Phase Transitions in Chromatin Organization that cause Cancer Progression

导致癌症进展的染色质组织的相变

基本信息

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
项目类别：
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

项目摘要

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.

项目概要尽管测序、成像和筛选技术取得了进步，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。健康的细胞总是呈椭球体，光滑的核形状和独特的染色质分布，而癌细胞的特点是不规则，锯齿状的核形状和破坏的染色质分布。相关地，最常见的突变之一人类癌症中的蛋白质是称为 ARID1A 的染色质重塑 BAF 复合物的组成部分。这些突变失去核小体滑动活性，导致转录组改变和癌症进展。作为一个 BAF 复合物的结构支架，ARID1A 中许多导致癌症的突变会导致早期癌症截断并导致 BAF 复合体组装丢失。然而，驱动突变也存在于相对 ARID1A 的未表征的本质无序区域，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和相分离决定整体核结构和组织，以及形成核体像核仁和染色质区室（如异染色质），但直到最近我们还无法控制该组织，或将其与染色质区室功能最终联系起来。布兰文实验室有开发了光遗传学工具，可以控制凝聚物的体内生物物理行为。作为马克癌症研究基金会的生命科学研究人员，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中的作用所发现的染色质包含、排除和压缩规则由相分离决定隔间。在这个提案中，我将扩展我的研究，以了解发生的生物物理变化 ARID1A 突变引起的这些核区室会导致癌症，以及这与它们的关系如何疾病表型。在目标 1 中，我将探究决定冷凝物如何与染色质相互作用的相互作用，并利用光触发的相分离来调节活细胞中的染色质压缩和转录。在目标 2，我将确定染色质聚合物如何引导相分离，以及核硬度如何影响核体体积和功能输出。在目标 3 中，在我的合作导师 Cigall Kadoch 博士的指导下，我将利用目标 1 和 2 中获得的知识构建 BAF 复合蛋白 ARID1A 的分子机制和 ARID1B 在肿瘤发生中的作用，包括它们的 IDR 在靶向 BAF 复合物活性中的作用以及癌症相关突变对缩合行为、序列靶向和转录输出的影响。在我的导师的支持以及普林斯顿大学和普林斯顿大学更大的研究环境下在达纳法伯癌症研究所，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分析。这些目标共同将提供一个新的对癌症核组织的看法可能会带来新的治疗方法。