{Reference Type}: Journal Article
{Title}: Whole-exome sequencing reveals novel cancer genes and actionable targets in biliary tract cancers in primary sclerosing cholangitis.
{Author}: Grimsrud MM;Forster M;Goeppert B;Hemmrich-Stanisak G;Sax I;Grzyb K;Braadland PR;Charbel A;Metzger C;Albrecht T;Steiert TA;Schlesner M;Manns MP;Vogel A;Yaqub S;Karlsen TH;Schirmacher P;Boberg KM;Franke A;Roessler S;Folseraas T;
{Journal}: Hepatol Commun
{Volume}: 8
{Issue}: 7
{Year}: 2024 Jul 1
{Factor}: 5.701
{DOI}: 10.1097/HC9.0000000000000461
{Abstract}: <B>BACKGROUND: </B>People with primary sclerosing cholangitis (PSC) have a 20% lifetime risk of biliary tract cancer (BTC). Using whole-exome sequencing, we characterized genomic alterations in tissue samples from BTC with underlying PSC.<BR><B>METHODS: </B>We extracted DNA from formalin-fixed, paraffin-embedded tumor and paired nontumor tissue from 52 resection or biopsy specimens from patients with PSC and BTC and performed whole-exome sequencing. Following copy number analysis, variant calling, and filtering, putative PSC-BTC-associated genes were assessed by pathway analyses and annotated to targeted cancer therapies.<BR><B>RESULTS: </B>We identified 53 candidate cancer genes with a total of 123 nonsynonymous alterations passing filtering thresholds in 2 or more samples. Of the identified genes, 19% had not previously been implicated in BTC, including CNGA3, KRT28, and EFCAB5. Another subset comprised genes previously implicated in hepato-pancreato-biliary cancer, such as ARID2, ELF3, and PTPRD. Finally, we identified a subset of genes implicated in a wide range of cancers such as the tumor suppressor genes TP53, CDKN2A, SMAD4, and RNF43 and the oncogenes KRAS, ERBB2, and BRAF. Focal copy number variations were found in 51.9% of the samples. Alterations in potential actionable genes, including ERBB2, MDM2, and FGFR3 were identified and alterations in the RTK/RAS (p = 0.036), TP53 (p = 0.04), and PI3K (p = 0.043) pathways were significantly associated with reduced overall survival.<BR><B>CONCLUSIONS: </B>In this exome-wide characterization of PSC-associated BTC, we delineated both PSC-specific and universal cancer genes. Our findings provide opportunities for a better understanding of the development of BTC in PSC and could be used as a platform to develop personalized treatment approaches.