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

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. For access to high resolution (single channel, composite, or ROI) images please contact the corresponding author or [e-mail]. RNA sequencing data and results for bulk RNA profiling can be accessed in study GSE150316. 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.