An Airway Organoid-Based Screen Identifies a Role for the HIF1α-Glycolysis Axis in SARS-CoV-2 Infection

SARS-CoV-2 causes the COVID-19 pandemic. It is urgent to develop disease models to dissect mechanisms regulating SARS-CoV-2 infection. Here, we derive airway organoids from human pluripotent stem cells (hPSC-AOs). The hPSC-AOs, particularly ciliated-like cells, are permissive to SARS-CoV-2 infection. Using this platform, we perform a high content screen and identify GW6471, which blocks SARS-CoV-2 infection. GW6471 can also block infection of the B.1.351 SARS-CoV-2 variant. RNA-seq analysis suggests that GW6471 blocks SARS-CoV-2 infection at least in part by inhibiting HIF1α, which is further validated by chemical inhibitor and genetic perturbation targeting HIF1α. Metabolic profiling identifies decreased rates of glycolysis upon GW6471 treatment, consistent with transcriptome profiling. Finally, xanthohumol, 5-(Tetradecyloxy)-2-furoic acid, and ND-646, three compounds that suppress fatty acid biosynthesis, also block SARS-CoV-2 infection. Together, a high content screen coupled with transcriptome and metabolic profiling reveals a key role of the HIF1α-glycolysis axis in mediating SARS-CoV-2 infection of human airway epithelium.

严重急性呼吸综合征冠状病毒2型（SARS-CoV-2）引发了新型冠状病毒肺炎（COVID-19）大流行。亟需开发疾病模型以解析调控SARS-CoV-2感染的分子机制。本研究中，我们从人类多能干细胞（human pluripotent stem cells）中制备得到气道类器官（airway organoids，以下简称hPSC-AOs）。该类器官，尤其是类纤毛细胞，对SARS-CoV-2感染具有易感性。依托该平台，我们开展了高内涵筛选（high content screen），鉴定出可阻断SARS-CoV-2感染的化合物GW6471。GW6471同时可阻断B.1.351型SARS-CoV-2变异株的感染。RNA测序（RNA-seq）分析显示，GW6471至少可通过抑制缺氧诱导因子1α（HIF1α）阻断SARS-CoV-2感染，该结论通过靶向HIF1α的化学抑制剂及基因扰动实验得到了进一步验证。代谢组学分析（metabolic profiling）显示，经GW6471处理后细胞的糖酵解（glycolysis）速率显著降低，这与转录组学分析（transcriptome profiling）结果一致。最后，黄腐酚（xanthohumol）、5-十四烷氧基-2-呋喃甲酸（5-(Tetradecyloxy)-2-furoic acid）以及ND-646这三种可抑制脂肪酸生物合成（fatty acid biosynthesis）的化合物，同样可阻断SARS-CoV-2感染。综上，本研究通过高内涵筛选结合转录组学与代谢组学分析，揭示了HIF1α-糖酵解轴在介导SARS-CoV-2感染人类气道上皮细胞过程中的关键作用。