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Start-ups

Watch out, CRISPR. The RNA editing race is on

Start-ups and academic labs are designing molecules that hijack our own enzymes to precisely edit RNA

by Ryan Cross
March 25, 2019 | APPEARED IN VOLUME 97, ISSUE 12

 

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Credit: ProQR Therapeutics
A model of the RNA-editing enzyme ADAR binding an antisense oligonucleotide and its target RNA

Joshua Rosenthal isn’t your typical biotech entrepreneur. The cephalopod scientist at the Marine Biological Laboratory in Woods Hole, Massachusetts, has spent most of his life studying the nervous systems of squid—along with the occasional octopus. But in April 2018, Rosenthal found himself in Boston pitching to investors at Atlas Venture an idea for a new kind of therapy, inspired by a mechanism that squid use to edit their RNA.

RNA, a short-lived cousin to its better-known partner DNA, is the blueprint for protein production in cells. Rosenthal told the Atlas investors about how squid and octopuses make prolific use of an enzyme called ADAR to catalyze thousands of single-letter changes to their RNA code. Those minor edits alter the structure and activity of proteins that control electrical impulses in the animals’ nerves.

Humans have ADAR enzymes in our bodies, too, where they do the same thing, just less prolifically. Rosenthal’s squid studies inspired him to hijack ADAR and program it for making precise edits to human RNA. By attaching a molecule called a guide RNA to ADAR, Rosenthal’s lab could direct the enzyme to edit a complementary RNA strand. It’s analogous to CRISPR gene editing, which uses a guide RNA to direct an enzyme called Cas9 to a complementary DNA strand.

Unlike DNA editing, which is permanent, the effects of RNA editing are reversible, since cells are constantly churning out new copies of RNA. If Rosenthal’s RNA editors work in humans, they could be used to repeatedly treat genetic diseases without confronting the unknown, long-term risks of permanent DNA editing with CRISPR. More importantly, they would offer a new strategy for treating conditions like pain or inflammation, in which a patient needs just a temporary fix. RNA editing could also be easier to turn into a therapy than CRISPR. Since ADAR already exists in our cells, in theory all that’s needed is a guide RNA to lasso the enzyme and tell it where to go.

The advantages must have been obvious to Nessan Bermingham, a venture partner at Atlas and the former CEO of Intellia Therapeutics, one of several firms developing CRISPR-based therapies. Atlas founded a new company, called Korro Bio, to develop RNA-editing therapies, with Bermingham as CEO and Rosenthal as a scientific adviser.

Korro is still in stealth mode, and Bermingham didn’t respond to interview requests, but it’s becoming clear that the excitement about RNA editing is mounting. At least four more biotech companies are developing RNA-editing therapies, and more academic labs are trying to design new RNA editors.

The concept of RNA editing isn’t new. In 1995, researchers at Ribozyme Pharmaceuticals discovered that synthetic strands of RNA, called antisense oligonucleotides, could recruit ADAR to make edits—albeit sloppily—on matching strands of RNA inside cells (Proc. Natl. Acad. Sci. U.S.A. 1995, DOI: 10.1073/pnas.92.18.8298). The team coined the term “therapeutic RNA editing.” The paper was cited once and then forgotten.

More than a decade later, two academic researchers—the MBL’s Rosenthal and Eberhard Karls University of Tübingen chemist Thorsten Stafforst—independently revived the idea of developing ADAR-based RNA editors. Each devised his own system for connecting a guide RNA to ADAR: Stafforst linked the two components chemically (Angew. Chem., Int. Ed. 2012, DOI: 10.1002/anie.201206489), and Rosenthal added a small RNA-binding protein to ADAR, which in turn bound the guide RNA (Proc. Natl. Acad. Sci. U.S.A. 2013, DOI: 10.1073/pnas.1306243110).

Both systems rely on ADAR’s natural ability to change one letter of the RNA code, an adenosine (A), into a different letter, called inosine (I). When cells use that edited RNA to make proteins, they interpret the unusual inosine as a normal letter, guanosine (G). The result is effectively the change of an A to a G. Although scientists can do a lot with this tool, it doesn’t allow them to make any edit they want. Other labs are looking for ways to edit the other letters in RNA.

But by the time Rosenthal’s research came out, CRISPR gene editing had been invented; it quickly overshadowed both labs’ work. People told Stafforst not to waste his time on RNA. “It was pretty difficult to actually publish this,” he says. “Everyone wanted to play around with CRISPR.”

While the CRISPR field exploded, Stafforst and Rosenthal continued refining their RNA editors. Early on, it became clear there might still be room for their approach: researchers discovered that CRISPR can sometimes introduce permanent unintended mutations in DNA. In contrast, off-target mutations in RNA are temporary, making RNA editing a potentially safer alternative to gene editing.

