Supplementary Material for: Human monocytes exposed to SARS-CoV-2 display features of innate immune memory producing high levels of CXCL10 upon restimulation

Introduction A role for innate immune memory in protection during COVID-19 infection or vaccination has been recently reported. However, no study so far has shown whether SARS-CoV-2 can train innate immune cells. The aim of this study was to investigate whether this virus can induce trained immunity in human monocytes. Methods Monocytes were exposed to inactivated (i)SARS-CoV-2 for 24 hours, followed by a resting period in medium only and a secondary stimulation on day 6 after which, the cytokine/chemokine and transcriptomic profiles were determined. Results Compared to untrained cells, the iSARS-CoV-2-trained monocytes secreted significantly higher levels of IL-6, TNF-α, CXCL10, CXCL9 and CXCL11 upon restimulation. Transcriptome analysis of iSARS-CoV-2 trained monocytes revealed increased expression of several inflammatory genes. As epigenetic and metabolic modifications are hallmarks of trained immunity, we analyzed the expression of genes related to these processes. Findings indicate that indeed SARS-CoV-2-trained monocytes show changes in the expression of genes involved in metabolic pathways including the tricarboxylic acid (TCA) cycle, amino acid metabolism and the expression of several epigenetic regulator genes. Using epigenetic inhibitors that block histone methyl and acetyl transferases, we observed that the capacity of monocytes to be trained by iSARS-CoV-2 was abolished. Conclusion Overall, our findings indicate that iSARS-CoV-2 can induce properties associated with trained immunity in human monocytes. These results contribute to the knowledge required for improving vaccination strategies to prevent infectious diseases.

近期有研究报道了固有免疫记忆在新型冠状病毒（SARS-CoV-2）感染或疫苗接种防护中的作用。然而，迄今为止尚无研究证实SARS-CoV-2能否诱导固有免疫细胞产生训练免疫（trained immunity）。本研究旨在探讨该病毒是否可在人单核细胞中诱导训练免疫。
方法 将单核细胞与灭活型SARS-CoV-2（iSARS-CoV-2）共培养24小时，随后更换为仅含培养基的体系进行静置培养，并于接种后第6天施加二次刺激，随后检测细胞因子/趋化因子表达谱与转录组学特征。
与未经过训练的细胞相比，经iSARS-CoV-2训练的单核细胞在二次刺激后，分泌的IL-6、TNF-α、CXCL10、CXCL9及CXCL11水平显著升高。对iSARS-CoV-2训练后的单核细胞进行转录组分析发现，多种炎症相关基因的表达水平显著上调。由于表观遗传修饰与代谢重塑是训练免疫的标志性特征，我们分析了与这两类过程相关的基因表达情况。研究结果显示，经SARS-CoV-2训练的单核细胞，其参与代谢通路（包括三羧酸循环（tricarboxylic acid cycle, TCA）、氨基酸代谢）的基因表达，以及多种表观遗传调控因子的表达均发生显著改变。使用可阻断组蛋白甲基转移酶与组蛋白乙酰转移酶的表观遗传抑制剂进行干预后，我们观察到单核细胞被iSARS-CoV-2诱导产生训练免疫的能力被完全消除。
结论 综上，本研究结果表明，iSARS-CoV-2可在人单核细胞中诱导与训练免疫相关的特性。上述结果为优化预防感染性疾病的疫苗接种策略提供了重要的理论依据。