Research Test-Bed Unit

科研试验台单元：项目总结 西北大学U54癌症染色质纳米成像中心(NU-CCNIC)的总体目标 是开发和部署多尺度染色质纳米成像平台，以及分子分析和 计算机建模以表征染色质结构和与之相关的转录模式 肿瘤干细胞(CSC)与耐药表型。建议的研究将立即得到应用 卵巢癌，一种需求未得到满足的恶性肿瘤。据推测，CSCs代表了来自 出现复发的、化疗耐药的肿瘤。该中心解决的关键生物学问题是 是否通过表观遗传和染色质组织调节转录组的重新编程 机制导致显著的转录可塑性，这是CSCs承受和生存的关键 肿瘤环境中的应激源，推动肿瘤的启动和进展。作为NU-CCNIC的一部分，这项研究 试验台单元(RTB)将为由 技术发展组(TECH)这些资源包括处于不同过渡点的细胞和组织 干细胞和非干细胞表型之间以及化疗敏感和耐药状态之间的差异。这个 RTB进行的研究将测试纳米级染色质成像和分析(Nano- Chia)平台，并提供反馈以优化其使用。此外，RTB还将表演最先进的 肿瘤干细胞和化疗耐药细胞的计算基因组分析，包括单细胞mRNA 测序和基因组图谱(例如，Hi-C、ATAC-测序和芯片测序)。具体的 本单位的目标是：1)确定CSC特有的表观基因组特征和3D染色质包装 整合染色质可及性、接触频率和基因的全基因组图谱的构象 表达网络具有高分辨率纳米级染色质成像功能。2)以确定是否 向化疗耐药状态的转变促进了茎状染色质的堆积和构象。轨迹 特定的表观遗传操作将与高分辨率成像技术相结合，以研究 抗性状态特异性3D染色质堆积及其与CSC状态的关系。3)了解全球化程度 小分子酶抑制剂诱导的表观基因组操作通过以下途径阻断茎和抗药性 染色质包装的改变。总之，通过染色质纳米成像对癌症的综合询问 方法(TECH)和全基因组作图(RTB)将发现CSCs和 耐化疗的癌细胞是受调控的。该项目通过使用高度创新的技术走在了该领域的前沿 分子和纳米级染色质成像技术更好地理解二者之间的关系 残留疾病中较高水平的染色质结构和干性和化疗耐药的关键驱动因素 致命且难以治疗。

Research Test-Bed Unit: PROJECT SUMMARY The overall goal of the U54 Northwestern University Center for Chromatin Nanoimaging in Cancer (NU-CCNIC) is to develop and deploy a multi-scale chromatin nanoimaging platform together with molecular analyses and computational modeling to characterize chromatin structure and transcriptional patterns associated with the cancer stem cell (CSC) and chemoresistance phenotype. The immediate application of the proposed studies will be ovarian cancer, a malignancy of unmet need. It has been speculated that CSCs represent the reservoir from which recurrent, chemotherapy-resistant tumors arise. The key biological question addressed by this Center is whether reprogramming of the transcriptome through epigenetic and chromatin organization-regulated mechanisms leads to significant transcriptional plasticity, which is critical for CSCs to withstand and survive stressors in the tumor environment, driving tumor initiation and progression. As part of NU-CCNIC, the Research Test-Bed Unit (RTB) will provide source materials for the nanoimaging technologies developed by the Technology Development Unit (TECH). These resources include cells and tissues at various transition points between stem cell and non-stem cell phenotypes and between chemotherapy-sensitive and resistant states. The studies conducted by the RTB will test the applicability of the Nanoscale Chromatin Imaging and Analysis (nano- ChIA) platform and provide feedback to optimize its use. In addition, the RTB will perform state-of-the-art computational genomic analyses of CSCs and chemotherapy-resistant cells, including single-cell mRNA sequencing and genome mapping (e.g., Hi-C, ATAC-sequencing and ChIP-sequencing). The specific objectives of this unit are: 1) To identify CSC-specific epigenomic features and 3D chromatin packing conformations by integrating genome-wide maps of chromatin accessibility, contact frequency and gene expression networks with high resolution nano-scale chromatin imaging features. 2) To identify whether the transition to a chemotherapy-resistant state promotes stemness-like chromatin packing and conformation. Locus specific epigenetic manipulations will be coupled with high resolution imaging technologies to investigate resistant-state specific 3D chromatin packing and its relation to the CSC state. 3) To discover how global epigenome manipulations induced by small enzymatic inhibitors block stemness and chemo-resistance through alterations of chromatin packing. In all, the integrated interrogation of cancer through chromatin nanoimaging methods (TECH) and genome-wide mapping (RTB) will discover how transcriptional plasticity of CSCs and chemo-resistant cancer cells is regulated. The project is at the forefront of the field by using highly innovative molecular and nanometer-scale chromatin imaging technologies to better understand the relationship between higher level chromatin structure and key drivers of stemness and chemo-resistance in a disease that remains lethal and difficult to treat.