A cleaner crisp(e)r way of editing the code!

We hear so much about CRISPR (discussed in a previous blog) and gene editing these days that it feels like the technique has been around for a decade (or more), and not something relatively unheard of before 2012.  Yet it's still an advance very much in its infancy, and one not without a healthy (no pun intended!) burden of controversy weighing it down. 

The heaviness surrounding the use of the CRISPR-Cas9 system lies in its potential not only to edit and correct disease-causing mutations or defective genes such that we revert to a normal genotype and phenotype, but also due to the fact that the technique may very well be open to "abuse" (or perhaps misuse) by those wishing to alter some part of their non-diseased phenotype. We want our baby to have blonde hair and blue eyes, for example. 

In a striking new development set to make the CRISPR technique an even more disruptive technology, one of the pioneers in the field just published a paper in Cell, yesterday, outlining the discovery of a new nuclease, Cpf1. Feng Zhang of the Broad Institute in Cambridge (MA) felt that as exciting and useful as the CRISPR-Cas9 system is, there was still benefit in seeking to refine it, and refine it he just did.

As technically brilliant as CRISPR editing is, there are a few drawbacks which clearly niggled at Zhang, who returned to the world of bacteria and went hunting for alternates to Cas9.  Having discovered Cpf1 in bacteria, his team isolated Cpf1 from some sixteen different bacterial strains and found two that could cut human DNA.Zhang then went about more fully characterising its properties in comparison to Cas9. 

One reason why Cas9 is not a perfect choice lies in the fact that it needs two guide RNAs to facilitate appropriate cutting of DNA; Cpf1 needs just one. Additionally, Cas9 is a considerably larger protein than Cpf1; coupled to the need for just one guide RNA, this makes Cpf1 easier to package and deliver to cells. Furthermore, and by no means least, Zhang discovered that both the sites of cleavage and their nature were distinct between the two nucleeases; this difference potentially makes the cutting and insertion of DNA by Cpf1 a much more accurate and efficient process - an explosive finding. 

Cas9 cuts both strands of DNA at the same position, leaving the DNA with blunt ends, the repair of which is hard to control and prone to errors. Cpf1 on the other hand leaves sticky end overhangs, which should make it much easier to control the appropriate insertion of the appropriate piece of exogenous DNA into a gene. As explained bu Zhang - "The sticky ends carry information that can direct the insertion of the DNA. It makes the insertion much more controllable" - which can only be a good thing. 

There's an unexpected bonus in all of this, which centres on the ongoing and brutal legal dispute over who-discovered-what in the CRISPR-Cas9 story. The two contenders in this dispute are the Broad Institute of MIT-Harvard (including Zhang et al.) and UC Berkeley, whose Jennifer Doudna is a major player along with her collaborator Emmanuelle Charpentier. In what may be true irony, even though Zhang and the Broad hold 10 patents on the technology, it is Doudna in particular who is often singled out by the media as the discoverer of CRISPR-Cas9. So one of the two sides is clearly winning the patent war and the other is winning most of the credit for the discovery. 

It may all come down to that staple of laboratory life - the lab notebook - given that the Regents of the University of California have asked the USPTO to approve "patent interference" to determine who was the inventor in those 10 patents belonging to Zhang and the Broad. It's going to get messy, almost certainly, and even the commercial end of this story is already messy, with both Zhang and Doudna originally listed as co-founders of Editas Medicine, a Cambridge-based biotech company set up to develop medicines based on the CRISPR system. Doudna has since exited, but not before selling her patent rights to another biotech, the UK's CRISPR Therapeutics, the founder of which is none other than, wait for it, a certain Emmanuelle Charpentier! 

There's gold in them hills, with Editas having raised additional funds totalling $120M in August, and a new player on the scene, Intellia, having raised some $70M in recent weeks. No shocker that Intellia is connected to Berkeley, by the way. But there's a lot more than mere millions at stake here, not least because scientists often care way more about credit, than their line of creidt! Some talking heads are already earmarking Doudna and Charpentier for the Nobel Prize, and you can bet that this rankles Zhang and MIT. 

It's fascinating stuff of course, and full of the passionate competitiveness and resulting drama that is at the heart of groundbreaking scientific discovery. With the recent patent interference request by the Regents of UC, it looks like it may well be a case whose outcome will come with its very own theme tune - "The Winner Takes It All" - because the USPTO is likely to come out squarely on one side or the other. This may just turn out to the scientific equivalent of the OJ Simpson trial and verdict, and you can expect some heavy duty (but non-violent!) fall-out if a severe injustice appears to have been done. 

Well, it's a simply gorgeous late September Saturday afternoon here in Montreal, and so I am off to get a few kilograms of baby back ribs onto the barbecue, smoking, as my trademarked "Belfast Cowboy Fiery Maple Hickory Smoke" sauce bubbles gently on the side. I've got some seriously hungry ranchers coming in later, so I better get to it. That's it for this one, so, until next time! :)