The DNA methylome of human vascular endothelium and its use in liquid biopsies

Vascular endothelial cells (EC) are an essential component of each tissue, contribute to multiple pathologies, and are targeted by important drugs. Yet, there is a shortage of biomarkers to assess EC turnover. To develop DNA methylation-based liquid biopsies for EC, we determined the methylome of EC isolated from freshly dissociated human tissues. A comparison to a human cell-type methylome atlas yielded thousands of loci that are uniquely unmethylated in EC. These sites are typically gene enhancers, often residing adjacent to EC-specific genes. We identified hundreds of genomic loci that are differentially methylated in organotypic EC, indicating that EC feeding specific organs are distinct cell types with a stable epigenetic identity. We established universal and lung-specific EC markers, and evaluated their presence in circulating cell-free DNA (cfDNA). Nearly 2.5% of cfDNA in the plasma of healthy individuals originates from EC. Sepsis, graft versus host disease and cardiac catheterization are associated with elevated levels of EC-derived cfDNA, indicative of vascular damage. Lung-specific EC cfDNA is selectively elevated in patients with COPD or lung cancer, revealing tissue-specific vascular turnover. EC cfDNA biomarkers inform vascular dynamics in health and disease, potentially contributing to early diagnosis and monitoring of pathologies, and assessment of drug activity.