Cholangiocarcinoma (CCA) is a hepatobiliary malignancy exhibiting high incidence in countries with endemic liver-fluke infection. We analysed 489 CCAs from 10 countries, combining whole-genome (71 cases), targeted/exome, copy-number, gene expression, and DNA methylation information. Integrative clustering defined four 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′UTR deletion as a mechanism of FGFR2 upregulation. Integration of non-coding 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.

The impact of different carcinogenic exposures on the specific patterns of somatic mutation in human tumors remains unclear. To address this issue, we profiled 209 cholangiocarcinomas (CCAs) from Asia and Europe, including 108 cases caused by infection with the liver fluke Opisthorchis viverrini and 101 cases caused by non-O. viverrini-related etiologies. Whole-exome sequencing (n = 15) and prevalence screening (n = 194) identified recurrent somatic mutations in BAP1 and ARID1A, neither of which, to our knowledge, has previously been reported to be mutated in CCA. Comparisons between intrahepatic O. viverrini-related and non-O. viverrini-related CCAs demonstrated statistically significant differences in mutation patterns: BAP1, IDH1 and IDH2 were more frequently mutated in non-O. viverrini CCAs, whereas TP53 mutations showed the reciprocal pattern. Functional studies demonstrated tumor suppressive functions for BAP1 and ARID1A, establishing the role of chromatin modulators in CCA pathogenesis. These findings indicate that different causative etiologies may induce distinct somatic alterations, even within the same tumor type.

Opisthorchis viverrini-related cholangiocarcinoma (CCA), a fatal bile duct cancer, is a major public health concern in areas endemic for this parasite. We report here whole-exome sequencing of eight O. viverrini-related tumors and matched normal tissue. We identified and validated 206 somatic mutations in 187 genes using Sanger sequencing and selected 15 genes for mutation prevalence screening in an additional 46 individuals with CCA (cases). In addition to the known cancer-related genes TP53 (mutated in 44.4% of cases), KRAS (16.7%) and SMAD4 (16.7%), we identified somatic mutations in 10 newly implicated genes in 14.8-3.7% of cases. These included inactivating mutations in MLL3 (in 14.8% of cases), ROBO2 (9.3%), RNF43 (9.3%) and PEG3 (5.6%), and activating mutations in the GNAS oncogene (9.3%). These genes have functions that can be broadly grouped into three biological classes: (i) deactivation of histone modifiers, (ii) activation of G protein signaling and (iii) loss of genome stability. This study provides insight into the mutational landscape contributing to O. viverrini-related CCA.

Cholangiocarcinoma (CCA) is a highly lethal, epithelial cell malignancy that occurs anywhere along the biliary tree and/or within the hepatic parenchyma. CCA displays features of cholangiocyte differentiation and probably arises predominantly from the epithelial cells lining the bile ducts, which are termed cholangiocytes; however, the cancers may also develop from peribiliary glands and hepatocytes, depending on the underlying liver disease and location [1][2][3][4] . These cancers are heterogeneous and are best classified according to the primary, anatomic subtype as intrahepatic CCA (iCCA), perihilar CCA (pCCA) or distal CCA (dCCA) 5,6 (Fig. 1). iCCA is located proximally to the second-order bile ducts within the liver parenchyma, pCCA is localized between the second-order bile ducts and the insertion of the cystic duct into the common bile duct, and dCCA is confined to the common bile duct below the cystic duct insertion. The true incidence of pCCA and iCCA is unclear owing to the extensive misclassification of pCCA as iCCA in national databases 6,7 . In addition, enhanced diagnostic capabilities have enabled increased clinical distinction between carcinoma of unknown primary and iCCA 8,9 . These factors have, in part, contributed to the reported increase in incidence of iCCA over the past two or three decades. Each of the anatomic subtypes is characterized by unique genetic aberrations, clinical presentations and management options 10 . However, many databases categorize both pCCA and dCCA as extrahepatic CCA. Most CCAs are adenocarcinomas and other histological subtypes, such as adenosquamous carcinoma or clear cell carcinoma, are encountered rarely 11 . These cancers are highly desmoplastic and are enmeshed in dense networks of inflammatory cells and matrix termed the tumour immune microenvironment [12][13][14] .The epidemiology of these cancers varies worldwide. Infections with specific trematodes (flatworm parasites, commonly called flukes) are a major cause of CCA in some regions. For example, in Southeast Asia, the liver fluke Opisthorchis viverrini is the leading cause of CCA 15 . CCA occurring secondary to fluke infestation can arise anywhere within the biliary tree and present as any one of the three anatomic subsets. Fluke-related CCA may have a specific pathogenesis, especially genetic aberrations, but the diagnosis and management are not different from non-fluke-related CCA. In the Western world, most patients with CCA do not have an identifiable risk factor, except for some with primary sclerosing cholangitis (PSC) 7,10 . Further insights into the epidemiology, risk factors and biology of CCA are needed to improve its prevention and therapy.In this Primer, we discuss the epidemiology and pathophysiological mechanisms of liver-fluke-related and non-liver-fluke-related CCA and associated risk factors and summarize diagnosis and management of C holangiocarcinoma

Opisthorchiasis is a neglected, tropical disease caused by the carcinogenic Asian liver fluke, Opisthorchis viverrini. This hepatobiliary disease is linked to malignant cancer (cholangiocarcinoma, CCA) and affects millions of people in Asia. No vaccine is available, and only one drug (praziquantel) is used against the parasite. Little is known about O. viverrini biology and the diseases that it causes. Here we characterize the draft genome (634.5 Mb) and transcriptomes of O. viverrini, elucidate how this fluke survives in the hostile environment within the bile duct and show that metabolic pathways in the parasite are highly adapted to a lipid-rich diet from bile and/or cholangiocytes. We also provide additional evidence that O. viverrini and other flukes secrete proteins that directly modulate host cell proliferation. Our molecular resources now underpin profound explorations of opisthorchiasis/CCA and the design of new interventions.