Investigation of ecDNA as a driver of intratumoral heterogeneity and treatment resistance in high-risk medulloblastoma

EcDNA 作为高危髓母细胞瘤瘤内异质性和治疗耐药性驱动因素的研究

• 批准号: 10709196
• 负责人: Lukas Chavez
• 金额: $ 66.05万
• 依托单位: SANFORD BURNHAM PREBYS MEDICAL DISCOVERY INSTITUTE
• 依托单位国家: 美国
• 财政年份: 2023
• 资助国家: 美国
• 起止时间: 2023-09-01 至 2028-08-31
• 项目状态: 未结题
• 来源: https://reporter.nih.gov/project-details/10709196
• 关键词: Biological; Biopsy; Bromodomains and extra-terminal domain inhibitor; Cancer Patient; Cell Nucleus; Cells; Chemotherapy and/or radiation; Child; Childhood Malignant Brain Tumor; Circular DNA; Clinical; Clustered Regularly Interspaced Short Palindromic Repeats; Code; Combined Modality Therapy; Computing Methodologies; DNA; DNA Repair; DNA-PKcs; Data; Dependence; Development; Disease; Disease Progression; Enhancers; Gene Amplification; Genes; Genetic Transcription; Human; Image; In Vitro; Individual; Institution; Investigation; MYCN gene; Malignant Neoplasms; Mediating; Methods; Mission; Molecular; Molecular Analysis; Molecular Evolution; Monitor; Neoplasm Metastasis; Nervous System Trauma; Nonhomologous DNA End Joining; Oncogenes; Oncoproteins; Outcome; Pathogenesis; Patients; Pediatric Hospitals; Poly(ADP-ribose) Polymerase Inhibitor; Predisposition; Prevention; Primary Neoplasm; Process; Proliferating; Property; Public Health; Relapse; Research; Resistance; Role; Sampling; Subgroup; Testing; Therapeutic; Treatment Efficacy; Treatment Failure; Tumor Biology; Tumorigenicity; United States National Institutes of Health; Untranslated RNA; Variant; Work; cancer genomics; cohort; combinatorial; data repository; detection method; developmental disease; experimental study; extrachromosomal DNA; genome sequencing; high risk; human disease; improved; in vivo; inhibitor; innovation; medulloblastoma; multiple omics; neoplastic cell; novel; novel therapeutic intervention; patient derived xenograft model; preclinical study; reconstruction; standard care; standard of care; targeted treatment; therapeutic target; therapy resistant; tumor; tumor growth; tumor heterogeneity; whole genome

The overall objective of this proposal is to investigate circular extrachromosomal DNA (ecDNA) as a potential driver of intratumoral heterogeneity and treatment resistance in medulloblastoma, the most common pediatric malignant brain tumor. Intratumoral heterogeneity is one of the leading determinants of therapeutic resistance and treatment failure and one of the main reasons for poor overall survival in cancer patients. However, the functional relevance of ecDNA as a driver of tumor heterogeneity and treatment resistance in medulloblastoma has hardly been studied. To analyze the clinical impact of ecDNA in the different molecular subgroups of medulloblastoma, we assembled a multi-institutional cohort of Whole Genome Sequencing data from 468 medulloblastoma patient samples. Using novel computational methods for the detection and reconstruction of ecDNA, we found ecDNA in 82 patients (18%) and observe that the presence of ecDNA is associated with significantly poorer outcomes. In addition, we find that individual medulloblastoma tumors often harbor multiple variants of ecDNA, each containing different amplified oncogenes along with co-amplified non-coding regulatory DNA (‘enhancers’). Based on our preliminary results, we propose the central hypothesis that ecDNA drives intratumoral heterogeneity and treatment resistance in high-risk medulloblastoma patients. The central hypothesis will be tested through the following three specific aims: To investigate the molecular evolution of ecDNA as a potential driver of treatment resistance (Aim 1); To evaluate combinatorial therapies targeted against mechanisms of ecDNA formation and clustering to reduce treatment resistance (Aim 2); To probe medulloblastoma tumor-dependencies by functional inhibition of coding and non-coding regulatory DNA co- amplified on ecDNA (Aim 3). The research proposed in this application has technical, conceptual, and biological innovations, including the analysis of ecDNA on the single-cell level using novel imaging and multiome single-nucleus sequencing methods in medulloblastoma tumors and in patient-derived xenograft (PDX) models. The proposed research is significant, because the current standard treatment for children with medulloblastoma causes developmental disorders, neurological damage, and secondary metastases. Novel therapeutic approaches are urgently needed. Our approach will test the impact of standard-of-care treatments on the molecular evolution of ecDNA and functionally test novel combination treatments targeted against ecDNA genesis and clustering. These preclinical studies have the potential to uncover novel mechanisms by which ecDNA contributes to the pathogenesis of medulloblastoma and to identify new scientific leads for the development of improved treatments. We expect that our studies will expose the contribution of ecDNA variants to the emergence of therapy resistance, reveal their selection advantages, validate recently described properties of ecDNA and their therapeutic susceptibilities, and identify novel tumor-dependency genes amplified on ecDNA in some of the most aggressive medulloblastoma tumors.

该提议的总体目的是研究循环外染色体DNA（ECDNA）作为潜力 肿瘤内异质性和治疗耐药性的驱动器，髓母细胞瘤，最常见的小儿 恶性脑肿瘤。肿瘤内异质性是治疗性抗性的主要决定剂之一 和治疗失败以及癌症患者总体生存不佳的主要原因之一。但是， eCDNA作为肿瘤异质性和抗治疗性耐药性的功能相关性 几乎没有研究。分析eCDNA在不同分子亚组中的临床影响 髓母细胞瘤，我们组装了468的整个基因组测序数据的多机构队列 髓母细胞瘤患者样品。使用新颖的计算方法检测和重建 eCDNA，我们发现82例患者（18％）的ecdna，并观察到ecdna的存在与 结果明显差。此外，我们发现单个髓母细胞瘤肿瘤通常具有多个 eCDNA的变体，每种含有不同的扩增癌基因以及共扩散的非编码 监管DNA（“增强剂”）。基于我们的初步结果，我们提出了一个中心假设，即eCDNA 在高危髓母细胞瘤患者中驱动肿瘤内异质性和耐药性。中央 假设将通过以下三个特定目的进行检验：研究的分子演化 ECDNA作为治疗耐药性的潜在驱动力（AIM 1）；评估针对性的组合疗法 反对eCDNA形成和聚类以降低治疗耐药性的机制（AIM 2）；证明 通过抑制编码和非编码调节DNA共同的髓母细胞瘤肿瘤依赖性 在ecdna上放大（AIM 3）。本应用程序中提出的研究具有技术，概念和 生物创新，包括使用新成像和 髓母细胞瘤肿瘤和患者衍生的异种移植物中的多重单核测序方法 （PDX）模型。拟议的研究很重要，因为目前针对患有儿童的标准治疗 髓母细胞瘤会引起发育障碍，神经系统损害和继发转移。小说 迫切需要治疗方法。我们的方法将测试护理标准治疗的影响 关于eCDNA的分子进化和功能测试针对的新型组合处理 eCDNA起源和聚类。这些临床前研究有可能通过 哪些eCDNA有助于髓母细胞瘤的发病机理，并确定新的科学铅 改进治疗的发展。我们预计我们的研究将揭示eCDNA的贡献 最近描述的抗疗法抗性的变体揭示了它们的选择优势 ECDNA及其治疗敏感性的特性，并鉴定出新的肿瘤依赖性基因 在某些最具侵略性的髓母细胞瘤肿瘤中在ECDNA上放大。