RNA Interference Comes of Age
RNA Interference Comes of Age

RNA Interference Comes of Age

The third FDA approval of an RNAi-based therapeutic marks the growing success of a technique that took two decades to get off the ground.

Diana Kwon
Diana Kwon
Dec 9, 2020

ABOVE: A newly approved RNAi-based therapy reduces the overproduction of oxalate among people who have a rare genetic disorder. The condition leads to kidney stones, which are formed by calcium oxalate crystals such as these, and tissue damage.
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Last month, the US Food and Drug Administration approved lumasiran (Oxlumo), a drug to treat a rare genetic disorder known as primary hyperoxaluria type 1. PH1 results in an overproduction of a substance known as oxalate by the liver, which can accumulate in the kidney and urinary tract and cause a wide range of effects, including kidney stones, widespread organ damage, and end-stage renal disease.

The only cure for PH1 is a liver transplant. Lumasiran, which was developed by Cambridge, Massachusetts-based Alnylam Pharmaceuticals, is the first drug that reduces oxalate levels in patients, thus reducing the risk of complications later in life. “This is really the first treatment that medically can address the underlying effect of this disease,” says Jeffrey Saland, a pediatric nephrologist at Mount Sinai Hospital in New York and an investigator on ILLUMINATE-A, one of Alnylam’s Phase 3 trials of lumasiran. It’s also only the third drug of its kind to gain regulatory approval.

Lumasiran harnesses a naturally occurring process known as RNA interference (RNAi), which hijacks the production of specific proteins by silencing mRNA, the genetic blueprints for proteins. The drug reduces the levels of oxalate production in the liver by blocking mRNA that encodes for glycolate oxidase, an enzyme involved in the synthesis of oxalate, with a fragment of double-stranded RNA known as small-interfering RNA (siRNA). 

The regulatory approval of another drug, which the FDA is expected to announce this month, would mark another milestone: RNAi’s first success in treating a common condition.

There were two Phase 3 clinical trials for lumasiran—ILLUMINATE-A, a multinational, randomized, placebo-controlled trial of 39 patients ages six and older, and ILLUMINATE-B, an open-label study of 16 patients under six years old. Patients in both trials had functioning kidneys. In the first trial, they received three monthly injections followed by a maintenance dose every three months, while in the second, dosing regimens were adjusted to patients’ weights.

After six months of treatment, lumasiran significantly lowered oxalate levels in both studies: in the first, patients who received the drug had a 65 percent reduction of oxalate in their urine on average, compared to a 12 percent reduction among those in the control group. Patients in the second study exhibited an average of a 71 percent decrease. No significant changes in kidney function or other clinical outcomes were seen during this period (aside from early signs of improvement in nephrocalcinosis, the level of calcium deposits in the kidneys). The company plans to continue to monitor patient outcomes in an extended, open label trial. The most common side effects were injection site reactions, which include symptoms such as redness, pain, and swelling.

There are two other FDA-approved RNAi therapies, and both belong to Alnylam. Patisiran (Onpattro), an RNAi treatment for a rare genetic disorder that causes buildup of the protein transthyretin in the nervous system, known as hereditary transthyretin amyloidosis, was approved in 2018. The second drug, givosiran (Givlaari), for acute hepatic porphyria, a rare genetic condition that leads to the buildup of toxic polypyrin molecules, received approval in 2019. All three drugs are expensive—lumasiran, for example, is priced at $493,000 per patient per year, and patients will likely need to take the drug for life to keep oxalate levels low.

It took two decades from the initial discovery of RNAi for the first treatment using this technology to get past regulatory scrutiny, and the field faced numerous obstacles and setbacks along the way. The approval of a third RNAi therapeutic “is a huge milestone for the RNAi field,” says Derek Dykxhoorn, a molecular geneticist at the University of Miami. “We’ve always seen the potential that this technology had—the ability to harness the cell’s own endogenous silencing mechanisms to be able to treat disease—but it’s been a long journey from those studies to actually having FDA-approved therapies.”

See “The Second Coming of RNAi

Boom and bust

More than 20 years ago, biologists Andrew Fire and Craig Mello uncovered the process of RNAi in the roundworm Caenorhabditis elegans—a groundbreaking discovery that earned the pair the 2006 Nobel Prize in Physiology or Medicine. The finding also generated a surge of interest in the early 2000s from researchers seeking to use RNAi as a technique for basic science and the development of therapeutics.

