Differential Contributions of Interferon Classes to Host Inflammatory Responses and Restricting Virus Progeny Production

Fundamental to mammalian intrinsic and innate immune defenses against pathogens is the production of Type I and Type II interferons, such as IFN-β and IFN-γ, respectively. The comparative effects of IFN classes on the cellular proteome, protein interactions, and virus restriction within cell types that differentially contribute to immune defenses are needed for understanding immune signaling. Here, a multilayered proteomic analysis, paired with biochemical and molecular virology assays, allows distinguishing host responses to IFN-β and IFN-γ and associated antiviral impacts during infection with several ubiquitous human viruses. In differentiated macrophage-like monocytic cells, we classified proteins upregulated by IFN-β, IFN-γ, or pro-inflammatory LPS. Using parallel reaction monitoring, we developed a proteotypic peptide library for shared and unique ISG signatures of each IFN class, enabling orthogonal confirmation of protein alterations. Thermal proximity coaggregation analysis identified the assembly and maintenance of IFN-induced protein interactions. Comparative proteomics and cytokine responses in macrophage-like monocytic cells and primary keratinocytes provided contextualization of their relative capacities to restrict virus production during infection with herpes simplex virus type-1, adenovirus, and human cytomegalovirus. Our findings demonstrate how IFN classes induce distinct ISG abundance and interaction profiles that drive antiviral defenses within cell types that differentially coordinate mammalian immune responses.在哺乳动物对抗病原体的固有免疫与天然免疫防御中，Ⅰ型和Ⅱ型干扰素（分别对应IFN-β与IFN-γ）的产生是核心基础。要深入理解免疫信号传导机制，亟需明确不同干扰素类别对免疫防御贡献各异的细胞类型内，其对细胞蛋白质组、蛋白质相互作用以及病毒限制作用的比较效应。本研究通过多层蛋白质组学分析结合生化与分子病毒学实验，实现了在多种常见人类病毒感染过程中，宿主对IFN-β与IFN-γ的应答及其相关抗病毒效应的区分鉴定。在分化成熟的巨噬细胞样单核细胞中，我们对受IFN-β、IFN-γ或促炎脂多糖（LPS）上调的蛋白质进行了分类。本研究利用平行反应监测（parallel reaction monitoring）技术，针对每类干扰素共有的与特有的干扰素刺激基因（ISG）特征，构建了蛋白质组特征肽库，可对蛋白质表达变化进行正交验证。热邻近共聚集分析（thermal proximity coaggregation）揭示了干扰素诱导的蛋白质相互作用的组装与维持机制。我们对巨噬细胞样单核细胞与原代角质形成细胞开展比较蛋白质组学分析及细胞因子应答检测，明确了这两种细胞在单纯疱疹病毒1型（herpes simplex virus type-1）、腺病毒（adenovirus）及人类巨细胞病毒（human cytomegalovirus）感染过程中限制病毒增殖的相对能力。本研究结果揭示了不同类别干扰素如何诱导特异性的干扰素刺激基因表达丰度与相互作用谱，进而在协同调控哺乳动物免疫应答的不同细胞类型中驱动抗病毒防御功能。