The CRISPR question mark

Since its discovery in 2012, the CRISPR/Cas9 gene editing tool has been used by countless laboratories globally. Five years on, an important question remains: who does it belong to?

 Illustration by Shruti Kotecha

Illustration by Shruti Kotecha

In the not-so-distant past, some intellectually strapping researchers figured out how to harness a bacterial defence mechanism and use it to advance science in previously unimaginable ways. Unfortunately, the researchers independently discovered and developed different parts of this technology and filed different patents. This has caused a drawn-out dispute over which scientists (and, importantly, which university) ‘own’ the versatile genetic tool that’s poised to change the world. This technology is CRISPR.

CRISPR/Cas is an acronym for (bear with me) Clustered Regularly Interspaced Short Palindromic Repeats/CRISPR-ASsociated proteins and it is the hot new gene editing technology on the block. In essence, we’ve harnessed a bacterial immune system that uses enzymes (those CRISPR-associated proteins) to recognize and digest the CRISPR regions of viral double-stranded DNA. While scientists have used other methods of editing genes for decades, this new tool is a leap into hyperspeed editing that requires comparatively less labour and resources to reach the same goal. 

The discovery and development of CRISPR was fairly recent, with initial results only published in 2012, but the impact it has had on molecular biology should not be understated. Since its discovery, we’ve already used this system to delete, disrupt, or edit genes in bacteria, plants, fungi, mice, and humans. Assistant Professor Dipali Sashital researches CRISPR’s role as a natural immune function in bacteria, and says “CRISPR has absolutely altered the landscape of molecular biology. It has greatly facilitated gene alterations that used to be time-consuming and/or cost-prohibitive. The ease of use has made genome editing of eukaryotic cells a standard technique in most genetics labs in just four years.” She goes on to say that CRISPR has “made it possible to perform large-scale genetic screens for disease phenotypes, to test the effects of drugs, to understand the function of non-coding DNA sequences … [demonstrating] the tremendous impact CRISPR technology will continue to have on the field of biology.”

 
  CRISPR/Cas9 acts like a pair of molecular scissors and gives researchers the ability to edit genes with less time and labour than most other molecular biology tools.   DBCLS TV/Wikimedia Commons  (CC BY 4.0)

CRISPR/Cas9 acts like a pair of molecular scissors and gives researchers the ability to edit genes with less time and labour than most other molecular biology tools. DBCLS TV/Wikimedia Commons (CC BY 4.0)

 

CRISPR technology allows us to edit the genomes of any animal — including humans — at a scale and specificity that has not been seen before. Christopher Weir, an Intellectual Property (IP) professional and writer at Mostly Science, speaks to the real-world effect, noting, “Outside of the research applications, you obviously have human health potential, which is where the real money-spinner is. Being able to cut out a detrimental or defective gene and replace it with a good copy is extremely attractive.” Dr Mark Summerfield, a registered patent attorney and IP consultant, agrees: “It is very clear that CRISPR technology underpins a potential multi-billion-dollar industry.” Indeed, CRISPR scientists have already begun preliminary research into the potential of this technology to improve outcomes for those with Duchenne muscular dystrophy and Huntington disease, among other afflictions. Research is moving fast: a Chinese group performed the first-ever human trial in October 2016, injecting an adult human with their own CRISPR-edited cells, and the National Institutes of Health approved a human trial in the United States.

With the scene set for the role that CRISPR could play in the future, it’s time to take a small step back into the past, to its entrance on the global stage. In May 2012, a team headed by Jennifer Doudna (University of California, Berkeley) and Emmanuelle Charpentier (University of Vienna) successfully used specific enzymes found naturally within bacteria to artificially alter a bacterial genome. In December of that year, Feng Zhang and his colleagues at the Broad Institute (affiliated with the Massachusetts Institute of Technology and Harvard University) achieved similar alterations of genomes of the more complex eukaryotic mouse and human stem cells, which sequester DNA in a nucleus. Both groups filed separate patents, but Zhang’s group requested an expedited review process, resulting in them being granted the patent in 2014, before Doudna and Charpentier.

While Doudna and Charpentier had shown that CRISPR worked in bacterial cells, the patent they filed extended to include the more complex eukaryotic cells, theoretically giving them intellectual ownership over that as well. Essentially, the patent filed by Berkeley covered all CRISPR/Cas9 techniques, guides, and resultant cells or organisms (excluding humans). However, without showing this work themselves, and with another patent challenging this assertion, the validity of their claim’s scope was brought into question. 

 
  In early 2012, researchers at the University of California, Berkeley used components of the bacterial immune system to successfully edit the genome of bacteria.   Brainchildvn/Wikimedia Commons  (CC BY 2.0)

In early 2012, researchers at the University of California, Berkeley used components of the bacterial immune system to successfully edit the genome of bacteria. Brainchildvn/Wikimedia Commons (CC BY 2.0)

 

Due to the overlap in their patent claims, the team at Berkeley were less than impressed that the Broad’s claim was granted, and started interference proceedings. Interference is usually a contest to see which group was the first to invent or discover a particular patentable device or process, but in this instance it’s asking whether, in 2012, it would have been “obvious” to develop CRISPR in eukaryotes following the initial work in bacteria by the Berkeley team. If it was obvious, the Broad’s patent to using CRISPR in more complex cells isn’t legitimate. If this next step wasn’t obvious, then there isn’t a dispute, and the Broad maintains their arguably more useful patent for the use of CRISPR in human cells.

