Gene Expression
Nebulas
Gene Expression NebulasSummary: Growing evidence suggests that conventional dendritic cells (cDCs) undergo aberrant maturation in COVID-19, which negatively affects T-cell activation. The presence of effector T cells in patients with mild disease and dysfunctional T cells in severely ill patients suggests that adequate T-cell responses limit disease severity. Understanding how cDCs cope with SARS-CoV-2 can help elucidate how protective immune responses are generated. Here, we report that cDC2 subtypes exhibit similar infection-induced gene signatures, with the upregulation of IFN-stimulated genes and IL-6 signaling pathways. Furthermore, comparison of cDCs between patients with severe and mild disease showed severely ill patients to exhibit profound downregulation of genes encoding molecules involved in antigen presentation, such as MHCII, TAP, and costimulatory proteins, whereas we observed the opposite for proinflammatory molecules, such as complement and coagulation factors. Thus, as disease severity increases, cDC2s exhibit enhanced inflammatory properties and lose antigen presentation capacity. Moreover, DC3s showed upregulation of anti-apoptotic genes and accumulated during infection. Direct exposure of cDC2s to the virus in vitro recapitulated the activation profile observed in vivo. Our findings suggest that SARS-CoV-2 interacts directly with cDC2s and implements an efficient immune escape mechanism that correlates with disease severity by downregulating crucial molecules required for T-cell activation.
Overall Design: Single-cell RNA sequencing of CD11c+ MHCII+ cells isolated from PBMCs of 3 COVID-19 patients and 2 healthy donors.
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| Growth Protocol: | - |
| Treatment Protocol: | - |
| Extract Protocol: | Myeloid cells were sorted (CD11c+ MHCII+) from 3 COVID-19 patients and 2 healthy donors using a MACSQuant Tyto (Miltenyi). 10,000 cells per sample were loaded on a Chromium Next GEM Chip G (10x Genomics). A Chromium controller (10x Genomics, Pleasanton, CA, USA) was used to generate single-cell GEMs, according to Chromium Next GEM Single Cell 5’ Library & Gel Bead Kit v1.1 protocol (PN-1000165; 10x Genomics). |
| Library Construction Protocol: | Full-length cDNA amplification and 5’ gene expression library construction were performed according to manufacturers’ instructions in a Veriti 96-well Thermal Cycler (Thermo Fisher Scientific). |
| Molecule Type: | polyA(+) RNA |
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| Library Layout: | PAIRED |
| Library Strand: | - |
| Platform: | ILLUMINA |
| Instrument Model: | Illumina NovaSeq 6000 |
| Strand-Specific: | - |
| Data Resource | GEN Sample ID | GEN Dataset ID | Project ID | BioProject ID | Sample ID | Sample Name | BioSample ID | Sample Accession | Experiment Accession | Release Date | Submission Date | Update Date | Species | Race | Ethnicity | Age | Age Unit | Gender | Source Name | Tissue | Cell Type | Cell Subtype | Cell Line | Disease | Disease State | Development Stage | Mutation | Phenotype | Case Detail | Control Detail | Growth Protocol | Treatment Protocol | Extract Protocol | Library Construction Protocol | Molecule Type | Library Layout | Strand-Specific | Library Strand | Spike-In | Strategy | Platform | Instrument Model | Cell Number | Reads Number | Gbases | AvgSpotLen1 | AvgSpotLen2 | Uniq Mapping Rate | Multiple Mapping Rate | Coverage Rate |
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