Chromatin mobility in response to DNA damage

DNA 损伤时的染色质迁移率

• 批准号: 10477011
• 负责人: Keith D Bonin
• 金额: $ 58.03万
• 依托单位: WAKE FOREST UNIVERSITY HEALTH SCIENCES
• 依托单位国家: 美国
• 财政年份: 2018
• 资助国家: 美国
• 起止时间: 2018-09-19 至 2024-08-31
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/10477011
• 关键词: 3-Dimensional; Acridines; Address; Affect; Affinity; Automobile Driving; Biogenesis; Biological Assay; Biometry; Biophysics; Cancer Patient; Cell Nucleus; Cell model; Cells; Cellular Assay; Cellular biology; Chemistry; Chemotherapy and/or radiation; Chromatin; Chromosomal Breaks; Chromosomes; Clinical; Communities; DNA; DNA Damage; DNA Repair; DNA Sequence Rearrangement; Data; Diffusion; Dimensions; Disease; Dyes; Dysmyelopoietic Syndromes; Elements; Engineering; Environment; Etiology; Exposure to; Freezing; Frequencies; Genome; Genomic Instability; Genomics; Goals; Hematopoietic stem cells; Image; Image Analysis; Kinetics; Knowledge; Label; Length; Light; Link; Lymphoma; Maintenance; Malignant Neoplasms; Maps; Measurement; Mediating; Methodology; Methods; Modeling; Motion; Movement; Myeloproliferative disease; Nuclear; Oncology; Optical Methods; Optics; Outcome; Patients; Pharmacology; Physical condensation; Polymers; Probability; Protocols documentation; Recurrence; Reporter; Research; Resolution; Resources; Rhodamine; Risk; Role; Sampling; Scanning; Second Primary Cancers; Survivors; System; Testing; Therapeutic; Three-Dimensional Imaging; Time; Tissues; Translations; base; biophysical model; cancer initiation; cancer therapy; clinically relevant; genetic approach; genomic aberrations; genomic predictors; imaging system; improved; in silico; insight; inter-individual variation; leukemia; mechanical properties; mortality; novel; novel strategies; prevent; protein distribution; response; therapy development; translational study; treatment choice

Project Summary Genomic translocations are well-established drivers of therapy-related myeloid neoplasms (t-MN) that affect survivors of primary malignancies. t-MN accounts for 10-20% of all myeloid malignancies and have very poor clinical outcomes. It is not possible to predict which patients treated for a primary cancer will develop t-MN, which constitutes a major clinical challenge. A method to assess the risk of translocations after patient exposures to DNA damaging chemotherapy and radiations would inform therapeutic decisions. Translocations depend on the movements of broken DNA ends on non-homologous chromosomes. We developed a method based on diffractive optical elements (DOE) to track photoactivated chromatin reporters (PACR) and map chromatin motions in the cell nucleus. Our preliminary data show that chromatin movements transiently decrease in response to DNA damage, which led to the hypothesis that chromatin `freezes' to facilitate the initial steps of the DNA damage response and reduce frequencies of genomic rearrangements. This effect may be mediated by reversible chromatin compaction and by chromatin interactions with structural nuclear elements. Inter-individual variability may determine genomic aberration frequencies and t-MN risk. The following specific aims will expand PACR assays and test this hypothesis: In Aim 1, methodology will be developed for 3D measurements of chromatin mobility, in order to improve tracking accuracy and to account for inhomogeneities of the nuclear environment in all three dimensions. Rapid light sheet imaging will be used, and a novel multifocus 3D system based on a rotating point spread function DOE will be built. New photoactivatable DNA dyes will be developed to expand the PACR approach to difficult-to-transfect cells and tissues. The goals for Aim 2 are to identify the mechanisms controlling chromatin motions after DNA damage and to assess the functional consequences for DNA repair and translocations of chromatin `freezing'. We will feed PACR measurements with high time resolution (before/during/after DNA damage) into biophysical polymer models to predict physical changes of chromatin (intramolecular forces, persistence length, etc.), then test the predictions using multidimensional maps of chromatin motions, compaction, and nucleoskeletal organization, as well as functional cell assays. Two approaches to alter chromatin diffusion will assess causality between chromatin motions, DNA repair, and genomic translocations. In Aim 3, we will use hematopoietic stem/progenitor cell samples from t-MN patients and healthy donors to test for clinically relevant associations between chromatin motions and genomic translocations. Characterizing the physical origins of genomic translocations may yield new methods to predict, and new targets to prevent, genomic rearrangements driving cancer initiation. Beyond the proposed research focused on chromatin motions during DNA repair, we anticipate broad applicability of our novel 3D imaging resources to study chromatin in multiple contexts.

