GSE159556: scRNA-seq analysis of SARS-CoV-2 infected human islets

scRNA-seq Viewer
Info Studies were incorporated in a barcode, matrix, feature format. This format can be found on the 10x Genomics website for processing of single cell studies to obtain the gene expression matrices. For each study, the metadata incorporated in GEO were manually curated into profiles and the samples were separated based on applicable groups and conditions. The expression data from the cells for the samples within the same profile and condition were aggregated into an expression matrix with the cell barcodes having the sample name appended to it to ensure unique cell names.

Description (from GEO)

Submission Date: Oct 19, 2020

Summary: Recent clinical data has suggestedsed a bi-directional relationship between Coronavirus disease 19 (COVID-19) and diabetes. Here, we showdemonstrateed the detection of SARS-CoV-2 in pancreatic endocrine cells in autopsy samples derived fromof COVID-19 patients. Single cell RNA-seq and immunostaining confirmed that multiple types of pancreatic islet cells can be infected byare susceptible to SARS-CoV-2, eliciting a cellular stress response and the induction of chemokines. SARS-CoV-2 infection causes the increase of chemokine response, cell stress, and interferon signal. Upon SARS-CoV-2 infection, beta cells show a the decreased expression of insulin and the increased expression of alpha and acinar cell markers, including glucagon and , and acinar cell markers, including PRSS1/trypsin1, respectfully, suggesting which suggests that infected beta cells undergocellular dedifferentiation. This was furtherCorroboration of these findings could be further validated using theinex vivo using single cell sequencing of pancreatic tissue from autopsy of COVID-19 patients autopsies. Trajectory analysis identifiedindicated that the EIF2 pathway that changess along withmediates beta cell dedifferentiation. Furthermore, a, and a high content screen identified trans-integrated stress response inhibitor (trans-ISRIB) that as decreasinges poly-hormonal cells. Finally, trans-ISRIB treatmentwhich rescueds beta cell dedifferentiation upon SARS-CoV-2 exposure. Together, it, suggestings that SARS-CoV-2 infection causes EIF2 pathway-mediated beta cell dedifferentiation. Altogether, tThis study provides a potential mechanism of new onset diabetes in upon the development of COVID-19.

GEO Accession ID: GSE159556

PMID: 34081913

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Info Preprocessing and downstream analysis were computed using the scanpy Python library and the steps of processing followed the Seurat vignette. Cells and genes with no expression or very low expression were removed from the dataset based on a predefined threshold. The data was then normalized across the expression within the cells and log normalized. The top 2000 highly variable genes were extracted to be used for downstream analysis. For each of these aggregated data matrices, the clusters were computed using the leiden algorithm. Scanpy was then used to compute the PCA, t-SNE, and UMAPs. The points in the plots are labelled by their corresponding cell type labels. The cell type labels were computed using the wilcoxon method as the differential gene expression method. The top 250 genes were then used for enrichment analysis against the CellMarker library in order to determine the most appropriate cell type label with the lowest p-value.
PCA, tSNE, and UMAP Visualizations Labeled by Cell Types:
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Differential Gene Expression Analysis
Info Differential gene expression can be computed for a single cell type labeled group of cells vs the rest. These include wilcoxon, DESeq2, or characteristic direction.
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