University of California/Berkeley Granted Yet Another CRISPR Patent

By Kevin E. Noonan --

On Tuesday, the U.S. Patent and Trademark Office granted U.S. Patent No. 10,385,360 to the University of California/Berkeley, directed to an aspect of its CRISPR technology (where CRISPR is an acronym for Clustered Regularly lnterspaced Short Palindromic Repeats).  The independent claims of the '360 patent read as follows:

1.  A nucleic acid molecule encoding a single molecule DNA-targeting RNA, wherein the single molecule DNA-targeting RNA comprises: (a) a DNA-targeting segment comprising a nucleotide sequence that is complementary to a target sequence in a target DNA molecule, and (b) a protein-binding segment comprising two complementary stretches of nucleotides that hybridize to form a double stranded RNA (dsRNA) duplex, wherein said two complementary stretches of nucleotides are covalently linked to one another with intervening nucleotides, wherein the DNA-targeting segment is positioned 5' of both of said two complementary stretches of nucleotides, and wherein the single molecule DNA-targeting RNA is capable of forming a complex with a Cas9 protein and targeting the complex to the target sequence of the target DNA molecule.

4.  A composition comprising: (1) a single molecule DNA-targeting RNA, or a nucleic acid encoding said single molecule DNA-targeting RNA, wherein the single molecule DNA-targeting RNA comprises: (a) a DNA-targeting segment comprising a nucleotide sequence that is complementary to a target sequence in a target DNA molecule, and (b) a protein-binding segment comprising two complementary stretches of nucleotides that hybridize to form a double stranded RNA (dsRNA) duplex, wherein said two complementary stretches of nucleotides are covalently linked to one another with intervening nucleotides, wherein the DNA-targeting segment is positioned 5' of both of said two complementary stretches of nucleotides, and wherein the single molecule DNA-targeting RNA is capable of forming a complex with a Cas9 protein and targeting the complex to the target sequence of the target DNA molecule; and (2) one or more of: (i) a nuclease inhibitor, (ii) a buffering agent, and (iii) a pharmaceutically-acceptable, non-toxic carrier or diluent.

The priority relationship of the '360 patent to the rest of the Berkeley portfolio is set forth on the face of the patent:

This application is a continuation of U.S. patent application Ser. No. 15/435,233 filed Feb. 16, 2017 (U.S. Patent No. 10,407,697, issue date Sep. 10, 2019), which is a continuation of U.S. patent application Ser. No. 15/138,604 filed Apr. 26, 2016 (U.S. Patent No. 10,113,167, issued Oct. 30, 2018), which is a continuation of U.S. patent application Ser. No. 14/685,502 filed Apr. 13, 2015 (U.S. Patent No. 10,000,772, issued Jun. 19, 2018), Ser. No. 14/685,504 filed Apr. 13, 2015 (U.S. Patent No. 10,301,651, issued May 28, 2019), Ser. No. 14/685,513 filed Apr. 13, 2015 (abandoned), Ser. No. 14/685,514 filed Apr. 13, 2015 (abandoned), Ser. No. 14/685,516 filed Apr. 13, 2015 (abandoned), and Ser. No. 14/942,782 filed Nov. 16, 2015 (U.S. Patent No. 10,227,611, issued Mar. 12, 2019), each of which is a continuation of U.S. patent application Ser. No. 13/842,859 filed Mar. 15, 2013 (U.S. Patent No. 10,266,850, issued Apr. 23, 2019), which claims the benefit of U.S. Provisional Patent Application Nos. 61/652,086 filed May 25, 2012, 61/716,256 filed Oct. 19, 2012, 61/757,640 filed Jan. 28, 2013, and 61/765,576, filed Feb. 15, 2013, each of which applications is incorporated herein by reference in its entirety.

None of these patents are involved in the recently declared interference, nor are they the subject of the Board's order to inform the Board and Senior Party, the Broad Institute, should they be allowed.  The claims correspond to an RNA component of a CRISPR-Cas9 complex for performing "gene editing" rather than the more comprehensive claims reciting the entire system.

The prosecution history shows no rejection on either the written description nor enablement provisions of 35 U.S.C. § 112(a), which is curious in view of the breadth of the claims (which can be read as comprising "a DNA-targeting segment comprising any nucleotide sequence that is complementary to any target sequence in a target DNA molecule").  In view of the recent penchant for the Federal Circuit to be concerned about claim breadth (see "Enzo Life Sciences, Inc. v. Roche Molecular Systems, Inc. (Fed. Cir. 2019)" and "Amgen Inc. v. Sanofi (Fed. Cir. 2017)").  These circumstances -- at least in theory -- leave these claims vulnerable to invalidation should Berkeley attempt to enforce them against a putative infringer (perhaps, for example, anyone licensing the Broad patents) or more immediately a post-grant review challenge before the Patent Trial and Appeal Board.

