On January 9th, Junior Party the University of California/Berkeley, the University of Vienna, and Emmanuelle Charpentier (collectively, "CVC") filed a Motion in Opposition to Senior Party The Broad Institute, Harvard University, and the Massachusetts Institute of Technology (collectively, "Broad") Substantive Motion No. 3 in support of the Patent Trial and Appeal Board ("Board") de-designating certain claims as not corresponding to Count 1 in Interference No. 106,155 as declared.

To recap, in its Motion No. 3, the Broad reiterated the arguments made in Motion No. 2, that there are two embodiments of CRISPR, one involving single-molecule RNA guide RNA that corresponds to Count 1 (which the Broad argues here is not recited in the claims it wants the Board to designate as not corresponding to the Count) and further that certain of the Broad's claims directed to "SaCas9" systems that require two or more nuclear localization signals (NLSs) do not correspond to the Count.  The Broad parsed the Broad's claims into three categories of claims that do not correspond to the Count, depending on how the Board rules on Substantive Motions Nos. 1 and 2:

• USP 8,865,406 – Claims 1-30 (all); 8,871,445 – Claims 1-30 (all); USP 8,889,356 – Claims 1-30 (all); USP 8,932,814 – Claims 1-30 (all); USP 8,945,839 – Claims 1-28 (all); USP 8,993,233 – Claims 1-43 (all); USP 8,999,641 – Claims 1-28 (all); USP 8,697,359 – Claims 1-3, 5-10, 12-17, and 19-20; USP 8,771,945 – Claims 1-4 and 6-29; USP 8,895,308 – Claims 1-9 and 11-28; USP 8,906,616 – Claims 1, 3-4, 6-30; USP 9,840,713 – Claims 1-7, 10-15, 17-26, and 28-41; and U.S. Patent Application No. 14/704,551: in the event that the Board denies both Motions No. 1 and 2

• USP 8,865,406 – Claims 1-30 (all) and USP 8,895,308 – Claims 1-30 (all): in any event, claims reciting Ca9 from Staphylococcus aureus

• USP 8,871,445 – Claims 1-30 (all); USP 8,932,814 – Claims 1-30 (all); USP 8,993,233 – Claim 7; USSN 14/704,551 – Claims 9-11: clams reciting two or more nuclear localization signal

And what would remain, should the Board grant this motion:

• U.S. Patent No. 8,697,359, claims 4, 11, and 18; U.S. Patent No. 8,795,965, claims 1-30 (all); U.S. Patent No. 8,771,945, claim 5; U.S. Patent No. 8,906,616, claims 2 and 5; and U.S. Patent No. 9,840,713, claims 8-9, 16, and 27

The Broad argued with regard to the first category of these claims (comprising the majority of the claims the Broad wants to have de-designated) that the Count of the interference as declared is directed to "single-molecule guide RNA molecule" embodiments of CRISPR that do not encompass these single-molecule guide RNA embodiments and thus do not corresponding to the Count.  The brief sets forth the Broad's understanding that, should the Board deny the Broad's Substantive Motions Nos. 1 and 2, then the interference will involve priority to such single-molecule guide RNA embodiments as a separate, patentable invention over claims that encompass both single-molecule and dual molecule embodiments (termed "generic guide" embodiments in the brief).  The Broad argues that its claims limited to dual-molecule embodiments do not correspond to the Count and the Board should so designate.

The Broad asserts as reasons/justifications for de-designating certain (most) of its claims:

• Count 1 is limited to the single-molecule invention, and would not be determining priority to generic, non-limited RNA embodiments of CRISPR, "violating" the "'primary purpose of an interference'" to make a priority determination of "each of the common [patentably distinct] inventions claimed by the parties,'" citing Godtfredsen v. Banner, 598 F. 2d 589, 592 (C.C.P.A. 1979).  The brief takes the opportunity to reiterate the unfairness of this outcome in view of the nature of their invention, e.g., a "breakthrough invention that revolutionized gene editing was the successful engineering of CRISPR-Cas9 systems for use in eukaryotic cells."

• There can be no interfering subject matter between the single-molecule RNA "invention" and generic, non-limited RNA CRISPR embodiments.  Under these circumstances, the brief argues a two-count interference should be declared with each invention to reiterate its allegation that CVC had made a strategic decision not to present claims to eukaryotic embodiments of CRISPR in the earlier, '048 interference.

• It would be unfair to put all the Broad's claims at risk under these circumstances because it would "t[ie] its hand to its best generic RNA proofs," which the brief characterizes as being "particularly egregious given that Broad could have relied on its best proofs during the 048 Interference, when the Count properly reflected the scope of the parties' claims."

The Broad also argued that its claims to SaCas9 embodiments and to claims requiring two or more nuclear localization sequences (NLS's) do not correspond to Count 1.  The Broad argues that these embodiments were not disclosed in the prior art and "provide[] a surprising combination of benefits not taught or suggested by the art" for both types of embodiments.

CVC's argument centers on proper application of Rule 207(b)(2):

A claim corresponds to a count if the subject matter of the count, treated as prior art to the claim, would have anticipated or rendered obvious the subject matter of the claim.  37 C.F.R. §41.207(b)(2).

This is the standard, and CVC argues first that on this basis the Board should deny the Broad's motion, and moreover that the Broad had not satisfied its burden that it is entitled to the relief requested under 37 C.F.R. §§ 41.121(b) and 41.208(b).  And the Broad will not be able to meet this burden, CVC argues, because a claim to a species (single-molecule guide RNA CRISPR embodiments) anticipates a claim to a genus (generic-guide RNA CRISPR embodiments), citing In re Gostelli, 872 F.2d 1008 (Fed. Cir. 1989).

