Integrative multiomics enhancer activity profiling identifies therapeutic vulnerabilities in cholangiocarcinoma of different etiologies

Abstract

ObjectivesCholangiocarcinoma (CCA) is a heterogeneous malignancy with high mortality and dismal prognosis, and an urgent clinical need for new therapies. Knowledge of the CCA epigenome is largely limited to aberrant DNA methylation. Dysregulation of enhancer activities has been identified to affect carcinogenesis and leveraged for new therapies but is uninvestigated in CCA. Our aim is to identify potential therapeutic targets in different subtypes of CCA through enhancer profiling.DesignIntegrative multiomics enhancer activity profiling of diverse CCA was performed. A panel of diverse CCA cell lines, patient-derived and cell line-derived xenografts were used to study identified enriched pathways and vulnerabilities. NanoString, multiplex immunohistochemistry staining and single-cell spatial transcriptomics were used to explore the immunogenicity of diverse CCA.ResultsWe identified three distinct groups, associated with different etiologies and unique pathways. Drug inhibitors of identified pathways reduced tumour growth inin vitroandin vivomodels. The first group (ESTRO), with mostly fluke-positive CCAs, displayed activation in estrogen signalling and were sensitive to MTOR inhibitors. Another group (OXPHO), with mostlyBAP1andIDH-mutant CCAs, displayed activated oxidative phosphorylation pathways, and were sensitive to oxidative phosphorylation inhibitors. Immune-related pathways were activated in the final group (IMMUN), made up of an immunogenic CCA subtype and CCA with aristolochic acid (AA) mutational signatures. Intratumour differences in AA mutation load were correlated to intratumour variation of different immune cell populations.ConclusionOur study elucidates the mechanisms underlying enhancer dysregulation and deepens understanding of different tumourigenesis processes in distinct CCA subtypes, with potential significant therapeutics and clinical benefits.

Cholangiocarcinoma: Recent Advances in Molecular Pathobiology and Therapeutic Approaches

“…Distinct patterns of DNA hypermethylation targeting either promoter CpG islands or promoter CpG shores were also observed in fluke-positive CCA cases and fluke-negative CCA cases, respectively [2], which highlights the prognostic value of DNA methylation in defining the molecular subtypes of CCA. More recently, genome-wide changes in DNA methylation and enhancer activities have proven valuable in deciphering different molecular subtypes to guide the therapeutic interventions in many other cancers [57][58][59]. In an epigenetic study by Tang and co-workers [60] on intrahepatic CCA, the collagen type XII alpha 1 chain (COL12A1) was identified as a specific biomarker for enrichment in the epithelial-mesenchymal transition pathway and advanced tumor stage.…”