Circulating DNA demethylation-derived cytosine analytes as emerging biomarkers

DNA methylation and demethylation in mammals are critical epigenetic processes that regulate gene expression and cellular function. Recent evidence suggests that DNA demethylation products such as 5-hydroxymethylcytosine (5hmC) are excreted into body fluids, highlighting their potential as circulating molecular biomarkers. In this review, we focus on cytosine derivatives generated during DNA demethylation, collectively referred to as circulating cytosine analytes, regardless of whether they are present as DNA-bound modifications (e.g., on cfDNA) or as free molecular species in biofluids. We summarize their underlying biological origins and discuss the potential clinical relevance of these analytes in disease diagnosis and therapeutic assessment. Specifically, we discuss the emerging applications of these excreted demethylation intermediates in cancer detection, neurological disorders, and treatment monitoring, alongside current technological challenges and future research directions. Further, the review covers the existing methods for detecting epigenetic modifications, including high-throughput sequencing and mass spectrometry, while emphasizing their limitations and recent technological advancements. Progress in this field may have the potential to advance precision medicine by providing insights into epigenetic regulation and its clinical implications. A schematic overview of circulating cytosine modification analytes and their roles in epigenetic regulation and precision medicine is presented in Scheme 1.