Mulling over latest CRISPR tumult, this one from Nat Biot pub on DNA lesions

If it seems to you like dramatic cautionary tales about CRISPR accompanied by all sorts of media are coming at us more frequently, it’s not your imagination. In the latest yesterday, it was reported in a new paper led by Allan Bradley that CRISPR-Cas9 results in sometimes large-scale chromosomal lesions at or even away from the target locus.

The media have really sunk their teeth into this one, just as in past situations where CRISPR has reportedly encountered anything from bumps in the road to supposed landmines. For instance, here and here are a couple of media stories on the latest CRISPR challenge.

It was just about a month ago that some panicked at a claimed CRISPR-cancer connection, which I wrote about on The Niche. When issues with gene editing are reported, we should pay close attention, but think about them logically rather than emotionally. Here’s what I wrote about some past reports of CRISPR hurdles:

“The initial gene editing “don’t panic” moment came when first one and then another paper came out indicating that the human body may have, to put it simply, some immunity to the key CRISPR protein component for standard gene editing, the nuclease Cas9. This is a real, sizable issue, but there are possible workarounds and in a way that news brought a needed taste of reality to the gene editing arena. The path ahead is not a smooth, linear one, but that’s OK.

Now two new research papers in Nature Medicine (here and here) are being portrayed as being some big new “bad news” connection between CRISPR and cancer. The first paper is “CRISPR–Cas9 genome editing induces a p53-mediated DNA damage response”, by a Swedish-UK team led by Jussi Taipale. The second paper is, “p53 inhibits CRISPR–Cas9 engineering in human pluripotent stem cells” from a team led by Ajamete Kaykas at Novartis.”

Ok, so what’s the deal with the latest CRISPR tech challenge?

CRISPR-Cas9 in a couple different cell types and with targeting of distinct loci, sometimes didn’t do what it was supposed to and the results of that misbehavior were striking. In fact, the authors report a surprisingly high rate of mistakes that sometimes are quite large in nature. I’d recommend reading the media posts above and especially that one by Julianna LeMieux for a good sense of just how wide the range of reactions to this paper has turned out to be, from basically this is probably no big deal to it being big trouble. The authors themselves suggest potential pathogenic consequences.

What an interesting paper that just came out in @natureBiotech from Allan Bradley’s group @tombergk on #CRISPR & on-target effects aka large deletions, chromosomal insertions after Cas9 double stranded break. Here is my take on this #genetherapy -> Thread https://t.co/AyrGAb2PCq

— Dr Gaetan Burgio, MD, PhD. (@GaetanBurgio) July 16, 2018

On Twitter there has also been a range of discussion. I found Gaetan Burgio’s thread on this (see tweet above, then scroll down once on Twitter)) to be valuable and notably he also indicates that additional data on this kind of problem is coming soon without going into details.

I also directly asked Gaetan as an expert for his take on this situation and he kindly provided this quote:

“In short my take home message of this paper is it an important contribution demonstrating we still have a lot to learn on the effect of Cas9 in cells before implementing the technology into the clinics.”

Clearly, overall we need to take this seriously, particularly in the translational bench-to-bedside context, but more broadly it should be on our radar screens too. This report is from a pioneering gene targeting lab and it sounds like the Nature Biotechnology editors were very demanding, probably appropriately so, before the pub could see the light of day.

Final note: this paper has some resonance for the Ma, et al. paper from the Mitalipov lab that reported supposed interhomolog repair for apparent CRISPR gene editing in human embryos, but was then challenged by an Egli, et al preprint. The authors of that preprint, including Allan Bradley (probably not by coincidence) raised some simple explanations for how the Ma, et al. paper’s main conclusions may have been wrong including for example the production of Indels (rather than corrected alleles) that make PCR amplification of alleles impossible, and so in turn skewing results to make it seem like all alleles present are WT. These hypothesized deletions could be like some of the genomic lesions mentioned in the new paper. Other cellular or technical events could also make the cells seem WT (presumed in the Ma paper to be due to gene editing-based mutant allele correction) in artifactual ways.

Remarkably, the Ma, et al. paper’s key points on CRISPR in human embryos remain in limbo, without having been recapitulated and if anything in more doubt at this point, but nothing further has been published to direct address it.