Integrated Genomics Profile of Relapsed Childhood Acute Lymphoblastic Leukemia

描述(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)的治愈率有了显著的提高，但每四到五个孩子中就有一个会复发，他们的预后很糟糕。事实上，反复发作的ALL是儿童非意外死亡的最常见原因。试图通过加强化疗来改善复发结果，包括使用干细胞移植，但未能治愈大多数儿童。虽然许多预后因素可以用于分层治疗，但只有免疫表型(T-ALL预后较差)、复发部位(骨髓低于孤立的髓外)和复发时间(早期复发定义为从首次诊断为较差的36个月相对于晚期复发)是预测挽救的因素。为了发现儿童耐药的潜在途径，我们使用高通量基因组技术分析了来自参加儿童肿瘤学小组(COG)方案的儿童的配对诊断/复发样本中全球基因表达和拷贝数异常(CNA)的差异。我们的早期结果表明，大多数早期复发的病例以增殖基因特征为特征，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/或表观遗传学改变而发生的。重要的是，我们已经为新的治疗方法确定了有吸引力的靶点，包括已经在临床前试验中得到验证的子集。本申请的目的是通过以下特定目标扩展这些观察并证实我们的假设：1)通过在四个诊断/复发对中通过直接转录组测序识别新的体细胞点突变和融合转录本来发现导致耐药疾病出现的生物学途径2)为了确定在目标1中识别的体细胞损伤是否代表与复发相关的复发遗传损伤，我们将使用直接测序和互补DNA和基因组DNA的Taqman分析的组合来筛选大量额外的诊断/复发对3)以优先处理那些最可能与耐药性相关的突变，我们将开发复发ALL的综合基因组分析，将AIMS 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相结合。这些研究的结果将有助于理解复发疾病的细胞起源以及导致治疗失败的途径。这些信息将导致发现可以在未来的试验中作为靶点的途径。 公共卫生相关性： 项目简介虽然大多数新诊断的急性淋巴细胞白血病(ALL)儿童现在已经治愈，但25%的病例会复发。大多数复发都是不可预测的，我们在治疗复发方面的成功远远落后于新诊断的疾病。事实上，只有大约三分之一的复发儿童ALL能长期存活。该项目的目标是更好地了解导致复发的分子遗传事件，以便利用这些知识来确定更有效的预防和治疗策略。

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.