Anti-inflammatory Chromatinscape Associated with Clinically Relevant Timing of Glucocorticoid Treatment [ChIP-seq]

Despite the widespread use of glucocorticoids (GCs) for treating inflammatory conditions, the underlying mechanisms of their anti-inflammatory effects are not understood. Moreover, the majority of molecular investigations have examined the effects of glucocorticoid receptor (GR) activation prior to inflammatory challenges. However, clinically relevant situations are emulated by a GC intervention initiated in the midst of rampant inflammatory responses. To characterize the effects of a late GC treatment, we performed systematic profiling of macrophage transcriptional and regulatory landscapes with Dexamethasone (Dex) treatment either before or after stimulation by lipopolysaccharide (LPS). GR activation by Dex following LPS stimulation had a similar anti-inflammatory profile in comparison to GR pre-activation, while ameliorating the disruption of metabolic genes. Unexpectedly, the chromatin occupancy pattern of GR is not predictive of the Dex-regulated expression changes and shows little evidence for the widely accepted 'trans-repression by tethering' model. Rather, we find that GR activation results in global blockade of NF-?B binding to chromatin. Integrative analyses of gene expression, transcription factor occupancy, and chromatin accessibility data highlight distinct mechanisms through which GR controls inflammatory macrophages: prevention of NF-?B chromatin occupancy and activation of negative regulators such as Nfkbia, Dusp1, Tnfaip3, and Tsc22d3. Our investigation with differentially timed GC treatments reveals molecular mechanisms underlying therapeutic actions of GR for modulating the 'inflamed epigenome'. Overall design: RNA-seq time course (0h, 4h, 10h) and DNase-seq sample replicates from macrophages; RelA/GR ChIP-seq time course sample replicates and input control DNA This is the ChIP-seq dataset.

尽管糖皮质激素（glucocorticoids, GCs）在炎症性疾病治疗中应用广泛，但其抗炎作用的具体分子机制尚未完全阐明。此外，绝大多数相关分子研究均聚焦于炎症刺激前糖皮质激素受体（glucocorticoid receptor, GR）的激活效应。然而临床实际诊疗场景中，往往是在炎症反应已全面爆发后才启动糖皮质激素干预。为阐明晚期糖皮质激素干预的效应特征，我们针对巨噬细胞的转录及调控图谱开展了系统性分析：分别在脂多糖（lipopolysaccharide, LPS）刺激前或刺激后给予地塞米松（Dexamethasone, Dex）处理。研究发现，相较于炎症刺激前的GR预激活，LPS刺激后经Dex诱导的GR激活可呈现相似的抗炎转录谱，但同时可改善代谢基因的表达紊乱。出乎意料的是，GR的染色质结合模式并不能预测Dex调控的基因表达变化，且几乎无法支持当前广为接受的tethering介导的反式抑制（trans-repression by tethering）模型。与之相反，我们发现GR激活可全局性阻断NF-κB与染色质的结合。通过整合基因表达、转录因子染色质结合及染色质开放状态的多组学数据分析，我们揭示了GR调控炎症巨噬细胞的双重分子机制：一是阻止NF-κB在染色质上的定位，二是激活包括Nfkbia、Dusp1、Tnfaip3及Tsc22d3在内的负调控因子。本研究通过差异化时序的糖皮质激素干预实验，阐明了GR通过调控‘炎症表观组’发挥治疗作用的分子机制。实验整体设计：巨噬细胞的RNA测序（RNA-seq）时序样本（0h、4h、10h）及DNase测序（DNase-seq）重复样本；RelA/GR 染色质免疫共沉淀测序（ChIP-seq）时序重复样本及输入对照DNA。本数据集属于ChIP-seq数据集。