Molecular classification and tumor microenvironment characterization of gallbladder cancer by comprehensive genomic and transcriptomic analysis

Abstract

Gallbladder cancer (GBC), a rare but lethal disease, is often diagnosed at advanced stages. So far, molecular characterization of GBC is insufficient, and a comprehensive molecular portrait is warranted to uncover new targets and classify GBC. We performed a transcriptome analysis of both coding and non‐coding RNAs from 36 GBC fresh‐frozen samples. The results were integrated with those of comprehensive mutation profiling based on whole‐genome or exome sequencing. The clustering analysis of RNA‐seq data facilitated the classification of GBCs into two subclasses, characterized by high or low expression levels of TME (tumor microenvironment) genes. A correlation was observed between gene expression and pathological immunostaining. TME‐rich tumors showed significantly poor prognosis and higher recurrence rate than TME‐poor tumors. TME‐rich tumors showed overexpression of genes involved in epithelial‐to‐mesenchymal transition (EMT) and inflammation or immune suppression, which was validated by immunostaining. One non‐coding RNA, miR125B1, exhibited elevated expression in stroma‐rich tumors, and miR125B1 knockout in GBC cell lines decreased its invasion ability and altered the EMT pathway. Mutation profiles revealed TP53 (47%) as the most commonly mutated gene, followed by ELF3 (13%) and ARID1A (11%). Mutations of ARID1A, ERBB3, and the genes related to the TGF‐β signaling pathway were enriched in TME‐rich tumors. This comprehensive analysis demonstrated that TME, EMT, and TGF‐β pathway alterations are the main drivers of GBC and provides a new classification of GBCs that may be useful for therapeutic decision‐making.