Use of chromatin accessibility maps to discover novel regulatory circuits in aggressive B cell lymphomas

使用染色质可及性图谱发现侵袭性 B 细胞淋巴瘤的新型调节回路

• 批准号: 9397178
• 负责人: Ashley Stephen Doane
• 金额: $ 4.4万
• 依托单位: WEILL MEDICAL COLL OF CORNELL UNIV
• 依托单位国家: 美国
• 财政年份: 2017
• 资助国家: 美国
• 起止时间: 2017-08-01 至 2019-07-31
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/9397178
• 关键词: ATAC-seq; Address; B-Cell Activation; B-Cell Lymphomas; B-Lymphocytes; Binding; CRISPR interference; CRISPR/Cas technology; Cell Line; Cells; ChIP-seq; Chromatin; Computer Analysis; Critical Pathways; DNA; Data; Databases; Elements; Epigenetic Process; Family; Gene Expression; Gene Expression Regulation; Gene Targeting; Genes; Genetic Transcription; Growth; IRF4 gene; In Vitro; Locus Control Region; Logic; Lymphoma; Maps; Mediating; Nucleosomes; Oncogenic; Pathogenesis; Phenotype; Plasmablast; Positioning Attribute; Reaction; Regulatory Element; Research; Role; Site; Structure of germinal center of lymph node; Testing; Therapeutic; Validation; Xenograft procedure; chemotherapy; cofactor; cohort; computer framework; defined contribution; design; differential expression; imprint; in vivo; large cell Diffuse non-Hodgkin' s lymphoma; novel; outcome forecast; overexpression; programs; standard of care; transcriptome sequencing; tumor

PROJECT SUMMARY/ABSTRACT Diffuse large B-cell lymphomas (DLBCL) arise from B-cells transiting different stages of the germinal center (GC) reaction. We have an incomplete picture of the regulatory logic and circuits that become disrupted in subtypes of DLBCL. This is especially true in Activated B-cell-like (ABC) subtype, an aggressive subset of tumors that respond poorly to standard-of-care chemotherapy and have a dismal prognosis. To uncover novel regulatory circuits we leverage chromatin accessibility maps (regulomes) produced by ATACseq and develop a computational framework to quantify gain or loss of accessibility across regulatory elements of expressed TFs. Here, we hypothesize that ABC-DLBCLs depend on the activity of BATF to drive their oncogenic transcriptional programs. We seek to uncover mechanisms of gene regulation by BATF including decipher the mechanisms by which BATF and co-factors assemble on chromatin cooperatively, the mechanisms that mediate a highly clustered chromatin accessibility imprint at critical ABC loci. Aim 1: To identify and validate the direct targets of BATF in B cell lymphoma. We will perform ATACseq and RNAseq in DLBCL cell lines and an additional cohort of DLBCL tumors and normal B-cells, and map regulatory elements including putative BATF targets and LCRs. Aim2. To determine the mechanisms though which BATF regulates gene expression in ABC-DLBCL. We hypothesize that BATF is essential in ABC-DLBCL and regulates gene expression by enabling chromatin accessibility, binding of additional factors, and accessibility and looping of LCRs. Aim3. To define the contribution of BATF to the ABC phenotype in vitro and in vivo. We will examine the role of BATF on the growth, survival, and differentiation of ABC cells after BATF depletion. We hypothesize that in the absence of BATF, ABC cell lines cannot maintain their identity and will die or differentiate.

项目摘要/摘要 弥漫性大B细胞淋巴瘤(DLBCL)起源于B细胞穿越生发的不同阶段 中心(GC)反应。我们对监管逻辑和电路的了解并不完整 在DLBCL的亚型中中断。在激活的B细胞样(ABC)亚型中尤其如此， 侵袭性肿瘤亚群，对标准护理化疗反应差，并有令人沮丧的 预后。为了发现新的调节电路，我们利用染色质可及性图(调节体) 由ATACseq产生，并开发了一个计算框架来量化可访问性的收益或损失 在表达的转录因子的调控元素之间。 在这里，我们假设ABC-DLBCL依赖于BATF的活性来驱动其致癌 转录程序。我们试图揭示BATF的基因调控机制，包括 破译BATF和辅助因子在染色质上协同组装的机制， 调节高度聚集的染色质可及性的机制印记在关键的ABC基因座上。目标 1.鉴定和验证BATF在B细胞淋巴瘤中的直接靶点。我们将执行ATACseq 和RNAseq在DLBCL细胞系和另外一组DLBCL肿瘤和正常B细胞中，以及 绘制监管要素图，包括假定的BATF目标和LCR。 AIM2.目的：探讨BATF调控ABC-DLBCL细胞基因表达的机制。 我们假设BATF在ABC-DLBCL中是必不可少的，并通过使 染色质可及性、附加因子的结合以及LCRs的可及性和环路。 Aim3.目的：明确BATF在体内外对ABC表型的贡献。 我们将研究BATF在BATF后对ABC细胞生长、存活和分化的作用 耗尽。我们假设，在没有BATF的情况下，ABC细胞株不能保持其特性 并将死亡或分化。