Genetic variation in IL-4 activated tissue resident macrophages alters the epigenetic state to determine strain specific synergistic responses to LPS [RNA-seq]

IL-4 activates tissue resident macrophages (TRMs) to mediate tissue repair and clearance of nematode infections in mice, but most studies have been performed on the C57BL/6 background. The natural genetic variation between C57BL/6 and BALB/c mouse strains can result in differences in allergic responses, parasite resistance, monocyte to macrophage conversion and response to IL-4 activation. Here, we investigated in vivo IL-4 activation in TRMs of the peritoneal cavity from C57BL/6 and BALB/c mice and find that C57BL/6 TRMs are surprisingly more transcriptionally responsive to IL-4 stimulation, with greater association of induced genes with super enhancers, induced enhancers and topologically associating domains (TAD) boundaries. IL-4-directed epigenomic remodeling showed NF-?B motif enrichment only in C57BL/6 TRMs. This resulted in an enhanced synergistic response upon in vitro lipopolysaccharide (LPS) exposure in IL-4 activated C57BL/6 TRMs but not for BALB/c, despite unstimulated BALB/c TRMs having a stronger transcriptional response to LPS than C57BL/6 TRMs. Single cell RNA sequencing (scRNAseq) analysis of mixed bone marrow chimeric mice indicates that transcriptional differences between C57BL/6 and BALB/c TRMs is cell intrinsic within the same tissue environment. Hence, genetic variation alters IL-4-induced cell intrinsic epigenetic reprogramming between C57BL/6 and BALB/c TRMs to regulate the magnitude of synergistic responses to LPS exposure. Overall design: RNA-seq was performed after IL4, H. polygyrus or LPS treatment in Bl/6 and BALB/c mice. Two or three replicates for each samples

白介素4（Interleukin-4, IL-4）可激活组织驻留巨噬细胞（tissue resident macrophages, TRMs），介导小鼠的组织修复与线虫感染清除，但绝大多数相关研究均基于C57BL/6遗传背景开展。C57BL/6与BALB/c小鼠品系间的自然遗传差异，可导致二者在过敏反应、寄生虫抗性、单核细胞向巨噬细胞转化以及对白介素4激活的应答等方面存在差异。本研究针对C57BL/6与BALB/c小鼠腹腔组织驻留巨噬细胞的体内IL-4激活状态展开探究，令人意外的是，C57BL/6来源的TRMs对IL-4刺激的转录响应更为显著，其诱导基因与超级增强子、诱导型增强子及拓扑关联结构域（topologically associating domains, TAD）边界的关联程度更高。IL-4介导的表观基因组重塑仅在C57BL/6 TRMs中呈现核因子κB（NF-κB）基序富集现象。这使得经IL-4激活的C57BL/6 TRMs在体外接受脂多糖（lipopolysaccharide, LPS）刺激时可产生更强的协同应答，而BALB/c TRMs则无此效应——尽管未受刺激的BALB/c TRMs对LPS的转录响应本身强于C57BL/6 TRMs。对混合骨髓嵌合小鼠开展的单细胞RNA测序（single cell RNA sequencing, scRNAseq）分析显示，C57BL/6与BALB/c TRMs之间的转录差异，在相同组织环境中属于细胞自主性差异。综上，遗传差异可改变C57BL/6与BALB/c TRMs间IL-4诱导的细胞自主性表观遗传重编程过程，进而调控其对LPS刺激的协同应答强度。整体实验设计：对C57BL/6与BALB/c小鼠分别施以IL-4、多形螺旋线虫（Heligmosomoides polygyrus, H. polygyrus）或LPS处理后开展RNA测序，每个样本设置2~3个生物学重复。