Cadherin-6 is a putative tumor suppressor and target of epigenetically dysregulated miR-429 in cholangiocarcinoma

Epigenetics. 2016 Nov;11(11):780-790. doi: 10.1080/15592294.2016.1227899. Epub 2016 Sep 3.


Cholangiocarcinoma (CC) is a rare malignancy of the extrahepatic or intrahepatic biliary tract with an outstanding poor prognosis. Non-surgical therapeutic regimens result in minimally improved survival of CC patients. Global genomic analyses identified a few recurrently mutated genes, some of them in genes involved in epigenetic patterning. In a previous study, we demonstrated global DNA methylation changes in CC, indicating major contribution of epigenetic alterations to cholangiocarcinogenesis. Here, we aimed at the identification and characterization of CC-related, differentially methylated regions (DMRs) in potential microRNA promoters and of genes targeted by identified microRNAs. Twenty-seven hypermethylated and 13 hypomethylated potential promoter regions of microRNAs, known to be associated with cancer-related pathways like Wnt, ErbB, and PI3K-Akt signaling, were identified. Selected DMRs were confirmed in 2 independent patient cohorts. Inverse correlation between promoter methylation and expression suggested miR-129-2 and members of the miR-200 family (miR-200a, miR-200b, and miR-429) as novel tumor suppressors and oncomiRs, respectively, in CC. Tumor suppressor genes deleted in liver cancer 1 (DLC1), F-box/WD-repeat-containing protein 7 (FBXW7), and cadherin-6 (CDH6) were identified as presumed targets in CC. Tissue microarrays of a representative and well-characterized cohort of biliary tract cancers (n=212) displayed stepwise downregulation of CDH6 and association with poor patient outcome. Ectopic expression of CDH6 on the other hand, delayed growth in the CC cell lines EGI-1 and TFK-1, together suggesting a tumor suppressive function of CDH6. Our work represents a valuable repository for the study of epigenetically altered miRNAs in cholangiocarcinogenesis and novel putative, CC-related tumor suppressive miRNAs and oncomiRs.

Keywords: Biliary tract cancer; DNA methylation; epigenomics; microRNA; patient survival.

MeSH terms

  • Adult
  • Aged
  • Aged, 80 and over
  • Cadherins / biosynthesis*
  • Cadherins / genetics
  • Cell Cycle Proteins / biosynthesis*
  • Cell Cycle Proteins / genetics
  • Cell Line, Tumor
  • Cholangiocarcinoma / genetics*
  • Cholangiocarcinoma / pathology
  • DNA Methylation / genetics*
  • Epigenesis, Genetic / genetics
  • F-Box Proteins / biosynthesis*
  • F-Box Proteins / genetics
  • F-Box-WD Repeat-Containing Protein 7
  • Female
  • GTPase-Activating Proteins / biosynthesis*
  • GTPase-Activating Proteins / genetics
  • Gene Expression Regulation, Neoplastic
  • Humans
  • Male
  • MicroRNAs / biosynthesis*
  • MicroRNAs / genetics
  • Middle Aged
  • Promoter Regions, Genetic
  • Signal Transduction / genetics
  • Tissue Array Analysis
  • Tumor Suppressor Proteins / biosynthesis*
  • Tumor Suppressor Proteins / genetics
  • Ubiquitin-Protein Ligases / biosynthesis*
  • Ubiquitin-Protein Ligases / genetics


  • Cadherins
  • Cell Cycle Proteins
  • DLC1 protein, human
  • F-Box Proteins
  • F-Box-WD Repeat-Containing Protein 7
  • FBXW7 protein, human
  • GTPase-Activating Proteins
  • MIRN429 microRNA, human
  • MicroRNAs
  • Tumor Suppressor Proteins
  • Ubiquitin-Protein Ligases
  • K cadherin