contexts, and do not mean the same thing for all purposes" seems similarly uncompelling compared with the Board's interpretation.  Broad also argues that using the term "aspects" does not require an interpretation to apply to all aspects; while this may be true it seems to be a heavy burden for the Court to rebut the Board's interpretation in the context of the other rationales used in the interference.  Finally, the brief parses the meaning of "the" in the phrase "the polynucleotide sequence."  The brief distinguishes the cases (Rumsfeld v. Padilla, 542 U.S. 426 (2004), Shum v. Intel Corp., 629 F.3d 1360 (Fed. Cir. 2010)) cited by CVC to support its interpretation.  On the basis of all these arguments, Broad contends that "[t]he question before the Court is whether "guide RNA" must exclusively be read as limited to the single-molecule configuration.  Taking the specifications as a whole, the answer to that question is a resounding 'no.'"

The brief then parses through various portions of Broad's specification(s) that disclose or could be construed to disclose dgRNA species as alternatives to sgRNA species and further argues the significance of dgRNA embodiments to Broad's proofs of earlier conception.  In doing so, Broad contends that the existence of examples of dgRNA CRISPR species is what is relevant, not experimental results and whether the skilled worker would have considered the dgRNA species to be operable.  Broad further argues that the PTAB erred under the rubric that "construction like the PTAB's here that reads out embodiments, especially preferred embodiments, is 'rarefy, if ever, correct,'" citing Vitronics Corp. v. Conceptronic, Inc., 90 F.3d 1576, 1583 (Fed. Cir. 1996); MBO Labs., Inc. v. Becton, Dickinson & Co., 474 F.3d 1323, 1333 (Fed. Cir. 2007); and Oatey Co. v. IPS Corp.,514 F.3d 1271, 1276 (Fed. Cir. 2008).  Finally, the brief cites disclosure in the specifications regarding dgRNA CRISPR embodiments that reflect experiments performed in 2011-2012 that provide an earlier priority date for the proposed Count having broadened scope that would result in Broad being awarded on that basis.

The Broad concludes this portion of the brief by asserting the Court's discretion to revisit the Board's claim construction even if it would not affect the judgment on appeal, citing Thorner.

The brief then counters CVC's argument that the Board had "independent bases" to reach its conclusions in denying Broad's Motions No. 2 and No. 3, asserting that claim construction is a "threshold issue" as recognized by the Board.  This is so because the motion were directed, the brief asserts, to "to bring the scope of the count of the interference in line with the scope of the involved claims, under the proper claim construction."  Moreover, in the event that the Board denied Motion No. 2 (which it did) Broad sought in Motion No. 3 to remove claims that were not limited to sgRNA (i.e., wherein inter alia the claims recited "guide RNA" which, in Broad's view encompassed both species and should be removed from the interference under a Count limited to sgRNA for that reason).  Denying both motions was error on this basis according to Broad and supported the Court reversing these decisions:

"By simultaneously retaining Count 1 (denying Motion 2), while keeping Broad's generic RNA claims in the interference (denying Motion 3), the PTAB created a disconnect: Count 1 was not commensurate in scope with the involved claims and this worked a significant unfairness to Broad.  Under the PTAB's decision, the interference was not fulfilling its 'primary purpose' of determining the priority over 'the common inventions claimed by the parties,'" [in contravention of this purpose as enunciated by] Godtfredsen v. Banner, 598 F.2d 589, 592 (C.C.P.A. 1979) (overruled on other grounds).

The Federal Circuit is expected to hear oral arguments by year's end.

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DISCLAIMER: Because of the generality of this update, the information provided herein may not be applicable in all situations and should not be acted upon without specific legal advice based on particular situations.

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