Multigene mutational profiling of cholangiocarcinomas identifies actionable molecular subgroups - PubMed (original) (raw)

. 2014 May 15;5(9):2839-52.

doi: 10.18632/oncotarget.1943.

Matteo Fassan, Andrea Ruzzenente, Andrea Mafficini, Laura D Wood, Vincenzo Corbo, Davide Melisi, Giuseppe Malleo, Caterina Vicentini, Giorgio Malpeli, Davide Antonello, Nicola Sperandio, Paola Capelli, Anna Tomezzoli, Calogero Iacono, Rita T Lawlor, Claudio Bassi, Ralph H Hruban, Alfredo Guglielmi, Giampaolo Tortora, Filippo de Braud, Aldo Scarpa

Affiliations

Multigene mutational profiling of cholangiocarcinomas identifies actionable molecular subgroups

Michele Simbolo et al. Oncotarget. 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.

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Figures

Figure 1

Figure 1. Mutation and immunohistochemical landscape of 153 primary biliary carcinomas

The series includes 70 intrahepatic cholangiocarcinomas (ICC), 57 extrahepatic cholangiocarcinomas (ECC), and 26 gallbladder carcinomas (GBC). Significantly mutated genes are listed vertically in decreasing order of prevalence of nonsilent mutation. Colored rectangles indicate mutation category observed in a given gene and tumour. Tumour classifications and molecular features are as indicated in the boxes on the right. Immunoistochemistry phenotypes and FISH analysis results are shown in the bottom tracks. White boxes indicate unknown status or missing data.

Figure 2

Figure 2. Representative examples of validation by Sanger sequencing of mutations identified using next generation sequencing

On the left of each sample is the representation of the results of next-generation sequencing where the reads are aligned to the reference genome as provided by the Integrative Genomics Viewer (IGV v.2.1, Broad Institute) software. On the right is the representation of the results of Sanger sequencing.

Figure 3

Figure 3. Somatic mutations detected in chromatin remodeling genes ARID1A, BAP1, and PBRM1

Schematic representation of ARID1A, BAP1, and PBRM1 genes with the indication of the site of the somatic mutations identified in our study. Genomic coordinates are shown at the bottom track for each gene. Gray arrow indicates gene transcriptional direction. In black are represented the exons for each gene. Vertically, in correspondence of genomic location, bar chart indicate the type and number of mutations. Bar chart color is specific for mutation type: red, non synonymous coding; green, deletion; blue, splice site; yellow, frameshift.

Figure 4

Figure 4. Immunohistochemical profiles of Egfr and mTOR pathway in cholangiocarcinomas

Representative examples of immunohistochemical staining in cholangiocarcinoma samples. The prevalence of positive cases within the different tumour types is shown. Original magnfications 20x.

Figure 5

Figure 5. Overall survival according to pathological and mutational features

Overall survival of 125 cholangiocarcinomas is significantly affected by tumour stage (_p_=0.0001) (A), tumour location (_p_=0.0176) (B), TP53 (_p_=0.0043) (C) and KRAS (_p_=0.0162) (D) mutational status. Vertical axis indicates percent survival; horizontal axis shows time expressed in months. Kaplan–Meier and log-rank statistics were used to determine levels of significance.

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