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

糖皮质激素(GC)与糖皮质激素受体(GR)结合，是治疗类风湿性关节炎、过敏和急性肺损伤等炎症性疾病的广泛处方药。然而，它们有益的抗炎作用伴随着严重的副作用(糖尿病、肝脏脂肪变性、骨质疏松症、肌肉萎缩等)。特别是在应用于化疗、慢性炎症或治疗严重冠状病毒病2019年的长期治疗计划中(新冠肺炎)。该项目旨在从细胞和分子水平上了解GC诱导的组织适应及其在长期GC治疗后在肝脏和肺中的可逆性。这对于患者预测GC治疗可能出现的并发症是相关的。因此，我们将通过将全基因组GR DNA结合数据(Bulk CHIP-SEQ)与单核ATAC-SEQ整合来建立细胞类型特异性GR序列，分析DNA在小鼠肝脏和肺内内源性GC浓度峰值以及长期GC治疗后的组织适应中的可及性。通过多组分析(10倍基因组学)的同步单核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基因敲除小鼠的数据，我们将能够在细胞分辨率上描述依赖GR的GC不良影响，从而允许靶向治疗和对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)内长期GC治疗后是否在体内是可逆的。我们计划调查在接受GC治疗的患者中，是否会发生可能导致“记忆”效应的持续性改变，其后果目前尚不清楚。我们将在长期GC治疗的小鼠肝脏中建立空间转录组，以绘制肝脏细胞适应过程的空间图谱，并将这些过程与我们的单核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，以及一个可浏览的数据界面。

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.