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

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

PROVIDER: PRJNA670568 | ENA |

REPOSITORIES: ENA

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

Project description: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 GeoMxSupport@nanostring.com. RNA sequencing data and results for bulk RNA profiling can be accessed in study GSE150316.

2020-11-01 | GSE159785 | GEO

Temporal and Spatial Heterogeneity of Host Response to SARS-CoV-2 Pulmonary Infection [gene expression]

Project description: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 RNA 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 NanoString GeoMx COVID19 Atlas RNA panel v1.0. This panel was then read out using Illumina sequencing following standard library preparation according to manufacturer protocols. Attached below are low-resolution images of each slide with placement of all ROIs, as well as individual images of each ROI, segments, and UV illuminated IF channels. For access to high resolution (single channel, composite, or ROI) images please contact GeoMxSupport@nanostring.com or the corresponding author of the study. RNA sequencing data and results for bulk RNA profiling can be accessed in study GSE150316.

2020-11-14 | GSE159787 | GEO

Temporal and Spatial Heterogeneity of Host Response to SARS-CoV-2 Pulmonary Infection

Project description:Temporal and Spatial Heterogeneity of Host Response to SARS-CoV-2 Pulmonary Infection

| PRJNA670503 | ENA

Temporal and Spatial Heterogeneity of Host Response to SARS-CoV-2 Pulmonary Infection [gene expression]

Project description:Temporal and Spatial Heterogeneity of Host Response to SARS-CoV-2 Pulmonary Infection [gene expression]

| PRJNA678298 | ENA

Temporal and Spatial Heterogeneity of Host Response to SARS-CoV-2 Pulmonary Infection.

Project description:The relationship of SARS-CoV-2 lung infection and severity of pulmonary disease is not fully understood. We analyzed autopsy specimens from 24 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 virus corresponded to distinct spatial expression of interferon response genes and immune checkpoint genes demonstrating the intra-pulmonary heterogeneity of SARS-CoV-2 infection.

| S-EPMC7402055 | biostudies-literature

Temporal and spatial heterogeneity of host response to SARS-CoV-2 pulmonary infection.

Project description:The relationship of SARS-CoV-2 pulmonary infection and severity of disease is not fully understood. Here we show analysis of autopsy specimens from 24 patients who succumbed to SARS-CoV-2 infection using a combination of different RNA and protein analytical platforms to characterize inter-patient and intra-patient heterogeneity of pulmonary virus infection. There is a spectrum of high and low virus cases associated with duration of disease. High viral cases have high activation of interferon pathway genes and a predominant M1-like macrophage infiltrate. Low viral cases are more heterogeneous likely reflecting inherent patient differences in the evolution of host response, but there is consistent indication of pulmonary epithelial cell recovery based on napsin A immunohistochemistry and RNA expression of surfactant and mucin genes. Using a digital spatial profiling platform, we find the virus corresponds to distinct spatial expression of interferon response genes demonstrating the intra-pulmonary heterogeneity of SARS-CoV-2 infection.

| S-EPMC7725958 | biostudies-literature

Temporal and Spatial Heterogeneity of Host Response to SARS-CoV-2 Pulmonary Infection

Project description:This SuperSeries is composed of the SubSeries listed below.

2020-11-01 | GSE159788 | GEO

Spatially resolved transcriptomic profiling: an experimental comparison of GeoMx Digital Spatial Profiling and Visium CytAssist spatial transcriptomics in three cancer types (GeoMx)

Project description:We performed Visium CytAssist (10X), GeoMx DSP (Nanostring) and Chromium Flex (10X Genomics) full transcriptome profiling on Breast Cancer (BC), Lung Cancer (LC) and diffuse large B cell lymphoma (DLBCL) samples from archival FFPE blocks. We explore the data quality across blocks with different storage times and DV200 values for all the three methods. We compared the cell type signature purity between ST methods Visium and GeoMx by utilising pathology annotations and scRNAseq. For the Visium and Chromium methods with a large number of data points we explored the heterogeneity between tissues. Finally, we demonstrate the discovery of patient-specific tumor-TME interactions across all three methods.

2024-11-01 | E-MTAB-14566 | biostudies-arrayexpress

GeoMX spatial transcriptomic on biphasic Malignant Pleural Mesothelioma

Project description:We applied a spatially resolved, high-dimensional transcriptomic approach to study MPM morpho-logical evolution. 139 regions across 8 biphasic MPMs (B-MPMs) were profiled using the GeoMx™Digital Spatial Profiler and Cancer Transcriptome Atlas to compare epithelioid and sarcomatoid components transcriptional profile and reconstruct the positional context of transcriptional activities and the spatial topology of MPM cells interactions.

2023-12-07 | E-MTAB-13043 | biostudies-arrayexpress

Spatial transcriptomics of in vivo invasive trancheobronchitis biopsies obtained from patients with influenza-associated pulmonary aspergillosis or COVID-19-associated pulmonary aspergillosis

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