Immune derived cell free DNA - a novel noninvasive method for studying immune cell dynamics in health and disease

Circulating biomarkers for monitoring inflammatory or immune responses are an essential part of diagnostic medicine and an important tool for studying physiological and pathological processes. These tools are largely based on blood cell counts. However, blood cell counts often fail to report on immune processes occurring in remote tissues such as bone marrow, lymph nodes or in a specific organ. Here we demonstrate the use of immune cell type-specific methylation patterns in circulating cell-free DNA (cfDNA) for studying immune cell dynamics. We characterized baseline levels of immune derived cfDNA, cross sectionally and longitudinally, in healthy individuals(N=242), which enabled us to define the healthy baseline of this new biomarker. We then demonstrated a selective elevation of immune-derived cfDNA upon perturbations of immune homeostasis. For example, patients with eosinophilic esophagitis (N=21) and B-cell lymphoma (N=27) have higher levels of eosinophil and B-cell cfDNA, undetectable by cell counts in blood. We also employed immune derived cfDNA biomarkers to characterize immune cell dynamics following influenza (N=92) and SARS-COV-2 (N=100) vaccination. The vaccines elicited a strong elevation of immune derived cfDNA, specifically B-cell derived cfDNA, which was correlated with antibody and memory B-cell formation - potentially reflecting vaccination efficacy. This work portrays how immune-derived cfDNA can serve as a novel biomarker for monitoring immune responses to physiological and pathological processes not accessible using conventional methods.