Transcriptomic profiling reveals hepatic stem-like gene signatures and interplay of miR-200c and epithelial-mesenchymal transition in intrahepatic cholangiocarcinoma

Abstract

Intrahepatic cholangiocellular carcinoma (ICC) is the second most common type of primary liver cancer. However, its tumor heterogeneity and molecular characteristics are largely unknown. In this study, we conducted transcriptomic profiling of 23 ICC and combined hepatocellular cholangiocarcinoma tumor specimens from Asian patients using Affymetrix mRNA and Nanostring microRNA microarrays to search for unique gene signatures linked to tumor subtypes and patient prognosis. We validated the signatures in additional 68 ICC cases derived from Caucasian patients. We found that both mRNA and microRNA expression profiles could independently classify Asian ICC cases into two main subgroups, one of which shared gene expression signatures with previously identified hepatocellular carcinoma (HCC) with stem cell gene expression traits. ICC-specific gene signatures could predict survival in Asian HCC cases and independently in Caucasian ICC cases. Integrative analyses of the ICC-specific mRNA and microRNA expression profiles revealed that a common signaling pathway linking miR-200c signaling to epithelial-mesenchymal transition (EMT) was preferentially activated in ICC with stem cell gene expression traits. Inactivation of miR-200c resulted in an induction of EMT while activation of miR-200c led to a reduction of EMT including a reduced cell migration and invasion in ICC cells. We also found that miR-200c and NCAM1 expression were negatively correlated and their expression levels were predictive of survival in ICC samples. NCAM1, a known hepatic stem/progenitor cell marker, was experimentally demonstrated to be a direct target of miR-200c. Conclusion: Our results indicate that ICC and HCC share common stem-like molecular characteristics and poor prognosis. We suggest that the specific components of EMT may be exploited as critical biomarkers and clinically relevant therapeutic targets for an aggressive form of stem cell-like ICC.

Isocitrate Dehydrogenase (IDH) Mutations Promote a Reversible ZEB1/MicroRNA (miR)-200-dependent Epithelial-Mesenchymal Transition (EMT)

“…This raises the possibility that mutant IDH1/2-and 2-HGmediated EMT may play a role in the pathology of these epithelial tumors, with cholangiocarcinoma in particular. Notably, a recent study finds that a subset of intrahepatic cholangiocarcinoma exhibit aspects of EMT, with miR-200c reduction as a central phenotype (61). It will be intriguing to determine whether IDH mutations track with this subtype of cholangiocarcinoma.…”

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

“…Interestingly, patients with IDH1 and IDH2 mutations were significantly enriched in P2-P3 subgroups of our proliferation subclass (15/45 versus 3/62 rest, Po0.001, Fisher's exact test, Fig. 6), which is associated with chromosomal instability, enrichment of a stem cell-like iCCA signature 27 and activation of EGFR signalling. Consistent with the functions of IDH1/2 enzymes, the pathways related to tricarboxylic acid cycle and electron transport were enriched in patients with IDH mutations (FDRo0.05, Supplementary Table 11).…”

“…Consistent with the functions of IDH1/2 enzymes, the pathways related to tricarboxylic acid cycle and electron transport were enriched in patients with IDH mutations (FDRo0.05, Supplementary Table 11). Moreover, a recently published iCCA signature with stem cell-like features 27 was significantly enriched in IDH mutant tumours 28 along with several oncogenic pathways including KRAS, MET, NOTCH and VEGF pathways. iCCA tumours harbouring the FGFR2 fusions did not show significant enrichment in any of the iCCA subclasses (Fig.…”

Down-Regulation of Nogo-B Expression as a Newly Identified Feature of Intrahepatic Cholangiocarcinoma

“…However, few new markers associated with prognosis or malignant behavior of ICC has been determined (Oishi et al 2012;Shimada et al 2010). In this study we studied Nogo-B, which has recently been identified as a potential marker of hepatic fibrosis (Zhang et al 2011;Gao et al 2013;Tashiro et al 2013;Men et al 2015) and as a potential enhancer of bile duct proliferation (Zhang Each survival rate is shown as % value, based on our analytical software.…”