Integrative molecular characterization of gallbladder cancer reveals microenvironment-associated subtypes

Abstract Background & Aims Gallbladder cancer (GBC) is the most common type of biliary tract cancer, but the molecular mechanisms involved in gallbladder carcinogenesis remain poorly understood. In this study, we applied integrative genomics approaches to characterize GBC and explore molecular subtypes associated with patient survival. Methods We profiled the mutational landscape of GBC tumors (whole-exome sequencing on 92, targeted sequencing on 98, in total 190 patients). In a subset (n=45), we interrogated the matched transcriptomes, DNA methylomes and somatic copy number alterations. We explored molecular subtypes identified through clustering tumors by genes whose expression were associated with survival in 47 tumors and validated subtypes on 34 publicly available GBC cases. Results Exome analysis revealed TP53 was the most mutated gene. The overall mutation rate was low (median 0.82 Mut/Mb). APOBEC-mediated mutational signatures were more common in tumors with higher mutational burden. Aflatoxin-related signatures tended to be highly clonal (present in ≥50% of cancer cells). Transcriptome-wide survival association analysis revealed a 95-gene signature that stratified all GBC patients into three subtypes that suggested an association with overall survival post-resection. The two poor-survival subtypes were associated with adverse clinicopathologic features (advanced stage, pN1, pM1), immunosuppressive microenvironments (myeloid-derived suppressor cell accumulation, extensive desmoplasia, hypoxia) and T cell dysfunction, while the good-survival subtype showed the opposite features. Conclusion These data suggest that the tumor microenvironment and immune profiles could play an important role in gallbladder carcinogenesis and should be evaluated in future clinical studies, along with mutational profiles.