Validation of RNA and DNA Biomarkers of Prognosis in Chronic Lymphocytic Leukemia

描述(申请人提供)：慢性淋巴细胞白血病(CLL)是西半球最常见的白血病。虽然它一直被认为是一种老年人的惰性疾病，但其临床过程是不同的，很难预测。中位生存期为9年，但可能短至1至2年。传统的预后因素不足以解释其临床异质性。最近的研究发现了有希望的新的预后标记物。使用FISH进行的细胞遗传学研究表明，大多数病例包含非随机异常。序列分析表明，其免疫球蛋白可变区基因存在体细胞突变的患者比细胞缺乏突变的患者存活时间更长。基因表达谱芯片研究已经确定了在CLL亚型中差异表达的基因，并可能具有预后意义。我们假设，通过结合来自RNA(基因表达谱)和DNA(分子细胞遗传学)的分子信号，可以最好地构建一种临床上有用的方法来确定CLL患者的预后。由于基因表达芯片的动态范围有限，不太可能在常规的临床环境中使用，我们建议使用微流控卡片上的半定量实时聚合酶链式反应(MF-QRT-PCR)来建立一种检测RNA生物标记物特征的临床方法。由于FISH是劳动密集型的，而且只能用于研究有限数量的细胞遗传学异常，我们建议使用单核苷酸多态(SNP)DNA图谱阵列进行染色体拷贝数分析，以建立一种DNA生物标志物特征的临床检测方法。因此，我们提出了一项具有以下特定目的的研究：(1)利用MF-QRT-PCR验证先前通过基因表达谱确定的CLL患者的候选预后生物标志物，以确定它们与临床预后指标的相关性如何，并将它们结合到基于RNA的多变量(MV)预后模型中；(2)在独立的测试集上前瞻性地验证基于RNA的预后模型；(3)使用SNP DNA图谱阵列收集未经治疗患者的DNA拷贝数图谱，以确认先前识别的标志物，确定它们与呈现时的临床预后指标的相关性如何，并将其组合成基于DNA的预后MV模型；(4)在独立的测试集上前瞻性地验证基于DNA的预后模型；(5)确定结合RNA和DNA标志物的模型是否比单独使用任一种模型产生更好的预后预测因子。相关性：慢性淋巴细胞性白血病是美国最常见的白血病，其临床病程难以预测。一些患者在没有治疗的情况下存活了很多年，另一些人很快就死了。我们正试图根据分子医学的新发现设计一种新的临床测试，以帮助医生识别可能需要在疾病病程早期进行积极治疗的患者。

DESCRIPTION (provided by applicant): Chronic lymphocytic leukemia (CLL) is the most common leukemia in the Western Hemisphere. Although it has been viewed as an indolent disease of older adults, its clinical course is heterogeneous and difficult to predict. The median survival is 9 years, but may be as short as 1 to 2 years. Traditional prognostic factors are insufficient to account for its clinical heterogeneity. Recent studies have identified promising new prognostic markers. Cytogenetic studies using FISH have shown that most cases contain non-random abnormalities. Sequence analysis has shown that patients whose CLL cells contain somatic mutations in their Ig variable region genes survive longer than patients whose cells lack mutations. Gene expression profiling microarray studies have identified genes that are differentially expressed in CLL subtypes, and may have prognostic significance. We hypothesize that a clinically useful assay to determine the prognosis of CLL patients can best be constructed by combining molecular signatures derived from RNA (gene expression profiling) and DNA (molecular cytogenetics). Because gene expression microarrays have limited dynamic range and are unlikely to be usable in a routine clinical setting, we propose using semi- quantitative real-time PCR on microfluidics cards (MF-QRT-PCR) to develop a clinical assay for RNA biomarker signatures. Because FISH is labor-intensive and can only be used to study a limited number of cytogenetic abnormalities, we propose using single nucleotide polymorphism (SNP) DNA mapping arrays to perform chromosome copy number analysis to develop a clinical assay for DNA biomarker signatures. Thus, we propose a study with the following Specific Aims: (1) To validate candidate biomarkers of prognosis, previously identified by gene expression profiling, in untreated CLL patients using MF-QRT-PCR, to determine how well they correlate with clinical prognostic indicators at presentation, and to combine them into an RNA-based multivariate (MV) model of prognosis; (2) To validate prospectively the RNA-based model of prognosis on an independent test set; (3) To collect DNA copy-number profiles of untreated patients using SNP DNA mapping arrays in order to confirm previously identified markers, to determine how well they correlate with clinical prognostic indicators at the time of presentation, and to combine them into a DNA-based MV model of prognosis; (4) To validate prospectively the DNA-based model of prognosis on an independent test set; (5) To determine whether a model that combines RNA and DNA markers produces a better predictor of prognosis than either model alone. Relevance: CLL is the most common leukemia in the U.S. Its clinical course is difficult to predict. Some patients live for many years without treatment; others succumb quickly. We are attempting to devise a new clinical test, based on new discoveries in molecular medicine, to help doctors identify patients who may need aggressive therapy early in their disease course.