Berkeley Files Responsive Motion to Broad's Substantive Motion No. 2 in Interference

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As previously discussed, Senior Party The Broad Institute (joined by Harvard University and MIT) on October 14th filed Substantive Motion No 2 (to substitute the count) in the current interference over CRISPR technology (No. 106,115).

Count 1 of the interference as declared is:

An engineered, programmable, non-naturally occurring Type II CRISPR-Cas system comprising a Cas9 protein and at least one guide RNA that targets and hybridizes to a target sequence of a DNA molecule in a eukaryotic cell, wherein the DNA molecule encodes and the eukaryotic cell expresses at least one gene product and the Cas9 protein cleaves the DNA molecules, whereby expression of the at least one gene product is altered; and, wherein the Cas9 protein and the guide RNA do not naturally occur togetherwherein the guide RNAs comprise a guide sequence fused to a tracr sequence.

or

A eukaryotic cell comprising a target DNA molecule and an engineered and/or non-naturally occurring Type II Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR)-— CRISPR associated (Cas) (CRISPR-Cas) system comprising
    a) a Cas9 protein, or a nucleic acid comprising a nucleotide sequence encoding said Cas9 protein; and
    b) a single molecule DNA-targeting RNA, or a nucleic acid comprising a nucleotide sequence encoding said single molecule DNA-targeting RNA; wherein the single molecule DNA-targeting RNA comprises:
        i) a targeter-RNA that is capable of hybridizing with a target sequence in the target DNA molecule, and
        ii) an activator-RNA that is capable of hybridizing with the targeter-RNA to form a double-stranded RNA duplex of a protein- binding segment,
    wherein the activator-RNA and the targeter-RNA are covalently linked to one another with intervening nucleotides; and
    wherein the single molecule DNA-targeting RNA is capable of forming a complex with the Cas9 protein, thereby targeting the Cas9 protein to the target DNA molecule, whereby said system is capable of cleaving or editing the target DNA molecule or modulating transcription of at least one gene encoded by the target DNA molecule.

The Broad's proposed Count 2 is:

A method, in a eukaryotic cell, of cleaving or editing a target DNA molecule or modulating transcription of at least one gene encoded by the target DNA molecule, the method comprising:
    contacting, in a eukaryotic cell, a target DNA molecule having a target sequence with an engineered and/or non-naturally-occurring Type II Clustered Regularly lnterspaced Short Palindromic Repeats (CRISPR)-CRISPR associated Cas) (CRISPR-Cas) system comprising:
        a) a Cas9 protein, and
        b) RNA comprising
            i) a targeter-RNA that is capable of hybridizing with the target sequence of the DNA molecule or a first RNA comprising (A) a first sequence capable of hybridizing with the target sequence of the DNA molecule and (B) a second sequence; and
            ii) an activator-RNA that is capable of hybridizing to the targeter-RNA to form an RNA duplex in the eukaryotic cell or a second RNA comprising a tracr sequence that is capable of hybridizing to the second sequence to form an RNA duplex in the eukaryotic cell,
    wherein, in the eukaryotic cell, the targeter-RNA or the first sequence directs the Cas9 protein to the target sequence and the DNA molecule is cleaved or edited or at least one product of the DNA molecule is altered.

The distinction the Broad made in its Motion is between embodiments of CRISPR methods that are limited to "single-molecule guide RNA" (aka "fused" or "covalently linked" species), versus embodiments that encompass single-molecule and "dual molecule" species (wherein the in the latter versions the "targeter-RNA" and "activator-RNA" as recited in the proposed Count are not covalently linked).  The Broad argued that this Count should be adopted by the Board because it "properly describes the full scope of the interfering subject matter between the parties because both parties have involved claims that are generic, non-limited RNA claims."  The brief also argued that proposed Count 2 "sets the correct scope of admissible proofs [i.e., their own] for the breakthrough invention described by the generic claims at issue in these proceedings—the successful adaption of CRISPR-Cas9 systems for use in eukaryotic environments," which The Broad contended current Court 1 (in either alternative) does not.

