Using human genome, scientists build CRISPR for RNA to open pathways for medicine

UChicago scientists invent method that could help treat diseases, injuries

Less than a decade ago, biology underwent one of those once-in-a-generation events that shakes up a scientific field, when the discovery of gene editing technology called CRISPR/Cas-9 made it possible to precisely alter the sequence of DNA in a living being.

But while DNA may be the raw blueprints for life, RNA is the architect—translating those ideas into reality for the cell through proteins and regulation. While CRISPR systems that target RNA have recently been discovered, none offers a single clear solution.

A group of scientists from the University of Chicago has announced a breakthrough method to alter RNA—and instead of using a protein from bacteria, like CRISPR, the new system is built out of parts from the human genome. Announced June 20 in Cell, the discovery could open new pathways for treating diseases or injuries by temporarily altering how the genetic template is carried out in the cell.

“People had delayed targeting RNA for a long time because it’s so complex in how it works,” said study author Bryan Dickinson, an associate professor of chemistry at UChicago. “But I think now we’re realizing that complexity is an opportunity to figure out how to exploit and change those pathways. In principle, you could make even more dramatic changes to the cell than with DNA, and now we finally have the tools to do so.”

Even as DNA-targeting CRISPR methods begin their initial clinical trials in humans, scientists have become increasingly interested in equivalent systems for RNA. An RNA-targeting method that can safely be applied to humans would be a valuable complement to CRISPR, Dickinson said.

“If you imagine the universe of diseases that CRISPR is going to correct, it’ll be really important ones, but only those that are based off of one single mutation in your DNA,” said Dickinson, whose work tries to create functional molecules that lead to biological breakthroughs. “There are many more diseases out there with multiple causes in the cell, which may be much more difficult to understand—and there will also be those where the risks associated with changing someone’s DNA permanently are just too high.”

Because the effects of RNA alteration are temporary rather than permanent, an RNA-CRISPR is inherently less risky, because doctors can simply stop the treatment if there are intolerable side effects. It could also be used for things like briefly boosting a person’s system to accelerate wound healing: “We know what to do for that—you would encourage processes for cell growth and proliferation,” Dickinson said. “But those are the same things that cause cancer, so you could never do that at the DNA level.”

But translating these microbial systems into therapeutics is going to be challenging, he said. “RNA-targeting drugs need to be continually administered, so the foreign nature of CRISPR/Cas systems is going to create an immune backlash when applied to humans.”

This presents key roadblocks for natural CRISPR systems, which Dickinson’s team realized it had an opportunity to correct by reengineering the whole system from scratch.

Because it’s a very large protein, CRISPR is generally too big to use the most common delivery system to insert genetic material into cells—“phages,” which originate from tiny viruses. This is a problem, especially if you need to deliver them continually. More critically, because CRISPR comes from a microbe, there are significant concerns about the human immune system reacting to it.

Instead, the team broke down CRISPR into its components based on what each part does, and looked for human versions of those proteins that did equivalent tasks. Then they cobbled those together into a cohesive whole—which is smaller than CRISPR, and made out of human material.

“Although there’s still a lot of work to do, the crazy thing is it actually works,” Dickinson said.

Their system succeeded in altering RNA in tests in the lab. The scientists plan to improve the system at a few points where the performance is not as good as CRISPR, they said, but they’re encouraged by the early results.

“As we learn more, you could imagine targeting multiple RNAs in different ways, and doing more complex reprogramming of the cell at the RNA level,” Dickinson said. “It’s a really exciting field right now.”

The first author was graduate student Simone Rauch; other co-authors were visiting scholar Michael Srienc, postdoctoral fellow Huiqing Zhou, high school student Emily He and graduate student Zijie Zhang.

The scientists are working with the Polsky Center for Entrepreneurship and Innovation at the University of Chicago to advance this discovery.

Citation: “Programmable RNA-guided RNA effector proteins built from human parts.” Rauch et al, Cell, June 20, 2019. DOI: 10.1016/j.cell.2019.05.049

Funding: University of Chicago, National Institutes of Health, Chicago Fellow Program.