Integrated Genomics Profile of Relapsed Childhood Acute Lymphoblastic Leukemia

描述（由申请人提供）：尽管最常见的儿童恶性肿瘤急性淋巴细胞白血病（ALL）的治愈率有显著提高，但四到五分之一的儿童会复发，其预后令人沮丧。事实上，复发性ALL是儿童非意外死亡的最常见原因。通过强化化疗（包括使用干细胞移植）来改善复发结果的尝试未能治愈大多数儿童。虽然许多预后因素可用于分层治疗，但只有免疫表型（T-ALL不良预后）、复发部位（骨髓低于离体髓外）和复发时间（早期复发定义为初始诊断< 36个月低于晚期复发）可预测挽救。为了发现介导儿童ALL耐药的潜在途径，我们使用高通量基因组技术分析了来自儿童肿瘤组（COG）方案的匹配诊断/复发配对样本中总体基因表达和拷贝数异常（CNAs）的差异。我们的早期结果表明，大多数早期复发病例的特征是增殖性基因特征，我们认为这些克隆在诊断时存在。相反，我们假设许多晚期复发病例是通过获得额外的遗传和/或表观遗传变化而发生的。重要的是，我们已经确定了新颖治疗方法的有吸引力的靶点，包括在临床前分析中得到验证的一个子集。本应用程序的目标是通过以下具体目标扩展这些观察结果并确认我们的假设：1)通过在四个诊断/复发对中进行直接转录组测序，通过鉴定新的体细胞点突变和融合转录物，发现负责耐药疾病出现的生物学途径2)确定aim 1中鉴定的体细胞病变是否代表与复发相关的复发性遗传病变；我们将使用互补DNA和基因组DNA的直接测序和Taqman分析相结合的方法筛选大量额外的诊断/复发对(3)，优先考虑那些最有可能与耐药性相关的突变，我们将开发复发性ALL的综合基因组分析，我们将整合目标1和2中开发的突变分析与我们之前的基因表达和拷贝数分析结果。这些研究的结果将有助于了解复发疾病的细胞起源和导致治疗失败的途径。这些信息将有助于在未来的试验中发现有针对性的途径。

DESCRIPTION (provided by applicant): In spite of dramatic improvements in cure rate for the most common childhood malignancy, acute lymphoblastic leukemia (ALL), one in four to five children will suffer disease reoccurrence and their prognosis is dismal. In fact relapsed ALL is the most common cause of non-accidental death in childhood. Attempts to improve relapse outcome by intensifying chemotherapy including the use of stem cell transplantation have failed to cure the majority of children. While many prognostic factors can be used to stratify therapy, only immunophenotype (T-ALL inferior prognosis), site of relapse (bone marrow inferior to isolated extramedullary) and timing of relapse (early relapse defined as < 36 months from initial diagnosis inferior compared to late relapse) are predictive of salvage. To discover the underlying pathways that mediate drug resistance in childhood ALL we have used high throughput genomic techniques to analyze differences in global gene expression and copy number abnormalities (CNAs) in matched diagnosis/relapse paired samples from children enrolled on Children's Oncology Group (COG) protocols. Our early results indicate that most cases of early relapse are characterized by a proliferative gene signature and we suggest that these clones exist at diagnosis. In contrast, we hypothesize that many cases of late relapse occur through acquisition of additional genetic and/or epigenetic changes. Importantly, we have identified attractive targets for novel therapeutic approaches including a subset that have been validated in preclinical assays. The goals of this application are to extend these observations and confirm our hypothesis through the following specific aims: 1) discover biological pathways responsible for the emergence of resistant disease by identifying novel somatic point mutations and fusion transcripts through direct transcriptome sequencing in four diagnosis/relapse pairs 2) to determine if the somatic lesions identified in aim 1 represent recurring genetic lesions associated with relapse, we will screen a large cohort of additional diagnosis/relapse pairs using a combination of direct sequencing and Taqman assays of complementary and genomic DNA 3) to prioritize those mutations that are most likely to be associated with drug resistance, we will develop an integrated genomic analysis of relapsed ALL where we will integrate the mutational analyses developed in aims 1 and 2 with our previous results from gene expression and copy number analysis. The results of these studies will lead to an understanding of the cellular origin of relapsed disease and the pathways that are responsible for treatment failure. Such information will lead to the discovery of pathways that can be targeted in future trials. PUBLIC HEALTH RELEVANCE: PROJECT NARRATIVE Although the majority of children who are newly diagnosed with acute lymphoblastic leukemia (ALL) are now cured, recurrences develop in 25% of cases. Most of these recurrences develop unpredictably and our success in treating relapse has significantly lagged behind that of newly diagnosed disease. In fact, only approximately one third of children with recurrent ALL survive long-term. The goal of this project is to develop a better understanding of the molecular genetic events that lead to relapse so that this knowledge can be used to identify more effective preventative and therapeutic strategies.