Single-nuclei characterization of pervasive transcriptional signatures across organs in response to COVID-19

Infection by coronavirus SARS-CoV2 is a severe and often deadly disease that has implications for the respiratory system and multiple organs across the human body. While the effects in the lung have been extensively studied, less is known about the impact COVID-19 has across other organs.

Here, a team led by the COVID Tissue Atlas Consortium contribute a single-nuclei RNA-sequencing atlas comprising six human organs across 20 autopsies where they analyzed the transcriptional changes due to COVID-19 in multiple cell types. The integration of data from multiple organs enabled the identification of systemic transcriptional changes.

Computational cross-organ analysis for endothelial cells and macrophages identified systemic transcriptional changes in these cell types in COVID-19 samples. In addition, analysis of gene modules showed enrichment of specific signaling pathways across multiple organs in COVID-19 autopsies.

Altogether, the COVID Tissue Atlas enables the investigation of both cell type-specific and cross-organ transcriptional responses to COVID-19, providing insights into the molecular networks affected by the disease and highlighting novel potential targets for therapies and drug development.

Availability – All data generated or analyzed in this study is available through the COVID Tissue Atlas (CTA) portal website. All code used in this study, including Jupyter notebooks for pre-processing, analysis, and visualization, is available on the CTA GitHub repository