Whole-genome profiling of age- and sex-associated DNA methylation signatures in human plasma cell-free DNA

BACKGROUND: Age and sex significantly impact DNA methylation patterns, however, existing datasets typically include only a subset of methylation sites in the human genome, hindering our thorough understanding. METHODS: We recruited 98 generally healthy adults aged from 22 to 77 and investigated the effects of age and sex on plasma cell-free DNA (cfDNA) methylation through whole-genome bisulfite sequencing (WGBS) and association analysis. RESULTS: Here we show 3,047 age-associated and 1,053 sex-associated CpGs on autosomes, corresponding to 1,587 and 324 genes, respectively. To the best of our knowledge, many of these CpGs are newly discovered to be age- and sex-related at the DNA methylation level. The discovered sex-differential cfDNA methylation patterns on the X chromosome are related to XCI status. Besides, a cfDNA epigenetic clock comprising 125 CpGs is developed, demonstrating relatively high accuracy in predicting chronological age. Tissue-of-origin analysis reveals that cfDNA derived from monocytes/macrophages, granulocytes, and hepatocytes is associated with age and sex. Several individuals with abnormal cfDNA proportions of some specific cell types are found to have individual health problems. CONCLUSIONS: Our discovered CpGs and genes help to explain age-related and sex-biased diseases such as psychiatric disorders, diabetes, and autoimmune diseases, and we demonstrate the potential of cfDNA methylation signatures as very promising biomarkers for health monitoring for the general population.