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Temporal and Spatial Heterogeneity of Host Response to SARS-CoV-2 Pulmonary Infection [GeoMx human protein]

UID: 10822

Author(s): Desai, Neil B.*, Neyaz, Azfar, Szabolcs, Annamaria, Shih, Angela R., Chen, Jonathan H., Thapar, Vishal, Nieman, Linda T., Solovyov, Alexander*, Mehta, Arnav, Lieb, David J., Kulkarni, Anupriya S., Jaicks, Christopher, Pinto, Christopher J., Juric, Dejan, Chebib, Ivan, Colvin, Robert B., Kim, Arthur Y., Monroe, Robert, Warren, Sarah E., Danaher, Patrick, Reeves, Jason W., Gong, Jingjing, Rueckert, Erroll H., Greenbaum, Benjamin D.*, Hacohen, Nir, Lagana, Stephen M., Rivera, Miguel N., Sholl, Lynette M., Stone, James R., Ting, David T., Deshpande, Vikram * MSK affiliated

Description
Summary from the GEO: "The relationship of SARS-CoV-2 lung infection and severity of pulmonary disease is not fully understood. We analyzed specimens from 24 autopsies from patients who succumbed to SARS-CoV-2 infection using a combination of different RNA and protein analytical platforms to characterize inter- and intra- patient heterogeneity of pulmonary virus infection. There was a spectrum of high and low virus cases that was associated with duration of disease and activation of interferon pathway genes. Using a digital spatial profiling platform, the intra-pulmonary spatial heterogeneity of the virus corresponded to focal expression of interferon response genes and association with immune checkpoint genes
In this dataset, we capture the GeoMx DSP protein profiling work done in conjunction with this study. The files here represent SARS-CoV-2 infected rapid autopsy patients (n = 6) which were profiled with the following nanoString GeoMx protein panels: Immune Cell Profiling Core v1.0, IO Drug Target Module v1.0, Immune Cell Typing Module v1.0, Immune Activation Status Module v1.0, PI3K/AKT Signaling Module v1.0, MAPK Signaling Module v0.9, and Cell Death Module v0.9. These panels were then read out using Nanostring nCounter quantification following standard HybCode panel profiling protocols."

Overall design from the GEO: "This dataset contains expression from localized sampling within 6 SARS-CoV-2 infected patient FFPE samples collected during rapid autopsy, with 3 non-infected control samples. Up to 48 segments were collected within each patient sample. RNA Scope on serial sections was used to guide ROI selection, and ROI ISH staining by RNA Scope is noted in the sample annotations."
Subject of Study
Homo sapiens
Subject(s)
COVID-19
Immune Checkpoint Proteins
Interferons
SARS-CoV-2
Access via GEO

Plain Text files with processed data from the experiment
Accession #: GSE159785

Access via BioProject

Additional information about the overall initiative.
Accession #: PRJNA670568

Access Restrictions
Free to All
Access Instructions
The NCBI Gene Expression Omnibus, SRA, and BioProject databases provide open access to these files. The SRA Run Selector link at the bottom of the page is a processing tool for raw data.
Associated Publications
Desai N, Neyaz A, Szabolcs A, et al. Temporal and spatial heterogeneity of host response to SARS-CoV-2 pulmonary infection. Nature Communications. 2020; 11:6319.
Data Type
Genomic
Equipment Used
NanoString GeoMx Human Protein for nCounter
Software Used
GEO2R

Use GEO2R to compare two or more groups of Samples in order to identify genes that are differentially expressed across experimental conditions. Results are presented as a table of genes ordered by significance.

Dataset Format(s)
Plain Text, TAR
Dataset Size
410 KB
Data Catalog Record Updated
2021-08-09