Intrahepatic cholangiocarcinoma (iCCA) is the second most prevalent primary liver cancer. While the genetic characterization of iCCA has led to targeted therapies for treating tumors with FGFR2 alterations and IDH1/2 mutations, only a limited number of patients can benefit from these strategies. Epigenomic profiles have emerged as potential diagnostic and prognostic biomarkers for improving treatment of cancers. In this study, we conducted whole-genome bisulfite sequencing on 331 iCCAs integrated with genetic, transcriptomic, and proteomic analyses, demonstrating the existence of four DNA methylation subtypes of iCCAs (S1-S4) that exhibited unique post-operative clinical outcomes. The S1 group was an IDH1/2-mutation-specific subtype with moderate survival. The S2 subtype was characterized by the lowest methylation level and the highest mutational burden among the four subtypes and displayed upregulation of a gene expression pattern associated with cell cycle/DNA replication. The S3 group was distinguished by high inter-patient heterogeneity of tumor immunity, a gene expression pattern associated with carbohydrate metabolism, and an enrichment of KRAS alterations. Patients with the S2 and S3 subtypes had the shortest survival among the four subtypes. Tumors in the S4 subtype, which had the best prognosis, showed global methylation levels comparable to normal controls, increased FGFR2 fusions/BAP1 mutations, and the highest copy number variant burdens. Further integrative and functional analyses identified GBP4 demethylation, which is highly prevalent in the S2 and S3 groups, as an epigenetic oncogenic factor that regulates iCCA proliferation, migration, and invasion. Together, this study identifies prognostic methylome alterations and epigenetic drivers in iCCA.

中文翻译：

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肝内胆管癌的全基因组 DNA 甲基化分析揭示了具有不同生物驱动因素的预后亚型

肝内胆管癌（iCCA）是第二常见的原发性肝癌。虽然 iCCA 的基因特征已经导致针对具有 FGFR2 改变和 IDH1/2 突变的肿瘤的靶向治疗，但只有有限数量的患者可以从这些策略中受益。表观基因组图谱已成为改善癌症治疗的潜在诊断和预后生物标志物。在这项研究中，我们对 331 个 iCCA 进行了全基因组亚硫酸氢盐测序，并结合遗传、转录组和蛋白质组分析，证明 iCCA 存在四种 DNA 甲基化亚型 (S1-S4)，这些亚型表现出独特的术后临床结果。S1 组是 IDH1/2 突变特异性亚型，具有中等生存率。S2 亚型的特点是四种亚型中甲基化水平最低和突变负荷最高，并表现出与细胞周期/DNA 复制相关的基因表达模式的上调。S3 组的特点是肿瘤免疫的患者间高度异质性、与碳水化合物代谢相关的基因表达模式以及 KRAS 改变的富集。S2和S3亚型患者的生存期在四种亚型中最短。S4 亚型肿瘤的预后最好，其整体甲基化水平与正常对照相当，FGFR2 融合/BAP1 突变增加，并且拷贝数变异负担最高。进一步的综合和功能分析发现 GBP4 去甲基化在 S2 和 S3 组中非常普遍，是调节 iCCA 增殖、迁移和侵袭的表观遗传致癌因子。总之，这项研究确定了 iCCA 中的预后甲基化改变和表观遗传驱动因素。