Interview with Dr. Blake Weidenheft at Keystone Symposia’s Precision Genome Engineering and Synthetic Biology: Designing Genomes and Pathways
The Early Days of CRISPR
I was one of the earlier people involved in the CRISPR– in CRISPR biology. And so we didn’t really come at this with the intent to try to develop some new genome engineering application. I was actually a grad student here in Bozeman, where I worked in the Thermal Biology Institute. And we were studying the viruses that infect bacteria in boiling acid environments. And so during that work, I got really interested in virus-host interactions, and a little bit more interested in Archaea. They’re kind of schizophrenic.
They’re single-celled prokaryotes, but they have a lot of information processing machinery that eukaryotes have. And so that got me thinking that maybe they would rely on small RNAs, and maybe an RNAi-like pathway, to regulate endogenous genes and maybe even exogenous genes.
And it was really my interest in RNAi that led me to Jennifer Doudna’s lab, where I did a post-doc as an HHMI fellow for Life Sciences Research Foundation, and where we started to work on CRISPRs. And initially, I started working on the aspect that Jennifer introduced in her talk about the acquisition of foreign genetic material into the CRISPR locus. Something that might prove to be a pretty exciting technology in the relatively near future, as well, but one that nobody’s really talking about just yet. But from there, I started to get into looking at RNA-guided DNA detection by these large surveillance complexes. And that’s really been the focus of my work ever since.
So a few years ago, I moved from Berkeley back to the Big Sky State here in Montana. And my lab has really been focused on understanding the mechanism RNA guided surveillance by these large multi-subunit complexes associated with the type 1 systems. So Cas9 become so popular, it’s almost synonymous with the word CRISPR now. And even bigger than that, it’s maybe even almost synonymous with genome engineering.
The Many Faces of CRISPR
But in the CRISPR system, there’s at least 10 different versions of the CRISPR system. And Cas9 is one of those systems. And we study the type called the type 1 systems. These systems involve these large macro-molecular machines, these RNA-guided surveillance complexes that I’ve been mentioning. And they function differently from Cas9 in that they find the DNA, the invading DNA target, and then they recruit a transacting nuclease, rather than the canonical Cas9 system where you have an enzyme that binds to a target DNA and then cleaves it itself. So we’ve been focused on a little bit different system than what we’re hearing so much about at the genome engineering meeting.
Initially, we were just interested in this from a basic science perspective, understanding how bacteria and their molecular parasites, viruses, interact. And what happens in this molecular arms race, how do they respond. And it was sort of fortuitous, or– the initial indications of this immune system came from some bioinformaticists who were just genome gazing, identified these short snippets of viral sequence that were integrated into the CRISPR locus. That gave way to this hypothesis that CRISPRs were a central component of this perhaps novel nucleic acid-based immune system. And then [? Borango ?] in 2007 provided this really watershed moment, or paper, that described the first example of adaptive immunity using bacteria from yogurt.
And from there, it was really just a team of scientists that went after trying to understand mechanism. And then, in the course of figuring out the mechanism, then it started to become clear, wow, we could maybe repurpose these things for targeted genome engineering. So it’s a– I don’t know of another example where basic science has led to an innovative new application in such a short time period. That’s really been game-changing.
Clearly, Cas9 has taken center stage. And I’m equally excited about the possibilities of using Cas9. I think what we’re seeing at this meeting is it going from just a tool where you can go into a genome and make a cut in a predictable place and maybe even change that allele in a predictable fashion, but to now start to apply this in a systems biology approach where people are integrating new gene circuits, or higher-order molecular capacity, into a genome, whether that be novel function or whatever. Not even just in an individual cell, but in entire microbial communities. So I think that the influence of the synthetic biology community with using these new tools is pretty exciting.
The outstanding hurdle is delivery. So how do you get your genome editing potential to the particular cell type in a multicellular organism. In a human that has CF, how do you correct the CFTR gene in the entire human. Or if there’s just particular cell types that you want to target, how do you do that. So I think that that’s going to be– that remains an exciting frontier for the field.