Gene Expression
Nebulas
Gene Expression NebulasSummary: mRNA-1273, an mRNA-based vaccine for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), is efficacious in mouse and non-human primate models of mild COVID-19. Hamsters exhibit more severe clinical disease from SARS-CoV-2, making it an important model to evaluate vaccine efficacy. Here we show that mock-vaccine treated hamsters infected with SARS-CoV-2 show weight loss and pulmonary infection with pathological changes and increased activated interstitial macrophages and other immune cell types. Prime-boost administration of mRNA-1273 elicited dose-independent robust binding and neutralizing antibodies, ameliorated weight loss and suppressed virus replication in the upper and lower airways. Vaccination largely prevented pulmonary pathological changes, antiviral immune cell activation and changes in cell type composition although increases in some immune cell types and activation of regulatory pathways were found and coincided with an anamnestic antibody response. The results characterize unexpected pulmonary cellular responses to SARS-CoV-2 in vaccinated animals that were shared but greatly attenuated, when compared to mock-vaccinated animals. The efficacy of mRNA-1273 is demonstrated as a two-dose vaccination schedule in a model of severe COVID-19.
Overall Design: Single cell RNA sequencing was conducted on fourteen samples of the Syrian golden hamster lung tissue. Samples were from naïve, mock-vaccinated + SARS-CoV-2 infected, and mRNA-1273 vaccinated + SARS-CoV-2 infected hamsters.
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| Growth Protocol: | - |
| Treatment Protocol: | - |
| Extract Protocol: | The cranial left lung sections taken at the time of necropsy at 4 dpi from the 5 µg prime-boost group (VI, n=5), mock vaccinated group (MI, n=5) and a naïve group (N, n=4) of hamsters that were mock infected via the IN route with 100 µL of media inoculum. Lung samples were enzymatically digested and homogenized using the Lung Dissociation kit, mouse (Miltenyi Biotec Cat No. 130-095-927) and GentleMACS Dissociator (Miltenyi Biotec) according to the manufacturers protocol. After 30 min of digestion, the samples were filtered through a 70 µM filter, and RBC lysis was performed (ThermoFisher, MA, Cat #00-4333-57). After two washes in PBS containing 0.05 mM EDTA, the cell pellet was re-suspended in 1ml of buffer and filtered through a 40 µM Flowmi Cell strainer (Bel-Art # H13680-0040). The cell viability and concentration were determined on a TC20 cell counter (Bio-Rad, CA). Dead cell removal was performed if the viability was lower than 80% using Dead Cell Removal Kit (Miltenyi Biotec, CA, Cat#130-090-101) as per manufacturers recommendations. |
| Library Construction Protocol: | Seven thousand cells were targeted for generation of barcoded gel bead emulsions using the Chromium Single Cell 3’ version 3.0 chemistry (10x Genomics, CA, Cat# 1000077). After reverse transcription, the cDNA was amplified and purified using SPRISelect magnetic beads (Beckman Coulter, CA, Cat#B23317). The purified cDNA was precipitated in 80% ethanol, removed from BSL-4 containment, tested for quality on Bioanalyzer, and 3’ gene expression libraries were prepared as per manufacturer’s instructions. Libraries were quantified, and pooled libraries were submitted for sequencing (~140,000 reads per sample) on Novaseq S1 Flow cell (New York Genome Center). |
| 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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