By Gilang Cahya 
In the realm of scientific inquiry, where the unexpected often dethrones the anticipated, a recent discovery by researchers at Memorial Sloan Kettering Cancer Center (MSK) and their collaborators at the Icahn School of Medicine at Mount Sinai has unveiled a surprising new mechanism for regulating gene expression. This finding, born from an experiment that yielded results contrary to expectations, offers a promising avenue for improving therapies that leverage small RNA molecules to silence disease-causing genes, with potential implications for a wide range of conditions, including cancer.
The research team, spearheaded by Seungjae Lee, PhD, a postdoctoral fellow in the laboratory of developmental biologist Eric Lai, PhD, at MSK’s Sloan Kettering Institute, embarked on a study to elucidate the role of the protein ALAS1 in the biogenesis of microRNAs. MicroRNAs are crucial small regulatory RNA molecules that play a significant role in cellular function by modulating gene expression. The prevailing scientific understanding at the time posited that ALAS1, known for its established function in heme synthesis, would directly influence the production of these microRNAs. The researchers hypothesized that by diminishing ALAS1 levels within cells, they would observe a corresponding decrease in microRNA abundance.
However, the experimental outcomes defied this prediction. Instead of a decline, the team observed a significant and unexpected increase in microRNA levels when ALAS1 was removed from the cellular environment. This counterintuitive result marked a pivotal moment, prompting a deeper investigation into the previously unrecognized functions of ALAS1. It suggested that ALAS1 possessed a role extending far beyond its well-documented involvement in the production of heme, a vital component in numerous biological processes including oxygen transport, energy metabolism, and, as now understood, microRNA synthesis. The groundbreaking findings of this research were subsequently published in the prestigious scientific journal Science.
The Precision of Small RNAs in Gene Silencing
To fully appreciate the significance of this discovery, it is essential to understand the fundamental mechanics of how small RNA snippets operate to silence genes. Both microRNAs (miRNAs) and their closely related counterparts, small interfering RNAs (siRNAs), are remarkably small RNA molecules, typically measuring just 21 or 22 nucleotides in length. Their therapeutic power lies in their ability to bind with exquisite specificity to messenger RNAs (mRNAs), the molecular intermediaries that carry genetic instructions from DNA to the protein-making machinery of the cell. Upon binding, miRNAs and siRNAs effectively repress the function of these target mRNAs, thereby silencing the genes they represent.
The intricate process of converting longer RNA molecules into these active, gene-silencing small RNAs involves a complex cascade of molecular players. Scientists have masterfully deciphered this cellular pathway, harnessing this knowledge to develop innovative therapeutic strategies. Small RNAs have been engineered into potent drugs capable of targeting and silencing genes that drive specific diseases.
A landmark achievement in this field was the U.S. Food and Drug Administration (FDA) approval of patisiran in 2018. This marked the advent of the first FDA-approved siRNA drug, designed to treat hereditary transthyretin amyloidosis, a debilitating genetic disorder. Since then, several other siRNA drugs have received regulatory approval, with a growing pipeline of candidates advancing through various stages of clinical trials. The medical community views siRNA-based medicines with immense optimism, foreseeing their application in treating both rare genetic conditions and more prevalent diseases. These siRNA drugs are often referred to as RNAi drugs, underscoring their mechanism of action: interfering with the accumulation of messenger RNA.
Unveiling the "Moonlighting" Enzyme: ALAS1’s Hidden Talent
The unexpected surge in microRNA levels observed in the Lai Lab, following the depletion of ALAS1, set in motion a series of meticulous experiments. Dr. Lee’s further investigations revealed a critical distinction: while the absence of ALAS1 dramatically altered microRNA levels, removing other enzymes within the heme biosynthesis pathway had no discernible effect on these regulatory RNAs. This crucial observation provided irrefutable evidence that ALAS1 possessed a distinct function, independent of its role in heme production, a function that had eluded scientific detection until this point.
"This told us that ALAS1 has another job outside of helping to make heme, which no one had realized," stated Dr. Lee, highlighting the novelty of their finding.
Dr. Lai elaborated on this revelation, characterizing the newly discovered function as a "moonlighting" role. "We can consider this a ‘moonlighting’ function," he explained. "And here we discovered that ALAS1 has this secret role regulating microRNAs that’s not connected to its normal role in heme synthesis." This "moonlighting" phenomenon, where a single protein performs multiple, seemingly unrelated functions, is a fascinating aspect of molecular biology, and the identification of ALAS1’s dual nature represents a significant advancement in understanding cellular regulation.
