Multigene mutational profiling of cholangiocarcinomas identifies actionable molecular subgroups

// Michele Simbolo 1,2,* , Matteo Fassan 1,2,* , Andrea Ruzzenente 3,* , Andrea Mafficini 1 , Laura D. Wood 4 , Vincenzo Corbo 1 , Davide Melisi 5 , Giuseppe Malleo 6 , Caterina Vicentini 1 , Giorgio Malpeli 1,3,6 , Davide Antonello 1,3,6 , Nicola Sperandio 1 , Paola Capelli 2 , Anna Tomezzoli 2 , Calogero Iacono 3 , Rita T. Lawlor 1,2 , Claudio Bassi 6 , Ralph H. Hruban 4 , Alfredo Guglielmi 3 , Giampaolo Tortora 5 , Filippo de Braud 7 , Aldo Scarpa 1,2 1 ARC-Net Research Centre, University and Hospital Trust of Verona, Verona, Italy 2 Department of Pathology and Diagnostics, University and Hospital Trust of Verona, Verona, Italy 3 Department of Surgery, General Surgery A, University of Verona, Verona, Italy 4 Department of Pathology, Johns Hopkins University and Sidney Kimmel Comprehensive Cancer Center, Baltimore, MD, USA 5 Department of Medical Oncology, University and Hospital Trust of Verona, Verona, Italy 6 Department of Surgery, General Surgery B, University of Verona, Verona, Italy 7 Medical Oncology Unit 1, Fondazione Istituto di Ricovero e Cura a Carattere Scientifico, Istituto Nazionale dei Tumori, Milan, Italy * shared first authorship Correspondence: Aldo Scarpa, email: // Keywords : cholangiocarcinoma; next-generation sequencing; molecular subclassification; target therapy; multigene mutational panels Received : April 2, 2014 Accepted : April 30, 2014 Published : May 1, 2014 Abstract One-hundred-fifty-three biliary cancers, including 70 intrahepatic cholangiocarcinomas (ICC), 57 extrahepatic cholangiocarcinomas (ECC) and 26 gallbladder carcinomas (GBC) were assessed for mutations in 56 genes using multigene next-generation sequencing. Expression of EGFR and mTOR pathway genes was investigated by immunohistochemistry. At least one mutated gene was observed in 118/153 (77%) cancers. The genes most frequently involved were KRAS (28%), TP53 (18%), ARID1A (12%), IDH1/2 (9%), PBRM1 (9%), BAP1 (7%), and PIK3CA (7%). IDH1/2 (p=0.0005) and BAP1 (p=0.0097) mutations were characteristic of ICC, while KRAS (p=0.0019) and TP53 (p=0.0019) were more frequent in ECC and GBC. Multivariate analysis identified tumour stage and TP53 mutations as independent predictors of survival. Alterations in chromatin remodeling genes ( ARID1A , BAP1 , PBRM1 , SMARCB1 ) were seen in 31% of cases. Potentially actionable mutations were seen in 104/153 (68%) cancers: i) KRAS/NRAS/BRAF mutations were found in 34% of cancers; ii) mTOR pathway activation was documented by immunohistochemistry in 51% of cases and by mutations in mTOR pathway genes in 19% of cancers; iii) TGF-ß/Smad signaling was altered in 10.5% cancers; iv) mutations in tyrosine kinase receptors were found in 9% cases. Our study identified molecular subgroups of cholangiocarcinomas that can be explored for specific drug targeting in clinical trials.