ISL2 is an epigenetically silenced tumor suppressor and regulator of metabolism in pancreatic cancer

Abstract

Pancreatic ductal adenocarcinoma (PDAC) remains one of the deadliest cancers. Uncovering mechanisms responsible for the heterogeneous clinical features of this disease is an essential step toward developing improved and more specific therapeutic approaches. Here, we sought to identify transcriptional regulators of aggressive PDAC growth through in vivo CRISPR screening of epigenetic and transcription factors in an orthotopic model. We identified the ISL LIM homeobox 2 (ISL2) gene as a tumor suppressor whose depletion enhances the proliferation of human PDAC cells in vitro and in vivo and cooperates with activated KRAS to initiate PDAC in a murine model. Conversely, the upregulation of ISL2 expression through CRISPR-mediated locus-specific epigenetic editing results in reduced cell proliferation. Importantly, ISL2 is epigenetically silenced through DNA methylation in ~60% of PDAC tumors, which correlates with poor patient outcome.Functional studies showed that ISL2 loss rewires metabolic gene expression, and consequently potentiates oxidative phosphorylation while reducing glycolysis. This metabolic shift creates selective vulnerability to small molecule inhibitors of mitochondrial respiration and fatty acid oxidation. Collectively, these findings reveal ISL2 as a novel tumor suppressor whose inactivation drives metabolic reprogramming in an aggressive PDAC subset and point to potential therapeutic vulnerabilities in these tumors.

MethReg: estimating the regulatory potential of DNA methylation in gene transcription

“…The MEIS1 homeodomain protein is a tumor suppressor and was observed to be downregulated in colorectal adenomas ( 68 ). Similarly, ISL2 is also a tumor suppressor, and ISL2 loss increased cell proliferation and enhanced tumor growth in pancreatic ductal adenocarcinoma cells ( 69 ). ETV4 belongs to a subfamily of the ETS family with well-known oncogenic properties ( 70 ).…”

MethReg: estimating the regulatory potential of DNA methylation in gene transcription

“…The MEIS1 homeodomain protein is a tumor suppressor and was observed to be down-regulated in colorectal adenomas [66]. Similarly, ISL2 is also a tumor suppressor and ISL2 loss increased cell proliferation and enhanced tumor growth in pancreatic ductal adenocarcinoma cells [67]. ETV4 belongs to a subfamily of the ETS family with well-known oncogenic properties [68].…”