Comprehensive Prostate Cancer Characterization by Genomic and Transcriptomic Prof

基因组学和转录组学教授对前列腺癌进行全面表征

• 批准号: 8309102
• 负责人: MARK A. RUBIN
• 金额: $ 59.4万
• 依托单位: WEILL MEDICAL COLL OF CORNELL UNIV
• 依托单位国家: 美国
• 财政年份: 2011
• 资助国家: 美国
• 起止时间: 2011-08-01 至 2014-07-31
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/8309102
• 关键词: Age; American; Area; Benign; Biological Assay; Biological Markers; Biopsy; Blood; Cancer Biology; Cancer Diagnostics; Cancer Etiology; Cancerous; Categories; Cessation of life; Clinical; Communities; Computational Biology; DNA; DNA Sequence Rearrangement; DNA copy number; Data; Data Set; Detection; Development; Diagnosis; Diagnostic; Diagnostic Neoplasm Staging; Diagnostic tests; Digital Rectal Examination; Disease; Disease Progression; Drug Delivery Systems; ERG gene; ETV1 gene; Early Detection Research Network; Epithelium; Equilibrium; Extraprostatic; Freezing; Frequencies; Gene Expression Profile; Gene Fusion; Gene Mutation; Gene Rearrangement; Genes; Genomics; Gleason Grade for Prostate Cancer; Goals; Grant; Hand; Health; Knowledge; Lead; Lesion; Licensing; Malignant Neoplasms; Malignant neoplasm of prostate; Messenger RNA; Michigan; Molecular; Molecular Biology; Needle biopsy procedure; Normal Cell; Normal Range; Oligonucleotide Microarrays; Oncogenes; Organ; Patients; Pattern; Phase; Population; Positioning Attribute; Process; Prostate; Prostate Cancer Prevention Trial; Prostate-Specific Antigen; Prostatic Intraepithelial Neoplasias; Prostatic Neoplasms; Protocols documentation; Published Comment; RNA; RNA Sequences; Reading; Recurrence; Research; Resolution; Resources; Reverse Transcriptase Polymerase Chain Reaction; SPINK1 gene; Sampling; Screening for Prostate Cancer; Screening procedure; Second Primary Cancers; Sensitivity and Specificity; Series; Serum; Single Nucleotide Polymorphism; Somatic Mutation; Specificity; Systems Biology; TMPRSS2 gene; Technology; Testing; Time; Tissue Microarray; Tissues; Transcript; Tumor stage; Urine; Validation; Work; base; benign state; cancer cell; computerized tools; design; fusion gene; genome-wide; improved; insight; internal control; men; neoplastic cell; next generation; novel; programs; psychologic; research study; sound; tool; transcriptomics; tumor

DESCRIPTION (provided by applicant): Approximately 55% of prostate cancers (PCA) harbor cancer specific gene fusions. This represents an important opportunity to develop a non-invasive highly specific test for the early detection of PCA. Implementation of a urine assay to detect the TMPRSS2-ERG gene fusion is already underway, demonstrating a high specificity. A logical next step in biomarker development is the exploration of novel cancer specific gene fusions and somatic alterations. The overall goal of this proposal is to discover and validate PCA specific biomarkers that can be non- invasively detected in the urine. We have taken a Systems Biology approach integrating state-of-the-art RNA-sequencing (RNA-seq) and DNA 6.0 single nucleotide polymorphism (SNP) arrays with novel computational approaches for analysis. In Aim 1, we will identify novel gene fusions with RNA-seq and in Aim 2 we will determine somatic copy number alterations (gains and losses) associated with altered gene transcript expression as determined by RNA-seq from Aim 1. We will use 100 frozen PCA samples and 25 paired benign prostate tissues in the discovery step of Phase 1 for initial discovery of PCA specific biomarkers. The PCA samples will be equally divided based Gleason Score (tumor grade), 6 (3+3), 7 (3+4), 7(4+3), and 8-10. We will also attempt to balance for age at time of biopsy, PSA levels, and tumor stage (organ confined (pT2) versus extraprostatic extension (pT3). Tumors will be evaluated for known ETS gene fusions (e.g., TMPRSS2- ERG, SLC45A3-ETV1, etc.). We will also attempt to balance samples based on known fusions versus no fusions based on the current knowledge of gene fusions. The verification step of Phase 1 will occur using FISH for the novel gene fusions and immunohistochemisty (IHC) and/or FISH for somatic alterations to determine PCA specificity on tissue microarrays with over 200 PCA samples and 400 benign tissues. We will also explore PCA specificity in 100 urine samples collected from men with and without PCA using a rigorous EDRN Protocol on local samples. RT-PCR assays for fusion genes and over or under expression of somatically altered genes will be tested using mRNA for PSA as an internal control. The biostatistical group will supervise all steps of the analysis and help prioritize the lead candidates in conjunction with the computational biology group. We anticipate nominating 20 candidates from each biomarker category per year and will hand off 5-10 for formal Phase 2 validation by the EDRN Clinical Validation Center of Harvard/Michigan/Weil Cornel (outside the scope of this application). Discoveries made in this proposal will be strong candidates for clinical validation as part of the Early Detection Research Network PCA program. This study will also generate important insight into the molecular biology of PCA, which has broad implications in understanding disease progression and identifying potential drug targets. Finally, the computational tools and dataset will be important resources for the research community at large.

