Multigene mutational profiling of cholangiocarcinomas identifies actionable molecular subgroups

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.

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

“…4, Supplementary Table 5). Somatic substitutions were predominantly C:G4T:A transitions as previously reported in iCCA and other cancers [7][8][9][10][11] . Of the mutations identified, 64% were missense, 28% were silent, 5% were nonsense and 3% were indels (Fig.…”

“…Novel mutations in chromatin remodelling genes (for example, ARID1A, BAP1 and PBMR1) have emerged and account for the most frequent mutations reported so far in iCCA (B25%) 8,9 as it has also been corroborated in recent studies where mutations in such genes have been identified even at higher frequency (34-46%) 10,20 . At the same time, already described mutations (for example, KRAS, IDH1/2, and EGFR) have been confirmed [7][8][9][10][11]20 . Notably, IDH1/ 2-activating mutations occur in B20% of the iCCA cases 4 -17% in our series-and tend to be mutually exclusive with other mutations.…”

“…Screening of our prevalence cohort for these two mutations along with the evaluation of the kinase domain revealed that overall 11% of the iCCA population harbours mutations in ARAF gene. These mutations are novel [7][8][9][10]20 , and their oncogenic potential needs to be properly investigated in experimental models.…”

“…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] . Nonetheless, none of the targetable mutations have been explored yet in early clinical trials.…”

CRISPR/Cas9 somatic multiplex-mutagenesis for high-throughput functional cancer genomics in mice

“…This distribution suggests that biologically relevant mutations are selected for in vivo. The high incidence of Pten mutations can indeed be explained by the key importance of PI3K signaling in hepatobiliary tumorigenesis in humans and mice (32)(33)(34). Likewise, the lack of Brca1/2 mutations reflects their extremely rare alteration in human ICC/HCC (SI Appendix, Table S1).…”