Key Super Enhancers Drive Tumor-Suppressing Transcription Feedback Programs in Mature B Cell Cancers (RNA array). Key Super Enhancers Drive Tumor-Suppressing Transcription Feedback Programs in Mature B Cell Cancers (RNA array)

Dynamic changes to the epigenome are essential regulators of B cell differentiation and, when perturbed, can lead to cancer. We compared three types of mature B cell lymphoma/leukemia (BCL) and normal lymphocytes to identify common and distinct epigenetic perturbations that promote oncogenesis. Purified malignant B cells from 52 patients (18 Follicular, 11 Diffuse Large B Cell, 23 Chronic Lymphocytic Lymphomas) and normal B cell subsets from 28 donor tonsils were subjected to chromatin immunoprecipitation and sequencing (ChIP-seq) for H3K4me1, H3K9/14ac, and H3K27ac; FAIRE-seq for open chromatin; RNA-seq; and genome copy number arrays. We identified a novel super enhancer (SE) connected to the aberrant expression of FCMR and PIGR in multiple BCL subtypes, which may drive the tissue-specific expression of the two immunoglobulin receptor genes. These integrative studies also revealed that loss of normal B cell SEs in BCL was associated with significant reduction in linked gene expression, the greatest impact among regulatory elements. Downregulation of crucial B cell transcription factors (TF) and tumor suppressors was consistent across BCL subtypes and linked to significantly diminished or absent active chromatin marks in adjacent SEs. These BCL-repressed SEs are enriched in binding sites for the same suppressed TFs that they regulate, suggesting transcriptional regulatory feedback loops for these key B cell identity genes. In sum, this study defined common alterations in the regulomes of mature B cell leukemias and lymphomas and implicate SEs as important hubs of tumor suppressing transcriptional feedback loops that are perturbed in B cell cancer. Overall design: Gene expression analysis was performed for chronic lymphocytic leukemia and tonsil-derived germinal center B cells using Affymetrix Human Gene 2.0 ST.

表观基因组的动态变化是B细胞分化的关键调控因素，当其受到扰动时，可引发癌症。
本研究对比了三种成熟B细胞淋巴瘤/白血病（B cell lymphoma/leukemia, BCL）样本与正常淋巴细胞，以筛选能够促进肿瘤发生的共有及特异性表观遗传扰动事件。
研究对52例患者的纯化恶性B细胞（18例滤泡性淋巴瘤、11例弥漫大B细胞淋巴瘤、23例慢性淋巴细胞白血病）以及28例供体扁桃体来源的正常B细胞亚群进行了多组学检测：针对组蛋白修饰H3K4me1、H3K9/14ac及H3K27ac的染色质免疫共沉淀测序（ChIP-seq）、检测开放染色质的FAIRE-seq、RNA测序（RNA-seq）以及基因组拷贝数阵列分析。
本研究在多种BCL亚型中发现了一个与FCMR、PIGR异常表达相关的新型超级增强子（super enhancer, SE），其可能介导这两个免疫球蛋白受体基因的组织特异性表达。
本整合分析还发现，BCL中正常B细胞超级增强子的丢失与其靶基因表达的显著下调相关，且该效应在各类调控元件中最为显著。
关键B细胞转录因子（transcription factor, TF）与肿瘤抑制因子的表达下调在所有BCL亚型中均一致存在，且与相邻超级增强子区域内活性染色质标记的显著减弱或缺失密切相关。
这些在BCL中被抑制的超级增强子，其富集有其所调控的、同样被抑制的转录因子结合位点，提示这些关键B细胞身份基因存在转录调控反馈环路。
综上，本研究明确了成熟B细胞白血病与淋巴瘤调控组的共有改变，并提示超级增强子是BCL中发生紊乱的肿瘤抑制性转录反馈环路的关键枢纽。
实验整体设计：本研究使用Affymetrix人类基因2.0 ST芯片，对慢性淋巴细胞白血病样本及扁桃体来源的生发中心B细胞进行了基因表达分析。