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: 10652280
• 负责人: Jane Amanda Skok
• 金额: $ 40.34万
• 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/10652280
• 关键词: 16q; 3-Dimensional; Acceleration; Acute; Acute T Cell Leukemia; Address; Affinity; Alleles; Animal Model; Architecture; B-Cell Lymphomas; B-Lymphocytes; Bacteria; Binding; Binding Sites; Biochemical; Biological Assay; 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; Heterozygote; Histones; Hour; Hybrids; Immunoglobulin Class Switching; Immunoglobulin Somatic Hypermutation; Immunoglobulin Switch Recombination; Knock-out; Length; Lymphoma; Malignant - descriptor; Malignant Neoplasms; Malignant neoplasm of prostate; Memory; Modeling; Mus; Mutate; Mutation; NOTCH1 gene; Oncogenic; Other Genetics; Outcome; Pattern; Phenotype; Physically Challenged; Plasma Cells; Play; Proliferating; 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; cancer genome; cancer initiation; carcinogenesis; cofactor; cohesin; epigenome; experimental study; in vivo; innovation; insight; malignant breast neoplasm; 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变化是高度变化的。 事实上，主要取决于基因组中表观遗传标记的模式和分布。 表观遗传学机制研究的焦点集中在组蛋白或 DNA 之间的相互作用 这些研究已经取得了丰硕的成果。 关于健康和疾病的基因调控的许多基本见解。 基因组以及对大量基因进行协调调节和转录的要求 因此，这种方式对细胞带来了重大的能量和身体挑战。 通过三维结构赋予表观基因组额外的关键控制水平 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控和癌症中发挥着至关重要的作用， 人们对连接这些的基本机制知之甚少，因为 CTCF 是这些的核心。 CTCF 控制基因组组织并与癌症有关。事实上，CTCF 的突变可在以下细胞中检测到。 许多癌症，但是它们扰乱 3D 染色体结构的程度和 我们发现每个 CTCF 突变都会改变 细胞功能以不同的方式取决于它是否与 (i) CTCF 完全丧失相关 结合，(ii) 结合亲和力的变化，(iii) 结合基序偏好的改变或 (iv) 方向 此外，我们提出突变，这种突变经常发生在没有结合的癌症中。 对结合或结合亲和力的明显影响将在破坏二聚化方面具有重要功能 CTCF 分子或重要辅助因子（例如粘连蛋白）的结合为了测试这些模型，我们的目标是。 使用三种创新方法来检查突变对 (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控，以及 (iii) 体内表型和 我们首先描述癌症相关 CTCF 的影响。 接下来我们将分析它们对细胞的功能影响。 最后，小鼠模型将解决关键问题。 癌症相关的 CTCF 突变是否单独会导致恶性肿瘤的问题 我们建议获得一种机制。 预测性了解 CTCF 癌症相关突变体的影响对于理解 这可能使一系列新的治疗方法能够抵消癌症基因组的影响。 突变蛋白结构的恶性效应。 !1