Computational analysis of Human High Grade Gliomas

描述(申请人提供)：胶质瘤是一种具有多种遗传和表观遗传改变的致命性疾病。这些变化在癌症的发展和进展中协调一致地发挥作用。癌症系统生物学是一门新兴学科，它将高通量基因组数据和计算方法相结合，以提供对导致同一癌症表型的不同途径失调的一致和系统的理解。这一新学科有望将医学实践从反应性转变为预测性。在这里，我们将应用逆向工程计算方法来解剖和验证驱动高级别胶质瘤间充质表型的转录网络。间充质和血管生成相关基因在恶性人脑胶质瘤中的表达与不良的临床预后有关。我们使用了哥伦比亚国家生物医学计算中心(MAGNET)开发的ARACNe(精确细胞网络重建算法)来识别与预后不良相关的调控间充质基因表达特征的转录因子。后者是通过对广泛收集的恶性胶质瘤微阵列表达谱进行分级聚类来鉴定的。我们的分析已经确定了一个由六个相互调节的转录因子以及绝大多数间充质基因组成的高度相互关联的模块。我们还将计算分析扩展到能够预测主转录调控因子的翻译后调节器的新算法(Mindy，网络动力学的调节器推理)。在这项提案中，我们将设计和使用新的计算工具来整合人类脑瘤的遗传、表观遗传和功能数据的许多来源。我们的目标是：重建和实验操作负责高级别胶质瘤间充质信号表达的转录和翻译后程序(目标1)；阐明高级别胶质瘤沉默间充质信号转录抑制因子ZNF238的机制，并测试ZNF238基因失活在小鼠胶质瘤形成中的作用(目标2)；通过计算识别和实验验证调节恶性胶质瘤间充质信号的“可用药”基因，并测试它们作为候选治疗靶点(目标3)；组装和传播一个全基因组的人脑胶质瘤交互作用组(HGI)，它将整合具有高级别胶质瘤间充质表型特征的遗传、表观遗传和功能改变的不同来源(目标4)。科学界将通过磁铁中心传播基础设施访问HGI。最终，我们的目标是利用通过计算推断和实验验证的胶质瘤侵袭性调节因子，作为治疗干预的宝贵新靶点。公共卫生相关性：高级别胶质瘤(也称为多形性胶质母细胞瘤)是人类中枢神经系统肿瘤中生长最快的类型。它们总是与不良的预后有关。最近，多形性胶质母细胞瘤的两个固有功能被认为是恶性肿瘤的关键特征，即侵袭邻近正常大脑并产生新血管的能力。人们普遍认为，目前治疗高级别胶质瘤的失败主要是由于缺乏有效的工具来对抗侵袭性脑瘤的这些特征。这项拨款提案使用了哥伦比亚大学医学中心最近开发的尖端计算技术，利用大量原发多形性胶质母细胞瘤的微阵列表达谱，并确定负责恶性胶质瘤最具侵袭性属性的关键基因主调控因子(“间充质特征”)。我们将在细胞培养系统和实验动物中进行一系列最先进的实验，以验证新算法所做的预测。我们预计，指导恶性胶质瘤最具侵袭性特征的主要基因程序的识别将为治疗干预提供最佳的可能靶点。

DESCRIPTION (provided by applicant): Glioma is a lethal disease with multiple genetic and epigenetic alterations. These changes work in concert in a coordinated fashion in cancer development and progression. Cancer Systems Biology is an emerging discipline in which high-throughput genomic data and computational approaches are integrated to provide a coherent and systematic understanding of the diverse pathway dysregulations responsible for the presentation of the same cancer phenotype. This new discipline promises to transform the practice of medicine from a reactive one to a predictive one. Here we will apply a reverse engineering computational approach to dissect and validate the transcriptional network that drives the mesenchymal phenotype of high-grade glioma. The expression of mesenchymal and angiogenesis-associated genes in malignant human glioma is associated with very poor clinical outcome. We have used ARACNe (Algorithm for the Reconstruction of Accurate Cellular Networks), one of the tools developed by the Columbia National Center for Biomedical Computing (MAGNet), to identify transcription factors regulating a mesenchymal gene expression signature associated with poor prognosis. The latter was identified by hierarchical clustering of a wide collection of microarray expression profiles of malignant glioma. Our analysis has identified a highly interconnected module of six transcription factors that regulate each other as well as the vast majority of the mesenchymal genes. We have also extended the computational analyses to new algorithms able to predict post-translational modulators of the master transcriptional regulators (MINDy, Modulator Inference by Network Dynamics). In this proposal we will design and use new computational tools to integrate the many sources of genetic, epigenetic and functional date available on human brain tumors. Our goals are: to reconstruct and experimentally manipulate the transcriptional and post-translational programs responsible for the expression of the mesenchymal signature of high-grade glioma (Aim 1); to elucidate the mechanism by which high-grade glioma silence ZNF238, a transcriptional repressor of the mesenchymal signature, and test the role of ZNF238 gene inactivation in gliomagenesis in the mouse (Aim 2); to computationally identify and experimentally validate "druggable" genes that regulate the mesenchymal signature in malignant glioma and to test them as candidate therapeutic targets (Aim 3); to assemble and disseminate a genome-wide, Human Glioma interactome (HGi) that will integrate the diverse sources of genetic, epigenetic, and functional alterations that characterize the mesenchymal phenotype of high-grade glioma (Aim 4). The HGi will be accessible to the scientific community via the MAGNet Center dissemination infrastructure. Ultimately, we aim to exploit the computationally inferred and experimentally validated regulators of glioma aggressiveness as invaluable new targets for therapeutic intervention. Public Health Relevance: High-grade gliomas (also known as glioblastoma mutiforme) are the fastest growing type of central nervous system tumors in humans. They are invariably associated with a bad prognosis. Recently, two intrinsic capabilities of glioblastoma multiforme have been recognized as key traits of malignancy, the ability to invade adjacent normal brain and produce new blood vessels. There is general agreement that the current failures in the treatment of high-grade gliomas are mostly caused by lack of effective tools against these features of aggressive brain tumors. This grant proposal uses cutting-edge computational technologies recently developed at Columbia University Medical Center to exploit microarray expression profiles from a large collection of primary glioblastoma multiforme and identify the key genetic master regulators responsible for the most aggressive attributes of malignant gliomas ("the mesenchymal signature"). We will perform a series of state-of-the-art experiments in cell culture systems and experimental animals to validate the predictions made by the new algorithms. We anticipate that the identification of the master genetic programs directing the most aggressive features of malignant gliomas will offer the best possible targets for therapeutic intervention.