Abstract
Biliary tract cancers (BTC) are rare but highly aggressive malignant epithelial tumors. In order to improve the outcome in this lethal disease, novel biomarkers for diagnosis, prognosis, and therapy response prediction are urgently needed. DNA promoter methylation of PITX2 variants (PITX2ab, PITX2c) and intragenic methylation of the PITX2 adjacent non-coding RNA (PANCR) were investigated by methylations-specific qPCR assays in formalin-fixed paraffin-embedded tissue from 80 patients after resection for BTC. Results were correlated with clinicopathologic data and outcome. PITX2 variants and PANCR showed significant hypermethylation in tumor vs. normal adjacent tissue (p < 0.001 and p = 0.015), respectively. In survival analysis, dichotomized DNA methylation of variant PITX2c and PANCR were significantly associated with overall survival (OS). Patients with high tumor methylation levels of PITX2c had a shorter OS compared to patients with low methylation (12 vs. 40 months OS; HR 2.48 [1.38–4.48], p = 0.002). In contrast, PANCR hypermethylation was associated with prolonged survival (25 vs. 19 months OS; HR 0.54 [0.30–0.94], p = 0.015) and qualified as an independent prognostic factor on multivariate analysis. The biomarkers investigated in this study may help to identify BTC subpopulations at risk for worse survival. Further studies are needed to evaluate if PITX2 might be a clinically useful biomarker for an optimized and individualized treatment.
Highlights
Biliary tract cancers (BTC) represent a heterogenous group of malignancies that include adenocarcinomas of the intra- and extrahepatic bile ducts, the ampullary region, and the gallbladder.PLOS ONE | DOI:10.1371/journal.pone.0165769 October 31, 2016pituitary homeobox 2 (PITX2) Methylation in Biliary Tract CancersDietrich receives inventor’s compensation from Epigenomics AG
DNA methylation within the PITX2 gene and its adjacent ncRNA PITX2 adjacent noncoding RNA (PANCR) were determined at three distinct genomic locations: promoters of the transcript variants PITX2a/b and PITX2c as well as in an intragenic GC-rich region located in an annotated promoter flanking site within the PANCR gene body (Fig 1)
The analytical performance of the PITX2c and PANCR DNA methylation assays were verified using mixtures of methylated and unmethylated bisulfite-converted DNA from sperm, which is known to be unmethylated at many loci [37]
Summary
Biliary tract cancers (BTC) represent a heterogenous group of malignancies that include adenocarcinomas of the intra- and extrahepatic bile ducts, the ampullary region, and the gallbladder.PLOS ONE | DOI:10.1371/journal.pone.0165769 October 31, 2016PITX2 Methylation in Biliary Tract CancersDietrich receives inventor’s compensation from Epigenomics AG. Biliary tract cancers (BTC) represent a heterogenous group of malignancies that include adenocarcinomas of the intra- and extrahepatic bile ducts, the ampullary region, and the gallbladder. Dietrich receives inventor’s compensation from Epigenomics AG. Dimo Dietrich is a consultant for AJ Innuscreen GmbH (Berlin, Germany), a 100% daughter company of Analytik Jena AG (Jena, Germany), and receives royalties from product sales. Dimo Dietrich is a consultant and receives or received compensation from Therawis GmbH (Munich, Germany), Oncgnostics GmbH (Jena, Germany), MDxHealth, Inc. (Irvine, CA, USA), Epigenomics AG (Berlin, Germany), and RBiopharm AG (Darmstadt, Germany). Therawis GmbH aims to commercialize the DNA methylation biomarker PITX2. This does not alter our adherence to all PLOS ONE policies on sharing data and materials
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