EGAGenomicsEpigeneticsCOVID-192019 novel coronavirus infectionSARS-CoV-22019-nCoV infectionsevere acute respiratory syndrome coronavirus 2coronavirus disease 2019SARS-coronavirus 2https://ega-archive.org/studies/EGAS00001006559EGAEGA study EGAS00001006559Single-cell omics data for COVID-19 patientsEGArestrictedsingle cell ATAC-sequencing, single-cell ATAC-seq, assay, Client., Patient, scATAC-seq, determination, Clients, ATAC-seq (single cell), single cell assay for transposase-accessible chromatin using sequencing, single cell ATAC-seq, chemical analysisSpi1, Non Protein Coding, SPI1, Materials, Peripheral Blood Mononuclear Cells, Virus Infection, CG30327, Social Controls, dmTAF[[II]]230, Noncoding RNA, Relative, DmelCG12298, ATGPR7, oxigeno, pulmones, SCRAMBLED, GRP7, RESP SYSTEM DISEASE NOS, [X]Chronic and other pulmonary manifestations due to radiation (disorder), TFIID TAF250, cel, Non-Protein-Coding RNA, mJe-r, Pneumoconiosis due to other inorganic dust, O, Oxygen-16, Coronavirus Disease 2019, Respiratory conditions due to other specified external agents, Respiratory System Disorder, Other respiratory system diseases (disorder), beta-CoVs, Respiratory Disorder, Epigenomic, Social, Oxygen, set, T16B24_18, Mononuclear, Non Coding, [OO], Homo sapiens disease, COVID 19 Virus Disease, 2019-nCoV Infections, dTAF[[II]]230, SARS-CoV-2 Viruses, Lung involvement in other diseases classified elsewhere, β-CoV, SPI-1, STRUBBELIG, familial, SARS-CoV-2, TAF200, Hospitalizations, respiratory disease, Coronavirus 2, CKR2, Respiratory disorder, 2019 nCoV Infection, COVID 19 Virus Infection, PBMC Peripheral Blood Mononuclear Cells, partial functionality, DmIKKgamma, Ckr2, SARS-CoV-2 Virus, dIKK, Non-Coding RNA, Relative Risks, CC-CKR-2, Dmel_CG6393, dioxygen, CD192, Pandemic, IKK-gamma, Controls, Non-Protein-Coding, ALVEOL PNEUMONOPATHY NOS, F2G1.4, Taf250, Material, 2019, 2019-nCoV Diseases, Spi-1, SPI-A, Epigenetics, TAF230, Dioxygen, Regulations, [X]Chronic and other pulmonary manifestations due to radiation, Nontranslated RNA, npcRNA, COVID-19, impaired, E-948, Trait Loci, SARS CoV 2 Virus, Transcription Factor, 31 kDa-transforming protein, dIKK-gamma, COVID19 Virus, Other diseases of respiratory system, Sfpi-1, disease of respiratory system, SARS, Other specified alveolar and parietoalveolar pneumonopathies, DmIKK-gamma, Severe Acute Respiratory Syndrome Coronavirus 2 Infection, disease or disorder, Tfpu.1, β-coronavirus, 2019-nCoV, respiratory system disease, Transcription, SARS Coronavirus 2, β-CoVs, Other respiratory system diseases, dTAF[[II]]250, cell, Non-Coding, mei-1794, dysfunction, COVID-19 Virus Infection, Other respiratory system diseases NOS (disorder), severe acute respiratory syndrome coronavirus 2, Trait Locus, SARS-CoV-2 Infection, dTAF250, COVID-19 Virus, LUNG INVOLV IN OTH DIS, ATGRP7, Mononuclear Leukocyte, 65K, Loci, CG42257, Dmel_CG30327, [X]Respiratory conditions due to other specified external agents, RESP SYSTEM DISEASE NEC, snp, constitutitional genetic, respiratory disorder, Dis-1, RNA, cg11478, Coronavirus Disease 19, 2019 Novel Coronavirus, SFFV proviral integration 1 protein, Oxygen 16, grupo, beta-CoV, disorders, RESP COND: EXT AGENT NOS, BG:DS00004.13, Factor, function, SARS-CoV-2 Infections, lungs, motif, Cell, oxygen, T16B24.18, dTAF230, COVID-19 Virus Disease, IKKgamma, Dis1, Severe Acute Respiratory Syndrome Coronavirus 2, Cmkbr2, Social Control, chemical analysis, TAF[[II]]250/230, condition, oxygene, Other diseases of mediastinum, OXYGEN MOLECULE, Relative Risk, Taf[[II]]250, Peripheral Blood Human Mononuclear Cells, Other alveolar and parietoalveolar pneumonopathy, O2, 2019 Novel, betacoronavirus, underdeveloped, ensemble, Dmikkgamma, Disorder of respiratory system, Dub, GR-RBP7, OF, set of lungs, COVID-19 Pandemics, COVID-19 Pandemic, CG16910, [X]Other diseases of the respiratory system, Locus, having decreased function, Respiratory disease, cinnamoyl coa reductase, Noncoding, regulation, E 948, hereditary, Severe, COVID 19, determination, Respiratory conditions due to unspecified external agent, and rna binding 2, CCR2B, CCR2A, ALVEOL PNEUMONOPATHY NEC, Other diseases of respiratory system NOS, 2019 novel coronavirus, Quantitative, Virus Disease, disorder of respiratory system, 2019 nCoV Disease, Unspecified alveolar and parietoalveolar pneumonopathy, respiratory system disease or disorder, SUB, dysfunctional, CG11478, RESP COND: EXT AGENT NEC, ATCRR2, diseases, 2019-nCoV Disease, Novel Coronavirus, Virus, diseases and disorders, lungs pair, Peripheral Blood Mononuclear Cell, E948, [X]Other diseases of the respiratory system (disorder), COVID 19 Pandemic, KIF20A, Formal Social Controls, IKKg, Chromatins, Ccr2b, KEY, Key, respiratory system disorder, Ccr2a, Unspecified