COVID-19 is a systemic disease involving multiple organs. We previously established a platform to derive organoids and cells from human pluripotent stem cells to model SARS-CoV-2 infection and perform drug screens^1,2. This provided insight into cellular tropism and the host response, yet the molecular mechanisms regulating SARS-CoV-2 infection remain poorly defined. Here we systematically examined changes in transcript profiles caused by SARS-CoV-2 infection at different multiplicities of infection for lung airway organoids, lung alveolar organoids and cardiomyocytes, and identified several genes that are generally implicated in controlling SARS-CoV-2 infection, including CIART, the circadian-associated repressor of transcription. Lung airway organoids, lung alveolar organoids and cardiomyocytes derived from isogenic CIART^−/− human pluripotent stem cells were significantly resistant to SARS-CoV-2 infection, independently of viral entry. Single-cell RNA-sequencing analysis further validated the decreased levels of SARS-CoV-2 infection in ciliated-like cells of lung airway organoids. CUT&RUN, ATAC-seq and RNA-sequencing analyses showed that CIART controls SARS-CoV-2 infection at least in part through the regulation of NR4A1, a gene also identified from the multi-organoid analysis. Finally, transcriptional profiling and pharmacological inhibition led to the discovery that the Retinoid X Receptor pathway regulates SARS-CoV-2 infection downstream of CIART and NR4A1. The multi-organoid platform identified the role of circadian-clock regulation in SARS-CoV-2 infection, which provides potential therapeutic targets for protection against COVID-19 across organ systems.

COVID-19 是一种涉及多个器官的全身性疾病。我们之前建立了一个平台，从人类多能干细胞中提取类器官和细胞，以模拟 SARS-CoV-2 感染并进行药物筛选^1,2。这提供了对细胞嗜性和宿主反应的深入了解，但调节 SARS-CoV-2 感染的分子机制仍不清楚。在这里，我们系统地检查了肺气道类器官、肺泡类器官和心肌细胞在不同感染复数下由 SARS-CoV-2 感染引起的转录谱变化，并确定了几个通常与控制 SARS-CoV-2 感染有关的基因，包括CIART，与昼夜节律相关的转录抑制因子。源自同基因CIART ^-/-人多能干细胞的肺气道类器官、肺泡类器官和心肌细胞对 SARS-CoV-2 感染具有显着抵抗力，与病毒进入无关。单细胞 RNA 测序分析进一步证实了肺气道类器官纤毛样细胞中 SARS-CoV-2 感染水平的降低。CUT&RUN、ATAC-seq 和 RNA 测序分析表明，CIART至少部分通过调节NR4A1来控制 SARS-CoV-2 感染, 一个基因也从多类器官分析中鉴定出来。最后，转录谱分析和药理学抑制导致发现维甲酸 X 受体通路调节 CIART 和 NR4A1 下游的 SARS-CoV-2 感染。多类器官平台确定了生物钟调节在 SARS-CoV-2 感染中的作用，这为跨器官系统预防 COVID-19 提供了潜在的治疗靶点。