ScRNA-seq of PBMC and whole blood samples reveals a dysregulated myeloid cell compartment in severe COVID-19

In a dual-center, two-cohort study, we performed single-cell RNA-sequencing of whole blood and peripheral blood mononuclear cells to determine changes in immune cell composition and activation in mild vs. severe COVID-19 over time. This study provides detailed insights into the systemic immune response to SARS-CoV-2 infection and reveals profound alterations in the myeloid cell compartment associated with severe COVID-19.

Type: Other
Archiver: European Genome-Phenome Archive (EGA)

1 Dataset 29 Publications

Click on a Dataset ID in the table below to learn more, and to find out who to contact about access to these data

Dataset ID	Description	Technology	Samples
EGAD00001006550	In a dual-center, two-cohort study, we performed single-cell RNA-sequencing of whole blood and peripheral blood mononuclear cells to determine changes in immune cell composition and activation in mild vs. severe COVID-19 over time. This study provides detailed insights into the systemic immune response to SARS-CoV-2 infection and reveals profound alterations in the myeloid cell compartment associated with severe COVID-19.	Illumina NovaSeq 6000	141

Publications	Citations
Severe COVID-19 Is Marked by a Dysregulated Myeloid Cell Compartment. Schulte-Schrepping J, Reusch N, Paclik D, Baßler K, Schlickeiser S, Zhang B, Krämer B, Krammer T, Brumhard S, Bonaguro L, De Domenico E, Wendisch D, Grasshoff M, Kapellos TS, Beckstette M, Pecht T, Saglam A, Dietrich O, Mei HE, Schulz AR, Conrad C, Kunkel D, Vafadarnejad E, Xu CJ, Horne A, Herbert M, Drews A, Thibeault C, Pfeiffer M, Hippenstiel S, Hocke A, Müller-Redetzky H, Heim KM, Machleidt F, Uhrig A, Bosquillon de Jarcy L, Jürgens L, Stegemann M, Glösenkamp CR, Volk HD, Goffinet C, Landthaler M, Wyler E, Georg P, Schneider M, Dang-Heine C, Neuwinger N, Kappert K, Tauber R, Corman V, Raabe J, Kaiser KM, Vinh MT, Rieke G, Meisel C, Ulas T, Becker M, Geffers R, Witzenrath M, Drosten C, Suttorp N, von Kalle C, Kurth F, Händler K, Schultze JL, Aschenbrenner AC, Li Y, Nattermann J, Sawitzki B, Saliba AE, Sander LE, Deutsche COVID-19 OMICS Initiative (DeCOI). Cell 182: 2020 1419-1440.e23	866
Optimized workflow for single-cell transcriptomics on infectious diseases including COVID-19. De Domenico E, Bonaguro L, Schulte-Schrepping J, Becker M, Händler K, Schultze JL. STAR Protoc 1: 2020 100233	10
Convalescent COVID-19 patients are susceptible to endothelial dysfunction due to persistent immune activation. Chioh FW, Fong SW, Young BE, Wu KX, Siau A, Krishnan S, Chan YH, Carissimo G, Teo LL, Gao F, Tan RS, Zhong L, Koh AS, Tan SY, Tambyah PA, Renia L, Ng LF, Lye DC, Cheung C. Elife 10: 2021 e64909	86
Longitudinal proteomic analysis of severe COVID-19 reveals survival-associated signatures, tissue-specific cell death, and cell-cell interactions. Filbin MR, Mehta A, Schneider AM, Kays KR, Guess JR, Gentili M, Fenyves BG, Charland NC, Gonye ALK, Gushterova I, Khanna HK, LaSalle TJ, Lavin-Parsons KM, Lilley BM, Lodenstein CL, Manakongtreecheep K, Margolin JD, McKaig BN, Rojas-Lopez M, Russo BC, Sharma N, Tantivit J, Thomas MF, Gerszten RE, Heimberg GS, Hoover PJ, Lieb DJ, Lin B, Ngo D, Pelka K, Reyes M, Smillie CS, Waghray A, Wood TE, Zajac AS, Jennings LL, Grundberg I, Bhattacharyya RP, Parry BA, Villani AC, Sade-Feldman M, Hacohen N, Goldberg MB. Cell Rep Med 2: 2021 100287	157
Transcriptional Changes in CD16+ Monocytes May Contribute to the Pathogenesis of COVID-19. Chilunda V, Martinez-Aguado P, Xia LC, Cheney L, Murphy A, Veksler V, Ruiz V, Calderon TM, Berman JW. Front Immunol 12: 2021 665773	18
