Emmanuelle Charpentier, PhD, director and scientific member at the Max Planck Institute of Infection Biology, Berlin.

An 11th U.S. patent covering CRISPR-Cas9 claims has been granted to the Regents of the University of California (UC), the University of Vienna, and CRISPR pioneer Emmanuelle Charpentier, PhD, director and scientific member at the Max Planck Institute of Infection Biology, Berlin.

U.S. Patent No. 10,385,360  “Methods and compositions for RNA-directed target DNA modification and for RNA-directed modulation of transcription,” was awarded on Tuesday by the U.S. Patent and Trademark Office (USPTO). The patent covers nucleic acid molecules encoding single-molecule guide RNAs, as well as CRISPR-Cas9 compositions comprising single-molecule guide RNAs or nucleic acid molecules encoding single-molecule guide RNAs.

The patent describes a DNA-targeting RNA that comprises a targeting sequence and, together with a modifying polypeptide, provides for site-specific modification of a target DNA and/or a polypeptide associated with the target DNA. The patent also covers site-specific modifying polypeptides, and further provides methods of site-specific modification of a target DNA and/or a polypeptide associated with the target DNA.

Also described in the patent are methods of modulating transcription of a target nucleic acid in a target cell, generally involving contacting the target nucleic acid with an enzymatically inactive Cas9 polypeptide and a DNA-targeting RNA.

The latest patent joins 10 others that relate to methods and compositions for CRISPR-Cas9 awarded to UC, U. Vienna, and Charpentier—also known collectively as CVC.

“At Least” Six Additional Patents

Charpentier is listed as one of four inventors on the patent. The other three are CRISPR pioneer Jennifer Doudna, PhD, of UC Berkeley; Martin Jinek, PhD, of University of Zurich, a onetime postdoctoral student of Doudna; and Krzysztof Chylinski, PhD, of University of Vienna, a onetime postdoctoral student of Charpentier.

UC said in a statement that it anticipated being awarded “at least six additional related patents issuing in the near future,” which would raise UC’s total portfolio to 17 patents. Those patents would span various compositions and methods including targeting and editing genes in any setting, such as within plant, animal, and human cells—as well as patents related to the modulation of transcription, according to the University.

UC’s statement also said the methods covered by the 11th patent, as well as the other methods claimed in UC’s previously issued patents and those it expects to be issued, were included by the Doudna-Charpentier inventor team in its U.S. Provisional Application No. 61/652,086, filed May 25, 2012.

“The USPTO has continually acknowledged the Doudna-Charpentier team’s groundbreaking work,” Eldora L. Ellison, PhD, lead patent strategist on CRISPR-Cas9 matters for UC and a Director at Sterne, Kessler, Goldstein & Fox, said in the UC statement. “True to UC’s mission as a leading public university, the patent granted today and others in its CRISPR-Cas9 portfolio will be applied for the betterment of society.”

Not Part of Interference

UC also stated that the 11 CVC patents issued to date had not been challenged, and are not part of the patent interference declared in June by USPTO’s Patent Trial and Appeal Board (PTAB).

That interference—the second in the bitter legal wrangle over who invented CRISPR gene-editing technology—came less than a year after the first interference proceeding resulted in a ruling by the U.S. Court of Appeals in September 2018 that upheld a PTAB judgment finding no interference-in-fact between UC claims and patents already issued to Broad, stating that the claims were not directed to the same subject matter.

The current interference was declared between 10 separate U.S. Patent applications owned by UC, the University of Vienna, and Charpentier, and 13 of the 15 patents held by the Broad Institute, Harvard University, and the Massachusetts Institute of Technology (MIT), plus one patent application.

A month later, Sigma-Aldrich, a unit of Merck KGaA, Darmstadt, Germany, petitioned for its own parallel interference between three pending patent applications and patents issued to UC related to CRISPR-Cas9-based methods in eukaryotic cells.

Merck KGaA has built up its own CRISPR patent portfolio, with the company’s Millipore-Sigma unit announcing August 19 that it had been awarded 20 CRISPR patents in the U.S. and eight other jurisdictions worldwide—a month after agreeing with the Broad to a framework through which they will offer nonexclusive licenses to CRISPR intellectual property for use in commercial research and product development.

Settlement Discussions

In the pending interference, both CVC and the Broad have filed lists of proposed motions in the latest interference proceeding. A decision on those motions had not been filed at deadline.

During an August 5 telephone conference between lawyers and Administrative Patent Judge Deborah Katz, Ellison discussed in part an additional CVC request to add four additional Patent applications to the interference: U.S. Application Nos. 16/276,361; 16/276,365; 16/276,368; and 16/276,374.

A lawyer representing the Broad Institute told Judge Katz it was his understanding that both sides have had settlement discussions.

“And those discussions have not yielded any results,” added Steven R. Trybus of the law firm Jenner & Block, representing the Broad, according to a transcript filed August 9.

“If you continue to talk and anything promising, please let us know,” Judge Katz told lawyers.

“We will let you know, Your Honor” Trybus replied.

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