Genomic Medicine Institute, Lerner Research Institute, Cleveland Clinic, Cleveland, OH, USA.
Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, NY, USA.
Nat Biotechnol. 2023 Jan;41(1):128-139. doi: 10.1038/s41587-022-01474-0. Epub 2022 Oct 10.
Studying viral-host protein-protein interactions can facilitate the discovery of therapies for viral infection. We use high-throughput yeast two-hybrid experiments and mass spectrometry to generate a comprehensive SARS-CoV-2-human protein-protein interactome network consisting of 739 high-confidence binary and co-complex interactions, validating 218 known SARS-CoV-2 host factors and revealing 361 novel ones. Our results show the highest overlap of interaction partners between published datasets and of genes differentially expressed in samples from COVID-19 patients. We identify an interaction between the viral protein ORF3a and the human transcription factor ZNF579, illustrating a direct viral impact on host transcription. We perform network-based screens of >2,900 FDA-approved or investigational drugs and identify 23 with significant network proximity to SARS-CoV-2 host factors. One of these drugs, carvedilol, shows clinical benefits for COVID-19 patients in an electronic health records analysis and antiviral properties in a human lung cell line infected with SARS-CoV-2. Our study demonstrates the value of network systems biology to understand human-virus interactions and provides hits for further research on COVID-19 therapeutics.
研究病毒-宿主蛋白-蛋白相互作用可以促进发现治疗病毒感染的方法。我们使用高通量酵母双杂交实验和质谱技术,生成了一个由 739 个高可信度二元和共复合物相互作用组成的全面的 SARS-CoV-2-人类蛋白质相互作用网络,验证了 218 个已知的 SARS-CoV-2 宿主因子,并揭示了 361 个新的宿主因子。我们的结果显示,与已发表的数据集相比,我们的交互作用伙伴的重叠率最高,与 COVID-19 患者样本中差异表达的基因的重叠率也最高。我们发现了病毒蛋白 ORF3a 与人类转录因子 ZNF579 之间的相互作用,这表明病毒对宿主转录有直接影响。我们对超过 2900 种 FDA 批准或正在研究的药物进行了基于网络的筛选,发现其中 23 种与 SARS-CoV-2 宿主因子具有显著的网络接近性。这些药物中的一种,卡维地洛,在电子健康记录分析中对 COVID-19 患者具有临床益处,并在感染 SARS-CoV-2 的人肺细胞系中具有抗病毒特性。我们的研究表明网络系统生物学在理解人类-病毒相互作用方面的价值,并为 COVID-19 治疗的进一步研究提供了线索。