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Gene expression data of alveolosphere/airway organoid and alveolosphere with SARS-CoV-2 or mock infection

ABSTRACT: Although the main cellular target of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection is thought to be alveolar cells, the absence of their tractable culture system has precluded the development of a clinically-relevant SARS-CoV-2 infection model. Here, we established an efficient human alveolosphere culture method and sphere-based drug testing platform for SARS-CoV-2. Alveolospheres exhibited indolent growth in a Wnt and R-spondin dependent manner. Gene expression, immunofluorescence and electron microscopy analyses revealed the presence of alveolar cells in alveolospheres. Alveolospheres expressed ACE2 and allowed SARS-CoV-2 to propagate nearly 100,000- fold in three days of infection. While lopinavir and nelfinavir, protease inhibitors used for the treatment of HIV infection, had a modest anti-viral effect on SARS-CoV-2, remdesivir, a nucleotide prodrug, showed anti-viral effect at the concentration comparable to the circulating drug level. These results demonstrated the validity of alveolosphere culture system for the development of therapeutic agents to combat SARS-CoV-2.

ORGANISM(S): Homo sapiens

PROVIDER: GSE171430 | GEO | 2021/05/17

REPOSITORIES: GEO

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Project description:The coronavirus disease 2019 (COVID-19) pandemic has affected nearly 700 million and claimed more than 6 million lives. However, the large heterogeneity in disease susceptibility and severity of illness (SOI) remains poorly understood. A growing body of evidence suggests that alveolar epithelial cell type 2 (AT2), which constitute 10-15% of all alveolar cells and are critical for alveolar homeostasis, are the primary targets of severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) infection and damage to AT2s may directly contribute to disease severity and poor prognosis in COVID-19 patients. Our in-vitro modeling of SARS-CoV-2 infection, in well-characterized, highly uniform, (r2 at 95% CI = 0.92 ± 0.03), induced pluripotent stem cell (iPSC) derived AT2s from 10 participants of our Mexican American Family Study, showed interindividual variability in infection susceptibility and the post-infection cellular viral load. To understand the underlying mechanism of the AT2’s capacity to regulate SARS-CoV-2 infection and cellular viral load, we performed a systematic characterization of the pre- and post-SARS-CoV-2 challenged AT2 transcriptomes. A total of 1,393 genes were found significantly (Oneway ANOVA FDR corrected p ≤ 0.05; FC abs ≥ 2.0) differentially expressed (DE) between pre- and post-SARS-CoV-2 infection-challenged AT2 and suggest significant upregulation of viral infection-related cellular innate immune response pathways (p-value ≤ 0.05; activation z-score ≥ 3.5), whilst the cholesterol and xenobiotic related metabolic pathways were significantly downregulated (p-value ≤ 0.05; activation z-score ≤ - 3.5). Interestingly, pre-infection expression of 238 DE genes showed a high correlation with the post-infection SARS-CoV-2 viral load (FDR corrected p-value ≤ 0.05, and r2-absolute ≥ 0.57). The 85 genes whose expression was negatively correlated with the viral load showed significant enrichment in viral recognition and cytokine-mediated innate immune GO biological processes (p-value range: 4.65x10-10 to 2.24x10-6). The 153 genes whose expression was positively correlated with the viral load showed significant enrichment in cholesterol homeostasis, extracellular matrix, and MAPK/ERK pathway-related GO biological processes (p-value range: 5.06x10-5 to 6.53x10-4). Overall, our results strongly suggest that AT2s pre-infection innate immunity and metabolic state affects their susceptibility to SARS-CoV-2 infection and viral load.

Dataset Information

Gene expression data of alveolosphere/airway organoid and alveolosphere with SARS-CoV-2 or mock infection

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