Table_2_Linking Cell Dynamics With Gene Coexpression Networks to Characterize Key Events in Chronic Virus Infections.xlsx

The host immune response against infection requires the coordinated action of many diverse cell subsets that dynamically adapt to a pathogen threat. Due to the complexity of such a response, most immunological studies have focused on a few genes, proteins, or cell types. With the development of “omic”-technologies and computational analysis methods, attempts to analyze and understand complex system dynamics are now feasible. However, the decomposition of transcriptomic data sets generated from complete organs remains a major challenge. Here, we combined Weighted Gene Coexpression Network Analysis (WGCNA) and Digital Cell Quantifier (DCQ) to analyze time-resolved mouse splenic transcriptomes in acute and chronic Lymphocytic Choriomeningitis Virus (LCMV) infections. This enabled us to generate hypotheses about complex immune functioning after a virus-induced perturbation. This strategy was validated by successfully predicting several known immune phenomena, such as effector cytotoxic T lymphocyte (CTL) expansion and exhaustion. Furthermore, we predicted and subsequently verified experimentally macrophage-CD8 T cell cooperativity and the participation of virus-specific CD8+ T cells with an early effector transcriptome profile in the host adaptation to chronic infection. Thus, the linking of gene expression changes with immune cell kinetics provides novel insights into the complex immune processes within infected tissues.

宿主抗感染免疫应答依赖于多种异质性细胞亚群的协同作用，这些细胞亚群可动态响应病原体威胁并发生适应性重塑。受限于此类免疫应答的高度复杂性，绝大多数免疫学研究此前仅聚焦于少数基因、蛋白质或细胞类型。随着组学（omic）技术与计算分析方法的发展，如今解析复杂免疫系统的动态特性已具备可行性。然而，对完整器官来源的转录组数据集进行细胞组分解构仍是当前面临的核心挑战之一。本研究将加权基因共表达网络分析（Weighted Gene Coexpression Network Analysis, WGCNA）与数字细胞定量器（Digital Cell Quantifier, DCQ）相结合，对急性与慢性淋巴细胞脉络丛脑膜炎病毒（Lymphocytic Choriomeningitis Virus, LCMV）感染模型中小鼠脾脏的时序转录组进行了分析。该策略使我们能够针对病毒诱导的宿主扰动后复杂的免疫调控机制生成可检验的假说。通过成功预测多种已知免疫现象——例如效应性细胞毒性T淋巴细胞（cytotoxic T lymphocyte, CTL）的扩增与耗竭——验证了该分析策略的可靠性。进一步而言，我们通过该策略预测并通过实验证实了巨噬细胞与CD8+ T细胞的协同互作，以及携带早期效应转录组特征的病毒特异性CD8+ T细胞在宿主适应慢性感染过程中的关键参与作用。综上，将基因表达变化与免疫细胞动力学特征相整合的研究思路，可为感染组织内的复杂免疫过程提供全新的认知维度。