BACKGROUND AND AIMS Cholangiocarcinoma (CCA), a deadly malignancy of the bile ducts, can be classified on the basis of its anatomical location into either intrahepatic (iCCA) or extrahepatic (eCCA), each with different pathogenesis and clinical management. There is marginal understanding of the molecular landscape of eCCA and no targeted therapy with clinical efficacy has been approved. We aimed to provide a molecular classification of eCCA and identify potential targets for molecular therapies. METHODS An integrative genomic analysis of an international multi-center cohort of 189 eCCA cases was conducted. Genomic analysis included whole-genome expression, targeted DNA-sequencing and immunohistochemistry. Molecular findings were validated in an external set of 181 biliary tract tumors from ICGC. RESULTS KRAS (36.7%), TP53 (34.7%), ARID1A (14%) and SMAD4 (10.7%) were the most prevalent mutations, with ∼25% of tumors having a putative actionable genomic alteration according to OncoKB. Transcriptome-based unsupervised clustering helped us define four molecular classes of eCCA. Tumors classified within the Metabolic class (19%) showed a hepatocyte-like phenotype with activation of the transcription factor HNF4A and enrichment in gene signatures related to bile acid metabolism. The Proliferation class (23%), more common in patients with distal CCA, was characterized by enrichment of MYC targets, ERBB2 mutations / amplifications and mTOR signaling activation. The Mesenchymal class (47%) was defined by signatures of epithelial-mesenchymal transition, aberrant TGF-β signaling and poor overall survival. Finally, tumors in the Immune class (11%) had a higher lymphocyte infiltration, overexpression of PD-1/PD-L1 and molecular features associated with a better response to immune checkpoint inhibitors. CONCLUSION An integrative molecular characterization identified distinct subclasses of eCCA. Genomic traits of each class provide the rationale for exploring patient stratification and novel therapeutic approaches.

中文翻译：

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肝外胆管癌的分子分类和治疗靶点

背景和目的胆管癌（CCA）是一种致命的胆管恶性肿瘤，根据其解剖位置可分为肝内（iCCA）或肝外（eCCA），每种都有不同的发病机制和临床治疗。对 eCCA 的分子状况了解甚少，并且尚未批准具有临床疗效的靶向治疗。我们的目的是提供 eCCA 的分子分类并确定分子治疗的潜在靶点。方法 对 189 例 eCCA 病例的国际多中心队列进行综合基因组分析。基因组分析包括全基因组表达、靶向 DNA 测序和免疫组织化学。分子研究结果在 ICGC 的 181 例外部胆道肿瘤组中得到了验证。结果 KRAS (36.7%)、TP53 (34.7%)、ARID1A (14%) 和 SMAD4 (10.7%) 是最常见的突变，根据 OncoKB，约 25% 的肿瘤具有假定的可操作基因组改变。基于转录组的无监督聚类帮助我们定义了 eCCA 的四种分子类别。代谢类肿瘤（19%）表现出肝细胞样表型，转录因子 HNF4A 被激活，并且与胆汁酸代谢相关的基因特征富集。增殖类 (23%) 在远端 CCA 患者中更为常见，其特点是 MYC 靶点富集、ERBB2 突变/扩增和 mTOR 信号传导激活。间质类 (47%) 的定义是上皮-间质转化特征、异常的 TGF-β 信号传导和较差的总体生存率。最后，免疫类肿瘤 (11%) 具有较高的淋巴细胞浸润、PD-1/PD-L1 过度表达以及与免疫检查点抑制剂更好反应相关的分子特征。结论 综合分子表征确定了 eCCA 的不同亚类。每个类别的基因组特征为探索患者分层和新的治疗方法提供了基础。