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

UID: 10742

Author(s): Chen, Shuibing, Tang, Xuming, Uhl, Skyler

Description
Summary from the GEO: "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."

Overall design from the GEO: "Human islets were infected with SARS-CoV-2 and analyzed using scRNA-seq"
Subject of Study
Homo sapiens
Subject(s)
Chemokines
COVID-19
Eukaryotic Initiation Factor-2
Islets of Langerhans
Access via GEO

MTX and TSV files of expression profiling by high throughput sequencing
Accession #: GSE159556

Access via SRA

RNA sequencing of 5 samples.
Accession #: SRP287500

Access via BioProject

Additional information about the overall inititative.
Accession #: PRJNA669693

Access Restrictions
Free to All
Access Instructions
The NCBI Gene Expression Omnibus, SRA and BioProject databases provide open access to these files. SRA and/or tar files can be downloaded directly from the site or viewed in the NCBI SRA Run Selector (link at bottom of page).
Associated Publications
Tang X, Uhl S, Zhang T, et al. SARS-CoV-2 infection induces beta cell transdifferentiation [published online ahead of print, 2021 May 19]. Cell Metab. 2021;S1550-4131(21)00232-1.
Data Type
Genomic
Equipment Used
Illumina NovaSeq 6000
Software Used
SRA Toolkit

The NCBI SRA Toolkit enables reading ("dumping") of sequencing files from the SRA database and writing ("loading") files into the .sra format.

Dataset Format(s)
TSV, SRA, TAR, MTX
Data Tool(s)
scRNA Seq
Dataset Size
272.9 MB (TAR of MTX, TSV), 41.3 Gb (SRA)
Data Catalog Record Updated
2023-12-07