Dissecting the common and compartment-specific features of COVID-19 severity in the lung and periphery with single-cell resolution. Overholt KJ, Krog JR, Zanoni I, Bryson BD. iScience 24: 2021 102738	6
An interactive single cell web portal identifies gene and cell networks in COVID-19 host responses. Jin K, Bardes EE, Mitelpunkt A, Wang JY, Bhatnagar S, Sengupta S, Krummel DP, Rothenberg ME, Aronow BJ. iScience 24: 2021 103115	11
Early IFN-α signatures and persistent dysfunction are distinguishing features of NK cells in severe COVID-19. Krämer B, Knoll R, Bonaguro L, ToVinh M, Raabe J, Astaburuaga-García R, Schulte-Schrepping J, Kaiser KM, Rieke GJ, Bischoff J, Monin MB, Hoffmeister C, Schlabe S, De Domenico E, Reusch N, Händler K, Reynolds G, Blüthgen N, Hack G, Finnemann C, Nischalke HD, Strassburg CP, Stephenson E, Su Y, Gardner L, Yuan D, Chen D, Goldman J, Rosenstiel P, Schmidt SV, Latz E, Hrusovsky K, Ball AJ, Johnson JM, Koenig PA, Schmidt FI, Haniffa M, Heath JR, Kümmerer BM, Keitel V, Jensen B, Stubbemann P, Kurth F, Sander LE, Sawitzki B, Deutsche COVID-19 OMICS Initiative (DeCOI), Aschenbrenner AC, Schultze JL, Nattermann J. Immunity 54: 2021 2650-2669.e14	137
Immune Response in Severe and Non-Severe Coronavirus Disease 2019 (COVID-19) Infection: A Mechanistic Landscape. Mukund K, Nayak P, Ashokkumar C, Rao S, Almeda J, Betancourt-Garcia MM, Sindhi R, Subramaniam S. Front Immunol 12: 2021 738073	22
Differential Co-Expression Network Analysis Reveals Key Hub-High Traffic Genes as Potential Therapeutic Targets for COVID-19 Pandemic. Hasankhani A, Bahrami A, Sheybani N, Aria B, Hemati B, Fatehi F, Ghaem Maghami Farahani H, Javanmard G, Rezaee M, Kastelic JP, Barkema HW. Front Immunol 12: 2021 789317	31
A human pluripotent stem cell-based model of SARS-CoV-2 infection reveals an ACE2-independent inflammatory activation of vascular endothelial cells through TLR4. Ma Z, Li X, Fan RLY, Yang KY, Ng CSH, Lau RWH, Wong RHL, Ng KK, Wang CC, Ye P, Fu Z, Chin AWH, Lai MYA, Huang Y, Tian XY, Poon LLM, Lui KO. Stem Cell Reports 17: 2022 538-555	18
Severe COVID-19 Shares a Common Neutrophil Activation Signature with Other Acute Inflammatory States. Schimke LF, Marques AHC, Baiocchi GC, de Souza Prado CA, Fonseca DLM, Freire PP, Rodrigues Plaça D, Salerno Filgueiras I, Coelho Salgado R, Jansen-Marques G, Rocha Oliveira AE, Peron JPS, Cabral-Miranda G, Barbuto JAM, Camara NOS, Calich VLG, Ochs HD, Condino-Neto A, Overmyer KA, Coon JJ, Balnis J, Jaitovich A, Schulte-Schrepping J, Ulas T, Schultze JL, Nakaya HI, Jurisica I, Cabral-Marques O. Cells 11: 2022 847	20
Single-cell transcriptomics reveal a unique memory-like NK cell subset that accumulates with ageing and correlates with disease severity in COVID-19. Guo C, Wu M, Huang B, Zhao R, Jin L, Fu B, Wang P, Wang D, Zheng M, Fang J, Wei H, Qu K, Ni F. Genome Med 14: 2022 46	20
The Genetic Risk for COVID-19 Severity Is Associated With Defective Immune Responses. Kuijpers Y, Chu X, Jaeger M, Moorlag SJCFM, Koeken VACM, Zhang B, de Nooijer A, Grondman I, Gupta MK, Janssen N, Mourits VP, de Bree LCJ, de Mast Q, van de Veerdonk FL, Joosten LAB, Li Y, Netea MG, Xu CJ. Front Immunol 13: 2022 859387	2
A systems biology approach identifies candidate drugs to reduce mortality in severely ill patients with COVID-19. Fava VM, Bourgey M, Nawarathna PM, Orlova M, Cassart P, Vinh DC, Cheng MP, Bourque G, Schurr E, Langlais D. Sci Adv 8: 2022 eabm2510	10
Identification of COVID-19-Associated DNA Methylation Variations by Integrating Methylation Array and scRNA-Seq Data at Cell-Type Resolution. Wang G, Xiong Z, Yang F, Zheng X, Zong W, Li R, Bao Y. Genes (Basel) 13: 2022 1109	6
