Research by University of California (UC), San Diego, School of Medicine scientists has demonstrated how RNA-binding proteins may represent a new class of drug target for cancers, including triple-negative breast cancer (TNBC), a particularly difficult-to-treat cancer because it lacks most other molecular drug targets. The researchers’ studies found that genetically deleting the RNA-binding protein YTHDF2 from human TNBC tumors transplanted into mice resulted in the tumors shrinking by approximately 10-fold in volume.
“We’re excited that RNA-binding proteins look like they could be a new class of drug targets for cancer,” said Gene Yeo, PhD, professor of cellular and molecular medicine at UC San Diego School of Medicine. “We’re not yet sure how easily druggable they are in this context, but we’ve built a solid framework to begin exploring them.” Yeo, together with Jaclyn Einstein, PhD, a graduate student, led the team’s studies, which are published in Molecular Cell, in a paper titled, “Inhibition of YTHDF2 triggers proteotoxic cell death in MYC-driven breast cancer.” Einstein will join a startup company spun out from the lab to explore the druggability of YTHDF2.
In cancer research, it’s a common goal to find something about cancer cells—some sort of molecule—that drives their ability to survive, and to determine if that molecule could be inhibited with a drug, halting tumor growth. Even better is if the molecule isn’t present in healthy cells, so the normal cells would remain untouched by the new therapy.
Plenty of progress has been made in this approach, known as molecular targeted cancer therapy. Some current cancer therapeutics inhibit enzymes that become overactive, allowing cells to proliferate, spread, and survive beyond their norm. The challenge is that many known cancer-driving molecules are “undruggable,” meaning their type, shape, or location prohibit drugs from binding to them.
RNA-binding proteins (RBPs) are critical regulators of post-transcriptional gene expression, the authors explained. After genes are transcribed into RNA, these proteins provide an extra layer of cellular control, determining which RNA copies get translated into other proteins and which don’t. Like many molecular systems that govern cell growth, RNA-binding proteins can contribute to tumor development when they malfunction.
“Changes in cellular growth rate and identity that occur during cancer progression are driven by specific gene expression signatures programmed by the activity of DNA-binding transcription factors (TFs) and RBPs,” the investigators wrote. However, “… aberrant RBP-RNA interactions can promote cancer progression.” And while mutations in transcription factors have been studied for decades, “… RBPs have been overlooked as drivers of disease and as therapeutically relevant targets,” the team pointed out. “RBPs remain largely unexplored as drug targets because their systematic evaluation has been limited by the lack of sensitive and efficient assays for phenotypic interrogation of individual RBPs.”
Yeo’s team has long studied the role of RNA-binding proteins in a number of other diseases. In 2016, they discovered that mutations in one such protein contribute to ALS by scrambling crucial cellular messaging systems. To explore RNA-binding proteins as cancer drug targets, the researchers harnessed a strategy known as synthetic lethality. They started with human breast cells engineered to overproduce another well-known cancer-driving molecule, MYC, and then looked for additional vulnerabilities specific to those cells.
The researchers systematically silenced RNA-binding proteins in the cancer cells one by one using CRISPR gene editing. They found 57 RNA-binding proteins that, when inhibited, led to death of cancer cells with the known hyperactive cancer-driver. The advantage of the synthetic lethal approach is that normal cells, which don’t produce that cancer-driving molecule, should be left untouched by the treatment. Of these 57 RNA-binding proteins, YTHDF2 appeared to be the most promising.
Yeo’s team also recently developed a new laboratory technique called Surveying Targets by APOBEC-Mediated Profiling (STAMP), which allows them to measure how RNA-binding proteins interact with RNA molecules within individual cells.
For their newly reported study, the researchers used STAMP to get a detailed look at how the various cells that make up a breast tumor behave without YTHDF2. “… we applied scRibo-STAMP to measure mRNA translation in individual tumor cells, which to our knowledge remains an outstanding challenge,” they commented. “scRibo-STAMP enabled the simultaneous quantification of transcriptomic and translational changes, and provided an early snapshot of changes occurring within tumor cells following YTHDF2 depletion and prior to widespread apoptosis.”
The approach revealed that YTHDF2-deficient cancer cells die by stress-induced apoptosis, a carefully controlled mechanism that cells use to destroy themselves. Apoptosis is supposed to shut down malfunctioning cells so tumors don’t arise, but it doesn’t always work. By removing YTHDF2, they managed to re-activate this cell death signal, leading to the death of cancer cells in vitro, and in vivo. “…we specifically found that depletion of YTHDF2 induced apoptosis in human triple-negative breast cancer (TNBC) cell lines and impeded xenografted tumor growth in vivo,” the team noted.
To test how safe it might be to treat cancer by inhibiting YTHDF2, the researchers engineered mice that lack YTHDF2 in every cell of the adult body, not just transplanted breast cancer cells. Encouragingly, the mice appeared completely normal, not only did they not have tumors, there were no changes in body weight or behavior. “… we demonstrate the efficacy and feasibility of depleting YTHDF2 as a potential therapeutic strategy by generating viable adult-life inducible systemic Ythdf2-knockout mice,” the authors noted. “Those otherwise healthy mice tell us that we might expect minimal adverse side effects of potential therapies that work by targeting YTHDF2,” Einstein said.
“Altogether, our studies reveal disease-promoting RBP-RNA interactions that are selectively essential for growth and survival of tumor cells but not somatic tissues and that targeting RBPs holds great promise for minimally toxic and highly specific treatment modalities in specific cancer subtypes,” the team concluded.