项目摘要 基因组易位是影响与治疗相关的髓系肿瘤(t-MN)的公认驱动因素 原发恶性肿瘤的幸存者。T-MN占所有髓系恶性肿瘤的10%-20%， 临床结果。不可能预测哪些接受原发癌症治疗的患者会发展成t-MN， 这构成了一个重大的临床挑战。一种评估患者术后易位风险的方法 暴露在DNA破坏性的化疗和辐射中将为治疗决定提供依据。易位 依赖于非同源染色体上断裂的DNA末端的运动。我们开发了一种方法 基于衍射光学元件(DOE)跟踪光激活染色质报告器(PACR)和MAP 染色质在细胞核内运动。我们的初步数据显示，染色质的运动是短暂的 对DNA损伤的反应减少，这导致了这样的假设：染色质“冻结”是为了促进 DNA损伤反应的初始步骤和减少基因组重排的频率。此效果可能 由可逆的染色质压缩和染色质与结构核的相互作用所介导 元素。个体间的差异可能决定了基因组的畸变率和t-MN风险。这个 以下具体目标将扩展PACR分析并检验这一假设：在目标1中，方法论将是 为染色质迁移率的3D测量而开发，以提高跟踪精度和计算 对于核环境在所有三个维度上的不均匀。将使用快速光片成像， 并建立了一种基于旋转点扩散函数DOE的新型多聚焦三维系统。新的 将开发可光激活的DNA染料，以将PACR方法扩展到难以转基因的细胞和 纸巾。目标2的目标是确定dna损伤后控制染色质运动的机制。 并评估染色质“冷冻”对DNA修复和移位的功能影响。我们会 将高时间分辨率的PACR测量(DNA损伤之前/期间/之后)送入生物物理 预测染色质的物理变化(分子内力、持续长度等)的聚合物模型，然后 使用染色质运动、紧凑和核骨骼的多维地图来检验预测 组织，以及功能细胞分析。两种改变染色质扩散的方法将评估 染色质运动、DNA修复和基因组易位之间的因果关系。在目标3中，我们将使用 T-MN患者和健康献血者的造血干/祖细胞样本检测临床相关性 染色质运动和基因组易位之间的关联。描述了……的物理起源 基因组易位可能产生预测基因组的新方法，以及预防基因组易位的新靶点 重排导致癌症的发生。除了拟议的研究外，还集中在染色质运动上 在DNA修复方面，我们预计我们的新3D成像资源将广泛适用于研究多发性硬化的染色质 上下文。

项目成果

Genomic heterogeneity in pancreatic cancer organoids and its stability with culture.

• DOI: 10.1038/s41525-022-00342-9
• 发表时间: 2022-12-19
• 期刊: NPJ GENOMIC MEDICINE
• 影响因子: 5.3
• 作者: Usman, Olalekan H.;Zhang, Liting;Xie, Gengqiang;Kocher, Hemant M.;Hwang, Chang-il;Wang, Yue Julia;Mallory, Xian;Irianto, Jerome
• 通讯作者: Irianto, Jerome

Differential modulation of cellular phenotype and drug sensitivity by extracellular matrix proteins in primary and metastatic pancreatic cancer cells.

原发性和转移性胰腺癌细胞中细胞外基质蛋白对细胞表型和药物敏感性的差异调节。

• DOI: 10.1091/mbc.e23-02-0075
• 发表时间: 2023
• 期刊: Molecular biology of the cell
• 影响因子: 3.3
• 作者: Usman,OlalekanH;Kumar,Sampath;Walker3rd,ReddickR;Xie,Gengqiang;Sumajit,HyejeC;Jalil,AbdelAzizR;Ramakrishnan,Subramanian;Dooling,LawrenceJ;Wang,YueJulia;Irianto,Jerome
• 通讯作者: Irianto,Jerome