Phase Transitions in Chromatin Organization that cause Cancer Progression

导致癌症进展的染色质组织的相变

• 批准号: 10572860
• 负责人: Amy Strom
• 金额: $ 12.05万
• 依托单位: PRINCETON UNIVERSITY
• 依托单位国家: 美国
• 财政年份: 2023
• 资助国家: 美国
• 起止时间: 2023-03-01 至 2025-02-28
• 项目状态: 未结题
• 来源: https://reporter.nih.gov/project-details/10572860
• 关键词: ARID1A gene; Affect; Agreement; Amino Acid Sequence; Area; Behavior; Binding; Binding Proteins; Binding Sites; Biological Assay; Biological Sciences; Biology; Biophysical Process; Biophysics; Bromodomain; Cancer Biology; Cancer Etiology; Cancerous; Cell Nucleolus; Cell Nucleus; Cells; Chromatin; Chromatin Fiber; Chromosomal Rearrangement; Common Neoplasm; Complex; DNA Binding Domain; DNA Sequence; Dana-Farber Cancer Institute; Defect; Disease; Environment; Epigenetic Process; Exclusion; Foundations; Functional disorder; Gene Expression Profile; Gene Order; Genetic; Genetic Transcription; Genome; Genomic Segment; Genomics; Heterochromatin; Human; Image; Investigation; Knowledge; Light; Link; Malignant Neoplasms; Mechanics; Mediating; Mentors; Methods; Modeling; Modification; Molecular; Morphology; Mutate; Mutation; Nuclear; Nuclear Lamina; Nuclear Structure; Nucleosomes; Oncogenic; Outcome; Output; Pattern; Phase; Phase Transition; Phenotype; Physical condensation; Polymers; Process; Protein Region; Proteins; RNA; Research; Role; Sampling; Shapes; Site; Slide; Specificity; Structure; Structure-Activity Relationship; System; Technology; Therapeutic; Training; Transcriptional Activation; Universities; Work; anticancer research; biophysical properties; body volume; cancer diagnosis; cell growth; density; disease phenotype; driver mutation; in vivo; next generation sequencing; novel; optogenetics; protein complex; protein crosslink; scaffold; screening; theories; tool; transcriptome; tumor progression; tumorigenesis; viscoelasticity

Project Summary Despite advances in sequencing, imaging and screening technologies, morphological changes in nuclear structure are still utilized as a common and reliable diagnosis of cancer. Healthy cells invariably have ellipsoid, smooth nuclear shape and distinctive chromatin distribution, while cancerous cells are characterized by irregular, jagged nuclear shape and disrupted chromatin distribution. Relatedly, one of the most commonly mutated proteins in human cancers is a component of the chromatin remodeler BAF complex known as ARID1A. These mutations lose nucleosome sliding activity, leading to altered transcriptome and cancer progression. As a structural scaffold of the BAF complex, many of the mutations in ARID1A that cause cancer result in early truncation and lead to loss of BAF complex assembly. However, driver mutations also exist in the relatively uncharacterized intrinsically disordered regions of ARID1A whose molecular mechanism is unknown. Investigations into nuclear organization have identified the importance of intrinsically disordered regions and phase separation in dictating overall nuclear structure and organization, as well as forming nuclear bodies like the nucleolus, and chromatin compartments like heterochromatin, but until recently we have not been able to control this organization, or link it conclusively to chromatin compartment function. The Brangwynne lab has developed optogenetic tools that allow for control of in vivo biophysical behavior of condensates. As a Life Science Research Fellow through the Mark Foundation for Cancer Research, I have determined the role of chromatin-chromatin crosslinking protein HP1a in determining nuclear shape and mechanics, as well as discovered rules for chromatin inclusion, exclusion, and compaction dictated by phase separated compartments. In this proposal I will expand my research to understand the biophysical changes that occur in these nuclear compartments upon ARID1A mutations that drive cancer, and how this is connected to their disease phenotype. In Aim 1, I will interrogate interactions that dictate how condensates interact with chromatin, and utilize light-triggered phase separation to modulate chromatin compaction and transcription in living cells. In Aim 2, I will determine how the chromatin polymer directs phase separation, and how nuclear stiffness influences nuclear body volume and functional output. In Aim 3, under the guidance of my co-mentor Dr. Cigall Kadoch, I will utilize knowledge gained in Aims 1 and 2 to build a molecular mechanism of BAF complex proteins ARID1A and ARID1B in oncogenesis, including the roles of their IDRs in targeting BAF complex activity and effects of cancer-associated mutations on condensation behavior, sequence targeting and transcriptional output. With the support of my mentors and the greater research environment at both Princeton University and the Dana Farber Cancer Institute, I will have access to unique tools, and will receive training in cancer biology methods, biophysical theory, and next-generation sequencing assays. Together, these aims will provide a new perspective on nuclear organization in cancer that may lead to novel venues of therapeutics.

项目摘要 尽管取得了测序，成像和筛选技术的进步，但核的形态变化 结构仍然被用作癌症的常见且可靠的诊断。健康的细胞总是具有椭圆形， 光滑的核形状和独特的染色质分布，而癌细胞的特征是不规则， 锯齿状的核形状和染色质分布破坏。相关，最常见的突变之一 人类癌症中的蛋白质是染色质重塑剂BAF复合物的组成部分，称为ARID1A。这些 突变失去了核小体滑动活性，导致转录组和癌症进展的改变。作为 BAF复合物的结构支架，ARID1a中许多引起癌症的突变导致早期 截断并导致BAF复合物组件的损失。但是，驱动程序突变也相对存在 ARID1A的固有无序区域的未表征，其分子机制尚不清楚。 对核组织的调查已经确定了本质上无序区域的重要性 以及指示整体核结构和组织以及形成核体的相位分离 像核仁和染色质隔室一样 控制该组织，或将其最终链接到染色质隔室功能。 Brangwynne实验室有 开发了光遗传学工具，可以控制冷凝水的体内生物物理行为。 作为Mark Cancer Research基金会的生命科学研究研究员，我已经确定 染色质 - 染色质交联蛋白HP1A在确定核形状和力学方面的作用 如发现的染色质包含，排除和压实的规则，由相分开决定 车厢。在此提案中，我将扩大研究，以了解 这些在促进癌症的ARID1A突变上的核区室，以及如何将其连接 疾病表型。在AIM 1中，我将询问相互作用，以决定冷凝水如何与染色质相互作用， 并利用光触发的相分离来调节活细胞中的染色质压实和转录。在 AIM 2，我将确定染色质聚合物如何指导相分离以及核刚度如何影响 核体积和功能输出。在AIM 3中，在我的同事Cigall Kadoch博士的指导下 将利用目标1和2中获得的知识来构建BAF复合蛋白ARID1A的分子机制 和ARID1b在肿瘤发生中，包括其IDR在靶向BAF复杂活性和影响的作用以及 癌症相关的突变对凝结行为，序列靶向和转录输出。 在我的导师和普林斯顿大学和更大的研究环境的支持下 Dana Farber癌症研究所，我将获得独特的工具，并将接受癌症生物学培训 方法，生物物理理论和下一代测序测定法。这些目标将共同提供新的 癌症中核组织的观点可能导致新的治疗场所。