Cholangiocarcinoma (CCA) is a hepatobiliary malignancy exhibiting high incidence in countries with endemic liver-fluke infection. We analyzed 489 CCAs from 10 countries, combining whole-genome (71 cases), targeted/exome, copy-number, gene expression, and DNA methylation information. Integrative clustering defined 4 CCA clusters—fluke-positive CCAs (clusters 1/2) are enriched in ERBB2 amplifications and TP53 mutations; conversely, fluke-negative CCAs (clusters 3/4) exhibit high copy-number alterations and PD-1/PD-L2 expression, or epigenetic mutations (IDH1/2, BAP1) and FGFR/PRKA-related gene rearrangements. Whole-genome analysis highlighted FGFR2 3′ untranslated region deletion as a mechanism of FGFR2 upregulation. Integration of noncoding promoter mutations with protein–DNA binding profiles demonstrates pervasive modulation of H3K27me3-associated sites in CCA. Clusters 1 and 4 exhibit distinct DNA hypermethylation patterns targeting either CpG islands or shores—mutation signature and subclonality analysis suggests that these reflect different mutational pathways. Our results exemplify how genetics, epigenetics, and environmental carcinogens can interplay across different geographies to generate distinct molecular subtypes of cancer.

SIGNIFICANCE: Integrated whole-genome and epigenomic analysis of CCA on an international scale identifies new CCA driver genes, noncoding promoter mutations, and structural variants. CCA molecular landscapes differ radically by etiology, underscoring how distinct cancer subtypes in the same organ may arise through different extrinsic and intrinsic carcinogenic processes. Cancer Discov; 7(10); 1–20. ©2017 AACR.

胆管癌（CCA）是一种肝胆恶性肿瘤，在地方性肝吸虫感染国家中发病率很高。我们分析了来自10个国家的489个CCA，结合了全基因组（71例），靶向/外显子组，拷贝数，基因表达和DNA甲基化信息。整合聚类定义了4个CCA聚类-阳性的CCA（聚类1/2）富含ERBB2扩增和TP53突变。相反，吸虫阴性CCA（簇3/4）表现出高拷贝数变化和PD-1 / PD-L2表达，或表观遗传突变（IDH1 / 2，BAP1）和FGFR / PRKA相关基因重排。全基因组分析突出FGFR2 3'非翻译区缺失是FGFR2上调的机制。非编码启动子突变与蛋白质-DNA结合图谱的整合表明，CCA中H3K27me3相关位点的普遍调节。聚类1和4表现出针对CpG岛或海岸的不同DNA高甲基化模式-突变特征和亚克隆性分析表明，它们反映了不同的突变途径。我们的结果证明了遗传学，表观遗传学和环境致癌物如何在不同地区相互作用，从而产生不同的癌症分子亚型。

意义：在国际范围内对CCA进行全基因组和表观基因组综合分析，可以确定新的CCA驱动基因，非编码启动子突变和结构变异。CCA分子格局在病因学上有根本不同，强调了同一器官中不同的癌症亚型可能通过不同的外在和内在的致癌过程而出现。巨蟹座Discov; 7（10）；1-20。©2017 AACR。