Remote immune processes revealed by immune-derived circulating cell-free DNA

Abstract

Blood cell counts often fail to report on immune processes occurring in remote tissues. Here we use immune cell type-specific methylation patterns in circulating cell-free DNA (cfDNA) for studying human immune cell dynamics. We characterized cfDNA released from specific immune cell types in healthy individuals (N=242), cross sectionally and longitudinally. Immune cfDNA levels had no individual steady state as opposed to blood cell counts, suggesting that cfDNA concentration reflects adjustment of cell survival to maintain homeostatic cell numbers. We also observed selective elevation of immune-derived cfDNA upon perturbations of immune homeostasis. Following influenza vaccination (N=92), B-cell-derived cfDNA levels increased prior to elevated B-cell counts and predicted efficacy of antibody production. Patients with Eosinophilic Esophagitis (N=21) and B-cell lymphoma (N=27) showed selective elevation of eosinophil and B-cell cfDNA respectively, which were undetectable by cell counts in blood. Immune-derived cfDNA provides a novel biomarker for monitoring immune responses to physiological and pathological processes that are not accessible using conventional methods.

WITHDRAWN: Nucleic acid biomarkers of immune response and cell and tissue damage in COVID-19 and MIS-C

“…In contrast, plasma cfRNA and cfDNA both measure levels and types of cell death from circulating cell types and peripheral tissues 17,39 . With respect to cells that are turning over or dying, cfDNA enables precise quantification of cell numbers, whereas cfRNA enables characterization of gene expression and pathways 40–42 . cfRNA profiling can leverage the extensive information regarding cell type specific gene expression that is available from recent large-scale human cell atlas projects, whereas reference data for cfDNA methylation profiling is currently more limited 17 .…”

Megakaryocyte and erythroblast DNA in plasma and platelets

“…In order to evaluate the contribution of these genomes to cfDNA, we obtained genome-wide methylation profiles of purified white blood cells (WBC) and cfDNA from 23 healthy individuals, sequenced at ∼85 coverage 16 . Methylation levels of genomic regions uniquely unmethylated in megakaryocytes were ∼26% less methylated in cfDNA compared to WBC-derived DNA ( Figure 1A ), suggesting that megakaryocyte genomes are major contributors to cfDNA.…”

Ultrasensitive tumour‐agnostic non‐invasive detection of colorectal cancer recurrence using ctDNA methylation

“…9 Second, cfDNA methylation carried non-tumour-derived, tumour-associated signals such as remote immune cell activation to enhance detection sensitivity. 10 The power of our conclusion is limited by a small number of patients with relatively short follow-up in this interim analysis. Additionally, such short follow-up has made the post-surgery cohort does not fully resemble pre-surgery cohort, which might impact the translation of prediction accuracy of DNAm for tumour load in cfDNA from the pre-surgery data towards post-surgery data.…”

“…Yu Xiao 1,2 Xiaodong Wang 3 Hong Weng Wei Jiang 1,10,12 Yunji Leng 8 Junpeng Zhao 8 Xinyue Cao 13 Minsheng Peng 14,15 Congqing Jiang 6,7…”