Non-Inflamed Tumor Microenvironment and Methylation/Downregulation of Antigen-Presenting Machineries in Cholangiocarcinoma

SIMPLE SUMMARY: Cholangiocarcinoma (CCA) is a chemotherapy-resistant cancer. Reportedly, combination chemotherapy that includes immune checkpoint inhibitors (ICIs) showed superior effects compared to conventional chemotherapy for the treatment of advanced CCA. Although the efficacy of ICIs is considered to be affected by the tumor immune microenvironment (TME), the genetic/epigenetic background associated with TME in CCA is unknown. Here, we find that downregulations of genes involved in antigen presentation are associated with a “non-inflamed” tumor; the downregulations are inversely correlated with their DNA methylation levels. All tumors in the “inflamed” group exhibited an upregulation/low-methylation pattern. In contrast, the majority of CCAs in the non-inflamed group represent a downregulation/high-methylation pattern in antigen-presenting machineries. In addition, unique gene mutations of CCA that should induce DNA methylation events, like those in IDH1/2, are exclusively observed in CCAs carrying a non-inflamed tumor phenotype. These results may prove to be a clue to develop novel biomarkers and combination therapies for the treatment of CCA using ICIs. ABSTRACT: Cholangiocarcinoma (CCA) is a refractory cancer; a majority of CCAs represents a non-inflamed tumor phenotype that should be resistant to treatment, including immune checkpoint inhibitors (ICIs). In this study, we aimed to understand the molecular characteristics associated with non-inflamed CCAs. The genetic/epigenetic status of 36 CCAs was obtained from the Cancer Genome Atlas (PanCancerAtlas). CCAs were classified based on immune class using hierarchical clustering analysis of gene expressions related to tumor-infiltrating lymphocytes. The associations between immune class and genetic/epigenetic events were analyzed. We found that the tumors with alterations in FGFR2 and IDH1/2 had a “non-inflamed” tumor phenotype. A significant association was observed between the non-inflamed group and the downregulation of genes involved in antigen presentation (p = 0.0015). The expression of antigen-presenting machineries was inversely correlated with their DNA methylation levels, where 33.3% of tumors had an upregulation/low-methylation pattern, and 66.7% of tumors had a downregulation/high-methylation pattern. All tumors in the “inflamed” group exhibited an upregulation/low-methylation pattern. In contrast, 24 of 30 tumors in the non-inflamed group represent the downregulation/high-methylation pattern (p = 0.0005). Methylation with downregulation of antigen-presenting machineries is associated with the “non-inflamed” tumor phenotype of CCAs. This evidence provides important insights for developing new strategies for treating CCA.