CRISPR Oral Arguments Recap, Cont’d

This week’s CRISPR patent hearing took a deep dive into the science of moving the gene-editing technology from prokaryotes to eukaryotic systems.

By | December 8, 2016

CRISPR patent hearingWIKIMEDIA, NATIONAL HUMAN GENOME RESEARCH INSTITUTEOn Tuesday (December 6), lawyers representing the Broad Institute of MIT and Harvard and the University of California, Berkeley, pled their respective clients’ cases to at the US Patent and Trademark Office, in the matter of who should own the intellectual property rights for the powerful—and increasingly lucrative—CRISPR-Cas9 gene editing technology.

The Scientist covered the oral arguments and the possible outcomes of the case, but there was much we left out of our initial article. Here’s the rest of the story:

Is the eukaryotic application obvious?

At the heart of this case is the question of whether or not the early prokaryotic and in vitro work on the CRISPR system—described by UC Berkeley’s Jennifer Doudna and colleagues in a 2012 patent application and published online in Science that June—could be used by a “person of ordinary skill in the art” of genome engineering to apply the pathway to eukaryotic cells with a “reasonable expectation of success.” If so, the later work of Feng Zhang at the Broad, patented in 2014 and published in Science in 2013, would not entitle the Broad to all of the intellectual property rights over CRISPR’s use in eukaryotes currently reserved by Zhang’s patent.

Here’s what each side had to say about this point:

UC Berkeley, represented by Todd Walters

The Broad Institute, represented by Steve Trybus

Doudna and colleagues’ 2012 paper identified the key components of the CRISPR system. The extrapolation of the pathway to eukaryotic cells depended entirely on this publication, Walters argued. Zhang’s patented work using CRISPR in eukaryotic cells was not innovative because it involved using “conventional techniques” and “conventional methods” on top of the information provided by the 2012 paper. “There’s no special sauce here,” he said multiple times in his rebuttal to Trybus’s arguments.

Many of the CRISPR components had already been identified, as far back as 2010, Trybus argued, and Zhang himself had already started on making CRISPR work in eukaryotic cells before the Doudna’s 2012 publication, as evidenced by an NIH grant application that Zhang submitted in 2012. Additionally, there was no guidance in Doudna’s paper for persons of ordinary skill on how to move the technology to eukaryotes.

Within six months of the publication, six groups, including Doudna’s, had successfully used CRISPR in eukaryotic cells, suggesting that a “person of ordinary skill” could apply the pathway to eukaryotes with “reasonable expectation of success.” Walters argued that scientists would not undertake an experiment without the expectation that it might work.

“These are all extraordinary people,” Trybus said of the scientists that succeeded in applying CRISPR to eukaryotes. Moreover, many of these groups, including Zhang’s, used different molecules than described in the 2012 paper. The work led to publications in high-impact journals as well as multiple patent applications, Trybus added, indicating that the researchers viewed these adaptations as innovative and patentable.

Doudna never said she didn’t believe CRISPR would work in eukaryotic cells. In fact, she said it was “now a very real possibility” after her 2012 paper. And we don’t know the context of what she referred to as her “many frustrations” regarding her early attempts to use the technique in human cells.

In a 2012 interview, Doudna said she wasn’t sure if CRISPR would work in eukaryotic cells—specifically, if the molecular machinery would get inside the nucleus. She also expressed “many frustrations” about her early attempts to use the technique in human cells, suggesting the application was not obvious.

UC Berkeley has submitted documentation about four proteins that were first discovered or used in prokaryotes and easily made the transition to eukaryotes, suggesting that application from prokaryotes to eukaryotes in similar cases could have been considered obvious.

CRISPR involves not just proteins, but RNAs and RNA-protein complexes, which can be more difficult to transition to a eukaryotic system than proteins alone. For example, bacterial protein-RNA complexes known as targetrons were never successfully used in eukaryotic cells despite “decades of research” attempting to do so, Trybus said. It was an “utter failure.”

Is there precedent for the prokaryotic-to-eukaryotic transition?

There is at least some precedent—and it seems to favor Zhang and the Broad. Jake Sherkow of New York Law School pointed to a 1999 case (Enzo Biochem, Inc. v. Calgene, Inc.) in which Enzo had patented an antisense RNA technology for both prokaryotic and eukaryotic use, despite having only demonstrated that it worked in E. coli.

“The trial court concluded that . . . Enzo’s patents were invalid for lacking something called ‘enablement’—they didn’t enable an average molecular biologist to use the invention in eukaryotes,” Sherkow wrote to The Scientist in an email. “This case seems to neatly dovetail with the CRISPR case. If it’s generally true that one needs to engage in a lot of experimentation to move a technology from prokaryotes to eukaryotes, then it stands to reason that success in eukaryotes is nonobvious—and therefore patentable—over previous experiments in prokaryotes. That’s an excellent case for the Broad.”

Another scientific matter on the table

In addition to determining whether a general patent on the use of CRISPR in prokaryotes and in vitro should subsume a patent on its use in eukaryotes, the court had another scientific matter to consider: that of single-molecule versus dual-molecule CRISPR techniques. In the natural bacterial pathway, two RNA molecules bind to the Cas9 enzyme and direct it to cut a targeted bit of DNA. Doudna and her colleagues bound the ends of each of these two RNAs together, and found that the simpler, single-molecule approach worked just fine.

UC Berkeley has requested that the Patent Trial and Appeal board consider adding this single-molecule tweak to the “count,” or the definition of the invention at the center of the investigation, arguing that this was a nonobvious innovation. The Broad, on the other hand, would prefer the single-molecule aspect be left out of the count, because much of Zhang’s early work used the dual-molecule approach and would thus be excluded from consideration if the invention was defined as the use of the single-molecule form of CRISPR gene editing.

In his rebuttal during the oral arguments, Trybus argued that the creation of the single molecule should be considered an “obvious” extension of the dual-molecule technique. He pointed to tetraloops, which he said were known to still be functional despite having multiple RNAs linked together.

Some logistical considerations

  • Could the case settle? Although many interference cases do settle, this one is unlikely to at this point, Sherkow said at a panel discussion held at the American University Washington College of Law following the hearing.
  • Could the decision be appealed? Theoretically, the losing side could appeal to the US Court of Appeals for the Federal Circuit. The likelihood of this is unclear, and may depend on the outcome of the interference proceedings, which may divvy up the intellectual property for CRISPR to both groups.
  • What are the next steps? The phase of the interference proceedings that is coming to a close is called the interlocutory phase, in which the court attempts to define the invention and determine which parties contributed. A second phase, called a testimonial phase, could involve interviews with the researchers involved, but in all likelihood the case will not proceed to this level. “I think that the chances of that are relatively slim,” Sherkow said.

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Avatar of: Paul Stein

Paul Stein

Posts: 221

December 8, 2016

As we see here, litigation shows how good any patent is.  Oftentimes, the patent writing is not too great, which allows for rejection.  So, what about the patents themselves?  Were they poorly written?  Were they too specific?  Were the claims not covering enough?  Were they too narrow?  I have a feeling that all this talk of not-in-the-patent research articles, interviews,etc. will be close to meaningless to the judges who rightly will focus on what the patents themselves say...unless the writing of all of the patents was horrible.

Avatar of: xtsam


Posts: 5

December 8, 2016

If you think evolution is right, then from prekaryotes to eukaryotes is not much of a big hurdle, I would argue. 

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