Early last month (November 7th), Junior Party the University of California, Berkeley; the University of Vienna; and Emmanuelle Charpentier; collectively, "CVC") filed its Responsive Motion (Contingent) to the Broad's motion no. 2, to be awarded priority to its earlier applications for the subject matter of proposed new Count 2.  (Careful readers with appreciate that in many ways this brief is substantially identical to CVC's Substantive Motion No. 1 filed to be accorded benefit to the same priority applications for the current Count.)  As required by the rather formulaic procedural rules of interferences, the brief is structured to address (and rebut) Senior Party's argument; the argument (simply stated) is that CVC is entitled to priority to the following priority applications: USSN 61/652,086, filed May 25, 2012 (P1); USSN 61/716,256, filed October 19, 2012 (P2): USSN 61/757,640, filed January 28, 2013 (P3);    USSN 13/842,859, filed March 15, 2013; USSN 14/685,504, filed April 13, 2015; or USSN 15/138,604, filed April 26, 2016.

Mirroring the Broad's motion, CVC sets forth in detail the disclosure in its earlier priority applications for at least one embodiment falling within the scope of proposed Count 2.  And as the Broad did in its motion, the brief hagiograhically recites the "ground-breaking" nature of their work, stating that the earliest priority document (P1) disclosed "the minimal components required to generate a functional CRISPR-Cas9 DNA-cleavage complex—Cas9, crRNA, and tracrRNA."  In addition, and addressing the Broad's argument that CVC's disclosure (and this interference) were directed to single-molecule embodiments of CRISPR, CVC argues that on the contrary this priority document "disclosed, for the first time, that complexes of Cas9 and a double- or single-molecule DNA-targeting RNA . . . are useful for targeted DNA cleavage and described numerous applications of this gene-editing technology, including modifying target DNA in eukaryotic cells" and that "[t]he CVC inventors immediately understood that the CRISPR-Cas9 DNA-cleavage complex could be used in a variety of different cellular and noncellular settings."  The brief recites (prophetic) Example 1 in the P1 specification, asserting that the failure of the P1 specification to show actual reduction to practice is not required to satisfy the requirement for entitlement benefit.  CVC also cautions the Board against any attempt by the Broad to "erroneously to link the issues in this motion to the PTAB's termination of Interference No. 106,048 due to no interference-in-fact," stating that "the legal and factual issues raised here are fundamentally different from those decided in the prior '048 proceeding" based on the PTAB's own prior statements of the grounds for its no interference-in-fact determination. Rather, according to CVC:

[A person of ordinary skill in the art] reading P1 in light of the state of the art at the time of filing would have understood that the application describes and enables at least one embodiment within the scope of Proposed Count 2.  Moreover, post-filing-date publications report successfully practicing CVC's claimed invention in eukaryotes using the very methods and components that P1 describes.  The Board should therefore accord CVC the benefit of P1's May 25, 2012 filing date with respect to Proposed Count 2.

What follows is a succinct statement of the Precise Relief Requests (pursuant to PTAB rules) and support in the P1 specification for this relief, recited in the alternative with the other priority documents recited in CVC's request for relief.  The standard, undisputed by the parties, is that to be accorded benefit of priority a prior application must show constructive reduction to practice (CRTP) regarding at least one embodiment falling within the scope of the count, citing Falkner v. Inglis, 448 F.3d 1357, 1362 (Fed. Cir. 2006).  After setting out the legal grounds for CRTP, the brief then applies these rubrics to the disclosure in P1 for subject matter falling within the scope of Count 2 (which CVC argues satisfies these requirements).  Along the way, the brief also suggests that "Broad will doubtlessly rely on cherry-picked quotes about whether or not the inventors or experts knew CRISPR would work in eukaryotic cells before testing it," rejecting these anticipated arguments on the ground that CTRP is grounded on what is disclosed in the specification.  The relevant P1 disclosure for CVC is that CRISPR is functional "when removed from its natural prokaryotic cellular milieu, which is highly relevant here because it establishes CVC's possession of the necessary and sufficient components for a functional CRISPR-Cas9 DNA-cleavage complex regardless of its environment" (emphasis in brief).

