CVC Files Substantive Preliminary Motion No. 3 to Substiture the Count

McDonnell Boehnen Hulbert & Berghoff LLP

McDonnell Boehnen Hulbert & Berghoff LLP

On November 19th, Junior Party the University of California, Berkeley; the University of Vienna; and Emmanuelle Charpentier (collectively, "CVC") filed its Substantive Preliminary Motion No. 3 in Interference No. 106,132 (which names Sigma-Aldrich as Senior Party), asking the Patent Trial and Appeal Board to substitute the Count of the interference pursuant to 37 C.F.R. §§ 41.121(a)(1)(iii) and 41.208(a)(1).

The present Count is set forth in the alternative either as Claim 156 on CVC's application-in-interference No. 15/981,807 (which claim also has been a portion of the Count in Interference No. 106,127 naming ToolGen as Senior Party) or Claim 31 in Sigma-Aldrich's involved Application No. 15/456,204*:

31. (previously presented) A method for modifying a chromosomal sequence in a eukaryotic cell by integrating a donor sequence, the method comprising introducing into the eukaryotic cell:
(i) a Clustered Regularly Interspersed Short Palindromic Repeats (CRISPR)/CRISPR-associated (Cas) (CRISPR-Cas) type II protein linked to only one nuclear localization signal (NLS) or a nucleic acid encoding the CRISPR-Cas type II protein linked to only one NLS, wherein the CRISPR-Cas type II protein is a Cas9 protein, and the nucleic acid encoding the CRISPR-Cas type II protein is codon optimized for expression in the eukaryotic cell;
(ii) a guide RNA or DNA encoding the guide RNA, wherein the guide RNA comprises a first region that is complementary to a target site in the chromosomal sequence, which target site in the chromosomal sequence is immediately followed by a protospacer adjacent motif (PAM), and a second region that interacts with the CRISPR-Cas type II protein, and wherein the guide RNA comprises a crRNA and a tracrRNA; and
(iii) a donor polynucleotide comprising the donor sequence and upstream and downstream sequences;
wherein the guide RNA guides the CRISPR-Cas type II protein to the target site in the chromosomal sequence, the CRISPR-Cas type II protein introduces a double stranded break at the target site, and repair of the double-stranded break by a DNA homology-directed repair (HOR) process leads to integration or exchange of the donor sequence into the chromosomal sequence.

In its motion, CVC proposes that this claim be substituted for claim 33, which has the additional limitation that "the guide RNA is a single molecule." CVC argues that substituting this Count is more symmetrical with CVC's portion of the Count and "avoids inconsistency" with the Counts in related interferences (see "CRISPR Battle Joined Again"; "The CRISPR Chronicles: Enter Toolgen"; and "Sigma-Aldrich Joins the CRISPR Interference Fray").

This "consistency" CVC seeks is that the Count reflect the limitation that the CRISPR complex recited therein comprise a single-molecule RNA species ("sgRNA") comprising the structural tracrRNA and the sequence-specific crRNA that, in combination with Cas9 protein introduces double-stranded breaks in DNA at specific sites in a target DNA. CVC notes that this consistent recitation of sgRNA species in Counts of the pending interferences is present whether the claims corresponding to the Count in each interference are limited to sgRNA or encompass "dual-molecule" RNA species (termed "generic-guide" claims). CVC argues that Sigma-Aldrich's claims are "outliers" in this regard, and that the Board has discretion to substitute the Count under appropriate circumstances (like these, according to CVC), citing Hitzman v. Rutter, 243 F.3d 1345, 1359 (Fed. Cir. 2001), without abusing its discretion.

In CVC's view, the benefits of substituting the Count as they suggest are "[e]fficiency, uniformity, and clarity" consistent with 37 C.F.R. § 41.1(b), while on the other hand "there are significant negative consequences of proceeding with this Interference if the Sigma side of the count is not conformed to the other pending interferences and continues to recite something other than a single guide system," naming two such negative consequences:

• First, proceeding with the existing count in this interference invites the parties to submit proofs that are different than those in the co-pending interferences. The inconsistency between the count in this interference and the co-pending interferences creates the possibility of irreconcilable decisions among interferences that involve the same claims for each party. Such inconsistency would be prejudicial to any party in CVC's position, and the public.

• Second, this uncertainty is magnified where the Sigma side of the count is subject to a disputed construction and is, as discussed in detail below, ambiguous as to whether it covers RNAs other than single-guide RNA. To avoid this ambiguity, the Board should substitute dependent claim 33 because it clearly recites a single-guide RNA molecule.

The brief explicates the details of these benefits and negative consequences with reference to the co-pending Interferences, their subject matter as defined by their Counts and the claims-in-interference in each, noting in addition that "[t]he PTAB chose to declare multiple, co-pending two-party interferences as an alternative to managing a single, multi-party interference" which would have avoided the possibility of [unnecessary differences in scope across the various counts [that] could lead to inconsistent results and . . . create uncertainty among the parties and the public."

In addition, CVC argues that the best use of so-called "McKelvey counts" as here is to choose claims from each party's pending or granted claims that are "as balanced and similar in scope as possible" (as, CVC argues, the Board has done in the '115, 126, and 127 interferences).

CVC argues that "Sigma will suffer no prejudice" by this substitution because its first provisional application (corresponding to the earliest priority date for which the Declaration of Interference gives the benefit of priority and Senior Party status) discloses sgRNA species-comprising CRISPR complexes (as well as dual-molecule species). Further, substituting this Count does not require the Board to de-designate any of the claims corresponding to the Count contained in the Interference Declaration, nor would substitution prevent the Board from granting (or denying) CVC's Motion No 4 to designate claims in Sigma-Aldrich's U.S. Patent Nos. 10,731,181 and 10,745,716 (arguing separately that these claims correspond to the Count). Nor would the substitution affect limitations in certain of Sigma-Aldrich's claims (using a codon-optimized nucleic acid to encode Cas9 protein having a nuclear localization sequence, for example), according to CVC.

The brief sets forth the claims of each party corresponding to Proposed Substitute Count 2 as follows:

CVC also notes that it is entitled to priority benefit as set forth in its Preliminary Motion No. 1 setting forth a table of correspondence between the express embodiments set forth in these provisional applications (U.S. Provisional Application 61/652,086 ("P1"), filed May 25, 2012 and, in the alternative, U.S. Provisional Application 61/716,256 ("P2"), filed October 19, 2012) and the limitations recited in Proposed Count 2:

as supported by particular disclosure in the specification and drawings as they would be understood by the skilled artisan in view of the teachings of the prior art.

Finally, pursuant to 37 C.F.R. § 41.208(c)(2), CVC argues that its proposed Substitute Count 2 is patentable over the prior art, inter alia, because it "is narrower than Count 1, and therefore does not raise any issues regarding patentability over the prior art."

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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