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Series GSE186888 Query DataSets for GSE186888
Status Public on Nov 26, 2021
Title Remote immune processes revealed by immune-derived circulating cell-free DNA
Organism Homo sapiens
Experiment type Methylation profiling by high throughput sequencing
Summary Blood cell counts often fail to report on immune processes occurring in remote tissues. Here we use 25 immune cell type-specific methylation patterns in circulating cell-free DNA (cfDNA) for studying 26 human immune cell dynamics. We characterized cfDNA released from specific immune cell types in 27 healthy individuals (N=242), cross sectionally and longitudinally. Immune cfDNA levels had no 28 individual steady state as opposed to blood cell counts, suggesting that cfDNA concentration reflects 29 adjustment of cell survival to maintain homeostatic cell numbers. We also observed selective elevation 30 of immune-derived cfDNA upon perturbations of immune homeostasis. Following influenza 31 vaccination (N=92), B-cell-derived cfDNA levels increased prior to elevated B-cell counts and 32 predicted efficacy of antibody production. Patients with Eosinophilic Esophagitis (N=21) and B-cell 33 lymphoma (N=27) showed selective elevation of eosinophil and B-cell cfDNA respectively, which 34 were undetectable by cell counts in blood. Immune-derived cfDNA provides a novel biomarker for 35 monitoring immune responses to physiological and pathological processes that are not accessible using 36 conventional methods.
 
Overall design To further examine the relative presence of immune cfDNA in plasma and whole blood, we employed an independent set of samples and an independent technology to measure and interpret methylation markers. We performed deconvolution of methylomes obtained by whole genome bisulfite sequencing (85x coverage), on genomic DNA from whole blood, and matched plasma cfDNA from 23 healthy donors.
*** Raw data is unavailable due to patient privacy concerns ***
 
Contributor(s) Fox-Fisher I, Piyanzin S, Ochana B, Klochendler A, Magenheim J, Peretz A, Loyfer N, Moss J, Cohen D, Drori Y, Friedman N, Mandelboim M, Rothenberg ME, Caldwell JM, Rochman M, Jamshidi A, Cann G, Lavi D, Kaplan T, Glaser B, Shemer R, Dor Y
Citation(s) 34842142
Submission date Oct 31, 2021
Last update date Nov 30, 2021
Contact name Tommy Kaplan
E-mail(s) tommy@cs.huji.ac.il
Organization name Hebrew University
Department School of Computer Science and Engineering
Street address Givat Ram Campus
City Jerusalem
ZIP/Postal code 91904
Country Israel
 
Platforms (1)
GPL24676 Illumina NovaSeq 6000 (Homo sapiens)
Samples (46)
GSM5663172 CNVS-NORM-110000263-WBC-WGBS-Rep1
GSM5663173 CNVS-NORM-110000264-WBC-WGBS-Rep1
GSM5663174 CNVS-NORM-110027051-WBC-WGBS-Rep1
Relations
BioProject PRJNA776644

Download family Format
SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE186888_RAW.tar 15.3 Gb (http)(custom) TAR (of BETA, BIGWIG)
GSE186888_blood_450k.csv.gz 31.5 Mb (ftp)(http) CSV
Raw data not provided for this record
Processed data provided as supplementary file
Processed data are available on Series record

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