Gene Expression
Nebulas
Gene Expression NebulasSummary: Study show that modified vaccinia Ankara (MVA)-based COVID-19 vaccine expressing membrane anchored pre-fusion stabilized spike (MVA/S) induces both neutralizing antibodies and CD8+ T cells in the blood and lung and protects from SARS-CoV-2 challenge. Single-cell RNA sequencing analysis of lung cells at day 4 post-infection revealed that MVA/S vaccination also protected macaques from infection-induced inflammation and B cell abnormalities, and lowered induction of interferon stimulated genes.
Overall Design: To test the immunogenicity and protective ability of the MVA/S vaccine, the researchers immunized rhesus macaques (n=5/group) either with MVA/S vaccine or MVA/Wt vaccine delivered intramuscularly on weeks 0 and 4. At week 8 (4 weeks after the boost) animals were challenged intranasally and intratracheally with live SARS-CoV-2 virus. To understand MVA/S vaccine offered inflammatory sequelae in the airway, the researchers performed single-cell RNA-Seq on the cellular fraction recovered from BAL at Day 4 after infection. This analysis shows MVA/S vaccination reduces transcripts associated with inflammation and hyperimmune activation in lung macrophages.
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| Growth Protocol: | Bronchoalveolar lavage (BAL), Day 4 Post SARS-CoV-2 challenge |
| Treatment Protocol: | Single cell suspensions from BAL at Day 4 after SARS-CoV-2 infection were collected from MVA/S vaccinated (n=4), and MVA/Wt control (n=5) macaques and were subjected to single cell RNA sequencing. These analyses were performed only once since the macaque study was done only once. |
| Extract Protocol: | Physiological saline, up to 50 ml was delivered through trachea to the lungs of anesthetized animals using a camera enabled fiberoptic bronchoscope. The flushed saline was re-aspirated 5 times before pulling out the bronchoscope. This collection was filtered through 70μm cell strainer and centrifuged at 2200 rpm for 5 minutes. Pelleted cells were suspended in 1ml R10 medium (RPMI(1X) and counted. |
| Library Construction Protocol: | BAL samples from 5 monkeys in each group were pooled together and two technical replicate 10X captures were performed. One replicate capture failed for the control group. The libraries were run on Nova Seq 6000 lanes and the resultant bcl files were converted to count matrices using Cell Ranger v3.1 |
| Molecule Type: | Poly(A)+ 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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