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

描述（由申请人提供）：慢性淋巴细胞白血病（CLL）是西半球最常见的白血病。虽然它一直被视为一种惰性疾病的老年人，其临床过程是异质性的，难以预测。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。最近的研究已经确定了有前途的新的预后标志物。使用FISH的细胞遗传学研究表明，大多数病例包含非随机异常。序列分析显示，CLL细胞在其IG可变区基因中含有体细胞突变的患者比细胞缺乏突变的患者存活更长时间。基因表达谱微阵列研究已经确定了在CLL亚型中差异表达的基因，并且可能具有预后意义。我们假设，一个临床上有用的测定，以确定CLL患者的预后，可以最好地通过结合来自RNA（基因表达谱）和DNA（分子细胞遗传学）的分子特征。因为基因表达微阵列具有有限的动态范围并且不太可能在常规临床环境中使用，所以我们提出在微流体卡上使用半定量实时PCR（MF-QRT-PCR）来开发用于RNA生物标志物特征的临床测定。由于FISH是劳动密集型的，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性（SNP）DNA作图阵列进行染色体拷贝数分析，以开发一种用于DNA生物标志物签名的临床检测。因此，我们提出了一项具有以下特定目的的研究：（1）使用MF-QRT-PCR在未经治疗的CLL患者中验证先前通过基因表达谱鉴定的预后候选生物标志物，以确定它们与临床预后指标的相关性，并将它们联合收割机组合成基于RNA的多变量（MV）预后模型;（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作图阵列收集未治疗患者的DNA拷贝数谱，以确认先前鉴定的标记，确定它们与临床预后指标的相关程度，并将它们联合收割机组合成基于DNA的MV预后模型：（4）在独立测试集上前瞻性地验证基于DNA的MV预后模型;（5）确定结合RNA和DNA标记物的模型是否比单独的模型产生更好的预后预测。相关性：CLL是美国最常见的白血病，其临床过程难以预测。有些病人可以活很多年而不接受治疗，有些则很快死亡。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，以帮助医生在疾病过程的早期识别可能需要积极治疗的患者。

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.