Discovery of novel DNA methylation biomarker panels for the diagnosis and differentiation between common adenocarcinomas and their liver metastases

Sep 21, 2026

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The study identifies DNA methylation biomarker panels for diagnosing and differentiating breast invasive carcinoma, cholangiocarcinoma, colorectal cancer, hepatocellular carcinoma, lung adenocarcinoma, pancreatic adenocarcinoma, and stomach adenocarcinoma, and extending this discrimination to corresponding liver metastases. Using a 2853-sample discovery dataset and a 782-sample independent verification dataset, the best panels reach high sensitivity and specificity for tumors and for tumor versus normal tissues. Selected hypermethylated regions are also detectable in cell-free DNA from liver metastasis patients, remaining unmethylated in healthy donors, supporting liquid biopsy applications.

LanguageEnglish

CategoryHealthcare

FormatPDF

Pages25

Reading Time1 h 3 min

AccessFree to download

Introduction

DNA methylation as an epigenetic mechanism

Differentially methylated regions and cancer implications

Clinical relevance and liquid biopsy potential

Methylation array platforms and measurement principles

[www. nature.com/scientificreports](www. nature.com/scientificreports) OPEN Discovery of novel DNA methylation biomarker panels for the diagnosis and differentiation between common adenocarcinomas and their liver metastases Tina Draškovič & Nina Hauptman * Differentiation between adenocarcinomas is sometimes challenging. The promising avenue for discovering new biomarkers lies in bioinformatics using DNA methylation analysis. Utilizing a 2853-sample identification dataset and a 782-sample independent verification dataset, we have identified diagnostic DNA methylation biomarkers that are hypermethylated in cancer and differentiate between breast invasive carcinoma, cholangiocarcinoma, colorectal cancer, hepatocellular carcinoma, lung adenocarcinoma, pancreatic adenocarcinoma and stomach adenocarcinoma. The best panels for cancer type exhibit sensitivity of 77.8–95.9%, a specificity of 92.7–97.5% for tumors, a specificity of 91.5–97.7% for tumors and normal tissues and a diagnostic accuracy of 85.3–96.4%. We have shown that the results can be extended from the primary cancers to their liver metastases, as the best panels diagnose and differentiate between pancreatic adenocarcinoma liver metastases and breast invasive carcinoma liver metastases with a sensitivity and specificity of 83.3–100% and a diagnostic accuracy of 86.8–91.9%. Moreover, the panels could detect hypermethylation of selected regions in the cell-free DNA of patients with liver metastases. Atthe same time, these were unmethylated in the cell-free DNA of healthy donors, confirming their applicability for liquid biopsies. Malignant liver tumors, which include primary liver tumors and liver metastases, are among the most common malignancies worldwide. Among primary malignant tumors, hepatocellular carcinoma is the most prevalent, followed by cholangiocarcinoma. Liver metastases include mostly carcinomas, the most common subtype being adenocarcinoma. The major sources of liver metastases are adenocarcinomas ofthe colon and rectum, followed by carcinomas ofthe pancreas, breast, lung and stomach. The disease has a poor prognosis and poor overall survival, especially with liver metastases1–4. Because of the variation in prognosis and treatment options, differentiation between malignant tumors ofthe liver and prediction of tumor origin in patients with carcinoma of unknown primary (CUP) in the liver are of vital importance. The correct diagnosis can be made using various methods; one of which is DNA methylation analysis. DNA methylation plays an important role as an epigenetic mechanism of cancer initiation, maintenance and progression. Normally, knowledge of the methylation status of a single CpG site is of limited value unless it is related to the status of neighboring CpG sites. Therefore, efforts in the field of cancer epigenetics have primarily focused on the detection of differentially methylated regions (DMRs) comprising multiple consecutive methylated CpG sites. DMRs can occur throughout the genome but have been identified primarily in the promoter regions of genes, within the body of genes and in intergenic regulatory regions5–8. Clusters Faculty of Medicine, Institute of Pathology, University of Ljubljana, Ljubljana, Slovenia. *email: nina.hauptman@ [mf.uni-lj.si](mf.uni-lj.si) [www. nature.com/scientificreports/](www. nature.com/scientificreports/) of hypermethylated CpG sites within a gene’s promoter region are commonly associated with gene silencing, while coordinated hypermethylation in intragenic regions is associated with gene upregulation5,7. In cancer, hypermethylation contributes to the disease phenotype through genetic inactivation of tumor suppressor genes and DNA repair genes, thereby increasing the rate of mutagenesis. These genes are frequently associated with the cell cycle, apoptosis, cell division, DNA repair and DNA replication8–10. DMRs and even single CpG sites with cancer-specific methylation changes have the potenti

FAQs

How were the DNA methylation biomarker panels identified and validated?

The panels were discovered using a 2853-sample identification dataset and validated with an independent 782-sample verification dataset based on DNA methylation analysis.

How well do the best panels perform for diagnosing and differentiating cancers?

The best panels achieve sensitivity of 77.8–95.9% and specificity of 92.7–97.5% for tumors, with diagnostic accuracy ranging from 85.3–96.4%.

Can these methylation biomarkers be applied to liver metastases and liquid biopsies?

Yes. The results extend from primary cancers to liver metastases, and hypermethylated regions can be detected in patient cell-free DNA while remaining unmethylated in healthy donors, supporting liquid biopsy use.

Sep 21, 2026

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