Development of deep proteomic sequencing platforms for molecular markers in DLBCL

DLBCL分子标记深度蛋白质组测序平台的开发

• 批准号: 8710119
• 负责人: Nika N Danial
• 金额: $ 22.15万
• 依托单位: DANA-FARBER CANCER INST
• 依托单位国家: 美国
• 财政年份: 2013
• 资助国家: 美国
• 起止时间: 2013-08-01 至 2015-07-31
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/8710119
• 关键词: Accounting; Address; Amino Acid Sequence; Archives; Biological Markers; Biopsy; Cell Line; Citric Acid Cycle; Classification; Clinical; Complex; Coupled; Dana-Farber Cancer Institute; Data; Detection; Development; Diagnostic; Disease; Disease Management; Disease Marker; Drug Metabolic Detoxication; Drug Targeting; Exhibits; Fractionation; Future; Gene Expression; Genetic; Genetic Markers; Genome; Genomics; Glutathione; Goals; Hematopoietic Neoplasms; Heterogeneity; Human; Lesion; Link; Liquid Chromatography; Lymphoma; Mass Spectrum Analysis; Mediating; Metabolic; Metabolic Pathway; Mitochondria; Modeling; Molecular; Molecular Diagnosis; Molecular Profiling; Non-Hodgkin' s Lymphoma; Nutrient; Oxidative Phosphorylation; Pathogenesis; Pathway interactions; Patients; Peptide Sequence Determination; Performance; Phenotype; Phosphorylation; Post-Translational Protein Processing; Predictive Value; Primary Neoplasm; Proteins; Proteome; Proteomics; Receptor Signaling; Receptors, Antigen, B-Cell; Relative (related person); Sampling; Signal Pathway; Signal Transduction; Somatic Mutation; Stratification; System; Technology; Testing; Therapeutic; Therapeutic Intervention; Tissues; Tricarboxylic Acids; Validation; base; cohort; fatty acid oxidation; human SYK protein; improved; insight; interest; large cell Diffuse non-Hodgkin' s lymphoma; member; molecular marker; mouse model; novel; prognostic; programs; protein expression; protein metabolite; protein purification; prototype; public health relevance; response; single molecule; therapeutic target; tumor; tumor growth

DESCRIPTION (provided by applicant): Development of deep proteomic sequencing platforms for molecular markers in DLBCL Diffuse large B cell lymphoma (DLBCL) is a genetically and clinically heterogeneous disease that comprises the most common non-Hodgkin's lymphoma. To date efforts to unearth the molecular pathogenesis of DBLCL, identify therapeutic targets, and stratify patients according to specific sets of molecular lesions have relied on genome-level analyses that identified distinct substructure classifications and pathogenic mechanisms, including B-cell receptor (BCR)-dependent survival signaling. The potential biomarkers that have emerged from these studies await further validation. Quantitative proteomics has the power to reveal additional, novel molecular signatures at the protein/pathway level that may otherwise escape detection through genome-based approaches due to post-transcriptional and post-translational mechanisms. However, use of quantitative proteomics to profile molecular signatures and facilitate biomarker discovery in clinical tissues has been hampered by critical barriers such as poor detection of low-abundance proteins, overly complex sample workflows that are often incompatible with the protein quantities available in primary tumors, and low throughput. We have developed a novel and very high peak capacity liquid chromatography system coupled directly to mass spectrometry that can address these barriers and achieve extensive and quantitative proteome coverage. In the fullness of time, this platform will enable analyses of sufficiently large clinical cohorts to provde statistically-powered identification of protein biomarkers. In preliminary studies, we utilized a prototype version of our deep proteome sequencing platform to interrogate the proteome of primary DLBCL tumor biopsies and patient derived DLBCL cell lines. This analysis revealed previously unappreciated pathway-level heterogeneity in nutrient/fuel utilization and associated proliferation and survival advantages that segregate with the presence/absence of functional BCR signaling. In response to FOA PA-12-220, which encourages development of "specific technologies for quantitative detection of novel biomarkers associated with hematopoietic malignancies," we propose to test, validate and improve our proteomics platform for systematic interrogation of both proteome (Aim 1) and phosphoproteome (Aim 2) signatures in primary DLBCL tumors. Our goal is to identify and validate coordinate pathways that are differentially enriched in molecular subsets of DLBCL. Our study plan will reveal putative new stratification markers for DLBCL and credential our deep protein sequencing LC-MS/MS platform for future use on much larger NHL patient cohorts.

描述（由申请人提供）：开发用于 DLBCL 分子标记的深度蛋白质组测序平台 弥漫性大 B 细胞淋巴瘤 (DLBCL) 是一种遗传和临床异质性疾病，包括最常见的非霍奇金淋巴瘤。迄今为止，挖掘 DBLCL 的分子发病机制、确定治疗靶点以及根据特定的分子病变对患者进行分层的努力都依赖于基因组水平的分析，该分析确定了不同的亚结构分类和致病机制，包括 B 细胞受体 (BCR)。依赖的生存信号。这些研究中出现的潜在生物标志物有待进一步验证。定量蛋白质组学有能力在蛋白质/通路水平上揭示额外的、新颖的分子特征，否则由于转录后和翻译后机制，这些特征可能会通过基于基因组的方法逃脱检测。然而，使用定量蛋白质组学来分析分子特征并促进临床组织中生物标志物的发现受到了一些关键障碍的阻碍，例如低丰度蛋白质的检测不佳、样品工作流程过于复杂，通常与原发性肿瘤中可用的蛋白质数量不相容，和低吞吐量。我们开发了一种新颖且非常高峰容量的液相色谱系统，直接与质谱联用，可以解决这些障碍并实现广泛和定量的蛋白质组覆盖。在时间成熟时，该平台将能够对足够大的临床队列进行分析，以提供蛋白质生物标志物的统计支持鉴定。在初步研究中，我们利用深度蛋白质组测序平台的原型版本来询问原发性 DLBCL 肿瘤活检和患者衍生的 DLBCL 细胞系的蛋白质组。该分析揭示了之前未被认识到的营养物/燃料利用的途径水平异质性以及相关的增殖和生存优势，这些优势与功能性 BCR 信号传导的存在/不存在相分离。为了响应鼓励开发“定量检测与造血系统恶性肿瘤相关的新型生物标志物的特定技术”的 FOA PA-12-220，我们建议测试、验证和改进我们的蛋白质组学平台，以系统地询问两种蛋白质组（目标 1）原发性 DLBCL 肿瘤中的磷酸化蛋白质组（目标 2）特征。我们的目标是识别和验证 DLBCL 分子亚群中差异富集的协调途径。我们的研究计划将揭示 DLBCL 的推定新分层标志物，并验证我们的深度蛋白质测序 LC-MS/MS 平台，以便将来在更大的 NHL 患者群体中使用。