The question of whether doing something in bacteria makes it obvious to do in more complex cells is something that even the experts disagree on. ‘Obviousness’ asks whether this jump would be straightforward for someone skilled in the art - in this case, the art of molecular biology. If you know how to use a knife to dice one vegetable, you can dice all vegetables, even if you have to throw different parts away or slightly alter your technique. In this case, the fact that Doudna and Charpentier mentioned eukaryotes in their initial patent claims suggests that perhaps it was obvious. However, Christopher Weir notes “[This] was not the first CRISPR patent applied for that mentioned its utility for eukaryotic gene editing.” Earlier patents include those by Stan Brounds (Wageningen Universiteit), which also date back to 2012 and cover different enzymes used in CRISPR gene editing

This interference matters substantially because not only is CRISPR popular with university researchers, but there are dramatically increasing numbers of patents being filed using CRISPR technology. While both of the disputed patent claims specify the Cas9 enzyme, many of Feng Zhang’s more recent patents also cover alternative enzymes that might make CRISPR more effective. Zhang is also a co-founder of Editas, which aims to use CRISPR to treat a rare form of blindness in humans this year. Both sides of this legal dispute have vested commercial interests: Doudna was involved in the formation of Caribou Biosciences and Intellia, and Charpentier is a founder and scientific advisor of CRISPR Therapeutics

With this number of side projects for Zhang, Doudna, and Charpentier, the question might then be asked if it is significant from a commercial perspective to be the holder of the initial patent for the use of CRISPR technology in eukaryotic cells. Summerfield suggests that “the income streams to UC and Broad will be from licensing to a range of users, not just companies with which they have some association... so long as there are commercial applications for CRISPR/Cas9, there will be associated revenues.” Even so, he adds, “From a marketing perspective, I am also sure that there is significant value in being confirmed as the true and first inventor.” Under the status quo, companies are already prepared for either eventuality, as Weir notes “competing CRISPR companies have been cross-licensing [IP] with each other as a prophylactic against any outcome over the CRISPR/Cas9 dispute”.

 
  In March 2017, the Patent Trial and Appeal Board agreed with the Broad Institute, a major development in the CRISPR dispute saga. Still, the story is not over yet.   Madcoverboy/Wikimedia Commons  (CC BY-SA 3.0)

In March 2017, the Patent Trial and Appeal Board agreed with the Broad Institute, a major development in the CRISPR dispute saga. Still, the story is not over yet. Madcoverboy/Wikimedia Commons (CC BY-SA 3.0)

 

It turns out that the Patent Trial and Appeal Board agrees with the Broad, ruling recently that “[University of California]’s claims would not have rendered Broad’s claims obvious” and that “one of ordinary skill in the art would not have reasonably expected a CRISPR/Cas9 system to be successful [in eukaryotes]”. Weir firmly thinks the Broad’s patent claim is obvious, commenting that “other gene editing techniques such as TALENs and Zinc-finger nucleases were not only first found in prokaryotes, but adapted for use in eukaryotic cells… typically, getting a eukaryotic enzyme to work in a prokaryote is tougher than the opposite” — suggesting that developing CRISPR/Cas9 for use in eukaryotes was “easier” than if the reverse had been required. Still, there are significant differences between CRISPR and other gene editing techniques and the case considered these points and concluded that the differences are sufficient to suggest ‘non-obviousness’ of developing CRISPR for eukaryote editing.

This has been described as a knockout punch, and shares in Editas jumped 29% after this announcement. However, it’s a long time before anything is completely finished in the legal system and this decision can be appealed to a higher circuit. Summerfield says that the key question is “in what circumstances might the parties change their positions and consider a settlement? So long as both parties believe they can win, a settlement is unlikely... only if both were to reach a point where they consider victory highly uncertain, and the risk no longer acceptable, is there an incentive to approach the negotiating table. There has been no sign of this to date.”

Not everyone in the scientific community agrees with the decision, and judging by how much both sides have riding on this, it’s quite likely there will be further appeals, both in the United States and beyond. But for academics, this might not mean very much. While A/Prof Sashital thinks “the patent dispute has slowed research at the industry level, due to uncertainty about the patents that they've licensed”, she still has an optimistic viewpoint, saying “the CRISPR community has been quite open in sharing resources and information with academic researchers, ensuring that the technology is available as quickly as possible. This openness has been instrumental in the rapid adoption of this technology in so many labs around the world.”

Although it’s still early days, scientists are already investigating how CRISPR technology can be used in the fight against both human and plant diseases. It is evident that CRISPR has the potential to dramatically alter healthcare, agriculture, and other fields. The relative speed and ease of genetic editing with this new technology will also accelerate the pace of molecular biology research as a whole. No matter what happens in the courts, we can look forward to a fascinating future shaped by CRISPR.

Edited by Ena Music