Integration of gene expression patterns, fusions, mutations, cytogenetics and other clinical variables for subtyping leukemias and targeting therapies

项目摘要/摘要 最近发现的儿童急性白血病(ALL)类Ph亚型是一项重大突破 在对这种疾病的理解和管理方面。这一亚群约占四分之一 在所有儿童中，高危人群是所有患者的罪魁祸首，他们一半以上的死亡都要对此负责。其特点 类Ph患者的基因表达特征使他们能够在诊断时被识别，并有助于 他们获得性潜在分子异常的深度特征，包括：涉及的基因融合 酪氨酸激酶基因及其途径、CRLF2的易位和缺失、JAK激酶和 IL7R的插入/删除。虽然这些融合的发现仍在进行中，但其中许多激酶事件 已经被证明对酪氨酸激酶抑制剂(TKI)和其他靶向治疗有反应，使他们的 鉴定在临床上至关重要。 所提议的工作既是类Ph情形刻画的继续，也是Ph类情形的应用 临床试验中的类pH基因表达分析可用于靶向药物的评价和开发 这些病人的治疗方法。这涉及到对诊断ALL的非常大的前瞻性队列的初始测试 样本以确定是否存在类Ph签名。与类Ph的鉴定同时进行 签名，还执行对最常见的CRLF2融合的测试以及确定 其他CRLF2重排的可能性。其余的类似Ph的病例(仅占约10%至15% 初始队列)，然后进行转录片段测序(RNA-Seq)以快速鉴定 表达的融合、突变和相关的插入/缺失。这一阶段的工作将扩大发现 新的融合技术，并允许将已知的融合技术用于靶向治疗。这两种技术的结合 这些具有完整基因表达信息的获得性事件的发现和表征也将使新的 有待开发的预测模型和分析方法。 在接下来的几年里，这项工作的高潮是将所有像Ph一样的患者从最糟糕的 最好的结果组。这方面的先例是针对BCR-ABL1患者的TKI疗法的出现。 在过去的十年里，这些患者已经从预后最差的群体发展到最好的群体之一。 结果，主要是由于适当的靶向药物的管理。要做到这一点，挑战在于 PH样患者的基因融合具有巨大的多样性(目前超过100种)，而且在 诊断并描述它们的特征。基因表达分析和测序策略的应用 本提案中描述的解决了这两个问题，并允许有针对性的融合立即 成为临床试验的一部分。

Project Summary/Abstract The recent discovery of the Ph-like subtype of childhood acute leukemia (ALL) represents a major breakthrough in the understanding and management of this disease. This subgroup accounts for approximately one quarter of all childhood high-risk ALL patients and is responsible for more than half of their deaths. The characteristic gene expression signature of the Ph-like patients allows them to be identified at diagnosis and facilitates an in depth characterization of their acquired underlying molecular abnormalities, including: gene fusions involving tyrosine kinase genes and their pathways, translocations and deletions of CRLF2, mutations of JAK kinases and insertions/deletions of IL7R. While the discovery of these fusions is still ongoing, many of these kinase events have been shown to be responsive to tyrosine kinase inhibitors (TKIs) and other targeted therapies, making their identification clinically crucial. The proposed work is both a continuation of the characterization of Ph-like cases and also the application of the Ph-like gene expression assay in clinical trials to permit the evaluation and development of targeted drug therapies for these patients. This involves the initial testing of a very large prospective cohort of diagnostic ALL samples to determine if the Ph-like signature is present. Simultaneously with the identification of the Ph-like signature, testing for the most common CRLF2 fusion is also performed as well as a determination of the likelihood of other CRLF2 rearrangements. The remaining Ph-like cases (comprising only about 10-15% of the initial cohort) will then be subjected to transcriptomic sequencing (RNA-Seq) for the rapid identification of expressed fusions, mutations and related insertions/deletions. This phase of the work will expand the discovery of new fusions and also permit the assignment of known fusions to targeted therapies. The combination of the discovery and characterization of these acquired events with full gene expression information will also allow new predictive models and assays to be developed. Within the next several years the culmination of this work is to transform the Ph-like ALL patients from the worst outcome group to the best. The precedent for this has been the advent of TKI therapy for BCR-ABL1 patients. Over the past ten years these patients have evolved from the poorest prognosis group to among the best outcomes, principally due to the administration of appropriate targeted drugs. The challenge in doing this with Ph-like patients has been the enormous diversity of gene fusions (currently more than 100) and the difficulty in diagnosing and characterizing them. The application of the gene expression assay and sequencing strategy described in this proposal address both of those issues and also allow for the targetable fusions to immediately become part of clinical trials.