Project 1: The biochemical, topological and functional impact of cancer associated Ctcfmutations and their contribution to cancer

项目 1：癌症相关 Ctcf 突变的生化、拓扑和功能影响及其对癌症的贡献

• 批准号: 10402271
• 负责人: Jane Amanda Skok
• 金额: $ 31.94万
• 依托单位: NEW YORK UNIVERSITY SCHOOL OF MEDICINE
• 依托单位国家: 美国
• 财政年份: 2019
• 资助国家: 美国
• 起止时间: 2019-06-12 至 2024-05-31
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/10402271
• 关键词: 16q; 3-Dimensional; Acute; Acute T Cell Leukemia; Address; Affinity; Alleles; Animal Model; Architecture; B-Cell Lymphomas; B-Lymphocytes; Bacteria; Binding; Binding Sites; Biochemical; Biological Assay; Breast; CCCTC-binding factor; Cell Nucleus; Cell Survival; Cell physiology; Cells; Chemicals; Chromatin; Chromosome Structures; Chromosomes; Collaborations; Complement; Complex; Coupled; DNA; DNA-Directed RNA Polymerase; Defect; Development; Developmental Process; Dimerization; Disease; Doxycycline; ES Cell Line; Enhancers; Epigenetic Process; Gene Expression; Gene Expression Regulation; Genes; Genetic Transcription; Genome; Germ-Line Mutation; Health; Histones; Hour; Hybrids; Immunoglobulin Class Switching; Immunoglobulin Somatic Hypermutation; Immunoglobulin Switch Recombination; Knock-out; Length; Lymphoma; Malignant - descriptor; Malignant Neoplasms; Memory; Modeling; Mus; Mutate; Mutation; NOTCH1 gene; Oncogenic; Other Genetics; Outcome; Pattern; Phenotype; Plasma Cells; Play; Prostate; Proteins; Radiation; Regulatory Element; Reporter Genes; Reporting; Role; Specificity; Structure; Structure of germinal center of lymph node; System; Testing; Tissues; Transcriptional Activation; Transgenes; Zinc Fingers; base; cancer genome; cancer initiation; cofactor; cohesin; epigenome; experimental study; in vivo; innovation; insight; malignant phenotype; mouse model; mutant; novel therapeutic intervention; preference; programs; promoter; protein function; recruit; small molecule; three dimensional structure; transcription factor; tumor; tumor initiation; tumor progression; tumorigenesis

SUMMARY – PROJECT 1 (SKOK) It is well established that changes in cellular phenotypes that occur during development are highly dependent on the patterning and distribution of epigenetic marks in the genome. Indeed, the major focus of mechanistic epigenetic studies has centered around the interplay between histone or DNA modifying proteins and transcription factors. These studies have been immensely fruitful and yielded many fundamental insights into gene regulation in health and disease. Yet the enormous length of the genome and the requirement for large sets of genes to be regulated and transcribed in a coordinated manner poses significant energetic and physical challenges to cells. It is thus not surprising that an additional critical level of control of the epigenome is conferred through the three dimensional structure of chromosomes and their organization within the nucleus. Though it is known that 3D genome organization plays a crucial role in gene regulation and cancer, the underlying mechanisms connecting these are poorly understood. CTCF is central to these, as it governs genome organization and is implicated in cancer. In fact mutations in CTCF are detected in numerous cancers, however the extent to which they perturb 3D chromosomal architecture and contribute to the malignant phenotype is unknown. We hypothesize that each CTCF mutation will alter cellular function in a different manner depending on whether it is associated with (i) total loss of CTCF binding, (ii) a change in binding affinity, (iii) an alteration in binding motif preference or (iv) orientation of binding. Furthermore, we propose that mutations, which occur frequently in cancers that have no apparent effect on binding or binding affinity will have important functions in disrupting dimerization of CTCF molecules or binding of important cofactors such as cohesin. To test these models we aim to use three innovative approaches that examine the impact of mutations on (i) binding affinity and target sequence specificity, (ii) chromosome structure and gene regulation, and (iii) in vivo phenotype and tumor initiation/progression. We will start by characterizing the impact of cancer associated CTCF mutations on their binding affinity and binding motif. Next we will analyze their functional effect on cell survival, gene expression and chromosome organization. Finally, mouse models will address the key question of whether cancer associated CTCF mutations alone can predispose to malignant transformation or whether cooperating mutations are required. We propose that gaining a mechanistic predictive understanding of the impact of CTCF cancer associated mutants is essential to understand cancer genomes. This may enable a range of novel therapeutic approaches to counteract the malignancy effects of mutant architectural proteins. !1

摘要 - 项目1（SKOK） 众所周知，发育过程中发生的细胞表型的变化高度高度 取决于基因组中表观遗传标记的图案和分布。确实，专业 机械表观遗传研究的重点集中在Hisstone或DNA之间的相互作用围绕 修饰蛋白质和转录因子。这些研究非常富有成果，并产生了 许多对健康和疾病基因调节的基本见解。然而巨大的长度 基因组和对大量基因进行调节和转录的要求 方式对细胞具有重大的能量和物理挑战。因此，毫不奇怪 三维结构赋予表观基因组的其他临界控制水平 染色体及其在细胞核内的组织。 尽管众所周知，3D基因组组织在基因调节和癌症中起着至关重要的作用，但 连接这些连接的基本机制知之甚少。 CTCF对这些是核心 控制基因组组织，并暗示癌症。实际上在CTCF中检测到 许多癌症，但是它们在摄取3D染色体体系结构的程度和 有助于恶性表型是未知的。我们假设每个CTCF突变都会改变 蜂窝函数以不同的方式取决于（i）CTCF的总损失是否与之相关 结合，（ii）结合亲和力的变化，（iii）结合基序偏好或（iv）方向的改变 结合。此外，我们提出，在没有的癌症中经常发生的突变 对结合或结合亲和力的明显影响将在破坏二聚 CTCF分子或重要辅助因子（例如粘着蛋白）的结合。为了测试这些模型，我们的目的是 使用三种创新的方法来检查突变对（i）结合亲和力和目标的影响 序列特异性，（ii）染色体结构和基因调节，以及（iii）体内表型和（iii） 肿瘤倡议/进展。我们将首先表征与癌症相关的CTCF的影响 其结合亲和力和结合基序的突变。接下来，我们将分析它们对细胞的功能影响 生存，基因表达和染色体组织。最后，鼠标模型将解决密钥 与癌症相关的CTCF突变是否可能易于恶性的问题 转换或是否需要合作突变。我们建议获得机械 对CTCF癌症相关突变体的影响的预测理解对于了解 癌症基因组。这可能使一系列新型的治疗方法来抵消 突变建筑蛋白的恶性影响。 ！1