Cadherin-6 is a putative tumor suppressor and target of epigenetically dysregulated miR-429 in cholangiocarcinoma.
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.
a Institute of Pathology, University Hospital Heidelberg , Germany.
Benjamin
B
Goeppert
b Division of Epigenomics and Cancer Risk Factors, German Cancer Research Center (DKFZ) , Heidelberg , Germany.
Christina
C
Ernst
b Division of Epigenomics and Cancer Risk Factors, German Cancer Research Center (DKFZ) , Heidelberg , Germany.
Constance
C
Baer
a Institute of Pathology, University Hospital Heidelberg , Germany.
Stephanie
S
Roessler
a Institute of Pathology, University Hospital Heidelberg , Germany.
Marcus
M
Renner
c Department of General , Visceral, and Transplantation Surgery, University Hospital Heidelberg , Germany.
Arianeb
A
Mehrabi
c Department of General , Visceral, and Transplantation Surgery, University Hospital Heidelberg , Germany.
Mohammadreza
M
Hafezi
d Department of Internal Medicine IV, Gastroenterology and Hepatology , University Hospital Heidelberg , Germany.
Anita
A
Pathil
a Institute of Pathology, University Hospital Heidelberg , Germany.
Arne
A
Warth
a Institute of Pathology, University Hospital Heidelberg , Germany.
Albrecht
A
Stenzinger
e Technical University of Munich, University Hospital, Institute for General Pathology and Pathological Anatomy , Germany.
Wilko
W
Weichert
b Division of Epigenomics and Cancer Risk Factors, German Cancer Research Center (DKFZ) , Heidelberg , Germany.
Marion
M
Bähr
f Genomics and Proteomics Core Facility, German Cancer Research Center (DKFZ) , Heidelberg , Germany.
Rainer
R
Will
a Institute of Pathology, University Hospital Heidelberg , Germany.
Peter
P
Schirmacher
b Division of Epigenomics and Cancer Risk Factors, German Cancer Research Center (DKFZ) , Heidelberg , Germany.
Christoph
C
Plass
b Division of Epigenomics and Cancer Risk Factors, German Cancer Research Center (DKFZ) , Heidelberg , Germany.
Dieter
D
Weichenhan
D000328:Adult; D000368:Aged; D000369:Aged, 80 and over; D015820:Cadherins / Q000096:biosynthesis* / Q000235:genetics; D018797:Cell Cycle Proteins / Q000096:biosynthesis* / Q000235:genetics; D045744:Cell Line, Tumor; D018281:Cholangiocarcinoma / Q000235:genetics* / Q000473:pathology; D019175:DNA Methylation / Q000235:genetics*; D044127:Epigenesis, Genetic / Q000235:genetics; D044783:F-Box Proteins / Q000096:biosynthesis* / Q000235:genetics; D000073979:F-Box-WD Repeat-Containing Protein 7; D005260:Female; D020690:GTPase-Activating Proteins / Q000096:biosynthesis* / Q000235:genetics; D015972:Gene Expression Regulation, Neoplastic; D006801:Humans; D008297:Male; D035683:MicroRNAs / Q000096:biosynthesis* / Q000235:genetics; D008875:Middle Aged; D011401:Promoter Regions, Genetic; D015398:Signal Transduction / Q000235:genetics; D046888:Tissue Array Analysis; D025521:Tumor Suppressor Proteins / Q000096:biosynthesis* / Q000235:genetics; D044767:Ubiquitin-Protein Ligases / Q000096:biosynthesis* / Q000235:genetics
D015820:Cadherins; D018797:Cell Cycle Proteins; C112352:DLC1 protein, human; D044783:F-Box Proteins; D000073979:F-Box-WD Repeat-Containing Protein 7; C513273:FBXW7 protein, human; D020690:GTPase-Activating Proteins; C546363:MIRN429 microRNA, human; D035683:MicroRNAs; D025521:Tumor Suppressor Proteins; D044767:Ubiquitin-Protein Ligases; C087310:K cadherin
Biliary tract cancer; DNA methylation; epigenomics; microRNA; patient survival