Integrated epigenetic biomarkers in circulating cell-free DNA as a robust classifier for pancreatic cancer

Abstract

Background: The high lethal rate of pancreatic cancer is partly due to a lack of efficient biomarkers for screening and early diagnosis. We attempted to develop effective and noninvasive methods using 5-methylcytosine (5mC) and 5-hydroxymethylcytosine (5hmC) markers from circulating cell-free DNA (cfDNA) for the detection of pancreatic ductal adenocarcinoma (PDAC). Results: A 24-feature 5mC model that can accurately discriminate PDAC from healthy controls (area under the curve (AUC) = 0.977, sensitivity = 0.824, specificity = 1) and a 5hmC prediction model with 27 features demonstrated excellent detection power in two distinct validation sets (AUC = 0.992 and 0.960, sensitivity = 0.786 and 0.857, specificity = 1 and 0.993). The 51-feature model combining 5mC and 5hmC markers outperformed both of the individual models, with an AUC of 0.997 (sensitivity = 0.938, specificity = 0.955) and particularly an improvement in the prediction sensitivity of PDAC. In addition, the weighted diagnosis score (wd-score) calculated with the 5hmC model can distinguish stage I patients from stage II-IV patients. Conclusions: Both 5mC and 5hmC biomarkers in cfDNA are effective in PDAC detection, and the 5mC-5hmC integrated model significantly improve the detection sensitivity.

Downregulation of 5‐hydroxymethylcytosine is an early event in pancreatic tumorigenesis

“…To our knowledge, this is the first comprehensive study investigating four well‐characterized human pancreatic precursor lesions. Other previous studies have further investigated 5hmC levels at specific gene loci in either PDAC tissue or cell‐free DNA, suggesting that such cancer‐associated 5hmC signatures are characteristic of specific cancer types and may serve as potential biomarkers [44–46]. In light of these findings, our results suggest that gene‐specific alterations in 5hmC distribution may occur even in the early stages of pancreatic carcinogenesis.…”

Liquid Biopsy in Pancreatic Cancer: Are We Ready to Apply It in the Clinical Practice?

“…In a study that included several tumors, it was found that the analysis of cfDNA methylome allowed their early diagnosis [ 52 ]. In a pilot study it was reported that a model combining the modifications in 5-methylcytosine (5mC) and 5-hydroxymethylcytosine (5hmC) in cfDNA achieved a sensitivity of 0.94 and a specificity of 0.95, with an AUC of 0.99 for the diagnosis of PDAC [ 101 ].…”

The Detection of Cancer Epigenetic Traces in Cell-Free DNA

“…The feasibility of this method for cancer detection was demonstrated in several studies ( 101 – 103 ). Moreover, a combination of cfMeDIP-seq and 5hm-Seal for simultaneous 5mC and 5hmC profiling in pancreatic cancer improved the prediction accuracy ( 104 ). MBD-seq takes advantage of the methyl-binding proteins such as MBD2 to capture methylated DNA ( 105 – 107 ).…”