Dissecting the role of DNA damage repair deficiency in Ewing sarcoma pathogenesis for improved risk stratification and treatment

项目总结 尤文肉瘤是影响儿童和儿童的第二种最常见的骨和软组织癌症 世界各地的青少年。这是一种侵袭性的恶性肿瘤，需要多模式治疗，具有显著的 转移性和复发性疾病的发病率和治愈率仍然很低。而尤因肉瘤是 在EWSR1-ETS基因融合的特征和驱动下，导致这些简单的生物因素 重排，以及在某些情况下称为染色络合体的复杂重排，并不是很好- 特色化的。我发现FANCC和其他DNA损伤修复(DDR)中的遗传致病变异 相对于其他儿科肉瘤亚型，尤文肉瘤患者的基因具有独特的丰富性 (Gillani等人，AJHG 2022)。要了解DNA损伤修复缺陷是如何发生的，还有很多工作要做 与尤文肉瘤的发病机制有关。这项研究提案的指导假设是DNA 损伤修复缺陷促进尤文肉瘤的发病，表现为一种独特的 易患生殖系变异和肿瘤基因组特征，是肿瘤发生的组成部分，并可以 可用于更知情的风险分层和治疗。 我们将应用计算和实验方法对来自慢性阻塞性肺疾病患者的数据集进行测序 尤文肉瘤和细胞系模型完成这项研究建议。在具体目标1中，我们将剖析 尤文肉瘤中影响DDR基因的较大种系结构变异的加性贡献 分析了301个亲本先证者三者的队列，并评估了生殖系结构变异的丰富性。 1180例与非肿瘤对照比较。在具体目标2中，我们将定义FANCC变体的表型 在尤文肉瘤患者的胚系中发现，并将这些变体敲入间充质干细胞系以 了解它们如何在存在遗传毒性应激的情况下导致基因组不稳定。在具体目标3中， 我们将获得基因组签名以获得对DNA损伤过程的进一步了解 尤文肉瘤和相关拷贝数签名与治疗反应和 旧病复发。最后，我们将进行体外药物治疗研究，以证明特定拷贝的效用。 数字签名作为DNA损伤反应靶向药物敏感性的生物标记物。 通过对生殖系和肿瘤的综合研究，我们打算推动新的 了解DNA损伤在尤文肉瘤发病机制中的作用，这些知识将是核心知识 改善这种侵袭性儿童癌症的风险分层和治疗。此外，在扩大我们的 更广泛地了解生殖系结构变异、杂合风险变异在癌症中的作用 易感性和拷贝数签名作为临床相关的生物标志物，这项工作也将具有很高的 与其他儿科癌症的相关性。

PROJECT SUMMARY Ewing sarcoma is the second most common bone and soft tissue cancer impacting children and adolescents worldwide. It is an aggressive malignancy requiring multimodal treatment that confers significant morbidity, and cure rates for metastatic and relapsed disease remain poor. While Ewing sarcoma is characterized and driven by EWSR1-ETS gene fusions, the biological factors contributing to these simple rearrangements, and complex rearrangements known as chromoplexy in a subset of cases, are not well- characterized. I found that inherited pathogenic variants in FANCC and other DNA damage repair (DDR) genes are uniquely enriched among patients with Ewing sarcoma relative to other pediatric sarcoma subtypes (Gillani et al., AJHG 2022). Much work is still needed to understand how DNA damage repair deficiency contributes to Ewing sarcoma pathogenesis. The guiding hypothesis of this research proposal is that DNA damage repair deficiency promotes Ewing sarcoma pathogenesis, manifesting as a unique pattern of predisposing germline variants and tumor genomic features that are integral to oncogenesis and can be utilized for more informed risk stratification and treatment. We will apply computational and experimental approaches to sequencing datasets from patients with Ewing sarcoma and cell line models to complete this research proposal. In Specific Aim 1, we will dissect the additive contribution of larger germline structural variants impacting DDR genes in Ewing sarcoma by analyzing a cohort of 301 parent-proband trios and evaluating the enrichment of germline structural variants in 1180 cases relative to cancer-free controls. In Specific Aim 2, we will define the phenotype of FANCC variants seen in the germline of Ewing sarcoma patients and knock these variants into mesenchymal stem cell lines to understand how they contribute to genomic instability in the presence of genotoxic stress. In Specific Aim 3, we will derive genomic signatures to gain additional insight into the DNA damage processes that are operant in Ewing sarcoma tumors and associate copy number signatures specifically with treatment response and relapse. Finally, we will conduct in-vitro drug treatment studies to demonstrate the utility of specific copy number signatures as biomarkers of sensitivity to DNA damage response targeting agents. Through integrative investigations spanning the germline and tumor, we intend to drive new understanding of how DNA damage operates in Ewing sarcoma pathogenesis, knowledge that will be central to improved risk stratification and treatment of this aggressive pediatric cancer. Moreover, in extending our broader understanding about germline structural variants, the role of heterozygous risk variants in cancer predisposition, and copy number signatures as clinically relevant biomarkers, this work will also have high relevance to other pediatric cancers.