Researchers from China identified methylated-differentially expressed genes and signaling pathways that are significantly associated with cholangiocarcinoma (CCA) using a series of bioinformatics databases and tools and published their findings in Medicine.

They also found 2 genes MYC and VWF that are hub genes, which possess potential predictive and prognostic value and therefore could be used as biomarkers based on their methylation status to accurately diagnose and treat the disease.

“This information may help to improve the understanding of the epigenetic regulation mechanism of CCA occurrence and development,” the authors of the study wrote.

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The researchers identified the differentially expressed and methylated genes using GEO2R, an interactive web tool that allows the comparison of 2 or more groups of samples in a Gene Expression Omnibus (GEO). 

Read more about the diagnosis of CCA

The team found a total of 81 hypermethylated, lowly expressed genes and 76 hypomethylated, highly expressed genes. The hypermethylated, lowly expressed genes were enriched in ion channel binding and transcription factor activity while the hypomethylated, highly expressed genes were enriched in cysteine-type endopeptidase activity.

Based on protein-protein interaction networks, the researchers identified MYC and VWF as hub genes for hypermethylated, lowly expressed genes but not hub genes for hypomethylated, highly expressed genes. They said that they now need to explore these genes further to confirm their function in CCA.

CCA is a heterogeneous group of rare malignant tumors originating from cells of the biliary tree. The disease does not have any obvious symptoms, especially in the early stages and most patients are found in the advanced stages of the disease, which results in a poor prognosis. A biomarker that is able to diagnose CCA early, therefore, holds great value.


Lin G, Xinhe Z, Haoyu T, Yiling L. Aberrantly methylated-differentially expressed genes and related pathways in cholangiocarcinoma. Medicine. 2022;101:25(e29379). doi:10.1097/MD.0000000000029379