A simple way to edit RNA

To correct single point mutations in RNA, researchers are designing antisense oligonu- cleotides that bind to an enzyme in our cells called ADAR. By also binding a complemen- tary strand of RNA, these oligonucleotides coax ADAR into changing a mutation in an adenosine (A) base of the RNA into an inosine (I), which the cell reads as guanosine (G).
Will Ludwig/C&EN

In 2017, one of CRISPR’s inventors, Feng Zhang from the Broad Institute of MIT and Harvard, created his own version of RNA editing that linked up the catalytic portion of the ADAR enzyme to a Cas protein and a guide RNA (Science 2017, DOI: 10.1126/science.aaq0180). Zhang’s superstar status lent an air of credibility to the RNA-editing field. In fact, two CRISPR companies, Beam Therapeutics—cofounded by Zhang—and Locana, are developing RNA-editing therapies that require Cas enzymes.

Those complex designs are creating opportunities for others to showcase improved and simpler versions of RNA editors. In December, University of California, Davis, chemist Peter Beal revealed a system in which an engineered ADAR enzyme and a chemically modified guide RNA interlock to reduce off-target mutations. “We’re really excited about this because it was the first thing we tried,” Beal says. “We think there’s a lot of room for improvement” (Cell Chem. Biol.2018, DOI: 10.1016/j.chembiol.2018.10.025).

Others are trying to simplify the delivery system to make it easier to turn it into a therapy. Until recently, the various flavors of RNA editors all had to get both ADAR and the guide RNA into cells, creating a drug-delivery headache. In fact, drug delivery remains one of the biggest challenges for the CRISPR gene-editing field. In January, Stafforst published a strategy for designing chemically modified guide RNAs with built-in structures that effectively lasso the ADAR proteins found naturally in our own cells (Nat. Biotechnol. 2019, DOI: 10.1038/s41587-019-0013-6).

And in February, Prashant Mali, a CRISPR researcher at the University of California, San Diego, published a similar study using engineered guide RNAs that bind ADAR and direct it to fix RNA mutations in mouse models of two genetic diseases: muscular dystrophy and ornithine transcarbamylase deficiency (Nat. Methods 2019, DOI: 10.1038/s41592-019-0323-0). Mali has also founded a company called Shape Therapeutics to develop RNA-editing therapies.

Stafforst’s and Mali’s recent approaches demonstrate RNA editing’s two big advantages over CRISPR gene editing. First, using only a guide RNA to hijack the body’s own ADAR circumvents the problem of introducing a foreign protein into the body—something that could pose problems for CRISPR, whose Cas proteins come from bacteria. Second, chemically synthesized guide RNAs are essentially the same thing as antisense oligonucleotides, a class of drugs well established for treating diseases of the brain, eye, and liver.

“An advantage of antisense oligos is that they’ve been studied for decades already,” says Daniel de Boer, CEO of the Dutch antisense oligo company ProQR Therapeutics. De Boer says his company has been designing antisense oligos to recruit the body’s own ADAR for RNA editing since 2014. The firm is keeping most details under wraps, but de Boer says its first RNA-editing program will be for a form of hearing and vision loss called Usher syndrome.

The RNA-editing field is starting to attract more researchers too. In January, a rare-disease organization called the Rett Syndrome Research Trust (RSRT) awarded more than $5 million to several academic labs to develop RNA-editor therapies for the neurological disease. Rett is driven by a mutation that causes insufficient production of a protein called MeCP2, which is essential for regulating genes in brain cells. RNA editors could fix the blueprints for making the protein.

The nonprofit is also funding gene therapy, which would add a new copy of the gene for MeCP2, and CRISPR gene-editing approaches, which would fix the gene’s DNA mutation. “It is an exciting time for Rett,” says Monica Coenraads, executive director of RSRT. “We don’t want to sit idle.”

For a genetic disease like Rett, RNA-editing therapies would need to be administered repeatedly. Gene-therapy and gene-editing approaches could offer one-and-done cures. But having just the right amount of MeCP2 protein in cells—not too much or too little—is critical, explains Gail Mandel from Oregon Health and Science University, who received funding from RSRT to develop RNA editors with UC Davis’s Beal. The gene-therapy approach carries the risk of making too much MeCP2, a liability avoided with RNA and DNA editors, she explains.

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Other groups are beginning to investigate RNA editing’s potential for temporary treatments. Stafforst, for instance, suggests that RNA editing could be used to boost or weaken inflammation as a cancer or immune disease treatment. And Rosenthal’s lab is designing RNA editors that can lower the sensitivity of pain receptors by making a single change to their RNA blueprints. If the idea is successful, it could lead to a painkiller that lasts days or weeks but is nonaddictive and reversible.

None of the RNA editors are perfect yet. “It will be quite a high burden to make this work decently, but the idea is that once you can do it, there are countless opportunities,” Stafforst says. RNA editing is just getting its start as a small field, and Stafforst thinks that over the next few years, as more researchers turn from DNA to RNA editing, more applications for the technology will become clear. As for his own entrepreneurial ambitions? “It is a bit too early to say,” he says. “But there will definitely be a company.”

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