Lymphocyte-specific chromatin accessibility pre-determines glucocorticoid resistance in acute lymphoblastic leukemia [WGBS]. Lymphocyte-specific chromatin accessibility pre-determines glucocorticoid resistance in acute lymphoblastic leukemia [WGBS]

Semi-synthetic glucocorticoids are used to treat a broad range of medical conditions including inflammation, autoimmunity, and lymphoid malignancies. While a large component of these effects can be attributed to glucocorticoid-induced apoptosis of normal and malignant lymphocyte, the molecular basis for the lymphocyte-specific apoptosis remains unclear. Moreover, the mechanisms of glucocorticoid resistance in lymphoid malignancy are poorly defined, and remain a significant barrier to cure. To address these issues, we first performed a global analysis of chromatin accessibility in lymphoid and non-lymphoid cells to map lymphocyte-specific open chromatin domains (LSOs). We then integrated these domains with glucocorticoid receptor (GR) binding-induced RNA transcription and chromatin modulation in an in vivo patient-derived xenograft (PDX) model of acute lymphoblastic leukemia (ALL). This led to the identification of LSOs associated with glucocorticoid resistance in ALL. One such LSO was at the pro-apoptotic BIM gene locus, where a chromatin architectural protein CTCF binding was found only in lymphocytes but not in other cell types. The GR cooperated with CTCF to mediate interactions between the BIM promoter and the LSO to direct DNA looping, thus triggering BIM transcription. Importantly, this LSO was heavily DNA methylated in glucocorticoid resistant PDXs and non-lymphoid cells. This study demonstrates for the first time that lymphocyte-specific chromatin accessibility pre-determines glucocorticoid resistance in ALL and proposes a model for the lack of glucocorticoid sensitivity in non-lymphoid cell types. This submission represents the WGBS component of the study. Overall design: Examination of binding profiles of GR, CTCF, H3K9ace, H3K27ace, H3K4me3 and H3K27me3 in combination with RNAseq, ATACseq and whole genome bisulfite sequencing data before and after Dex treatment in ALL xenograft cells.

半合成糖皮质激素（Semi-synthetic glucocorticoids）被用于治疗涵盖炎症、自身免疫疾病及淋巴系统恶性肿瘤在内的多种临床病症。尽管这类药物的多数药理效应可归因于糖皮质激素诱导正常及恶性淋巴细胞发生凋亡，但淋巴细胞特异性凋亡的分子机制仍未阐明。此外，淋巴系统恶性肿瘤中糖皮质激素耐药的机制尚不清楚，这仍是临床治愈该类疾病的重大障碍。为解决上述问题，本研究首先对淋巴细胞与非淋巴细胞开展染色质开放性全基因组分析，以绘制淋巴细胞特异性开放染色质区域（lymphocyte-specific open chromatin domains，简称LSOs）的图谱。随后，我们将这些区域与糖皮质激素受体（glucocorticoid receptor, GR）结合诱导的RNA转录及染色质调控相结合，所用模型为急性淋巴细胞白血病（acute lymphoblastic leukemia, ALL）的在体患者来源异种移植（patient-derived xenograft, PDX）模型。通过上述分析，我们鉴定出了与ALL中糖皮质激素耐药相关的LSOs。其中一处LSO位于促凋亡蛋白BIM基因位点，研究发现染色质架构蛋白CTCF仅在淋巴细胞中结合该位点，而非其他细胞类型。GR与CTCF协同介导BIM启动子与该LSO之间的染色质相互作用，指导DNA环化，进而启动BIM基因的转录。值得注意的是，该LSO在糖皮质激素耐药的PDX模型及非淋巴细胞中存在显著的DNA甲基化修饰。本研究首次证实，淋巴细胞特异性的染色质开放性可预先决定ALL患者的糖皮质激素耐药性，并提出了非淋巴细胞类型糖皮质激素敏感性缺失的作用模型。本提交内容为该研究的全基因组亚硫酸氢盐测序（Whole Genome Bisulfite Sequencing, WGBS）部分。研究整体设计：我们对ALL异种移植细胞在地塞米松处理前后的GR、CTCF、组蛋白H3K9乙酰化（H3K9ac）、组蛋白H3K27乙酰化（H3K27ac）、组蛋白H3K4三甲基化（H3K4me3）及组蛋白H3K27三甲基化（H3K27me3）结合谱，结合RNA测序（RNAseq）、ATAC测序（ATACseq）及全基因组亚硫酸氢盐测序数据进行了整合分析。