Gene Expression
Nebulas
Gene Expression NebulasSummary: A dysregulated immune response against the SARS-CoV-2 virus plays a critical role in severe COVID-19. However, the molecular and cellular mechanisms by which the virus causes lethal immunopathology are poorly understood. Here, we utilize multi-omics single-cell analysis to probe dynamic immune responses in patients with stable or progressive manifestations of COVID-19, and assess the effects of tocilizumab, an anti-IL-6 receptor monoclonal antibody. Coordinated profiling of gene expression and cell lineage protein markers reveals a prominent type-1 interferon response across all immune cells, especially in progressive patients. An anti-inflammatory signature in monocytes and a pre-exhaustion phenotype in activated T cells are hallmarks of progressive disease. Single-cell T and B cell receptor repertoire analysis reveal a skewed clonal distribution of CD8 T cells and a primary B cell response with possible contribution from memory B cells. Our in-depth immune profiling reveals dyssynchrony of the innate and adaptive immune interaction in progressive COVID-19, which may contribute to delayed virus clearance and has implications for therapeutic intervention.
Overall Design: 18 PBMC samples from 10 patients at various time points were studied. Age and sex matched healthy subjects (n=13) whose samples were collected before the COVID-19 pandemic were used as controls. Single-cell RNA sequencing (scRNA-seq) was performed, as well as surface protein libraries (CITE-seq), T cell receptor (TCR) libraries and B cell receptor (BCR) libraries. The processed data for the control samples exist solely within the Seurat Rds file. There are no additional metadata or processed data files for the control samples, as there are for the COVID-19 samples.
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| Extract Protocol: | PBMCs were isolated from whole blood using density gradient centrifugation, and immediately cryopreserved. They were later thawed, DMSO was removed, cells were filtered and loaded to the 10x chromium platform |
| Library Construction Protocol: | Libraries were prepared using the 10X Genomics Chromium Next GEM Chip G, according to the manufacturer’s user guide (document number CG000208, revision E, February 2020) |
| 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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