Remote immune processes revealed by immune-derived circulating cell-free DNA
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Curated by eLife
Evaluation Summary:
This manuscript introduces a novel method for the monitoring of immune dynamics from blood, based on a measurement of the burden of cell-free DNA derived from seven key immune cell types in blood. The authors demonstrate the possibility to quantify the specific amounts of cell-free DNA by assaying cell-type specific CpG methylation marks via a targeted DNA sequencing assay. Assays of specific immune cell counts in blood are commonplace in modern diagnostic medicine. Rather than counting cells, the assay reported in this manuscript measures the burden of DNA released by dying immune cells, and this new assay may provide information about the immune system beyond what is possible with mere cell counting. The authors test their assay in three different settings (vaccination, inflammation and cancer), and provide significant support for the utility of their assay for immune monitoring in health and disease.
(This preprint has been reviewed by eLife. We include the public reviews from the reviewers here; the authors also receive private feedback with suggested changes to the manuscript. The reviewers remained anonymous to the authors.)
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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.
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Evaluation Summary:
This manuscript introduces a novel method for the monitoring of immune dynamics from blood, based on a measurement of the burden of cell-free DNA derived from seven key immune cell types in blood. The authors demonstrate the possibility to quantify the specific amounts of cell-free DNA by assaying cell-type specific CpG methylation marks via a targeted DNA sequencing assay. Assays of specific immune cell counts in blood are commonplace in modern diagnostic medicine. Rather than counting cells, the assay reported in this manuscript measures the burden of DNA released by dying immune cells, and this new assay may provide information about the immune system beyond what is possible with mere cell counting. The authors test their assay in three different settings (vaccination, inflammation and cancer), and provide …
Evaluation Summary:
This manuscript introduces a novel method for the monitoring of immune dynamics from blood, based on a measurement of the burden of cell-free DNA derived from seven key immune cell types in blood. The authors demonstrate the possibility to quantify the specific amounts of cell-free DNA by assaying cell-type specific CpG methylation marks via a targeted DNA sequencing assay. Assays of specific immune cell counts in blood are commonplace in modern diagnostic medicine. Rather than counting cells, the assay reported in this manuscript measures the burden of DNA released by dying immune cells, and this new assay may provide information about the immune system beyond what is possible with mere cell counting. The authors test their assay in three different settings (vaccination, inflammation and cancer), and provide significant support for the utility of their assay for immune monitoring in health and disease.
(This preprint has been reviewed by eLife. We include the public reviews from the reviewers here; the authors also receive private feedback with suggested changes to the manuscript. The reviewers remained anonymous to the authors.)
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Reviewer #1 (Public Review):
This is an interesting manuscript in which Fox-Fisher et al report a novel method for minimally invasive monitoring of the dynamics of the human immune system, based on profiling of cell-type specific cell-free DNA methylation marks. This method implements targeted DNA sequencing of a small panel of cell-type specific CpG markers and has the potential to be useful for the monitoring of a wide range immune-related diseases. The authors have tested the utility of this assay in three settings: influenza vaccination, Eosinophilic Esophagitis and B cell lymphoma. The experiments are well described and well powered, and the results are compelling. Nonetheless, this submission can be improved in several areas, most importantly, i) the presentation of the data in some of the Figures, ii) the statistical analysis of …
Reviewer #1 (Public Review):
This is an interesting manuscript in which Fox-Fisher et al report a novel method for minimally invasive monitoring of the dynamics of the human immune system, based on profiling of cell-type specific cell-free DNA methylation marks. This method implements targeted DNA sequencing of a small panel of cell-type specific CpG markers and has the potential to be useful for the monitoring of a wide range immune-related diseases. The authors have tested the utility of this assay in three settings: influenza vaccination, Eosinophilic Esophagitis and B cell lymphoma. The experiments are well described and well powered, and the results are compelling. Nonetheless, this submission can be improved in several areas, most importantly, i) the presentation of the data in some of the Figures, ii) the statistical analysis of B cell dynamics after vaccination in Figure 3, iii) the discussion of the challenges for diagnostic testing related to the significant inter- and intra-individual variation in immune cfDNA levels observed, and iv) the lack of discussion of other immune monitoring methods that have previously been described in the scientific literature or that are used in diagnostic medicine.
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Reviewer #2 (Public Review):
The authors try to dissect the contributions of various types of immune cells in cfDNA. They have mined cell-type-specific DNA methylation biomarkers for 7 common immune cells and validated their assays in 3 clinical scenarios, arguing that the signal in cfDNA could provide better assessment of the immune response in the body than cell counts.
B-cells also have lots of subtypes which could be very different from each other (e.g., plasma B cell vs naive B cell), the authors did not differentiate them while 2 of the clinical applications in the article are closely related to B-cells. Therefore the results need to reinterpreted using more precise measurements.
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