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.

这项建议的总体目标是研究环状染色体外dna(Ecdna)作为一种潜在的 儿童最常见的髓母细胞瘤的瘤内异质性和治疗耐药性的驱动因素 恶性脑瘤。肿瘤内的异质性是治疗耐药性的主要决定因素之一。 治疗失败也是癌症患者总体存活率较低的主要原因之一。然而， 髓母细胞瘤中ecDNA作为肿瘤异质性和治疗耐药的驱动因素的功能相关性 几乎没有人研究过。分析ecDNA在不同分子亚群中的临床影响 髓母细胞瘤，我们收集了468个全基因组测序数据的多机构队列 髓母细胞瘤患者样本。使用新的计算方法来检测和重建 我们在82名患者(18%)中发现了ecDNA，并观察到ecDNA的存在与 结果要糟糕得多。此外，我们还发现，单个髓母细胞瘤常伴有多发性 EcDNA的变种，每个变种包含不同的扩增癌基因以及共扩增的非编码基因 监管DNA(“增强剂”)。基于我们的初步结果，我们提出了ecDNA的中心假设 导致高危髓母细胞瘤患者肿瘤内的异质性和治疗耐药性。中环 假说将通过以下三个具体目标进行检验：研究 EcDNA作为治疗耐药的潜在驱动因素(目标1)；评估有针对性的联合治疗 针对ecDNA的形成和聚集机制以减少对药物的耐药性(目标2)；探索 髓母细胞瘤编码和非编码调节性DNA协同功能抑制与肿瘤的相关性 在ecDNA上扩增(目标3)。本申请中提出的研究具有技术、概念和 生物创新，包括使用新的成像技术在单细胞水平上分析ecDNA 髓母细胞瘤和患者来源的异种移植中的多组单核测序方法 (PDX)型号。这项拟议的研究意义重大，因为目前对儿童的标准治疗 髓母细胞瘤会导致发育障碍、神经损伤和继发性转移。小说 迫切需要治疗方法。我们的方法将测试标准护理治疗的影响 论ecDNA的分子进化及靶向靶向的新型联合治疗 EcDNA的起源和聚集性。这些临床前研究有可能通过以下方式揭示新的机制 哪种ecDNA在髓母细胞瘤的发病机制中起作用并为 开发改进的治疗方法。我们期望我们的研究将揭示ecDNA的作用。 出现治疗耐药的变异，揭示其选择优势，验证最近描述的 EcDNA的性质及其治疗敏感性，并鉴定新的肿瘤依赖基因 在一些最具侵袭性的髓母细胞瘤的ecDNA上扩增。