Integrative Molecular Analysis of Intrahepatic Cholangiocarcinoma Reveals 2 Classes That Have Different Outcomes

Abstract

BACKGROUND & AIMS Cholangiocarcinoma, the second most common liver cancer, can be classified as intra-hepatic cholangiocarcinoma (ICC) or extrahepatic cholangiocarcinoma. We performed an integrative genomic analysis of ICC samples from a large series of patients. METHODS We performed a gene expression profile, high-density single-nucleotide polymorphism array, and mutation analyses using formalin-fixed ICC samples from 149 patients. Associations with clinicopathologic traits and patient outcomes were examined for 119 cases. Class discovery was based on a non-negative matrix factorization algorithm and significant copy number variations were identified by GISTIC analysis. Gene set enrichment analysis was used to identify signaling pathways activated in specific molecular classes of tumors, and to analyze their genomic overlap with hepatocellular carcinoma (HCC). RESULTS We identified 2 main biological classes of ICC. The inflammation class (38% of ICCs) is characterized by activation of inflammatory signaling pathways, overexpression of cytokines, and STAT3 activation. The proliferation class (62%) is characterized by activation of oncogenic signaling pathways (including RAS, mitogen-activated protein kinase, and MET), DNA amplifications at 11q13.2, deletions at 14q22.1, mutations in KRAS and BRAF, and gene expression signatures previously associated with poor outcomes for patients with HCC. Copy number variation– based clustering was able to refine these molecular groups further. We identified high-level amplifications in 5 regions, including 1p13 (9%) and 11q13.2 (4%), and several focal deletions, such as 9p21.3 (18%) and 14q22.1 (12% in coding regions for the SAV1 tumor suppressor). In a complementary approach, we identified a gene expression signature that was associated with reduced survival times of patients with ICC; this signature was enriched in the proliferation class (P < .001). CONCLUSIONS We used an integrative genomic analysis to identify 2 classes of ICC. The proliferation class has specific copy number alterations, many features of the poor-prognosis signatures for HCC, and is associated with worse outcome. Different classes of ICC, based on molecular features, therefore might require different treatment approaches.

BRAF V600E-specific immunohistochemistry reveals low mutation rates in biliary tract cancer and restriction to intrahepatic cholangiocarcinoma

“…Our findings are in line with recently published smaller series detecting BRAF mutations in 1% to 4% of evaluated cases. [26][27][28] We cannot confirm the exceedingly high mutation rates detected in early BRAF studies of European cohorts, 29,30 and conclude that the previously assumed regional difference in the genetics of biliary tract cancer in Europe versus the Americas is not existent. 2 Our data further demonstrate that BRAF mutations are restricted to intrahepatic cholangiocarcinomas and account for 3% in this subgroup.…”

“…In two previously analyzed cholangiocarcinoma cohorts, tumors with BRAF mutations other than V600E have been reported that may potentially also respond to targeted therapy. For BRAF V600K (detected in one intrahepatic cholangiocarcinoma by Sia et al 27 ) response of melanoma metastases has been observed in a phase II trial, 37 and for BRAF V600D (detected in two cholangiocarcinomas not otherwise specified by Tannapfel et al 29 ) in vitro inhibitor Figure 2 Overall survival probability in intrahepatic cholangiocarcinoma patients in correlation with BRAF V600E status. Kaplan-Meier curves show no difference in overall survival of patients in correlation with BRAF V600E status in intrahepatic cholangiocarcinoma (P ¼ 0.38).…”

“…Considering that B70 000 new cases of intrahepatic cholangiocarcinoma are diagnosed globally every year, B2000 to 3000 patients are expected to harbor BRAF V600E-mutated tumors. 27 These patients may benefit from targeted therapies, and BRAF mutation screening approaches-like the one presented in this studyshould be evaluated for design of prospective trials for such low BRAF mutation frequency populations.…”

Massive parallel sequencing uncovers actionable FGFR2–PPHLN1 fusion and ARAF mutations in intrahepatic cholangiocarcinoma

“…To provide an overview of the genomic landscape of molecular alterations in iCCA, we integrated exome-and RNA-seq data with our previously published iCCA molecular classification 5 . IDH1 and IDH2 mutations were observed in 11 (11/107, 10%) and 7 patients, respectively (7/107, 7%, Supplementary Table 10).…”

“…Of late, there has been a significant improvement in our understanding of the molecular basis of iCCA 4 . Large-scale molecular profiling studies have enabled the first molecular classifications to emerge 5,6 . Furthermore, deepsequencing studies have provided a preliminary description of somatic mutations for iCCA [7][8][9][10] : novel mutations in chromatin remodelling genes (BAP1, ARID1A and PBRM1) have been recently unveiled, whereas frequent mutations in KRAS, IDH1 and IDH2 have been confirmed [8][9][10][11] .…”