COVID-19 methylation
1 Main goals
This notebook is aimed to provide a list of available resources where methylation array data can be found for COVID-19 patients. The studies listed here were performed with different goals and propose to answer different scientific questions. Our main objective is to collect and download these data in order to perform specific analyses on them, tailored to our research needs.
2 List of available studies and data sources
2.1 Genome-wide DNA methylation analysis of COVID-19 severity
Genome-wide DNA methylation analysis of COVID-19 severity using the Illumina HumanMethylationEPIC microarray platform to analyze over 850,000 methylation sites, comparing COVID-19 patients with patients presenting with respiratory symptoms, but negative for COVID-19, using whole blood tissue.
Number of patients: 124
Platform: Illumina HumanMethylationEPIC
Citation: Balnis, Joseph et al. “Blood DNA methylation and COVID-19 outcomes.” Clinical epigenetics vol. 13,1 118. 25 May. 2021, doi:10.1186/s13148-021-01102-9
Age: needs to be checked
2.2 Epigenome-Wide Association Study of COVID-19 Severity with Respiratory Failure
Patients infected with the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), responsible for the coronavirus disease 2019 (COVID-19), exhibit a wide spectrum of disease behavior. Since DNA methylation has been implicated in the regulation of viral infections and the immune system, we performed an epigenome- wide association study (EWAS) to identify candidate loci regulated by this epigenetic mark that could be involved in the onset of COVID-19 in patients without comorbidities.
Number of patients: 407
Platform: Infinium MethylationEPIC
Citation: Castro de Moura, Manuel et al. “Epigenome-wide association study of COVID-19 severity with respiratory failure.” EBioMedicine vol. 66 (2021): 103339. doi:10.1016/j.ebiom.2021.103339
Age: available
2.3 Host methylation predicts SARS-CoV-2 infection and clinical outcome
Genome-wide DNA methylation profiling of peripheral blood from 164 SARS-CoV-2 positive, 296 SARS-CoV-2 negative, and 65 other respiratory infection patient samples. Samples were profiled on a custom Illumina Infinium HumanMethylation BeadChip array including all MethylationEPIC-B4 probes and additional custom content targeting immune genes. SARS-CoV-2 positivity is defined by a positive RT-PCR test. “Other infection” samples are SARS-CoV-2 negative and were tested with a panel of common human acute respiratory infection pathogens.
Number of patients: 525
Platform: Illumina Infinium HumanMethylation BeadChip
Citation: Konigsberg, Iain R et al. “Host methylation predicts SARS-CoV-2 infection and clinical outcome.” Communications medicine vol. 1,1 (2021): 42. doi:10.1038/s43856-021-00042-y
Age: needs to be checked
2.4 Longitudinal multi-omics identifies responses of megakaryocytes, erythroid cells and plasmablasts as hallmarks of severe COVID-19 trajectories
To help characterise the temporal dynamics of host response during COVID-19, we performed a longitudinal DNA methylation analysis in a cohort of 12 patients. DNA was extracted from peripheral blood sampled at up to 5 time points per patient. At each sample point, a patient’s disease trajectory, “pseudotime”, was categorised according to clinical parameters. DNA methylation profiling by Illumina Bead Arrays was performed on each sample. We found CpG sites hypomethylated during COVID-19 were highly enriched in cis of transcripts related to positive regulation of TNF secretion and innate immune signalling, indicating potential long-term regulation of immunological misfiring by epigenetic processes.
Number of patients: 6+6
Platform: Illumina Bead Array
Citation: Bernardes, Joana P et al. “Longitudinal Multi-omics Analyses Identify Responses of Megakaryocytes, Erythroid Cells, and Plasmablasts as Hallmarks of Severe COVID-19.” Immunity vol. 53,6 (2020): 1296-1314.e9. doi:10.1016/j.immuni.2020.11.017
Age: needs to be checked
2.5 Epigenetic Clocks Are Not Accelerated in COVID-19 Patients
Accession “GSE161988” is currently private and is scheduled to be released on Nov 23, 2023.
Number of patients: 9
Platform: Illumina Bead Array
Citation: Franzen, Julia et al. “Epigenetic Clocks Are Not Accelerated in COVID-19 Patients.” International journal of molecular sciences vol. 22,17 9306. 27 Aug. 2021, doi:10.3390/ijms22179306
Age: available