描述（由申请人提供）： 大约 55% 的前列腺癌 (PCA) 含有癌症特异性基因融合。这为开发用于早期检测 PCA 的非侵入性高度特异性测试提供了重要机会。检测 TMPRSS2-ERG 基因融合的尿液检测已经在进行中，显示出高度的特异性。生物标志物开发的合理下一步是探索新型癌症特异性基因融合和体细胞改变。该提案的总体目标是发现并验证可在尿液中非侵入性检测的 PCA 特异性生物标志物。我们采用系统生物学方法，将最先进的 RNA 测序 (RNA-seq) 和 DNA 6.0 单核苷酸多态性 (SNP) 阵列与新颖的计算分析方法相结合。在目标 1 中，我们将通过 RNA-seq 识别新的基因融合，在目标 2 中，我们将确定与目标 1 中的 RNA-seq 确定的基因转录表达改变相关的体细胞拷贝数改变（增加和丢失）。我们将在第一阶段的发现步骤中使用 100 个冷冻 PCA 样本和 25 个配对良性前列腺组织，以初步发现 PCA 特异性生物标志物。 PCA样本将根据格里森评分（肿瘤分级）、6（3+3）、7（3+4）、7（4+3）和8-10等分。我们还将尝试平衡活检时的年龄、PSA水平和肿瘤分期（器官局限性（pT2）与前列腺外扩展（pT3））。将对肿瘤进行已知ETS基因融合（例如，TMPRSS2-ERG、SLC45A3-ETV1等）的评估。我们还将尝试根据已知融合与无融合的当前知识来平衡样本。 基因融合。第一阶段的验证步骤将使用 FISH 进行新型基因融合和免疫组织化学 (IHC) 和/或 FISH 进行体细胞改变，以确定组织微阵列上超过 200 个 PCA 样本和 400 个良性组织的 PCA 特异性。我们还将对当地样本使用严格的 EDRN 方案，探索从患有和未患有 PCA 的男性收集的 100 个尿液样本中的 PCA 特异性。逆转录聚合酶链反应 将使用 PSA 的 mRNA 作为内部对照来测试融合基因以及体细胞改变基因的过度或不足表达的测定。生物统计小组将监督分析的所有步骤，并与计算生物学小组一起帮助确定主要候选者的优先顺序。我们预计每年从每个生物标志物类别中提名 20 名候选人，并将将 5-10 名候选人交给 EDRN 临床验证中心进行正式的 2 期验证。 哈佛大学/密歇根州/Weil Cornel（不属于本申请的范围）。作为早期检测研究网络 PCA 计划的一部分，该提案中的发现将成为临床验证的有力候选者。这项研究还将产生对 PCA 分子生物学的重要见解，这对于了解疾病进展和识别潜在药物靶点具有广泛的影响。最后，计算工具和数据集将成为整个研究界的重要资源。