Remote immune processes revealed by immune-derived circulating cell-free DNA
- The Hebrew University-Hadassah Medical School, Israel
- The Hebrew University of Jerusalem, Israel
- Chaim Sheba Medical Center, Israel
- University of Cincinnati, United States
- GRAIL, United States
- Hadassah Hebrew University Medical Center, Israel
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.
Data availability
All data generated or analyzed during this study are included in the manuscript and supporting files.The whole-genome bisulfite sequencing data reported in the paper, from 46 samples, is uploaded to GEO as described. The paper also reports data from PCR reactions that were analyzed by massively parallel sequencing. This is a very large set of data that is extremely low in information content and is of little interest to readers or even to people interested in replicating our results or interrogating them further. The key information (methylation status) in each sample is provided in the supplementary information, and we also uploaded the analysis algorithm and some sequence data. The entire set of raw sequencing data is available in the Dor lab to anyone interested.Please contact Prof. Yuval Dor dor@huji.ac.il . All information will be shared. There is no need for any paperwork.Code is uploaded to GitHub as described in the paper.The methylation status of each marker in each sample is provided in Supplementary file 1. This data was used to generate the graphs shown in the paper. Sheets in this file indicate which figure they relate to.
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Funding
No external funding was received for this work.
Ethics
Human subjects: This study was conducted according to protocols approved by the Institutional Review Board at each study site (Hadassah Medical Center: HMO-14-0198. A Method to Diagnose Cell Death Based on Methylation Signature of Circulating Cell-Free DNA, Cininnati Children's Hospital: CCHMC IRB protocol 2008-0090: Eosinophils and Inflammation, an Expanded Study), with procedures performed in accordance with the Declaration of Helsinki. Blood and tissue samples were obtained from donors who have provided written informed consent. When using material from deceased organ donor those with legal authority were consented. Subject characteristics are presented in Supplementary File 1.
Copyright
© 2021, Fox-Fisher et al.
This article is distributed under the terms of the Creative Commons Attribution License permitting unrestricted use and redistribution provided that the original author and source are credited.
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Remote immune processes revealed by immune-derived circulating cell-free DNA
eLife 10:e70520.
https://doi.org/10.7554/eLife.70520
Further reading
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N6-methyladenosine (m6A) in eukaryotic RNA is an epigenetic modification that is critical for RNA metabolism, gene expression regulation, and the development of organisms. Aberrant expression of m6A components appears in a variety of human diseases. RNA m6A modification in Drosophila has proven to be involved in sex determination regulated by Sxl and may affect X chromosome expression through the MSL complex. The dosage-related effects under the condition of genomic imbalance (i.e. aneuploidy) are related to various epigenetic regulatory mechanisms. Here, we investigated the roles of RNA m6A modification in unbalanced genomes using aneuploid Drosophila. The results showed that the expression of m6A components changed significantly under genomic imbalance, and affected the abundance and genome-wide distribution of m6A, which may be related to the developmental abnormalities of aneuploids. The relationships between methylation status and classical dosage effect, dosage compensation, and inverse dosage effect were also studied. In addition, we demonstrated that RNA m6A methylation may affect dosage-dependent gene regulation through dosage-sensitive modifiers, alternative splicing, the MSL complex, and other processes. More interestingly, there seems to be a close relationship between MSL complex and RNA m6A modification. It is found that ectopically overexpressed MSL complex, especially the levels of H4K16Ac through MOF, could influence the expression levels of m6A modification and genomic imbalance may be involved in this interaction. We found that m6A could affect the levels of H4K16Ac through MOF, a component of the MSL complex, and that genomic imbalance may be involved in this interaction. Altogether, our work reveals the dynamic and regulatory role of RNA m6A modification in unbalanced genomes, and may shed new light on the mechanisms of aneuploidy-related developmental abnormalities and diseases.
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