GSE162911
A single-cell and spatial atlas of autopsy tissues reveals pathology and cellular targets of SARS-CoV-2 [gene expression levels]
The SARS-CoV-2 pandemic has caused over 1 million deaths globally, mostly due to acute lung injury and acute respiratory distress syndrome, or direct complications resulting in multiple-organ failures. Little is known about the host tissue immune and cellular responses associated with COVID-19 infection, symptoms, and lethality. To address this, we collected tissues from 11 organs during the clinical autopsy of 17 individuals who succumbed to COVID-19, resulting in a tissue bank of approximately 420 specimens. We generated comprehensive cellular maps capturing COVID-19 biology related to patients' demise through single-cell and single-nucleus RNA-Seq of lung, kidney, liver and heart tissues, and further contextualized our findings through spatial RNA profiling of distinct lung regions. We developed a computational framework that incorporates removal of ambient RNA and automated cell type annotation to facilitate comparison with other healthy and diseased tissue atlases. In the lung, we uncovered significantly altered transcriptional programs within the epithelial, immune and stromal compartments and cell intrinsic changes in multiple cell types relative to lung tissue from healthy controls. We observed evidence of alveolar type 2 (AT2) differentiation replacing depleted alveolar type 1 (AT1) lung epithelial cells, as previously seen in fibrosis, and a concomitant increase in myofibroblasts reflective of defective tissue repair. Viral reads were enriched in lung mononuclear phagocytic cells and endothelial cells, and these cells expressed distinct viral RNA host response transcriptional programs. We corroborated the compositional and transcriptional changes in lung tissue through spatial analysis of RNA profiles in situ and distinguished unique tissue host responses between regions with and without viral RNA, and in COVID-19 donor tissues relative to healthy lung. Finally, we analyzed genetic regions implicated in COVID-19 GWAS with transcriptomic data to implicate specific cell types and genes associated with disease severity. Overall, our COVID-19 cell atlas is a foundational dataset to better understand the biological impact of SARS-CoV-2 infection across the human body and empowers the identification of new therapeutic interventions and prevention strategies. Overall design: This dataset contains gene expression levels from ROIs from 9 SARS-CoV-2 infected patient LUL FFPE samples collected during rapid autopsy, and 3 non-infected control parenchyma samples. In addition to this core sample set we report one trachea CTA slide, one heart left ventricle WTA slide, one LUL CTA repeat with different segmentation, one LLL slide and one RUL slide. Up to 26 ROIs were collected within each patient sample, segmented to AOIs according to the descriptions below. In total we report n = 375 AOIs for CTA and n = 409 AOIs for WTA. RNA Scope on serial sections was used to guide ROI selection. Additional sample properties, and mapping to protein data in this super series is reported in sheets of Nanostring_Count_Matrices.xlsx.