Promoter hypermethylation of SHOX2 and SEPT9 is a potential biomarker for minimally invasive diagnosis in adenocarcinomas of the biliary tract

Abstract

BackgroundBiliary tract carcinoma (BTC) is a fatal malignancy which aggressiveness contrasts sharply with its relatively mild and late clinical presentation. Novel molecular markers for early diagnosis and precise treatment are urgently needed. The purpose of this study was to evaluate the diagnostic and prognostic value of promoter hypermethylation of the SHOX2 and SEPT9 gene loci in BTC.MethodsRelative DNA methylation of SHOX2 and SEPT9 was quantified in tumor specimens and matched normal adjacent tissue (NAT) from 71 BTC patients, as well as in plasma samples from an independent prospective cohort of 20 cholangiocarcinoma patients and 100 control patients. Receiver operating characteristic (ROC) curve analyses were performed to probe the diagnostic ability of both methylation markers. DNA methylation was correlated to clinicopathological data and to overall survival.Results SHOX2 methylation was significantly higher in tumor tissue than in NAT irrespective of tumor localization (p < 0.001) and correctly identified 71% of BTC specimens with 100% specificity (AUC = 0.918; 95% CI 0.865–0.971). SEPT9 hypermethylation was significantly more frequent in gallbladder carcinomas compared to cholangiocarcinomas (p = 0.01) and was associated with large primary tumors (p = 0.01) as well as age (p = 0.03). Cox proportional hazard analysis confirmed microscopic residual tumor at the surgical margin (R1-resection) as an independent prognostic factor, while SHOX2 and SEPT9 methylation showed no correlation with overall survival. Elevated DNA methylation levels were also found in plasma derived from cholangiocarcinoma patients. SHOX2 and SEPT9 methylation as a marker panel achieved a sensitivity of 45% and a specificity of 99% in differentiating between samples from patients with and without cholangiocarcinoma (AUC = 0.752; 95% CI 0.631–0.873).Conclusions SHOX2 and SEPT9 are frequently methylated in biliary tract cancers. Promoter hypermethylation of SHOX2 and SEPT9 may therefore serve as a minimally invasive biomarker supporting diagnosis finding and therapy monitoring in clinical specimens.Electronic supplementary materialThe online version of this article (doi:10.1186/s13148-016-0299-x) contains supplementary material, which is available to authorized users.

Cytology Smears in the Era of Molecular Biomarkers in Non–Small Cell Lung Cancer: Doing More With Less

“…55 Quantitative methylation-specific real-time PCR is currently being used to detect aberrant patterns of DNA methylation of several genes, including p16-INK4a and SHOX2. 33,56,57 This technique needs a relatively high amount of bisulfite-converted DNA (~50 ng), which is often difficult to obtain from small specimens. Additionally, bisulfite conversion will reduce even more the final fraction of good DNA needed for methylation studies.…”

Epigenetic biomarkers of promoter DNA methylation in the new era of cancer treatment

“…Liquid biopsy using such HRMG showed superior diagnosis (73%‐91%) and high specificity (95%‐100%) compared to the conventional cytology test (58%‐63%). Recently, additional HRMG with high performance have been identified, including SFRP1 , OPCML and SHOX2 (Table ), and additional optimization of the HRMG analyses may yield further improvements in performance.…”

RNA sequencing (RNA-Seq) of lymph node, spleen, and thymus transcriptome from wild Peninsular Malaysian cynomolgus macaque (Macaca fascicularis)

“…The CCL20-CCR6 ligand–receptor pair is responsible for the chemotaxis of lymphocytes, neutrophils, proinflammatory IL17 producing helper T-cells (Th17), and the regulatory T-cells in response to inflammation ( Frick et al, 2016 ). SHOX2 , a gene which codes for Short stature homeobox protein 2, is a transcriptional factor involved in various embryological development processes ( Branchi et al, 2016 ), and is implicated in Turner syndrome, whereby gene knockout of SHOX2 in mice results in skeletal growth abnormalities and short stature phenotypes ( Gu et al, 2008 ). SHISA3 , which codes for protein shisa-3 homolog, is a member of the Shisa family of proteins that modulate WNT and FGF signalling in developmental processes ( Chen et al, 2014 ).…”