Whole blood DNA methylation analysis reveals respiratory environmental traits involved in COVID-19 severity following SARS-CoV-2 infection. Barturen G, Carnero-Montoro E, Martínez-Bueno M, Rojo-Rello S, Sobrino B, Porras-Perales Ó, Alcántara-Domínguez C, Bernardo D, Alarcón-Riquelme ME. Nat Commun 13: 2022 4597	16
scFeatures: multi-view representations of single-cell and spatial data for disease outcome prediction. Cao Y, Lin Y, Patrick E, Yang P, Yang JYH. Bioinformatics 38: 2022 4745-4753	5
Longitudinal characterization of circulating neutrophils uncovers phenotypes associated with severity in hospitalized COVID-19 patients. LaSalle TJ, Gonye ALK, Freeman SS, Kaplonek P, Gushterova I, Kays KR, Manakongtreecheep K, Tantivit J, Rojas-Lopez M, Russo BC, Sharma N, Thomas MF, Lavin-Parsons KM, Lilly BM, Mckaig BN, Charland NC, Khanna HK, Lodenstein CL, Margolin JD, Blaum EM, Lirofonis PB, Revach OY, Mehta A, Sonny A, Bhattacharyya RP, Parry BA, Goldberg MB, Alter G, Filbin MR, Villani AC, Hacohen N, Sade-Feldman M. Cell Rep Med 3: 2022 100779	28
Neutrophil profiles of pediatric COVID-19 and multisystem inflammatory syndrome in children. Boribong BP, LaSalle TJ, Bartsch YC, Ellett F, Loiselle ME, Davis JP, Gonye ALK, Sykes DB, Hajizadeh S, Kreuzer J, Pillai S, Haas W, Edlow AG, Fasano A, Alter G, Irimia D, Sade-Feldman M, Yonker LM. Cell Rep Med 3: 2022 100848	23
Protocol for bulk RNA sequencing of enriched human neutrophils from whole blood and estimation of sample purity. Gonye ALK, LaSalle TJ, Freeman SS, Reyes M, Hacohen N, Villani AC, Sade-Feldman M. STAR Protoc 4: 2023 102125	2
Benchmarking of analytical combinations for COVID-19 outcome prediction using single-cell RNA sequencing data. Cao Y, Ghazanfar S, Yang P, Yang J. Brief Bioinform 24: 2023 bbad159	2
Atlas-scale single-cell multi-sample multi-condition data integration using scMerge2. Lin Y, Cao Y, Willie E, Patrick E, Yang JYH. Nat Commun 14: 2023 4272	7
scDeepInsight: a supervised cell-type identification method for scRNA-seq data with deep learning. Jia S, Lysenko A, Boroevich KA, Sharma A, Tsunoda T. Brief Bioinform 24: 2023 bbad266	7
Interferon response and profiling of interferon response genes in peripheral blood of vaccine-naive COVID-19 patients. Huang B, Huang J, Chiang NH, Chen Z, Lui G, Ling L, Kwan MYW, Wong JSC, Mak PQ, Ling JWH, Lam ICS, Ng RWY, Wang X, Gao R, Hui DS, Ma SL, Chan PKS, Tang NLS. Front Immunol 14: 2023 1315602	0
Iron dysregulation and inflammatory stress erythropoiesis associates with long-term outcome of COVID-19. Hanson AL, Mulè MP, Ruffieux H, Mescia F, Bergamaschi L, Pelly VS, Turner L, Kotagiri P, Cambridge Institute of Therapeutic Immunology and Infectious Disease–National Institute for Health Research (CITIID–NIHR) COVID BioResource Collaboration, Göttgens B, Hess C, Gleadall N, Bradley JR, Nathan JA, Lyons PA, Drakesmith H, Smith KGC. Nat Immunol 25: 2024 471-482	6
Thinking process templates for constructing data stories with SCDNEY. Cao Y, Tran A, Kim H, Robertson N, Lin Y, Torkel M, Yang P, Patrick E, Ghazanfar S, Yang J. F1000Res 12: 2023 261	0
A unified model for interpretable latent embedding of multi-sample, multi-condition single-cell data. Madrigal A, Lu T, Soto LM, Najafabadi HS. Nat Commun 15: 2024 6573	0
Defining the optimal setting for transcriptomic analyses on blood samples for response prediction in immunotherapy-treated NSCLC patients. Marcos Rubio Á, Oh S, Roelandt S, Stevens D, Van Damme E, Vermaelen K, De Preter K, Everaert C. Sci Rep 14: 2024 26026	0