Deciphering the 3D genome of pediatric brain tumors

项目摘要 在患有实体肿瘤的儿童中，儿童脑肿瘤是最常见的发病原因。重要的是， 积极的治疗方案往往会导致衰弱的神经效应。意识到 对大脑发育至关重要的发育过程也被解除了调控，癌症提供了新的希望 用于了解和治疗脑瘤。事实上，单细胞RNAseq分析进一步证明了 缺陷在儿童脑肿瘤家族决定中的作用。为了发现肿瘤发生的新驱动因素， 我们将集中于三维(3D)基因组折叠在儿童脑肿瘤中的功能。事实上，3D 染色质相互作用参与基因表达调控，基因组折叠的变化与 发育过程中细胞身份的获取。虽然人们对阐明3D的功能越来越感兴趣 在发育过程和癌症中的基因组结构，3D基因组是如何组织在 不同的儿童脑肿瘤及其在肿瘤形成和发展中的作用尚不清楚。我们假设 在胚胎或出生后发育过程中扰乱3D基因组折叠会改变基因表达，导致 发育中大脑中的异常细胞分化和肿瘤发生。为了检验我们的假设，我们将 全面询问儿童脑肿瘤的基因组以寻找可能影响3D的非编码变体 基因组折叠。我们将使用一个名为Akita的深度学习模型来预测3D染色质相互作用 仅来自基因组序列的频率。因为秋田只需要DNA序列作为输入，所以我们可以预测 适应单核苷酸变体(SNV)的单个框架内的任何变体的影响， 插入/删除(Indels)和结构变异(Svs)。秋田将用于儿科脑全基因组 来自Gabriella Miller Kids First(KF)的序列(WGS)以及染色质捕获、表观遗传和表达数据 来自4D核组(4DN)和基因-组织表达(GTEx)计划的目标如下：1) 确定不典型畸胎样/横纹肌样瘤AT/RT肿瘤的三维基因组结构。我们已经发起了我们的 使用AT/RT的研究，肿瘤被认为是由于早期发育缺陷11和最常见的大脑 肿瘤发生在六个月以下的儿童。1.a.我们将开发一条生物信息学管道，使用Akita来 量化一个基因变异在多大程度上被预测为扰乱AT/RT肿瘤的3D染色质相互作用。1.B.我们 将验证和确定在AT/RT肿瘤中观察到的3D基因组折叠中断的功能相关性。 2)确定儿童恶性肿瘤的三维基因组结构。我们将扩展我们对秋田的分析 为了增加儿童脑肿瘤的恶性，重点针对这一试点项目进行恶性程度最高的治疗 难治性肿瘤。这个创新的项目，使用一种新的深度学习工具Akita，将导致新的研究 假说，并将加速发现儿科癌症肿瘤发生的其他调节因素，从而 这些毁灭性疾病的潜在治疗策略。

Project Summary Pediatric brain tumors are the most frequent cause of morbidity in children with solid tumors. Importantly, the aggressive therapeutic regiments often lead to debilitating neurological effects. The realization that developmental processes critical to brain development are also deregulated in cancer has provided new hope for understanding and treating brain tumors. Indeed, single cell-RNAseq analyses have further demonstrated the role of defects in lineage determination for pediatric brain tumors. To discover novel drivers of tumorigenesis, we will focus on the function of three-dimensional (3D) genome folding in pediatric brain tumors. Indeed, 3D chromatin interactions are involved in gene expression regulation, and changes in genome folding are linked to cell identity acquisition during development. While there is increasing interest in elucidating the function of 3D genome architecture during developmental processes and in cancer, how the 3D genome is organized in different pediatric brain tumors and its roles in tumor formation and progression are unknown. We hypothesize that disrupted 3D genome folding during embryonic or postnatal development alters gene expression leading to abnormal cell differentiation and tumorigenesis in the developing brain. To test our hypothesis, we will comprehensively interrogate the genomes of pediatric brain tumors for non-coding variants that may affect 3D genome folding. We will use a deep-learning model called Akita that predicts 3D chromatin interaction frequencies from genome sequence alone. Because Akita only requires DNA sequence as input, we can predict the effect of any variant within a single framework that accommodates single-nucleotide variants (SNVs), insertion/deletions (indels), and structural variation (SVs). Akita will be used with pediatric brain whole genome sequences (WGS) from Gabriella Miller Kids First (KF) plus chromatin capture, epigenetic, and expression data from the 4D Nucleome (4DN) and Genotype-Tissue Expression (GTEx) programs in the following aims: 1) Determine the 3D genome architecture of Atypical teratoid/rhabdoid tumor AT/RT tumors. We have initiated our study using AT/RT, tumors thought to be due to defects in early development11 and the most common brain tumor in children less than six months of age. 1.A. We will develop a bioinformatics pipeline that uses Akita to quantify how much a genetic variant is predicted to disrupt 3D chromatin interactions in AT/RT tumors. 1.B. We will validate and determine the functional relevance of 3D genomic folding disruptions observed in AT/RT tumors. 2) Determine the 3D genome architecture of malignant pediatric tumors. We will extend our analyses with Akita to additional malignant pediatric brain tumors, focusing for this pilot project on the most malignant and treatment refractory tumors. This innovative project, using a new deep-learning tool Akita, will lead to, novel research hypotheses and will accelerate the discovery of additional regulators of pediatric cancer tumorigenesis and thus to potential therapeutic strategies for these devastating diseases.