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Series GSE188573 Query DataSets for GSE188573
Status Public on Nov 01, 2022
Title Epigenetic and transcriptomic remodeling in monocytes of severe COVID-19 patients mirrors systemic changes in cytokines and immune cell crosstalk
Organism Homo sapiens
Experiment type Methylation profiling by array
Summary COVID-19 manifests with a wide spectrum of clinical phenotypes ranging from asymptomatic and mild to severe and critical. Severe and critical COVID-19 patients are characterized by a marked dysregulation in the myeloid compartment, especially monocytes; however, little is known about the epigenetic regulation of these cells in relation to hyperinflammatory responses in severe COVID-19 patients. In this study, we obtained the DNA methylome and transcriptome of monocytes from severe COVID-19 patients. We observed drastic DNA methylation changes encompassing impairment of type-I interferons (IFN), antigen presentation functions among others, in concordance with gene expression changes supporting the relevance of DNA methylation alterations in the dysregulation of the myeloid compartment. These changes were similar to those occurring in bacterial sepsis, although specific functions resulting from viral infection were also identified. Also, a progressive relationship of DNA methylation alterations and Sequential Organ Failure Assessment (SOFA) score was found related with IFNγ production and T-helper 1 cell cytokine production. Analysis of the single cell transcriptomes of other immune cell types allowed inferring dysregulation of communication between monocytes and other cell types like NK cells, plasma B cells and T cells, which can partly explain monocyte epigenome dysregulation, perpetuating a dysregulated response in these patients.
 
Overall design Monocytes from 48 severe COVID19 patients and 11 healthy donors were sorted and DNA methylation analysis was performed.
 
Contributor(s) Godoy-Tena G, Barmada A, Morante-Palacios O, de la Calle-Fabregat C, Ciudad L, Ruiz-Sanmartín A, Martínez-Gallo M, Frank-Bertoncelj M, Ferrer R, Ruiz-Rodriguez JC, Rodríguez-Ubreva J, Vento-Tormo R, Ballestar E
Citation(s) 36443794
Submission date Nov 10, 2021
Last update date Dec 15, 2022
Contact name Esteban Ballestar
Organization name Josep Carreras Research Institute (IJC)
Lab Epigenetics and Immune Disease
Street address Ctra de Can Ruti, Camí de les Escoles s/n
City Badalona, Barcelona
State/province N/A = Not Applicable
ZIP/Postal code 08916
Country Spain
 
Platforms (1)
GPL21145 Infinium MethylationEPIC
Samples (59)
GSM5685685 Monocytes From HD number 5
GSM5685686 Monocytes from severe COVID19 patient number 49
GSM5685687 Monocytes from severe COVID19 patient number 35
Relations
BioProject PRJNA779439

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
GSE188573_Matrix_processed.txt.gz 452.6 Mb (ftp)(http) TXT
GSE188573_Matrix_signal.txt.gz 302.1 Mb (ftp)(http) TXT
GSE188573_RAW.tar 1001.4 Mb (http)(custom) TAR (of IDAT)
Processed data are available on Series record

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