Highlights d A hPSC-derived cell and organoid platform is used to study SARS-CoV-2 tissue tropism d Human pancreatic alpha and beta cells are permissive to SARS-CoV-2 infection d Human hepatocyte and cholangiocyte organoids are permissive to SARS-CoV-2 infection d hPSC-derived cells/organoids show similar chemokine responses as COVID-19 tissues

There is an urgent need to create novel models using human disease-relevant cells to study SARS-CoV-2 biology and to facilitate drug screening. As SARS-CoV-2 primarily infects the respiratory tract, we developed a lung organoid model using human pluripotent stem cells (hPSC-LOs). The hPSC-LOs, particularly alveolar type II-like cells, are permissive to SARS-CoV-2 infection, and showed robust induction of chemokines upon SARS-CoV-2 infection, similar to what is seen in COVID-19 patients. Nearly 25% of these patients also have gastrointestinal manifestations, which are associated with worse COVID-19 outcomes 1. We therefore also generated complementary hPSC-derived colonic organoids (hPSC-COs) to explore the response of colonic cells to SARS-CoV-2 infection. We found that multiple colonic cell types, especially enterocytes, express ACE2 and are permissive to SARS-CoV-2 infection. Using hPSC-LOs, we performed a high throughput screen of FDA-approved drugs and identified entry inhibitors of SARS-CoV-2, including imatinib, mycophenolic acid (MPA), and quinacrine dihydrochloride (QNHC). Treatment at physiologically relevant levels of these drugs significantly inhibited SARS-CoV-2 infection of both hPSC-LOs and hPSC-COs. Together, these data demonstrate that hPSC-LOs and hPSC-COs infected by SARS-CoV-2 can serve as disease models to study SARS-CoV-2 infection and provide a valuable resource for drug screening to identify candidate COVID-19 therapeutics. The development of anti-SARS-CoV-2 drugs could change the scope of the ongoing COVID-19 pandemic. While this strategy is being pursued, high throughput screens are typically performed in transformed cell lines which fail to capture the physiologically relevant dynamics of human SARS-CoV-2 infection. To overcome limitations of these cell lines, several adult organoid models have been developed to study SARS-CoV-2 2-4. Here, we developed human pluripotent stem cell-derived lung and colonic organoids (hPSC-LOs and hPSC-COs) optimized as in vitro platforms for high throughput drug screening. hPSC-LOs are permissive to SARS-CoV-2 We differentiated hPSCs to lung organoids (hPSC-LOs) based on previously reported stepwise strategies 5-13 (Extended Data Fig. 1a-1c). qRT-PCR and RNA-seq profiling validates the expression of alveolar type II (AT2) cell markers in the hPSC-LOs (Extended Data Fig. 1d, 1e). Intra-cellular flow cytometry further confirmed the presence of Pro-SP-C + cells in hPSC-LOs (Extended Data Fig. 1f). Single cell transcriptomic profiles of hPSC-LOs identified AT2-like cells, which were enriched for adult human lung AT2 cell markers (Fig. 1a-1c and Extended Data Fig. 2a-2c).

Cells derived from pluripotent sources in vitro must resemble those found in vivo as closely as possible at both transcriptional and functional levels in order to be a useful tool for studying diseases and developing therapeutics. Recently, differentiation of human pluripotent stem cells (hPSCs) into brain microvascular endothelial cells (ECs) with blood–brain barrier (BBB)-like properties has been reported. These cells have since been used as a robust in vitro BBB model for drug delivery and mechanistic understanding of neurological diseases. However, the precise cellular identity of these induced brain microvascular endothelial cells (iBMECs) has not been well described. Employing a comprehensive transcriptomic metaanalysis of previously published hPSC-derived cells validated by physiological assays, we demonstrate that iBMECs lack functional attributes of ECs since they are deficient in vascular lineage genes while expressing clusters of genes related to the neuroectodermal epithelial lineage (Epi-iBMEC). Overexpression of key endothelial ETS transcription factors (ETV2, ERG, and FLI1) reprograms Epi-iBMECs into authentic endothelial cells that are congruent with bona fide endothelium at both transcriptomic as well as some functional levels. This approach could eventually be used to develop a robust human BBB model in vitro that resembles the human brain EC in vivo for functional studies and drug discovery.

ParagraphThe SARS-CoV-2 virus has caused already over 3.5 million COVID-19 cases and 250,000 deaths globally. There is an urgent need to create novel models to study SARS-CoV-2 using human disease-relevant cells to understand key features of virus biology and facilitate drug screening. As primary SARS-CoV-2 infection is respiratory-based, we developed a lung organoid model using human pluripotent stem cells (hPSCs) that could be adapted for drug screens. The lung organoids, particularly aveolar type II cells, express ACE2 and are permissive to SARS-CoV-2 infection.Transcriptomic analysis following SARS-CoV-2 infection revealed a robust induction of chemokines and cytokines with little type I/III interferon signaling, similar to that observed amongst human COVID-19 pulmonary infections. We performed a high throughput screen using hPSC-derived lung organoids and identified FDA-approved drug candidates, including imatinib and mycophenolic acid, as inhibitors of SARS-CoV-2 entry. Pre-or post-treatment with these drugs at physiologically relevant levels decreased SARS-CoV-2 infection of hPSC-derived lung organoids. Together, these data demonstrate that hPSC-derived lung cells infected by SARS-CoV-2 can model human COVID-19 disease and provide a valuable resource to screen for FDAapproved drugs that might be repurposed and should be considered for COVID-19 clinical trials.was not certified by peer review) is the author/funder. All rights reserved. No reuse allowed without permission.

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