Project 3: Modeling tumor evolution and drug response in bladder cancer organoids

项目摘要/摘要 肿瘤的异质性和克隆进化在癌症进展和对 心理治疗。然而，克隆进化很难在实体肿瘤中进行研究，例如膀胱癌。 由于缺乏顺从的模式系统。在这个项目中，我们建议使用患者来源的膀胱肿瘤 有机化合物作为一种新的模型系统用于肿瘤进化的纵向研究及其在药物中的作用 反应和抵抗。在初步研究中，我们已经为建立 从乳头状非侵袭性肿瘤到膀胱癌组织的患者衍生的器官系 肌肉浸润性癌症，并表明这些器官样线概括了组织病理学和 其相应亲本肿瘤的分子特征。特别是，我们发现这些有机化合物 在培养的连续传代过程中，品系表现出与克隆一致的突变谱变化 进化论。我们进一步证明了这些株系可以用来分析药物反应，并且这些 这些有机物在体内的原位异种移植中的反应可以得到验证。 我们现在将使用这些患者衍生的膀胱癌器官模型来研究克隆进化。 和药物反应在膀胱癌中追求三个特定的目标：1)异质性和肿瘤分析 通过检测连续传代过程中异质性的维持来研究膀胱癌有机体的进化 并通过研究基因组不稳定性和表观遗传失调如何驱动克隆进化；2) 通过分析核苷酸的作用研究膀胱癌有机化合物的化疗反应 切除修复途径基因ERCC2在顺铂治疗差异反应中的作用；3)克隆分析 慢病毒介导的条形码和单细胞技术在膀胱癌耐药中的应用 用RNA测序法对药物出现期间的克隆肿瘤群体进行纵向分析 文化中的抗药性。这些研究将极大地促进患者来源的器官样品系的生物库 以及将由膀胱癌模型核心、组织病理学和靶向外显子产生的异种移植 由分子病理学核心执行的测序，以及来自 管理核心。我们的工作也将与项目1和2通过我们对 表观遗传调控因子KDM6A和ARID1A在推动肿瘤异质性和进化中的潜在作用 同时，我们对患者来源的膀胱肿瘤有机化合物的研究将提供有价值的试剂。 以及对其他项目的见解。

Project Summary/Abstract Tumor heterogeneity and clonal evolution play key roles in cancer progression and the response to therapy. However, clonal evolution has been difficult to study in solid tumors such as bladder cancer, in part due to the lack of amenable model systems. In this Project, we propose to use patient-derived bladder tumor organoids as a new model system to pursue longitudinal studies of tumor evolution and its role in drug response and resistance. In preliminary studies, we have developed culture conditions for the establishment of patient-derived organoid lines from bladder cancer tissues that range from papillary non-invasive tumors to muscle-invasive cancer, and have shown that these organoid lines recapitulate the histopathological and molecular features of their corresponding parental tumors. In particular, we have found that these organoid lines display changes in mutational profiles during serial passaging in culture that are consistent with clonal evolution. We have further demonstrated that these lines can be used to assay drug response, and that these responses can be validated in orthotopic xenografts from these organoids in vivo. We will now use these patient-derived bladder cancer organoid models to investigate clonal evolution and drug response in bladder cancer by pursuing three specific aims: 1) Analysis of heterogeneity and tumor evolution in bladder cancer organoids by examining the maintenance of heterogeneity during serial passaging and by investigating how genome instability and epigenetic dysregulation drive clonal evolution; 2) Investigation of chemotherapy response in bladder cancer organoids by analyzing the role of the nucleotide excision repair pathway gene ERCC2 in differential response to cisplatin treatment; and 3) Analysis of clonal evolution in drug resistance of bladder cancer organoids using lentiviral-mediated barcoding and single-cell RNA sequencing to perform longitudinal analyses of clonal tumor populations during the emergence of drug resistance in culture. These studies will be greatly facilitated by the biobank of patient-derived organoid lines and xenografts that will be generated by the Bladder Cancer Models Core, histopathology and targeted exome sequencing performed by the Molecular Pathology Core, and bioinformatic and biostatistical support from the Administrative Core. Our work will also be highly integrated with Projects 1 and 2 through our analyses of the potential roles of the epigenetic regulators KDM6A and ARID1A in driving tumor heterogeneity and evolution, while at the same time, our studies of patient-derived bladder tumor organoids will provide valuable reagents and insights for the other Projects.