The argument is illustrated by Figures from the P1 application:

Figures
And explicit disclosure compared with the elements of proposed Count 2.

The brief then sets forth specific disclosure related to the elements of Count 2 (also provided in Appendix 3 entitled "Exemplary Evidence of Constructive Reduction to Practice of Proposed Count 2 in the P1 '068 Application"), and CVC further asserts that "[t]he inventors fully grasped the broad utility of such a method as aptly illustrated by the many types of 'target cells of interest' suitable for the methods described in P1, including a variety of eukaryotic cells (elements [1]-[2]) such as a fish, human, and fruit fly cell," noting that "[t]hese features are not merely recited in P1, but diagrammed, discussed, and specifically exemplified showing the inventors' possession" based on express disclosure cited with particularity in the brief (including specifically the prophetic use of CRISPR in fish cells).  CVC presents explicit argument relating to what the skilled worker would understand CVC possessed and would be able to accomplish without undue experimentation with regard to the CRTP requirement for being accorded benefit.  Finally in this regard, the brief asserts that post-filing evidence (much of it by third parties) further supports a conclusion of constructive reduction to practice in the P1 disclosure:

Within a year of CVC publishing that Cas9 and a [single guide RNA] such as chimera A (or a double-molecule RNA) formed a functional DNA-cleavage complex (Ex. 3202), other researchers used materially the same components and methods disclosed in P1 to practice the fish cell embodiment—objectively confirming that P1 enables practicing the method of E4.  While the studies described below published after P1's May 25, 2012 filing

 

Table_1

date, post-priority date evidence "may show, for example, that practicing the invention did not require undue experimentation," citing Amgen, Inc. v. Sanofi, 872 F.3d 1367, 1379 (Fed. Cir. 2017); see also, In re Wands, 858 F.2d 731, 739 (Fed. Cir. 1988); In re Hogan, 559 F.2d 595, 605 (Fed. Cir. 1977).

CVC supports its allegations of what the skilled person would understand from the disclosure in the P1 specification by declaration testimony an expert, Dr. Peterson (who eventually will be subject to cross-examination by the Broad in this interference).  Specifically, Dr. Peterson attests extensively to the applicability of CRISPR as set forth in P1 to use in human cells, which CVC asserts is also shown by third-party success in applying CRISPR to human cells, and fruit fly cells.  Thus, CVC asserts "[i]n sum, the great weight of evidence compels a finding that P1 describes and enables each of the fish (E4), human (E5), and fruit fly (E6) cell methods, any one of which, on its own provides a CRTP of Proposed Count 2."

The brief then turns on the distinction between what was required for the Broad to prevail (as it did) in the earlier interference and in this one:

Broad's previously asserted arguments wrongly impose a reasonable expectation of success standard (obviousness) on §112, first paragraph, which contains no such standard.  Obviousness "turns on . . . whether the claimed invention would have been obvious in view of the prior art."  Allergan, Inc. v. Sandoz, Inc., 796 F.3d 1293, 1310 (Fed. Cir. 2015) (emphasis in original).  "In contrast, the enablement inquiry turns on whether the skilled artisan, after reading the specification, would be able to make and use the claimed invention without undue experimentation."  Id. (emphasis in original).  Similarly, "[t]he standard for satisfying the written description requirement is whether the disclosure 'allow(s) one skilled in the art to visualize or recognize the identity of the subject matter purportedly described.'"  Alcon, 745 F.3d at 1190 (emphasis added; citation omitted); see also, Ariad, 598 F.3d at 1351.  Any argument to the contrary erroneously conflates obviousness with written description and enablement.

Finally, the brief argues in the alternative that the other applications CVC asserts for priority contain the P1 disclosure relied upon for priority in this brief, and thus for the same reasons (set forth in brief for each reference) CVC is entitled to priority to these applications, based on the "continuous chain" of priority in these CVC applications.

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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