The "Reasons for Allowance" of these claims is instructive regarding at least how the USPTO is thinking about CRISPR:

The instant claims recite "a single molecule DNA-targeting RNA" comprising "a DNA targeting segment" and "a protein-binding segment," wherein the protein-binding segment comprises "two complementary stretches of nucleotides that hybridize to form a double stranded RNA (dsRNA) duplex, wherein said two complementary stretches of nucleotides are covalently linked to one another with intervening nucleotides" and wherein the "single molecule DNA targeting RNA is capable of forming a complex with a Cas9 protein and targeting the complex to the target sequence of the target DNA molecule".

The closest prior art is Siksnys (US 9,637,739) and Siksnys (WO 2013/141680) each of which claim priority to US 61/625,420 (filed April 17, 2012) and US 61/613,373 (filed March 20, 2012), which are both prior to the instant effective filing date of May 25, 2012.  These priority documents describe a method of assembling a CRISPR-Cas9 DNA cleavage complex by combining Cas9, crRNA, tracrRNA, and RNase III (see Example 2) or just Cas9, crRNA, and tracrRNA (see Example 3).  Siksnys further discloses the criticality of the tracrRNA molecule to the assembly of a functional Cas9-crRNA DNA cleavage complex (see Figure 16).  These disclosures are supported by US 61/613,373 filed March 20, 2012.  In addition, Deltcheva (Deltcheva et al. (2011) Nature, 471:602-607 and supplementary data published online March 30, 2011) is a relevant prior art.  Deltcheva teaches that "tracrRNA is required for crRNA maturation in S. pyogenes" (see Figure 1).  Deltcheva further illustrates that "Co-processing of tracrRNA and pre-crRNA requires both endogenous RNase III and Csnl in vivo" (see Figure 2), wherein Csnl is a synonym for Cas9. Deltcheva illustrates that this crRNA maturation occurs via hybridization between the crRNA and the tracrRNA to form a dsRNA duplex (see Figure 1).  These disclosures indicate that the prior art recognized both the dsRNA duplex formation between crRNA and tracrRNA and further recognized the criticality of the tracrRNA to the maturation of the crRNA and to the assembly of the Cas9-crRNA cleavage complex.

However, the prior art did not sufficiently describe or recognize the presence of the tracrRNA molecule in the Cas9-crRNA DNA cleavage complex itself.  This is supported by Siksnys' characterization of the DNA cleavage complex as a "Cas9-crRNA complex" (see Figure 15), which refers only to two components, and the characterization of a "ternary complex" (see description of Figure 14), which refers to the Cas9-crRNA in a complex with the target dsDNA (see Figure 14), for example.  Because the prior art as a whole did not sufficiently describe or recognize the presence of the tracrRNA molecule in the Cas9-crRNA DNA cleavage complex, one of ordinary skill in the art would not have had sufficient motivation to "covalently link" the crRNA and the tracrRNA molecule together with "intervening nucleotides" to form a "single molecule" DNA-targeting RNA as required by the instant claims.  The claims recite eligible subject matter at least because naturally occurring crRNAs and tracrRNAs that hybridize to form a dsRNA duplex capable of forming a complex with a Cas9 protein are not "covalently linked to one another with intervening nucleotides" to form a "single-molecule" DNA-targeting RNA as required by the instant claims.  Accordingly, this structural feature renders the claimed subject matter markedly different from its naturally occurring counterpart.

This allowance is consistent with the PTAB's judgment of no interference-in-fact in Interference No. 106,048, affirmed by the Federal Circuit, stating "Broad has provided sufficient evidence to show that its claims, which are all limited to CRISPR-Cas9 systems in a eukaryotic environment, are not drawn to the same invention as UC's claims, which are all directed to CRISPR-Cas9 systems not restricted to any environment.  Specifically, the evidence shows that the invention of such systems in eukaryotic cells would not have been obvious over the invention of CRI SPR-Cas9 systems in any environment, including in prokaryotic cells or in vitro, because one of ordinary skill in the art would not have reasonably expected a CRISPR-Cas9 system to be successful in a eukaryotic environment.  This evidence shows that the parties' claims do not interfere." (see Interference No. 106,048, "Decision on Motions" mailed February 15, 2017, page 2).  The PTAB's judgment involved and was applicable to all claims of US Patent 8,906,616.

Accordingly, because the claims of US 8,906,616 have been deemed to be "limited to . . . a eukaryotic environment", and because the instant claims are not limited to a eukaryotic environment, the instant claims do not interfere with the claims of US Patent 8,906,616 or any other claim deemed to be "limited to . . . a  eukaryotic environment."

Comments

[Atari Man]

I don't get it. Everything in claim 1 was known, except for the covalent linker between the two complementary RNA strands. But we "know" from Myriad that covalent bonds like that are irrelelvant - in Myriad SCOTUS, with its wealth of experience in science, taught us that the hydrogens at the ends of the cleaved DNA in Myriad were no different from the additional nucleotides at those ends that were present in nature. So why was claim 1 here not considered to be abstract or a product of nature, per SCOTUS in Myriad/Alice?

/end sarcasm/

I am grateful that the PTO now seems to be applying 101 in a slightly more sane manner than it was doing 3-5 years ago.

[Skeptical]

ping and pong, Atari Man (your sense of gratitude is very much premature).