CfDNA methylation profiling in blood following moderate-to-severe traumatic brain injury using brain cell type–enriched signatures: A pilot study

The human brain consists of diverse cell types that collaboratively perform complex functions and form intricate neuronal networks. When traumatic brain injury (TBI) occurs, multiple molecular pathways involving diverse cell types are activated in response to injury. Understanding how brain cell composition is altered during TBI may help improve patient outcomes. Upon brain trauma, neurovascular disruption leads to the release of brain-derived cell-free DNA (cfDNA) into peripheral blood. The tissue-specific DNA methylation patterns in this cfDNA have the potential to serve as candidate markers for studying brain injury. To characterize brain cell type–enriched methylation features, we analyzed the methylomes of five major brain cell types—neurons, astrocytes, oligodendrocytes, microglia, and vascular endothelial cells (VECs)—using whole-genome bisulfite sequencing (WGBS). Cellular enrichment analysis showed that differentially methylated genes (DMGs) exhibited reference-defined cell type–enriched patterns. Gene Ontology pathway analysis further supported the biological plausibility of these methylation features. To demonstrate the feasibility of applying cfDNA methylation profiling in TBI, we analyzed a limited pilot dataset comprising healthy controls and samples collected at acute (1 day), subacute (1 month), and chronic (6 months) post-injury time points from patients with moderate-to-severe TBI (msTBI). These analyses identified candidate brain cell type–enriched cfDNA methylation features that differed across post-injury sampling groups. Together, our findings highlight that brain cell type-enriched methylation signatures may provide a powerful tool for characterizing distinct cell populations and nominating candidate brain cell-associated cfDNA methylation biomarkers in TBI.