5-Hydroxymethylome in Circulating Cell-Free DNA as A Potential Biomarker for Non-Small-Cell Lung Cancer

Abstract

Non-small-cell lung cancer (NSCLC), the most common type of lung cancer accounting for 85% of the cases, is often diagnosed at advanced stages owing to the lack of efficient early diagnostic tools. 5-Hydroxymethylcytosine (5hmC) signatures in circulating cell-free DNA (cfDNA) that carries the cancer-specific epigenetic patterns may represent the valuable biomarkers for discriminating tumor and healthy individuals, and thus could be potentially useful for NSCLC diagnosis. Here, we employed a sensitive and reliable method to map genome-wide 5hmC in the cfDNA of Chinese NSCLC patients and detected a significant 5hmC gain in both the gene bodies and promoter regions in the blood samples from tumor patients compared with healthy controls. Specifically, we identified six potential biomarkers from 66 patients and 67 healthy controls (mean decrease accuracy >3.2, P < 3.68E−19) using machine-learning-based tumor classifiers with high accuracy. Thus, the unique signature of 5hmC in tumor patient’s cfDNA identified in our study may provide valuable information in facilitating the development of new diagnostic and therapeutic modalities for NSCLC.

Detection of early stage pancreatic cancer using 5-hydroxymethylcytosine signatures in circulating cell free DNA

“…The 5hmC signal was readily found to overlap in gene-centric functional regions (enrichment in promoter, exons, UTR and TTS), as well as transposable elements like SINEs (enriched) and LINEs (depleted) (Figure 2A, B). Such hydroxymethylcytosine changes in functional regions have been reported in cfDNA from colorectal 24 , esophageal 23,33 and lung cancer 23 . In a similar manner, PDAC specific gains or losses in hydroxymethylation were observed in functional regions in our data.…”

“…More recently, detailed understanding of demethylation has been enabled with precision around intermediate states during demethylation activation 19,20 . Specifically, discovery of TET enzyme-mediated methyl-cytosine oxidation to 5-hydroxymethyl cytosine (5hmC) has yielded novel signatures that have enabled the definition of cellular states 21 , as well as the identification of cancer in the cell free state [22][23][24] .…”

The interplay of circulating tumor DNA and chromatin modification, therapeutic resistance, and metastasis

“…Research has also shown that 5-hydroxymethylcytosine signatures in cfDNA developed by genome-wide profiling of 5 hmC can distinguish features of specific cancer types and stages and are superior to conventional protein biomarkers and concordant with 5 hmC biomarkers from tissue biopsies. This approach has been performed in lung cancer, hepatocellular carcinoma, pancreatic cancer, colorectal cancer and gastric cancer [50,67,97,98].…”

5-Hydroxymethylcytosine signatures in circulating cell-free DNA as diagnostic and predictive biomarkers for coronary artery disease

“…And motif information was obtained from the Homer motif database internally. For the result of motif enrichment in DhMRs, according to the enriched P value and the percentage of target sequences enriched with the binding motif which indicated transcription factor, top enriched known transcription factor binding motifs were shown which followed the approach of Zhang et al [46].…”

“…The out-of-bag (OOB) error was used to optimize the parameter and evaluate the stability of the model. To further select the most reliable hydroxymethylation marker genes, both mean decrease accuracy (MDA) and the significance (P value) of two-tailed t tests were used to filter top candidate genes to show the classification capabilities of 5hmC marks which followed the approach of Zhang et al [46]. Briefly, the MDA of each gene which showed feature importance and contribution to the model was calculated internally by the model, and high MDA values referring to greater importance.…”