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

Abstract

Intrahepatic cholangiocarcinoma (iCCA) is a fatal bile duct cancer with dismal prognosis and limited therapeutic options. By performing RNA-and exome-sequencing analyses, we report a novel fusion event, FGFR2-PPHLN1 (16%), and damaging mutations in the ARAF oncogene (11%). Here we demonstrate that the chromosomal translocation t(10;12)(q26;q12) leading to FGFR2-PPHLN1 fusion possesses transforming and oncogenic activity, which is successfully inhibited by a selective FGFR2 inhibitor in vitro. Among the ARAF mutations, N217I and G322S lead to activation of the pathway and N217I shows oncogenic potential in vitro. Screening of a cohort of 107 iCCA patients reveals that FGFR2 fusions represent the most recurrent targetable alteration (45%, 17/107), while they are rarely present in other primary liver tumours (0/100 of hepatocellular carcinoma (HCC); 1/21 of mixed iCCA-HCC). Taken together, around 70% of iCCA patients harbour at least one actionable molecular alteration (FGFR2 fusions, IDH1/2, ARAF, KRAS, BRAF and FGF19) that is amenable for therapeutic targeting.

Human hepatic organoids for the analysis of human genetic diseases

“…Second, since virtually all (>97%) of the cells express endodermal (SOX17) or hepatoblast (TBX3) markers at the appropriate developmental stage, this system is quite efficient at inducing organoid formation. Of note, TBX3 is expressed by a subpopulation of proliferating and self-renewing cells in the liver that are responsible for homeostatic hepatocyte renewal (46). Third, the iPSCs differentiate into HOs through stages that resemble liver during its embryonic development.…”

Biliary cancer: intrahepatic cholangiocarcinoma vs. extrahepatic cholangiocarcinoma vs. gallbladder cancers: classification and therapeutic implications

“…These receptors bind to one of 18 secreted glycoprotein ligands, or fibroblast growth factors (FGFs), to their extracellular domain (71). Several FGFR2 chromosomal fusions, with several genomic partners, have been identified in IHCC (72)(73)(74)(75)(76)(77). Preclinical studies have identified several FGFR2 fusions (FGFR2-PPHLN1, FGFR2-BICC1, FGFR2-TACC3, AHCYL1) specifically in intrahepatic BC, where genomic sequencing identified an incidence ranging up to 50% of intrahepatic BC patients.…”

Cholangiocarcinoma: current knowledge and future perspectives consensus statement from the European Network for the Study of Cholangiocarcinoma (ENS-CCA)

“…The genomic heterogeneity of CCA (TABLE 1) is not only related to the diverse anatomical location of the tumour (that is, intrahepatic, perihilar or distal) but also to the various risk factors and associated pathologies 29,[67][68][69][70][71][72][73][74][75] . The most prevalent genetic alterations identified in CCA affect key networks such as DNA repair (TP53) 72,73,75 , the WNT-CTNNB1 pathway 67 , tyrosine kinase signalling (KRAS, BRAF, SMAD4 and FGFR2) 29,68,70,[73][74][75] , protein tyrosine phosphatase (PTPN3) 71 , epigenetic (IDH1 and IDH2) 69,70,72,74,75 and chromatin-remodelling factors (histone-lysine N-methyltransferase 2C, also known as MLL3) 73 , including the SWI/SNF complex (ARID1A, PBRM1 and BAP1) 69,70,72,75 and deregulated Notch signalling, which is a key component in cholangiocyte differentiation and biliary duct development.…”

“…Finally, an integrative RNA-sequencing and exome-sequencing analysis revealed the presence of another novel fusion product, FGFR2-PPHLN1 (REF. 74). This study demonstrated that FGFR2 fusions might represent the most recurrent targetable alteration in CCA.…”

“…The most prevalent genetic alterations identified in CCA affect key networks such as DNA repair (TP53) 72,73,75 , the WNT-CTNNB1 pathway 67 , tyrosine kinase signalling (KRAS, BRAF, SMAD4 and FGFR2) 29,68,70,[73][74][75] , protein tyrosine phosphatase (PTPN3) 71 , epigenetic (IDH1 and IDH2) 69,70,72,74,75 and chromatin-remodelling factors (histone-lysine N-methyltransferase 2C, also known as MLL3) 73 , including the SWI/SNF complex (ARID1A, PBRM1 and BAP1) 69,70,72,75 and deregulated Notch signalling, which is a key component in cholangiocyte differentiation and biliary duct development. Recurrent genetic variants have also been identified in the promoter of the human telomerase reverse transcriptase (TERT) 70 , which for CCA is found to be associated with chronic hepatitis 70 .…”