Inhibition of EZH2 causes retrotransposon derepression and immune activation in porcine lung alveolar macrophages [ChIP-seq]

Alveolar macrophages (AMs) form the first defense line against a variety of respiratory pathogens, and their immune response has profound impact on the outcome of respiratory infection. It is of critical importance to clarify the immune regulation in AMs. Enhancer of Zeste Homolog 2 (EZH2), which catalyzes the trimethylation of H3K27 for epigenetic repression, has gained increasing attentions about their roles in immune regulation. However, the molecular mechanism underlying the immune regulation role of EZH2 in AMs remains largely unclear. Using porcine 3D4/21 alveolar macrophage cells as model, this study combined transcriptomic and epigenomic techniques to decipher the molecular function of EZH2 in AMs. Transcriptomic comparison revealed that inhibition of EZH2 in AMs causes transcriptional activation of dozens of immune genes which indicates an enhanced antiviral state, and as expected, we found that the infection of influenza A viruses can be remarkably affected. Interestingly, about one hundred families of transposable elements, particularly LTRs/ERVs and LINEs which belong to retrotransposons, get derepressed after EZH2 inhibition. Given that derepression of ERVs promotes innate immune activation in many tumors through the “viral mimicry” mechanism, the derepression of retrotransposon in AMs may also contribute to the coincided immune activation after EZH2 inhibition. Overall, this study improves the mechanistical understanding on the EZH2-dependent immune regulation in AMs and provides novel insights for the epigenetic regulation of retrotransposons in pigs. Overall design: ChIP-Seq (H3K27ac) and RNA-Seq data are generated for porcine 3D4/21 alveolar macrophages with or without the treatment of the EZH2 inhibitor GSK126

肺泡巨噬细胞（alveolar macrophages, AMs）是机体抵御多种呼吸道病原体的第一道防线，其免疫应答状态直接影响呼吸道感染的预后转归，阐明肺泡巨噬细胞的免疫调控机制具有重要的科学意义。zeste基因增强子同源物2（Enhancer of Zeste Homolog 2, EZH2）可催化H3K27三甲基化以介导表观遗传抑制，其在免疫调控中的功能愈发受到学界关注。然而，EZH2在肺泡巨噬细胞中发挥免疫调控作用的分子机制仍未完全阐明。本研究以猪源3D4/21肺泡巨噬细胞为模型，结合转录组与表观基因组学技术，解析EZH2在肺泡巨噬细胞中的分子功能。转录组比较分析显示，抑制肺泡巨噬细胞中的EZH2可激活数十个免疫相关基因的转录，提示细胞抗病毒状态增强；正如预期，研究发现甲型流感病毒的感染过程可被显著影响。值得注意的是，EZH2抑制后，约100个转座因子（transposable elements）家族的表达被去抑制，其中尤以逆转录转座子（retrotransposons）中的长末端重复序列/内源性逆转录病毒（LTRs/ERVs）和长散在核元件（LINEs）最为显著。鉴于内源性逆转录病毒的去抑制可通过"病毒模拟（viral mimicry）"机制促进多种肿瘤中的先天免疫激活，肺泡巨噬细胞中逆转录转座子的去抑制或许也参与了EZH2抑制后伴随的免疫激活过程。综上，本研究加深了对EZH2依赖型肺泡巨噬细胞免疫调控机制的理解，同时为猪源逆转录转座子的表观遗传调控提供了全新视角。实验设计：本研究针对经EZH2抑制剂GSK126处理与未处理的猪源3D4/21肺泡巨噬细胞，分别获取了染色质免疫沉淀测序（ChIP-Seq, H3K27ac）与RNA测序（RNA-Seq）数据。