Bulk RNA sequencing of SARS-CoV-2 infected alveolar type I- and type II like cells

Bulk RNA sequencing was performed on control and SARS-CoV-2 infected 2D bronchioalveolar-like and small airway cultures Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), which causes coronavirus disease 2019 (COVID-19), may result in acute respiratory distress syndrome (ARDS), multi-organ failure and death. The alveolar epithelium is a major target of the virus, but representative models to study virus host interactions in more detail are currently lacking. Here, we describe a human 2D air-liquid interphase culture system which was characterized by confocal-, electron-microscopy and mRNA expression analysis. In this model, alveolar type I- (ATI-L) and type II-like (ATII-L) cells, but also basal cells, neuroendocrine cells and club cells, are grown from 3D self-renewing lung bud tip organoids. These cultures were readily infected by SARS-CoV-2 with both ATI-L and ATII-L cells being targeted. Consequently, significant viral titers were detected and mRNA expression analysis revealed induction of a type I/III interferon response program. Hence, these cultures represent an experimental model for SARS-CoV-2 infection and can be applied for drug screens. Overall design: RNA was extracted from 2D pulmonary cultures that were either grown in expansion conditions (EXP) or differentiation conditions (DIF) and were not treated or SARS-CoV-2 for 72 hours. After this, RNA was collected.