(Reversible) cellular and genomic alterations induced by long-term glucocorticoid treatment

糖皮质激素（GCs）与糖皮质激素受体（GR）结合，被广泛用于治疗类风湿性关节炎、过敏和急性肺损伤等炎症性疾病。然而，它们有益的抗炎作用伴随着严重的不良反应（糖尿病、肝脂肪变性、骨质疏松症、肌肉萎缩等），特别是在化疗、慢性炎症或治疗2019年严重冠状病毒病（COVID-19）的长期治疗方案中。该项目旨在从细胞和分子水平上了解长期GC治疗后肝和肺中GC诱导的组织适应及其可逆性。这与患者预测GC治疗可能出现的并发症有关。因此，我们将通过整合全基因组GR DNA结合数据（bulk ChIP-seq）和单核ATAC-seq，建立细胞类型特异性GR细胞池，分析DNA在内源性GC浓度峰值时和长期GC处理后组织适应后在小鼠肝脏和肺部的可及性。通过多组分析（10xGenomics）的同时单核RNA表达分析（snRNA-seq），我们将在基因水平上将细胞类型特异性GR结合与细胞类型特异性GC反应联系起来。通过整合来自GR敲除小鼠的数据，我们将能够在细胞分辨率上描述GR依赖的GC不良反应，从而实现靶向治疗和对GC介导的组织改变的新见解。此外，我们将阐明gr诱导的细胞（细胞类型组成）和表观遗传（DNA可及性）适应在肝脏（以及潜在的肺）长期GC治疗后是否在体内可逆。我们计划研究在接受GC治疗的患者中，是否会发生持续性改变，从而导致迄今未知后果的“记忆”效应。我们将在长期GC处理的小鼠肝脏中建立空间转录组，以绘制肝脏中细胞的空间适应过程，并将其与我们的单核RNA-seq结果进行比较。最后，我们计划为科学界提供高质量的单核RNA和ATAC-seq参考数据集，用于开发工具和建模算法以及可浏览的数据接口。

Glucocorticoids (GCs) bind to the glucocorticoid receptor (GR)and are widely prescribed drugs to combat inflammatory disease like rheumatoid arthritis, allergies and acute lung injury. However, their beneficial anti-inflammatory effects are accompanied by severe adverse effects (diabetes, liver steatosis, osteoporosis, muscle atrophy etc.) especially in long-term treatment schemes applied in chemotherapy, chronic inflammation or treatment of severe Coronavirus Disease 2019 (COVID-19). The project aims to understand GC-induced tissue adaptations and their reversibility in liver and lung after long-term GC treatment on a cellular and molecular level. This is relevant for patients to anticipate possible complications of GC therapy. Therefore, we will establish a cell type specific GR cistrome by the integration of whole-genome GR DNA binding data (bulk ChIP-seq) with single nuclei ATAC-seq, profiling the DNA’s accessibility, in murine liver and lung at the peak of endogenous GC concentrations and after tissue adaptation in response to long-term GC treatment. By simultaneous single nuclei RNA expression analysis (snRNA-seq) via the multiome assay (10xGenomics), we will link the cell type specific GR binding to cell type specific GC responses on the gene level. By integrating data from GR knockout mice, we will be able to describe the GR-dependent GC adverse effects at cellular resolution allowing for targeted therapy and novel insights into GC-mediated tissue alterations. Furthermore, we will elucidate if GR-induced cellular (cell type composition) and epigenetic (DNA accessibility) adaptations upon long-term GC treatment within the liver (and potentially the lung) are reversible in-vivo. We plan to investigate if persistent alterations occur which might lead to a “memory” effect with so far unknown consequences for patients undergoing GC therapy. We will establish the spatial transcriptome in murine livers upon long-term GC treatment to map cellular adaptation processes spatially in the liver and compare those to our single nuclei RNA-seq results. In the end, we plan to provide the scientific community with high quality single nuclei RNA- and ATAC-seq reference datasets for the development of tools and modeling algorithms as well as a browsable data interface.