CRISPR Pioneer Zhang Details New Editing System Downstream From DNA

Xconomy Boston — 

[Updated 10/25/17 4:26pm ET] Researchers at the Broad Institute have adapted the CRISPR-Cas gene editing system so that it can change the sequence of RNA, rather than edit DNA. RNA transports instructions from DNA in the nucleus to the cell’s protein-making machinery.

CRISPR/Cas9-based drugs, which aim to correct genetic disease by making permanent changes to a cell’s DNA, will likely be tested in humans for the first time in the U.S. next year. There is a running debate among experts in the field about the risks of inadvertent genetic changes that could lead to cancer and other dangerous conditions.

But the Broad researchers, led by CRISPR pioneer Feng Zhang, say in a new paper that a CRISPR system that edits RNA can be used to correct genetic defects without permanently altering the genome. This, they say, could avoid potential safety issues. Their paper was published today in the journal Science.

Zhang’s team worked with cells in a dish, which means they are a long way from knowing if the new development will work in people. They used a human cell line, introducing mutated genes that are linked to Fanconi anemia and a rare kidney disorder called X-linked nephrogenic diabetes insipidus. Within those experimental cells, they used their new type of CRISPR system to repair the mutations at the RNA level.

CRISPR has been used to target and cut RNA, but scientists have struggled to get CRISPR to edit RNA, says Gaetan Burgio, a genome editing expert at Australian National University in Canberra. “To my knowledge this is the first time a correction of a disease in a cell line system is being performed using a CRISPR RNA editing system,” he adds.

The system, which the Broad team calls REPAIR, uses a different version of the Cas enzyme, which acts as molecular scissors. (In CRISPR-Cas systems, the Cas enzyme is guided to the right spot by another component—a string of programmable “guide” RNA that matches up with the targeted site.) Zhang and his group tested various Cas13 enzymes and selected one produced naturally by Prevotella bacteria.

But the naturally occurring Prevotella Cas13 went through a lot of changes before it would do what Zhang and his team wanted. First, the researchers inactivated the enzyme’s ability to chop RNA. They only wanted it to identify and bind to specific RNA sequences, like a person scanning for the name of a loved one among a vast wall of names. To do the editing at the identified site, the researchers brought in a different enzyme, called ADAR2, which swaps out a single “letter” A (adenosine) for an I (inosine) in RNA (hence the moniker REPAIR, for RNA Editing for Programmable A to I Replacement). Single-letter I-to-A mutations in RNA have been linked to a variety of genetic diseases.

The authors say the REPAIR system could potentially work in a wider range of cells than other gene-editing techniques. It might also be a technique to treat diseases or conditions that only require a temporary fix, such as local inflammation. “Treatment at the level of RNA can be more flexibly administered to control dosage better, allowing treatment to be stopped when no longer needed,” says Zhang.

Burgio says the REPAIR system seems to be about as efficient and accurate as classical CRISPR-Cas9 DNA editing, but it’s not quite as efficient and specific as more optimized CRISPR DNA-editing systems used by academic labs. He also cautions that the study was done only in cell lines. “There is a long way to go before envisaging the use of RNA editing as potential for therapeutics,” he says. In cases where a permanent genetic correction is needed, RNA editing might not be ideal, but it could potentially be better controlled than DNA editing, says Burgio. “I believe RNA and DNA editing are complementary approaches to potentially correct diseases.”

In their Science paper, Zhang (who co-founded Editas Medicine (NASDAQ: EDIT), which could be the first U.S company to test a CRISPR-based treatment in humans next year) and his team write that there is plenty more tinkering to do on REPAIR. They are now working to boost its efficiency and shrink its components so that it can be packaged and delivered into cells for animal testing.

[This paragraph has been added.] In addition to the paper from Zhang’s group, David Liu of Harvard University and his team showed in a paper published today in Nature that they could edit single letters of the DNA code using modified CRISPR-Cas9 components. Such CRISPR “base editors” can edit smaller sections of DNA more efficiently and cleanly than traditional genome editing techniques. Previous such CRISPR “base editors” developed over the last couple of years by Liu and others could change C-G DNA base pairs to T-A. The latest editors in the Nature paper can do the reverse.