A clever genetic tool tackles new troubles

Stanley Qi
Stanford University

By disabling the DNA-cutting enzyme in the CRISPR system, Stanley Qi, featured in 2019, created a new and versatile tool. Attaching a range of molecules to these “dead Cas” enzymes has yielded an entire toolbox worth of DNA and RNA manipulators.

Is the strategy of disabling Cas molecules still popular among researchers?
I feel it’s getting more popular, for a number of reasons: One, people use … this tool to study how the genome works. Two, there are some new efforts using the tool to treat some genetic diseases. And three, there are some other exciting uses of this tool to think about other diseases, other topics that we can possibly tackle.

For example, this CRISPR system came from bacteria cells, right? They were used as weapons by the bacteria to fight against invading viruses. So we said, “OK, humans also have many foes like invading viruses. Can we repurpose this CRISPR to help us fight our infectious diseases?” That was the idea before the COVID-19 pandemic. We practiced first on influenza, seasonal flu…. We adapted a type of CRISPR system that targets a specific RNA molecule, and it works pretty well. I remember it working in January [2020] when the news started reporting, “Oh, there’s a new virus, it’s an RNA virus,” and we thought immediately, “What if we use this tool on this new RNA virus?”

Instead [of using the live virus], we used synthetic biology to mimic the RNA sequence.… [And we found] we can still very rapidly cleave and destroy this RNA virus and its fragments in the human lung cells. We were really excited. Since then we’ve been working very hard to follow up on the idea, to make this as fast as possible into a possible antiviral. We called it PAC-MAN.

Can you talk a bit about how the dead Cas, or dCas, approach has been improved and adapted?
One bigger use is for treating disease like a gene therapy. However, there’s still a number of features that have not been ideal for easy use or testing in clinics.… [For patient care,] people always think about making the system very, very compact and suitable into a nanoparticle or into a viral particle, so we can deliver them with ease into the human body. So that requires a miniaturization of the CRISPR system. And we actually did some work on that…. They are like two-thirds smaller than what people use.

And second is, many of these natural proteins from bacteria don’t work very well [in human cells].… So we did some protein engineering. Following these efforts, we actually created some highly compact, yet highly efficient dCas systems that can be easily delivered into the human body to turn on or off genes.

What are the greatest challenges you’ve faced in the last couple of years?
We are bioengineers and we think our strength is in creating stuff, modifying. Now as we step into the domain of applying these tools to solve real-world problems, the challenge is how to build a bridge between where we are to where we want to go. That usually requires learning a significant amount about a disease, about a new field, and thinking creatively on how to interface two fields.

— Interview by Ashley Braun