敲低调控条形码使巨噬细胞极化从 M1 转向 M2，并增加金黄色葡萄球菌感染后的病原负荷
Knockdown of a regulatory barcode shifts macrophage polarization destination from M1 to M2 and increases pathogen burden upon S. aureus infection
整合网络分析流程基于巨噬细胞对 28 种刺激的转录组重建人类基因调控网络，识别出 13 个极化状态聚类，M1 与 M2 位于两端。该流程为每种极化状态给出核心调控因子（RF）组合，其中 CEBPB、NFE2L2 和 BCL3 三个 RF 足以将极化去向从 M1 改为 M2。在 THP1 来源的 M0 细胞中，即使暴露于 M1 刺激物，siRNA 敲低这 3 个 RF 仍显著减弱向 M1 的转变并提高 M2 标志物表达，单独敲低每个 RF 也呈相似趋势。该 3-RF 敲低使巨噬细胞对金黄色葡萄球菌感染高度易感，表明这些因子在调控免疫反应中的重要性。
来源：eLife · doi.org
Macrophages are driven to form distinct functional phenotypes in response to different immunological stimuli, in a process widely referred to as macrophage polarization. Transcriptional regulators that guide macrophage polarization in response to a given trigger remain largely unknown. In this study, we interrogate the programmable landscape in macrophages to find regulatory panels that determine the precise polarization state that a macrophage is driven to. Toward this, we configure an integrative network analysis pipeline that utilizes macrophage transcriptomes in response to 28 distinct stimuli, reconstructs contextualized human gene regulatory networks, and identifies epicenters of perturbations in each case. We find that these contextualized regulatory networks form a spectrum of 13 distinct clusters, with M1 and M2 at the two ends. Using our computational pipeline, we identify combinatorial panels of epicentric regulatory factors (RFs) for each polarization state. We demonstrate that a set of three RFs, that is, CEBPB , NFE2L2 , and BCL3 , is sufficient to change the polarization destination from M1 to M2. siRNA knockdown of the 3-RF-set in THP1-derived M0 cells, despite exposure to an M1 stimulant, significantly attenuated the shift to M1 phenotype and instead increased the expression of M2 markers. Single knockdown of each RF also showed a similar trend. The siRNA-mediated knockdown of the 3-RF-set rendered the macrophages hyper-susceptible to Staphylococcus aureus infection, demonstrating the importance of these factors in modulating immune responses. Overall, our results provide insights into the transcriptional mechanisms underlying macrophage polarization and identify key RFs that may be targeted to modulate immune responses.