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| Status |
Public on Feb 17, 2022 |
| Title |
Identification of distinct immune cell subsets associated with various clinical presentations, disease severity and viral persistence of SARS-CoV-2 infection |
| Organism |
Homo sapiens |
| Experiment type |
Expression profiling by high throughput sequencing
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| Summary |
The clinical presentations and outcomes of SARS-CoV-2 infection are highly variable, ranging from asymptomatic infections to severe conditions, and the underlying mechanisms remain largely unknown. In this study, we performed the single-cell RNA sequencing to examine the profiles of the peripheral blood mononuclear cells (PBMCs) from the healthy controls (HC), asymptomatic individuals (AS) and symptomatic COVID-19 patients (SM) with various clinical features and disease severity. We first identified nine major cell types, including T cells, B cells, monocytes, natural killer (NK) cells, dendritic cells (DC), platelets, neutrophils, plasma cells and stem cells from a total of 119,799 single cells captured and filtered for the final analysis, and then divided these cell types into separate cell clusters and sub-clusters, respectively. We revealed that SARS-CoV-2 infection resulted in profound alternations in various cellular compartments and identified a number of distinct immune cell subsets that were associated with various clinical presentations, disease severity and viral persistence of COVID-19. (NCAM1+CD160+) NK cells increased significantly in AS and SM individuals compared with the HC. SM patients showed a significant increase in (LAG3+CD160+CD8+) NKT cells and a decrease in (CD4-CD8-) double negative T cells compared with the AS subjects. (CD68-CSF1R-IL1BhiCD14+) classical monocytes were significantly higher in patients with severe disease (SD) than the patients with moderate disease (MD). (CD68-CSF1R-IL1BhiCD14+) classical monocytes and (CLEC10A-S100A9lo)pDC were positively and negatively correlated with the age-related disease severity of COVID-19 patients, respectively. Increases in (CD33-HLA-DMA-CD14+) classical monocytes and (CLEC10A-S100A9lo)pDC were associated with long-term nucleic acid test positive (LTNP) patients compared with the short-term nucleic acid test positive (STNP) individuals. Increases in (LAG3+CD160+CD8+) NKTcells and (FOXP3+IL2RA+IL7R+CD4+) Treg cells were observed in a patient lacking B cells and plasma cells. Dramatic increases in neutrophils, (CD33-HLA-DMA-CD14+) classical monocytes, and (CD68-CSF1R-IL1BhiCD14+) classical monocytes were detected at a later stage of a fatal patient. Our findings may enhance our understanding of the immune cell alternations involved in the pathogenesis of COVID-19 and the protective immune responses against SARS-CoV-2 infection.
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| Overall design |
53 peripheral blood mono-nuclear cell (PBMC) samples including 42 COVID-19 patients derived samples and 11 healthy controls (HCs) derived samples
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| Contributor(s) |
Zhang C |
| Citation(s) |
35281000, 35716403, 36055412 |
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https://doi.org/10.1016/j.bcmd.2022.102678
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| Submission date |
Jan 19, 2021 |
| Last update date |
Sep 15, 2022 |
| Contact name |
chengsheng zhang |
| E-mail(s) |
cszhang99@126.com
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| Organization name |
First Affiliated Hospital of Xi 'an Jiaotong University
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| Department |
precision medicine center
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| Street address |
277 West Yanta Road, Xi'an, Shaanxi, P.R.China
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| City |
Xian |
| State/province |
Shaanxi |
| ZIP/Postal code |
710061 |
| Country |
China |
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| Platforms (1) |
| GPL24676 |
Illumina NovaSeq 6000 (Homo sapiens) |
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| Samples (53)
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| Relations |
| BioProject |
PRJNA693201 |
| SRA |
SRP302338 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE165080_barcodes.tsv.gz |
910.7 Kb |
(ftp)(http) |
TSV |
| GSE165080_cell_batch.tsv.gz |
1.0 Mb |
(ftp)(http) |
TSV |
| GSE165080_genes.tsv.gz |
445.8 Kb |
(ftp)(http) |
TSV |
| GSE165080_matrix.mtx.gz |
1.0 Gb |
(ftp)(http) |
MTX |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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