Table_5_A Network-Based Analysis Reveals the Mechanism Underlying Vitamin D in Suppressing Cytokine Storm and Virus in SARS-CoV-2 Infection.xlsx

BackgroundSARS-CoV-2 causes ongoing pandemic coronavirus disease of 2019 (COVID-19), infects the cells of the lower respiratory tract that leads to a cytokine storm in a significant number of patients resulting in severe pneumonia, shortness of breathing, respiratory and organ failure. Extensive studies suggested the role of Vitamin D in suppressing cytokine storm in COVID-19 and reducing viral infection; however, the precise molecular mechanism is not clearly known. In this work, bioinformatics and systems biology approaches were used to understand SARS-CoV-2 induced cytokine pathways and the potential mechanism of Vitamin D in suppressing cytokine storm and enhancing antiviral response.
ResultsThis study used transcriptome data and identified 108 differentially expressed host genes (DEHGs) in SARS-CoV-2 infected normal human bronchial epithelial (NHBE) cells compared to control. Then, the DEHGs was integrated with the human protein-protein interaction data to generate a SARS-CoV-2 induced host gene regulatory network (SiHgrn). Analysis of SiHgrn identified a sub-network “Cluster 1” with the highest MCODE score, 31 up-regulated genes, and predominantly associated immune and inflammatory response. Interestingly, the iRegulone tool identified that “Cluster 1” is under the regulation of transcription factors STAT1, STAT2, STAT3, POU2F2, and NFkB1, collectively referred to as “host response signature network”. Functional enrichment analysis with NDEx revealed that the “host response signature network” is predominantly associated with critical pathways, including “cytokines and inflammatory response”, “non-genomic action of Vitamin D”, “the human immune response to tuberculosis”, and “lung fibrosis”. Finally, in-depth analysis and literature mining revealed that Vitamin D binds with its receptor and could work through two different pathways: (i) it inhibits the expression of pro-inflammatory cytokines through blocking the TNF induced NFkB1 signaling pathway; and (ii) it initiates the expression of interferon-stimulating genes (ISGs) for antiviral defense program through activating the IFN-α induced Jak-STAT signaling pathway.
ConclusionThis comprehensive study identified the pathways associated with cytokine storm in SARS-CoV-2 infection. The proposed underlying mechanism of Vitamin D could be promising in suppressing the cytokine storm and inducing a robust antiviral response in severe COVID-19 patients. The finding in this study urgently needs further experimental validations for the suitability of Vitamin D in combination with IFN-α to control severe COVID-19.

研究背景：新型冠状病毒（SARS-CoV-2）引发了持续大流行的2019冠状病毒病（COVID-19），该病毒会侵染人体下呼吸道细胞，在大量患者体内引发细胞因子风暴，进而导致重症肺炎、呼吸困难、呼吸衰竭及多器官功能衰竭。既往大量研究表明，维生素D（Vitamin D）可抑制COVID-19患者体内的细胞因子风暴并减轻病毒感染，但具体的分子机制尚未明确。本研究采用生物信息学与系统生物学方法，解析SARS-CoV-2感染引发的细胞因子通路，以及维生素D抑制细胞因子风暴、增强抗病毒应答的潜在分子机制。
研究结果：本研究通过转录组数据分析，在感染SARS-CoV-2的正常人支气管上皮（normal human bronchial epithelial, NHBE）细胞中筛选得到108个差异表达宿主基因（differentially expressed host genes, DEHGs），并以未感染细胞作为对照。随后，将上述DEHGs与人类蛋白质相互作用数据进行整合，构建出SARS-CoV-2诱导的宿主基因调控网络（SARS-CoV-2 induced host gene regulatory network, SiHgrn）。对该SiHgrn进行分析后，发现具有最高MCODE评分的子网络"聚类1（Cluster 1）"，其包含31个上调基因，且主要富集于免疫与炎症应答相关通路。值得注意的是，iRegulone工具分析显示，"聚类1（Cluster 1）"受转录因子STAT1、STAT2、STAT3、POU2F2及NFkB1调控，该调控网络被统称为"宿主应答特征网络"。通过NDEx进行功能富集分析后发现，"宿主应答特征网络"主要富集于多条关键通路，包括"细胞因子与炎症应答"、"维生素D的非基因组作用"、"人类对结核分枝杆菌的免疫应答"以及"肺纤维化"。最终，通过深入分析与文献挖掘发现，维生素D可通过与其受体结合，经由两条不同通路发挥作用：其一，通过阻断肿瘤坏死因子（TNF）诱导的NFkB1信号通路，抑制促炎细胞因子的表达；其二，通过激活干扰素-α（IFN-α）诱导的Janus激酶-信号转导与转录激活因子（Jak-STAT）信号通路，启动干扰素刺激基因（interferon-stimulating genes, ISGs）的表达，从而启动抗病毒防御程序。
研究结论：本综合研究明确了SARS-CoV-2感染引发细胞因子风暴的相关通路。本研究提出的维生素D潜在作用机制，有望在重症COVID-19患者中抑制细胞因子风暴并诱导强效抗病毒应答。本研究的发现亟需进一步实验验证，以明确维生素D联合IFN-α用于治疗重症COVID-19的适用性。