CVC further parses the language of the Rule to distinguish that this section does not set forth a (rebuttable) presumption despite the title of this rule being "Presumptions."  CVC draws a parallel with Rule 207(a), wherein subsection (1) sets forth the presumptions and subsection (2) sets forth the standard (for priority in subsection (a) and for claim correspondence in subsection (b)); the brief recited several citations to case law to support this interpretation, including Yorkey v. Diab, 601 F.3d 1279, 1286-87 (Fed. Cir. 2010), citing Bosies v. Benedict, 27 F.3d 539, 541 (Fed. Cir. 1994); and Brown v. Barbacid, 276 F.3d 1327, 1333 (Fed. Cir. 2002).  In addition, the brief asserts that a plain text reading of Rule 207(b)(2) is enough and controlling with regard to the Board's decision, citing Octane Fitness LLC v. ICOM Health & Fitness, Inc., 572 U.S. 545, 553 (2014), and the Standing Order Para. 208.3.2.  The brief also counters the Broad's arguments regarding comments made during rulemaking, that such comments cannot override the text of the rule, citing two Executive Orders from the Trump Administration (E.O. 13891, Promoting the Rule of Law through Improved Agency Guidance Documents, 84 Fed. Ref. 55235 (Oct. 15, 2019) and 13892, Promoting the Rule of Law through Transparency and Fairness in Civil Administrative Enforcement and Adjudication, 84 Fed. Reg. 55239 (Oct. 15, 2019)).

CVC counters the Broad's arguments that the Board should grant its Motion No. 3 because Count 1 does not correspond to its "best proofs" because, inter alia, the Broad hasn't offered any evidence that it has better proofs that it would be able to offer under Count 1.  CVC also asserts that the Broad assumes, without proving or even arguing, that the generic-guide claims are patentably distinct over single-molecule guide embodiments of CRISPR.  In addition, CVC argues that the Broad's assertion of this argument is inconsistent with the Broad's argument in its Substantive Motion No. 2 that claims to single-molecule guide embodiments of CRISPR are not patentably distinct over generic-guide embodiments.  "Broad cannot have it both ways," says CVC with regards to these allegedly inconsistent arguments.  Further, with regard to the Broad's "best proofs" argument, CVC contends that it is fair to have all the Broad's claims stand or fall in this interference because the Broad has not established its "best proofs" argument and it has the burden to do so to be entitled to the relief of de-designating the claims.

Turning to the Broad's expert testimony, CVC asserts that the Board cannot, and should not rely on the Broad's experts because these experts did not review documentary evidence supporting the Broad's assertions that the Broad inventors practiced generic-guide RNA CRISPR in 2011 (prior to CVC's earliest priority date), as the Broad alleges in its motion.  There are also contradictions, according to CVC, between what the expert testified is disclosed in an NIH grant proposal in this interference and what the Broad declared before the USPTO during ex parte prosecution of USSN 14/704,551 regarding this document.  The declarations submitted during prosecution were the basis for the Examiner to determine that the Broad could antedate CVC's earlier single-molecule guide RNA disclosures and thus were patentable over them.  And CVC contends that the Board should consider these declarations in ex parte prosecutions to be admissions.  The brief also argues that judicial estoppel precludes the Broad from relying on the purportedly contradictory expert testimony, citing Zedner v. U.S. and setting forth how circumstances in this interference satisfy the Supreme Court's Zedner test.  Specifically, estoppel should lie when a party's legal position is "clearly inconsistent with" a prior position; the party prevailed based on its prior position; and the opposing party (here, CVC) would be clearly disadvantaged, imposing an unfair detriment against them, by permitting a party to take a position in this proceeding contrary to its position in the earlier proceeding.  All those factors align in CVC's favor, according to their brief, under circumstances regarding the position the Broad has taken with regard to this brief in this interference and the contrary position taken by Senior Party during ex parte prosecution.

These circumstances also seem to put the Broad's experts in a bad position because they were not given access to information that might have reduced or eliminated their ability to make the representations they did in their testimony in this interference, including ones showing that Broad inventors had not been able to practice CRISPR in eukaryotic cells in the June 2012 timeframe.

CVC notes (in a "sauce for the goose" manner) that should the Board determine that the Broad's generic-guide claims be de-designated, then CVC's generic guide claims should be de-designated as well, requiring the Board to provide another interference count or declare another interference.  However, the presumption is that the PTAB properly designated the claims corresponding to the count and the burden is on a party requesting de-designation relief to establish they are entitled to such relief.  Much of these issues depend on claim construction, and according to CVC the term "guide RNA" did not have a plain and ordinary meaning but was dependent on definitions in the Broad's specification(s) that don't support Broad's construction.  Furthermore, the Broad's arguments in this regard should fail, according to CVC's brief, because all the claims recite "chimeric" RNA which comprise single-molecule embodiments, citing definitions in the specifications of the Broad's patents and applications in interference.

With regard to the Broad's arguments concerning S. aureus Cas9 claims and claims reciting multiple nuclear localization signal (NLS), that the Broad argues should be de-designated as not corresponding to Count 1, CVC makes its case that these proteins were known in the art and their smaller size and capacity to be introduced using adeno-associated virus (AAV) vectors would have motivated a person of ordinary skill in the art (POSA) to use them for eukaryotic CRISPR and further that there would be a reasonable expectation of success in doing so.  CVC also makes a detailed case with regard to why the Sa Cas9 species are not patentably distinct, and makes similar arguments regarding CRISPR embodiments comprising multiple NLS species.

Finally, throughout the brief CVC reiterates the theme that the Broad's motions are all attempts to avoid having the Board determine priority of eukaryotic cell embodiments of CRISPR.