IRF1 governs the differential Interferon-Stimulated Gene responses in human monocytes and macrophages by regulating chromatin accessibility (ATAC - Differentiation)

Myeloid lineage cells use TLRs to recognize and respond to diverse microbial ligands. Although unique transcription factors dictate the outcome of specific TLR signaling, whether lineage-specific differences exist to further modulate the quality of TLR-induced inflammation remains unclear. Comprehensive analysis of global gene transcription in human monocytes, monocyte-derived macrophages and monocyte-derived dendritic cells stimulated with various TLR ligands identifies multiple lineage-specific, TLR-responsive gene programs. Monocytes are hyperresponsive to TLR7/8 stimulation that correlates with higher expression of the receptors. While macrophages and monocytes express similar levels of TLR4, macrophages, but not monocytes, upregulate Interferon-Stimulated Genes (ISGs) in response to TLR4 stimulation. We find that TLR4 signaling in macrophages uniquely engages transcription factor IRF1, which facilitates opening of ISG loci for transcription. This study provides a critical mechanistic basis for lineage-specific TLR responses and uncovers IRF1 as a master epigenetic regulator for the ISG transcriptional program in human macrophages. Overall design: ATAC-seq anlaysis of epigenomic changes in monocytes, MDMs and MDDCs during differentiation from monocytes to MDMs or MDDCs

髓系细胞（myeloid lineage cells）通过Toll样受体（Toll-like receptors, TLRs）识别并响应多种微生物配体。尽管特定转录因子决定了TLR信号通路的具体结局，但是否存在谱系特异性差异以进一步调控TLR诱导的炎症反应质量，目前仍不明确。
对经不同TLR配体刺激的人类单核细胞、单核细胞来源巨噬细胞（monocyte-derived macrophages, MDMs）及单核细胞来源树突状细胞（monocyte-derived dendritic cells, MDDCs）开展全基因组转录分析，鉴定出多种谱系特异性TLR应答基因程序。
单核细胞对TLR7/8刺激呈现高应答性，该特性与其受体的高表达水平相关。尽管巨噬细胞与单核细胞的TLR4表达水平相近，但巨噬细胞（而非单核细胞）可在TLR4刺激下上调干扰素刺激基因（Interferon-Stimulated Genes, ISGs）。
研究发现，巨噬细胞中的TLR4信号通路可特异性激活转录因子IRF1，后者可促进ISG基因座的染色质开放以启动转录。本研究为谱系特异性TLR应答提供了关键的机制基础，并揭示IRF1可作为人类巨噬细胞中ISG转录程序的核心表观遗传调控因子。
实验整体设计：对单核细胞向MDMs或MDDCs分化过程中，单核细胞、MDMs及MDDCs的表观基因组变化开展转座酶可及性测序（Assay for Transposase-Accessible Chromatin using sequencing, ATAC-seq）分析。