Accurate differentiation between cholangiocarcinoma (CCA) and benign biliary stricture is of paramount importance. Biliary brush cytology is a simple and safe diagnostic approach that provides relatively high specificity; however, sensitivity is limited. Previous reports indicated the aberrations of DNA methylation in CCA. This study was aimed to investigate the diagnostic performance of the methylation index (MI) of HOXA1, NEUROG1 gene promoters in CCA.

Patients with biliary stricture who underwent endoscopic retrograde cholangiopancreatography (ERCP) with brush cytology in Siriraj Hospital from September 2016 to December 2019 were prospectively enrolled. The MI of HOXA1 (MI_H) and MI of NEUROG1 (MI_N) were determined by quantitative methylation-specific polymerase chain reaction. The diagnostic power for CCA was tested for MI from both genes and serum CA19-9.

A total of 67 patients were included in the study; 41 patients had a final diagnosis of CCA, and 26 patients were determined to have a benign biliary stricture. The results showed that both MI_H and MI_N had higher sensitivity/accuracy (95.1%/82.3% and 90.2%/89.5%, respectively) than brush cytology (61.5%/78.1%) and CA19-9 (69.4%/77.8%). The combination of brush cytology, both methylation markers and CA19-9 increased sensitivity/accuracy to 97.4%/91.0%. Methylation markers were positive in 5 out of 6 patients with confirmed CCA whose cytology and CA19-9 were negative.

DNA methylation increased sensitivity for the diagnosis of CCA; therefore, the usage of DNA methylation is promising for diagnosis of CCA in patients with biliary strictures. A future validation study is warranted to assess its role in clinical practice.