This study complies with all relevant ethical regulations. Postmortem brain tissue specimens from individuals with COVID-19 were collected through a protocol for waived consent for the use of excess tissue approved by the Mass General Brigham Institutional Review Board NeuroBioBank, which does not require IRB approval; postmortem human brain research of de-identified samples is not considered human subjects research).
Frozen tissue was processed using Biosafety Level 2+ procedures approved by the Beth Israel Deaconess Medical Center Institutional Biosafety Committee. Brain tissues were homogenized using TRIzol reagent and RNA were extracted from tissues by phase separation. Total RNA was quantified by NanoDrop and TapeStation 4200 .Severe COVID-19 was determined by meeting the NIH criteria for severe or critical illness .
To assess the expression of SARS-CoV-2, primers against the SARS-CoV-2 nucleocapsid gene and primer set nCOV_N2 ) and were synthesized as recommended by the US Centers for Disease Control and Prevention. The 2019-nCoV_
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Epigenetic and transcriptomic reprogramming in monocytes of severe COVID-19 patients reflects alterations in myeloid differentiation and the influence of inflammatory cytokines - Genome MedicineBackground 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 marked changes in the myeloid compartment, especially monocytes. However, little is known about the epigenetic alterations that occur in these cells during hyperinflammatory responses in severe COVID-19 patients. Methods In this study, we obtained the DNA methylome and transcriptome of peripheral blood monocytes from severe COVID-19 patients. DNA samples extracted from CD14 + CD15- monocytes of 48 severe COVID-19 patients and 11 healthy controls were hybridized on MethylationEPIC BeadChip arrays. In parallel, single-cell transcriptomics of 10 severe COVID-19 patients were generated. CellPhoneDB was used to infer changes in the crosstalk between monocytes and other immune cell types. Results We observed DNA methylation changes in CpG sites associated with interferon-related genes and genes associated with antigen presentation, concordant with gene expression changes. These changes significantly overlapped with those occurring in bacterial sepsis, although specific DNA methylation alterations in genes specific to viral infection were also identified. We also found these alterations to comprise some of the DNA methylation changes occurring during myeloid differentiation and under the influence of inflammatory cytokines. A progression of DNA methylation alterations in relation to the Sequential Organ Failure Assessment (SOFA) score was found to be related to interferon-related genes and T-helper 1 cell cytokine production. CellPhoneDB analysis of the single-cell transcriptomes of other immune cell types suggested the existence of altered crosstalk between monocytes and other cell types like NK cells and regulatory T cells. Conclusion Our findings show the occurrence of an epigenetic and transcriptional reprogramming of peripheral blood monocytes, which could be associated with the
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