Because RNAi could, in theory, target the production of any disease-causing protein—as long as the sequence of the gene encoding it is known—scientists began investigating it as a weapon against a wide range of ailments, including rare genetic disorders, cancer, and infectious diseases.

Despite a deluge of research, the results of early clinical trials were disappointing; low efficacy and harmful side effects meant treatments failed to progress far. One of the first treatments to make it to a Phase 3 clinical trial—an RNAi therapeutic for macular degeneration from the Florida-based company OPKO Health—was shut down in 2009 after disappointing early results. By 2010, pharma began to turn away from this technique, with large companies such as Roche, Pfizer, and Merck shuttering their RNAi research programs. Independent biotech consultant Dirk Haussecker described this period to The Scientist in 2014 as “the era of doubts and despair.”

RNAi therapies with targets outside the liver have yet to make it far in clinical trials.

The main obstacle the field faced was figuring out how to deliver siRNAs to the right cells in the body at high enough concentrations to be therapeutically relevant, Dykxhoorn says. A key issue is that siRNAs are readily degraded by enzymes in the bloodstream. To address this issue, scientists focused on identifying ways of packaging siRNAs. One of the first effective techniques involved coating them in droplets of fat called lipid nanoparticles (LNPs). But these LNPs had their limitations, says Phillip Zamore, director of the RNA Institute at the University of Massachusetts School of Medicine and cofounder of Alnylam. One drawback, he explains, was that although the LNPs would accumulate in the liver because a lot of blood—which carries the RNAi payload—flows through it, they did not explicitly target that organ. But what researchers wanted was a highly selective method of delivering the drug to tissues.

Alnylam developed another technique, dubbed GalNac, which involves linking a sugar, N-acetylgalactosamine, to the siRNA. Receptors on the surface of liver cells recognize N-acetylgalactosamine, enabling the conjugated molecules to reach those cells with a high level of specificity while limiting off-target effects. Many of Alnylam’s therapeutics, including lumasiran, use this technology, and for that reason treatments for liver-related conditions have been the first to advance clinically. “It’s clear now that everyone is using some strategy that involves conjugating a ligand to an siRNA to get it to the tissue of interest,” Zamore says. “For liver, it works incredibly well.”

See “Oligonucleotide Therapeutics Near Approval

To the liver and beyond

With new, effective methods of delivery, the RNAi field began to finally see some successes, namely, Alnylam’s three approved drugs. Another of Alnylam’s therapeutics is nearing the end of the pipeline: inclisiran, an RNAi treatment for high cholesterol that inhibits the liver’s production of PCSK9, an enzyme involved in cholesterol metabolism. (Alnylam designed inclisiran, but pharmaceutical giant Novartis has acquired the license for it.) The regulatory approval of this drug, which the FDA is expected to announce this month, would mark another milestone: RNAi’s first success in treating a common condition.

“I think everyone who follows this field is certain that it’s going to be approved,” says Judy Lieberman, a professor of pediatrics at Harvard Medical School who studies the use of RNAi in cancer and infectious diseases. “The Phase three data are so incredibly strong.” (Lieberman is a former member of Alnylam’s scientific advisory board.)

Alnylam’s successes reveal that RNAi has become a platform technology, Zamore says. “We now know it’s possible to have a global strategy that can be applied to any disease where reducing the concentration of something in the liver will provide clinical benefit.” Other biotech companies, such as Dicerna Pharmaceuticals and Arrowhead Pharmaceuticals, also have several RNAi drugs in their pipelines.

Expanding beyond the liver is the next big test. RNAi therapies with targets outside the liver have yet to make it far in clinical trials, according to Lieberman. The GalNac technique is specific to liver cells, so in order to get to other organs, researchers need to find methods that can target other tissues in a similar way. Many groups, including Lieberman’s, are developing and testing various methods of getting siRNA to other tissues, such as attaching antibodies and aptamers that, like GalNac, are recognized by cell-surface receptors that are unique to particular tissues, or by using lipid conjugates that home in on specific tissues.

In addition to several more drugs in the pipeline for liver-related conditions, including other genetic conditions and infectious diseases such as hepatitis B, Alnylam also has therapies in development with targets outside the liver. Currently, the company is also focused on developing RNAi treatments that work in the central nervous system and the eye, says Pritesh Gandhi, vice president and general manager of Alnylam’s lumasiran program.

“There’s a lot more to come,” Gandhi says. “This is just the beginning.”