disease of respiratory system, DmelCG42257, Immune Processes, Immune Responses, human disease, disease or disorder of respiratory system, long, hypoplasia, Coronavirus Disease-19, genetic, Monocyte, Immune, Mononuclear Leukocytes, GLYCINE RICH PROTEIN 7, chromosome scaffold, INORG DUST PNEUMOCON NEC, nuclear chromatin, Process, COVID-19 Viruses, Pu.1, SFPI1, 2019 Novel Coronavirus Disease, TAFII-250, ATCCR2, TAF250/230, Respiratory system diseases NOS (disorder), Quantitative Trait, COVID19 Viruses, F23A5.17, TAFII250, Sauerstoff, PU.1, Quantitative Trait Locus, CG6393, Kenny, Diseases, Genetic Materials, Coronavirus, NOS, F23A5_17, COVID-19 Virus Infections, Non-Peptide-Coding, Genetic Material, Sfpi1, Disauerstoff, Factors, Risk, cold, Epigenetic, Coronavirus Disease 2019 Virus, [X]Respiratory conditions due to unspecified external agent, Control, Nontranslated, CCR-2, lacks function of type, CG17603, Lung involvement in conditions classified elsewhere, Other respiratory system diseases NOS, TAF[[II]], low functionality, disease, DmelCG16910, Patient, SR3-5, MCP-1-R, 2019 Novel Coronavirus Infection, Cistron, inherited genetic, Regulation, Interferon, Gruppe, AT1G11140, COVID19, other disease, cytoplasmic chromatin, d230, Gene, COVID-19 Virus Diseases, dTAFII250, 8O, circadian rhythm, EfW1, CG12298, Client., reduced, dioxygene, dmTAF1, Taf230, heredity, SARS CoV 2 Infection, tiny, dmIKKgamma, IKK[[gamma]], Ckr2b, Ckr2a, 2019 Novel Coronaviruses, TAF250, study, Taf200, Genetic, Viruses, Disease of respiratory system, Tcfpu1, Wuhan Seafood Market Pneumonia Virus, Taf1p, non-neoplastic, [X]Respiratory conditions due to unspecified external agent (disorder), Immune Response, IKK, CKR2B, grupos, CKR2A, Clients, disorder, SRF9, Quantitative Trait Loci Genes, TAF, Immune Process, [X]Respiratory conditions due to other specified external agents (disorder), SARS Coronavirus 2 Infection, Wuhan Coronavirus, molecular oxygen, small, Disease, TAF[[II]]250, Leukocyte, Formal Social Control, Non Peptide Coding, not elsewhere classified, Other diseases of trachea and bronchus, l(3)84Ab, Other diseases of respiratory system NOS (disorder), CMKBR2, CRINKLY4 related 2, medical condition, Cistrons, Client, DISEASES OF THE RESPIRATORY SYSTEM, CHR PUL MANIF D/T RADIAT, group, STRUBBELIG-RECEPTOR FAMILY 9, 2019-nCoV Infection, Non-Peptide-Coding RNA, p230, Infection, Respiratory system diseases NOS, TFIID, GLYCINE-RICH RNA-BINDING PROTEIN 7, Untranslated RNA, Cc-ckr-2, Disease 2019, TAF[[II]]230, Exhibit, PNEUMOCONIOSES AND OTHER LUNG DISEASES DUE TO EXTERNAL AGENTS, Risks, Rest, INSDC_qualifier:other, TAF[II]250, Wuhan, Disease of respiratory system (disorder), SARS-coronavirus 2, Respiratory conditions due to other and unspecified external agents, Chronic and other pulmonary manifestations due to radiation, DmelCG17603, Disorder of respiratory system (disorder), MEDIASTINUM DISEASE NEC, Response, COVID 19 Virus, Lungs, assay, T19D16.8, groupe, SCM, TAF1falseSingle-cell ATAC-seq analysis for COVID19 patientsWhile SARS-CoV-2 infection causes mild respiratory disease in most individuals, a small group of patients develops severe COVID-19. Dysfunctional innate immune responses have been identified to contribute to differences in COVID-19 severity, but the key regulators are still unknown. Here, we present an integrative single-cell epigenetics, transcriptomic, and genetics analysis of peripheral blood mononuclear cells from hospitalized and convalescent COVID-19 patients. In classical monocytes, we identified 41.3% of significantly up-regulated genes in hospitalized COVID-19 patients potentially induced by differential chromatin accessibility. Sub-clustering and motif-enrichment analyses of monocytes reveal disease condition-specific regulation by transcription factors, such as C/EBPs and SPI1, and their targets, including a long-noncoding RNA LUCAT1, which further regulates interferon responses and is associated with the need for oxygen supply of COVID-19 patients. The interaction between C/EBPs and LUCAT1 was validated through loss-of-function experiments. Finally, we investigated genetic risk variants that exhibit allele-specific open chromatin (ASoC) in promoters/enhancers of COVID-19 patients. Integrating our data with publicly available expression quantitative trait loci and chromosomal interactions indicates that ASoC SNP rs6800484-C is associated with lower expression of CCR2, which may contributeto higher viral loads in lungs and higher risk of COVID-19 hospitalization. Altogether, our study highlights the diverse genetic and epigenetic regulators that contribute to the innate immune responses of different COVID-19 patients.2022-10-14 14:26:43EGAS000010065599606MONDO_0100096EGAD00001009331EGAC00001002844