hPSC-derived Airway Organoids-based Screen Reveals the Role of HIF1/Glycolysis Axis in SARS-CoV-2 Infection [bulk RNA-seq]

SARS-CoV-2, the virus causing recently pandemic, primarily infects the respiratory tract. There is an urgent need to develop platforms using disease relevant human cells to dissect the molecular mechanism regulating SARS-CoV-2 infection and perform drug screen. Here, we derived airway organoids from human pluripotent stem cells (hPSC-AO). The hPSC-AOs, particularly ciliated cells, express ACE2 and are permissive to SARS-CoV-2 infection. Using hPSC-AOs, we performed a high content screen and identified GW6471, which blocks SARS-CoV-2 infection. RNA-seq analysis suggested that GW6471 blocking SARS-CoV-2 infection by inhibiting HIF1α, which is further validated by chemotin, another HIF1α inhibitor. Furthermore, metabolic profiling identified that the downregulation of glycolysis upon GW6471 treatment, which is further validated by RNA-seq. Finally, xanthohumol, a prenylated flavonoid suppressing fatty acid and cholesterol biosynthesis, blocks SARS-CoV-2 infection. Together, we applied the high content screen, RNA-seq and metabolic profiling to define the key role of HIF1α-glycolysis axis in SARS-CoV-2 infection, which provides a target pathway for anti-viral drug development. HPSCs derived airway organoids (AOs) or colonic organoids (COs) were treated with control or 10 uM GW6471 in the presence of SARS-CoV-2 infection.

严重急性呼吸综合征冠状病毒2型（SARS-CoV-2）是引发近期全球大流行的病毒，主要感染呼吸道。目前亟需构建基于疾病相关人类细胞的研究平台，以解析调控SARS-CoV-2感染的分子机制并开展药物筛选。在此，我们从人类多能干细胞（human pluripotent stem cells, hPSC）中诱导得到气道类器官（hPSC-AO）。该hPSC来源的气道类器官，尤其是纤毛细胞，可表达血管紧张素转换酶2（ACE2），并对SARS-CoV-2感染具有易感性。利用该气道类器官，我们开展了高内涵筛选，鉴定出可阻断SARS-CoV-2感染的GW6471。RNA测序（RNA-seq）分析表明，GW6471通过抑制缺氧诱导因子1α（HIF1α）发挥阻断病毒感染的作用，该结论可通过另一款HIF1α抑制剂chemotin得到验证。此外，代谢组学分析发现，经GW6471处理后糖酵解通路被下调，该结果亦通过RNA-seq得到验证。最后，黄腐酚（xanthohumol）——一种可抑制脂肪酸与胆固醇生物合成的异戊烯基黄酮类化合物——同样可阻断SARS-CoV-2感染。综上，我们结合高内涵筛选、RNA测序及代谢组学分析，明确了HIF1α-糖酵解轴在SARS-CoV-2感染中的关键作用，该发现可为抗病毒药物研发提供靶标通路。本研究中，将人类多能干细胞来源的气道类器官（AOs）或结肠类器官（COs）在SARS-CoV-2感染条件下，分别以对照试剂或10 μM GW6471进行处理。