Basic science discovery could pave the way for better interfering RNA therapies

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

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

“Sometimes you do an experiment,” says developmental biologist Eric Lai, Ph.D. “You think you’re testing an idea, but when it doesn’t turn out the way you planned, it may lead you to come up with something else , much more interesting.”

In this case, the researchers, led by Seungjae Lee, Ph.D., a postdoctoral researcher in the Lai Lab at MSK’s Sloan Kettering Institute, were testing how a protein called ALAS1 helped make small regulatory RNAs called microRNAs. When they removed the protein from the cells, they expected to see microRNA levels drop.

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

This counterintuitive result led to the discovery of a previously unknown role for ALAS1 beyond its well-known role in heme production. (Heme plays an important role in many biological processes, including the transport of oxygen (which gives hemoglobin its name), energy production, and the manufacture of microRNAs.)

The team’s findings were published in Science.

How small RNA snippets silence genes

MicroRNAs and the related class of small interfering RNAs (siRNAs) are small snippets of RNA, only 21 or 22 nucleotides long, that bind to and repress specific messenger RNAs (mRNAs).

There are a multitude of players that together convert longer RNA molecules into tiny active products, and one of the key takeaways is that scientists have harnessed this knowledge to turn small RNAs into drugs capable of silence genes responsible for 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 disease called hereditary transthyretin amyloidosis. A handful of additional siRNA-based drugs have since been approved, and more are in clinical trials. Doctors see great potential in developing siRNA-based drugs against rare and more common diseases (siRNA-based drugs are sometimes called RNAi drugs, meaning they work by interfering with accumulation of messenger RNA).

An enzyme in the dark

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

“This showed us that ALAS1 had a role other than helping to make heme, which no one had realized,” says Dr. Lee.

“We can think of this as a function of ‘moonlighting’,” adds Dr Lai. “And here we discovered that ALAS1 has this secret role in regulating microRNAs that is not related to its normal role in heme synthesis.”

Potential to improve the effectiveness of siRNA drugs

The discovery led MSK researchers to team up with colleagues at the Icahn School of Medicine at Mount Sinai who specialize in heme regulation and ALAS.

And in mice, again, deletion of ALAS (particularly in liver cells) led to an overall increase in microRNAs.

“The emerging picture is that ALAS acts as a brake on microRNA production,” says Dr. Lai. “So we thought, now that we know how to remove this brake, maybe we could use it to improve the effectiveness of siRNA drugs and their ability to silence their target genes.”

In theory, this knowledge could help boost the activity of siRNA drugs against any problematic overactive genes in the disease, Dr. Lai says. Potentially, this could include oncogenes known to cause cancer.

“But we’re not there yet,” he says. “Therapeutic siRNA drugs do not work well enough against all targets and are currently limited in where they can be used in the body.” In fact, all six siRNA drugs approved by the FDA target hepatocytes in the liver.

“It’s easy to get medications into the liver, which serves as a filter for the body,” says Dr. Lai.

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 this also enhanced the silencing activity of another siRNA model compound delivered to mice.

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

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

Why Discovery Science Matters

In December 2024, Harvard geneticist Gary Ruvkun, Ph.D., was awarded the Nobel Prize with Victor Ambros, Ph.D., for their joint discovery of microRNA and its role in gene regulation in the early 1990s At that time, Dr. Lai was doing his undergraduate thesis in Dr. Ruvkun’s lab (on another class of genetic regulators) and he credits him with launching his own career.

“I had my first real exposure to how science was actually done and gained a lifelong interest in developmental biology and small RNAs,” says Dr. Lai, adding that his mentor’s recent honor highlights the importance of curiosity-driven research.

“Dr. Ruvkun didn’t start out looking for microRNAs,” says Dr. Lai. “Like Dr. Ambros, he was studying the development of nematodes, the tiny worms that live in the soil. Not only did this uncover a whole new paradigm for how genes are controlled, but the field they launched ultimately resulted in a new class of human therapies.

“When people ask why we don’t spend all of our research dollars directly studying diseases like cancer, why we fund research on the cells and processes of model organisms like fruit flies, yeast and bacteria , it’s a great example of how scientific discovery fuels the greatest advances,” he continues.

“And I think it’s especially critical to keep this conversation active, given the uncertainty and disagreements that exist within society and government about how much public funding for scientific research is going on and in what areas. Hopefully there will be continued support to keep the basic research engine strong.