Unexpected discovery opens doors for improved siRNA therapies

In everyday life, when things turn out the opposite of what you expect, it's usually cause for frustration. In science, it's often the starting point for discovery.

That's what happened to a team of researchers from Memorial Sloan Kettering Cancer Center (MSK) and their collaborators at the Icahn School of Medicine at Mount Sinai. Their unexpected findings in the lab point to an opportunity to improve therapies that use small RNAs to silence disease-causing genes, potentially including those involved in cancer.

Sometimes you do an experiment. You think you're testing one idea, but when it doesn't turn out the way you planned, it can lead you to find something else that's much more interesting."

Eric Lai, PhD, developmental biologist 

In this case, the researchers -; led by Seungjae Lee, PhD, a postdoctoral fellow in the Lai Lab at MSK's Sloan Kettering Institute -; were testing how a protein called ALAS1 helps to make small regulatory RNAs called microRNAs. When they removed the protein from cells, they expected to see levels of microRNAs drop.

"But instead, we were surprised to see them increase," Dr. Lai says.

That counterintuitive result led to the discovery of an unrecognized role for ALAS1 beyond its well-known role in the production of heme. (Heme is an important player in many biological processes, including in oxygen transport -; giving hemoglobin its name -; in energy production, and in making microRNAs.)

The team's findings were published in Science, one of the world's most prestigious scientific journals.

How little RNA snippets silence genes

Both microRNAs and the related class of small interfering RNAs (siRNAs) are small snippets of RNA -; just 21 or 22 nucleotides long -; that bind to specific messenger RNAs (mRNAs) and repress them.

There's a bucket brigade of players that together convert longer RNA molecules into the tiny active products, and a key takeaway is that scientists have harnessed this knowledge to turn small RNAs into drugs that can silence genes that cause specific diseases.

The first siRNA drug, patisiran, was approved by the U.S. Food and Drug Administration (FDA) in 2018 to treat a debilitating genetic disorder called hereditary transthyretin amyloidosis. A handful of additional siRNA drugs have been approved since, with more moving their way through clinical trials. Doctors see great potential to develop siRNA medicines against both rare diseases and more common ones (siRNA drugs are sometimes called RNAi drugs, meaning they work by interfering with messenger RNA accumulation).

A moonlighting enzyme

Back in the Lai Lab, Dr. Lee had discovered that upon removing ALAS1 from cells, they made more microRNAs. And further experiments showed that removing any of the other enzymes in the heme biosynthesis pathway did not affect microRNA levels.

"This told us that ALAS1 has another job outside of helping to make heme, which no one had realized," Dr. Lee says.

"We can consider this a 'moonlighting' function," Dr. Lai adds. "And here we discovered that ALAS1 has this secret role regulating microRNAs that's not connected to its normal role in heme synthesis."

Potential to make siRNA drugs work better

The discovery led the MSK researchers to partner with colleagues from the Icahn School of Medicine at Mount Sinai who specialize in heme regulation and ALAS genes -; Makiko Yasuda, MD, PhD, Robert Desnick MD, PhD, and postdoctoral fellow Sangmi Lee, PhD. This allowed the MSK researchers to extend their findings from cell culture into custom animal models that the Mount Sinai group were developing.

And in mice, again, removing ALAS (specifically in liver cells) led to a global increase in microRNAs.

"The emerging picture is that ALAS acts as a brake on the production of microRNAs," Dr. Lai says. "So we thought, now that we know how to remove this brake, maybe we can use that to improve the efficacy of siRNA drugs and their ability to silence their target genes."

In theory, this knowledge might help boost the activity of siRNA drugs against any problematic gene that is overactive in disease, Dr. Lai explains. Potentially this could include oncogenes known to drive cancer.

"But we're not quite there yet," he says. "Therapeutic siRNA drugs don't work well enough against all targets and are currently limited in where they can be used in the body." In fact, all six of the FDA-approved siRNA drugs target hepatocytes in the liver.

"It's straightforward to get drugs into the liver, which serves as a filter for the body," Dr. Lai says.

So, as a proof-of-concept, the team showed that not only could they deplete mouse liver cells of ALAS, leading to an increase in microRNAs, but doing so also enhanced the silencing activity of another model siRNA compound delivered to the mice.

Coincidentally, one of the six approved siRNA drugs turns off ALAS1 to treat acute hepatic porphyrias. Dr. Yasuda and Dr. Desnick worked on the preclinical and clinical trials for the drug, which is known as givosiran. Since an siRNA against ALAS1 works effectively and safely in humans, this raises the possibility of combining such an agent to enhance other siRNA drugs. Dr. Lai notes that this strategy could be generally applicable to any siRNA.

And if siRNA drugs can be made to work better, this could improve their cost-effectiveness, reduce side effects by making them effective at lower doses, and perhaps help to target additional cell types beyond liver cells, he adds.

Why discovery science matters

In December 2024, Harvard geneticist Gary Ruvkun, PhD, was awarded the Nobel Prize with Victor Ambros, PhD, for their joint discovery of microRNA and its role in gene regulation in the early 1990s. Dr. Lai did his undergraduate thesis research in Dr. Ruvkun's lab at that time (on another class of gene regulator) and credits him for launching his own career.

"I got my first real exposure to how science was actually done and gained lifelong interests in developmental biology and small RNAs," Dr. Lai says, adding that his mentor's recent accolade underscores the importance of curiosity-driven research.

"Dr. Ruvkun didn't start out looking for microRNAs," Dr. Lai says. "Like Dr. Ambros, he was investigating the development of nematodes, these tiny worms that live in the soil. And not only did this unveil an entirely new paradigm for how genes are controlled, the field they started eventually resulted in a novel class of human therapies.

"When people ask why we're not spending all of our research dollars directly studying diseases like cancer, why we're funding research into cells and processes in model organisms like fruit flies, yeast, and bacteria -; this is a great example of how discovery science fuels the biggest breakthroughs," he continues. "And I think it is especially critical to keep this conversation active, given how much uncertainty and disagreement there is in society and government about how much to publicly fund scientific research and in what areas. Hopefully, there will be continued support to keep the engine of foundational research strong."

Funding and disclosures

Funding for the research includes grants from the National Institutes of Health (R01DK134783, R01-GM083300, P30-CA008748); a Cooperative Centers of Excellence in Hematology pilot grant (10040500-05S1); and a NYSTEM training award (C32559GG).

The researchers have filed a patent application on their methods for enhancing the efficacy of RNAi therapy by targeting ALAS1/ALAS2 (WO2024148236A1).

Drs. Yasuda and Desnick are also co-inventors of a patent for RNAi therapy of acute hepatic porphyrias. They also report pharmaceutical consulting work. Please see the study for full details.