A Collaborative Leap Towards Enhanced Therapeutic Efficacy
The implications of this discovery were profound, prompting the MSK researchers to forge a partnership with leading experts in heme regulation and ALAS genes at the Icahn School of Medicine at Mount Sinai. This collaboration brought together the expertise of Makiko Yasuda, MD, PhD, Robert Desnick, MD, PhD, and postdoctoral fellow Sangmi Lee, PhD. The Mount Sinai team’s specialized knowledge and their development of custom animal models were instrumental in enabling the MSK researchers to transition their findings from in vitro cell culture studies to more complex in vivo investigations.
The results in the animal models mirrored those observed in cell culture. In mice, the targeted removal of ALAS, specifically within liver cells, consistently led to a widespread increase in microRNA levels. This confirmed the conserved nature of ALAS1’s regulatory role across species.
"The emerging picture is that ALAS acts as a brake on the production of microRNAs," Dr. Lai articulated, providing a clear analogy for ALAS1’s function. "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."
The theoretical framework suggested that this newfound understanding could potentially amplify the effectiveness of siRNA drugs against any gene that is abnormally overactive in a disease state. This includes oncogenes, which are known drivers of cancer development. The potential to enhance the power of these therapies could translate into more effective treatments for a broader spectrum of diseases.
However, Dr. Lai tempered this optimism with a dose of scientific realism. "But we’re not quite there yet," he cautioned. "Therapeutic siRNA drugs don’t work well enough against all targets and are currently limited in where they can be used in the body." A significant limitation currently faced by approved siRNA drugs is their targeting specificity, with all six FDA-approved siRNA drugs primarily targeting hepatocytes in the liver. This hepatic tropism is largely due to the liver’s role as the body’s primary filtration organ, making it a relatively accessible target for drug delivery.
As a demonstration of their concept, the research team conducted a proof-of-concept experiment. They successfully depleted ALAS in mouse liver cells, confirming the resultant increase in microRNA levels. Crucially, they then demonstrated that this manipulation also significantly enhanced the gene-silencing efficacy of a model siRNA compound administered to the mice. This provided compelling evidence that inhibiting ALAS1 could indeed potentiate the activity of other siRNA-based therapeutics.
A remarkable coincidence emerged during their research: one of the six FDA-approved siRNA drugs, known as givosiran, is specifically designed to turn off ALAS1 to treat acute hepatic porphyrias. Drs. Yasuda and Desnick were instrumental in the preclinical and clinical development of givosiran, underscoring their deep involvement in ALAS1-targeted therapies. The fact that an siRNA targeting ALAS1 has already proven effective and safe in human patients opens a tantalizing possibility: combining such an agent with other siRNA drugs to bolster their therapeutic impact. Dr. Lai suggested that this combinatorial strategy could be broadly applicable to any siRNA therapy, regardless of its specific target.
The potential benefits of such a strategy are manifold. Enhanced efficacy could lead to the use of lower doses of siRNA drugs, potentially reducing the incidence of side effects and improving cost-effectiveness. Furthermore, a more potent therapeutic effect might enable siRNA drugs to effectively target cell types beyond the liver, expanding their reach and therapeutic potential to a wider array of diseases and anatomical locations.
The Enduring Importance of Discovery Science
The recent Nobel Prize awarded to Harvard geneticist Gary Ruvkun, PhD, and Victor Ambros, PhD, in December 2024 for their pioneering discovery of microRNA and its role in gene regulation in the early 1990s, serves as a potent reminder of the value of fundamental, curiosity-driven research. Dr. Lai, who conducted his undergraduate thesis research in Dr. Ruvkun’s lab during that formative period, credits his mentor with igniting his own passion for scientific exploration.
"I got my first real exposure to how science was actually done and gained lifelong interests in developmental biology and small RNAs," Dr. Lai remarked, emphasizing how his mentor’s recent accolade underscores the profound impact of research that follows intellectual curiosity.
He further elaborated on the serendipitous nature of groundbreaking discoveries: "Dr. Ruvkun didn’t start out looking for microRNAs. 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."
This narrative powerfully illustrates the essence of discovery science. "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," Dr. Lai asserted. He stressed the critical importance of maintaining robust support for foundational research, particularly in an era marked by societal and governmental uncertainty regarding the allocation of public funding for scientific endeavors. "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 Declarations
The research underpinning this discovery was supported by 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 pertaining to their methods for enhancing the efficacy of RNAi therapy by targeting ALAS1/ALAS2, with the publication number WO2024148236A1.
Drs. Yasuda and Desnick are also co-inventors on a patent related to RNAi therapy for acute hepatic porphyrias. They have also disclosed pharmaceutical consulting work.