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

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-κB 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-κB 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）广泛用于炎症性疾病的治疗，但其抗炎作用的潜在分子机制仍未完全阐明。此外，绝大多数分子生物学研究均聚焦于炎症刺激前糖皮质激素受体（glucocorticoid receptor, GR）激活的效应。然而临床真实诊疗场景中，糖皮质激素干预通常是在炎症反应已显著活跃的阶段启动，与此前研究的给药时序存在差异。为了阐明晚期糖皮质激素给药的调控效应，我们针对巨噬细胞的转录组与调控组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，相较于炎症刺激前激活糖皮质激素受体的方案，脂多糖刺激后通过地塞米松激活受体同样可呈现相似的抗炎特征，同时还能改善代谢基因的表达紊乱。出乎意料的是，糖皮质激素受体的染色质结合模式并不能预测地塞米松调控的基因表达变化，也几乎未发现支持广为人知的“拴留介导的反式抑制（trans-repression by tethering）”模型的相关证据。与之相反，我们发现糖皮质激素受体激活会全局性阻断NF-κB与染色质的结合。通过对基因表达、转录因子结合及染色质开放度数据的整合分析，我们揭示了糖皮质激素受体调控炎症性巨噬细胞的双重核心机制：一是阻止NF-κB在染色质上的定位结合，二是激活包括Nfkbia、Dusp1、Tnfaip3及Tsc22d3在内的负调控因子。本研究通过差异化给药时序的糖皮质激素干预实验，阐明了糖皮质激素受体通过调控“炎症表观基因组（inflamed epigenome）”发挥治疗作用的分子机制。整体实验设计：来源于巨噬细胞的RNA-seq时序样本（0h、4h、10h）及DNase-seq重复样本；RelA/GR ChIP-seq时序重复样本及输入对照DNA。本数据集为ChIP-seq数据集。