Functionizing the epigenome in Ewing sarcoma

尤文肉瘤中表观基因组的功能化

• 批准号: 8658180
• 负责人: ANDREW L KUNG
• 金额: $ 16.36万
• 依托单位: COLUMBIA UNIVERSITY HEALTH SCIENCES
• 依托单位国家: 美国
• 财政年份: 2012
• 资助国家: 美国
• 起止时间: 2012-04-01 至 2015-03-31
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/8658180
• 关键词: Academia; Cancer Model; Cell Culture Techniques; Cell Death; Cell Line; Cells; Clinical; Cutaneous; DNA Methylation; Development; Disease; Drug Targeting; Emerging Technologies; Enzymes; Ewings sarcoma; Explosion; Feasibility Studies; Frequencies; Gene Expression; Genes; Goals; Growth; Histone Deacetylase Inhibitor; Immunodeficient Mouse; In Vitro; Industry; Infection; Libraries; Malignant Neoplasms; Modification; Nature; Pharmaceutical Preparations; Proteins; Publishing; Sampling; Subfamily lentivirinae; T-Cell Lymphoma; Tertiary Protein Structure; Therapeutic; Translations; Tumorigenicity; Validation; Work; Xenograft procedure; base; cancer cell; cell growth; cell type; drug development; drug discovery; drug mechanism; epigenome; genetic regulatory protein; in vivo; innovation; interest; loss of function; neoplastic cell; next generation sequencing; non-genetic; nucleoside analog; small hairpin RNA; success; therapeutic target; tumor growth; tumor xenograft; tumorigenesis; tumorigenic

DESCRIPTION (provided by applicant): There is an increasing understanding that epigenetic changes contribute to cancer development. Because epigenetic changes are by definition reversible, and because many epigenetic modifying enzymes are highly amenable to drug discovery, there is an explosion in interest in developing epigenetic-targeted therapies. Despite being highly "druggable", a major impediment to clinical translation of epigenetic therapies is the lack of understanding as to the clinical diseases to which these drugs should be applied. We are therefore at a crossroad in which multiple entities within academia and industry are actively developing drugs targeting epigenetic modifying proteins, but the diseases to which they should be applied are as yet poorly defined. We hypothesize that a comprehensive and systematic assessment of which epigenetic regulating proteins are critical for in vivo tumor growth will help define the epigeneti targets appropriate for therapeutic application in specific cancer sub-types. In this proposal, we will use pooled shRNA analysis to systematically determine, which epigenetic-modifying proteins are critical for the in vitro and in vivo growth of Ewing sarcoma cells. In the first Specific Aim, we have used gene annotation and protein domain analysis to identify 449 gene products that have known or putative epigenetic regulatory function (the epigenome). We will package a shRNA library composed of 3040 shRNAs targeting the epigenome and controls. In the second Specific Aim, we will use this pooled library to transduce 4 Ewing sarcoma cell lines that have been iteratively selected for high tumorigenicity. Next-generation sequencing will be used to determine the frequency of all shRNAs in an input sample compared to samples selected after in vitro growth in cell culture and in vivo growth as xenograft tumors. An analysis pipeline will identify genes products essential for in vitro and in vivo tumor cell growth. In the third Specific Aim we will fully assess the cellular effects associated with loss o function of specific high priority epigenetic regulatory proteins identified in the preceding Aims, and will assess therapeutic targeting in established Ewing sarcoma xenografts. Together, the overall goal of these studies is to systematically determine which epigenetic regulatory proteins are required for Ewing sarcoma growth and to achieve in vivo proof-of-concept for therapeutic targeting of Ewing sarcoma with epigenetic therapies. Success in these studies will establish a paradigm that can be readily applied to almost all other cancer sub-types.

描述（由申请人提供）： 越来越多的人认识到表观遗传变化有助于癌症的发展。 由于表观遗传变化根据定义是可逆的，并且由于许多表观遗传修饰酶非常适合于药物发现，因此开发表观遗传靶向疗法的兴趣激增。 尽管表观遗传疗法是高度“可用药”的，但临床转化的主要障碍是缺乏对表观遗传疗法的理解， 这些药物应应用于哪些临床疾病。 因此，我们正处于一个十字路口，学术界和工业界的多个实体正在积极开发针对表观遗传修饰蛋白的药物，但它们应该应用于的疾病尚未明确。 我们假设，一个全面和系统的评估，表观遗传调节蛋白是至关重要的在体内肿瘤生长将有助于确定表观遗传的目标，适用于特定的癌症亚型的治疗应用。 在本提案中，我们 将使用合并的shRNA分析来系统地确定哪些表观遗传修饰蛋白对尤文肉瘤细胞的体外和体内生长至关重要。 在第一个特定目标中，我们使用基因注释和蛋白质结构域分析来识别449个具有已知或推定的表观遗传调控功能（表观基因组）的基因产物。 我们将包装一个由3040个靶向表观基因组和对照的shRNA组成的shRNA文库。 在第二个特定目标中，我们将使用这个汇集的文库来筛选4个尤文肉瘤细胞系，这些细胞系已经被反复选择为高致瘤性。 将使用下一代测序来确定输入样品中所有shRNA的频率，与在细胞培养物中体外生长和作为异种移植肿瘤体内生长后选择的样品相比。 分析管道将识别体外和体内肿瘤细胞生长所必需的基因产物。 在第三个具体目标中，我们将充分评估与在前述目标中鉴定的特定高优先级表观遗传调节蛋白的功能丧失相关的细胞效应， 并将评估在已建立的尤文肉瘤异种移植物中的治疗靶向。 总之，这些研究的总体目标是系统地确定尤文肉瘤生长所需的表观遗传调节蛋白，并实现尤文肉瘤表观遗传疗法治疗靶向的体内概念验证。 这些研究的成功将建立一个范式，可以很容易地应用于几乎所有其他癌症亚型。