NEW YORK — Researchers have identified how gene regulatory regions called super-enhancers can fuel the growth of pancreatic ductal adenocarcinoma (PDAC), which accounts for over 90 percent of all pancreatic cancer cases.
In a study published in Nature Communications on Wednesday, a team led by researchers from the Salk Institute for Biological Studies investigated PDAC cell lines and found several active super-enhancers that lead to a cascade of protein upregulation leading to the cancer phenotype.
Super-enhancers are regions of DNA with high transcription factor binding densities that are critical drivers of tumorigenesis. While previous studies have found transcription factors driven by super-enhancers that play a role in PDAC, those that cause a durable increase in translation required for proliferation are still unexplored, the authors wrote.
"This is the first time anyone has looked in such detail at the role of super-enhancers in pancreatic cancer," co-corresponding author Ronald Evans, director of Salk’s Gene Expression Laboratory, said in a statement.
For their study, Evans and colleagues mapped the locations of super-enhancers in 16 human pancreatic cancer cell lines by using H3K27ac as an identifier, finding 876 super-enhancers in total. One of the most active ones was associated with the gene heterogeneous nuclear ribonucleoprotein F (HNRNPF), a regulator of alternative splicing, polyadenylation, and RNA stability. They corroborated this finding with immunohistochemistry experiments and analysis of publicly available human single-cell RNA-seq data and aneuploid epithelial tumor cell nuclei obtained from a PDAC patient biopsy.
Next, to establish the role of this super-enhancer in driving HNRNPF expression, the researchers deleted 1,800 bases spanning the 5' distal enhancer in a PDAC cell line and noted an 80 percent reduction in HNRNPF transcript levels that caused a 35 percent reduction in protein levels, resulting in a dramatic slowing of cancer cell growth.
Meanwhile, they also used CRISPR-Cas9 editing to knock out HNRNPF in the cell line. Subsequent transcriptomic analysis revealed that 62 percent of genes downregulated were accounted for by the deletion of the super-enhancer, highlighting its significance in regulating hnRNP F levels.
This protein mediates the stability of protein arginine methyltransferase 1 (Prmt1), they wrote, which modifies ubiquitin-associated protein 2-like (Ubap2l), an RNA binding protein that in turn directly regulates translation. "This interlinked super-enhancer cascade at any of the downstream nodes is sufficient to suppress protein translation and inhibit cancer progression," they wrote.
Furthermore, they also used an experimental drug targeting Prmt1 and noted that it could control the growth of pancreatic tumor cells in the lab and in mice.
Experiments also showed that the Myc gene was the activator of the HNRNPF super-enhancer. Although Myc, like KRAS, is a known oncogenic driver of PDAC, developing drugs against it has been difficult. The new findings show that entities downstream of this pathway could be targeted instead to stop the cancer growth, the authors suggested.
"These results demonstrate that this super-enhancer is relevant in humans and could even be used as a marker to monitor pancreatic cancer progression," Evans said.