Chromunities Drive Transcriptional Reprogramming in Humoral Immunity and B-cell Lymphomas

项目摘要/摘要 弥漫性大B细胞淋巴瘤(DLBCL)起源于生发中心不同阶段的B细胞 (GC)反应。很明显，这些肿瘤可以选择正常B细胞的调节电路来驱动 他们自己的恶性表型。先前的研究观察到，在两种情况下 重编程过程中的转录激活和基因附近的拓扑重组程度 轨迹。这表明3D基因组的重组对B细胞的发育至关重要，并突出了 它在DLBCL中的重要性。监管中心是增强剂的高度互动区域，可以形成 与拓扑相关结构域(TADS)内的多个基因相互作用诱导基因激活 在相同的TAD内，比成对的非相互作用的基因更高的概率。集线器通常在单元期间重新布线 命运的转变。最近的研究还表明，广泛互动网络的组织达到了一个新的水平，称为 染色质，这被认为允许跨境共享信息和更广泛的基因 对细胞身份至关重要的监管信息。对于理解驱动变化的机制至关重要 基因网络是研究大规模的染色体重排(结构变异，SVS)如何协同 选择调节元件形成异常或从头开始的染色单体，从而驱动异常基因 表情。而复杂结构变体(SVS)的解释主要集中在基因上 剂量和异常TAD结构的破坏，关于SVS在重编程中的作用知之甚少 调控中心及其目标基因。研究染色质及其相关中枢在细胞中的作用 命运转换和肿瘤发生，我们将利用染色质构象捕捉相互作用图(pcHiC， Pore-C)开发一个计算框架，以提名增强子和增强子的染色单体和图谱网络 推动表观遗传和转录重编程的启动子。我们还将整合染色质联系地图 用WGS数据研究复合体SVS在淋巴瘤细胞染色体重编程中的作用。在这里，我们 假设染色体调节元件的生理性重新编程产生从头开始的协调 在体液免疫过程中建立特定细胞状态和表型所需的多组基因之间 响应和发生在DLBCL中SVS改变这些中枢结构或创建新的中枢结构导致选择性 恶性克隆的优势。在我们的第一个目标中，我们将整合转录、表观遗传和染色质 构象捕获分析以确定与以下相关的染色单体及其调控元件 在GC反应中建立细胞身份。在我们的第二个目标中，我们将描述基因组 B细胞淋巴瘤的重新排列情况以及这些如何直接与中枢和染色质联系在一起 通过生成匹配的WGS、Pole-C和RNA-Seq数据来建立患者来源的异种移植模型。

PROJECT SUMMARY/ABSTRACT Diffuse large B-cell lymphomas (DLBCL) arise from B-cells transiting different stages of the germinal center (GC) reaction. It has become clear that these tumors can co-opt regulatory circuits of normal B-cells to drive their own malignant phenotype. Prior studies observe an inverse correlation between the timing of transcriptional activation during reprogramming and the degree of topological reorganization near the gene locus. This suggests that the reorganization of the 3D genome is critical for B-cell development and highlights its importance in DLBCL. Regulatory hubs are highly interactive regions of enhancers that can form interactions with multiple genes within topologically associating domains (TADs) to induce gene activation at a higher probability than pairs of non-interacting genes within the same TAD. Hubs are often rewired during cell fate transitions. Recent work also suggests a new level of organization into broadly interactive networks called chromunities, which putatively allow for transboundary sharing of information and more extensive gene regulatory information critical for cell identity. Critical to understanding the mechanisms driving changes in gene networks is the study of how large-scale chromosomal rearrangements (structural variants, SVs) can co- opt regulatory elements to form aberrant or de novo chromunities, consequently driving aberrant gene expression. While the interpretation of complex structural variants (SVs) has focused primarily on gene dosage and disruption by aberrant TAD structures, little is known regarding the role of SVs in reprogramming regulatory hubs and their target genes. To investigate the role of chromunities and its associated hubs in cell fate transitions and oncogenesis, we will leverage chromatin conformation capture interaction maps (pcHiC, Pore-C) to develop a computational framework to nominate chromunities and map networks of enhancer and promoters driving epigenetic and transcriptional reprogramming. We will also integrate chromatin contact maps with WGS data to investigate the role of complex SVs in reprogramming chromunities in lymphomas. Here, we hypothesize that physiological reprogramming of chromunity regulatory elements creates de novo coordination between sets of genes required to establish specific cell states and phenotypes during the humoral immune response and that SVs occurring in DLBCL alter these hub structures or create new ones leading to selective advantage of malignant clones. In our first aim, we will integrate transcriptional, epigenetic, and chromatin conformation capture assays to identify chromunities and their regulatory elements associated with establishing cell identity in the GC reaction. In our second aim, we will characterize the genomic rearrangement landscapes of B-cell lymphomas and how these directly link to hubs and chromunities using patient-derived xenograft models by generating matched WGS, Pore-C, and RNA-seq data.