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

基本信息

批准号：
8515754
负责人：
MARK A. RUBIN
金额：
$ 55.75万
依托单位：
WEILL MEDICAL COLL OF CORNELL UNIV
依托单位国家：
美国
项目类别：
财政年份：
2011
资助国家：
美国
起止时间：
2011-08-01 至 2015-07-31
项目状态：
已结题

来源：
https://reporter.nih.gov/project-details/8515754
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 Targeting 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 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 computerized tools design fusion gene genome-wide improved insight internal control men neoplastic cell next generation novel programs prostate cancer cell psychologic research study screening sound tool transcriptome sequencing transcriptomics tumor

项目摘要

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 确定的基因转录本表达改变相关的体细胞拷贝数改变（增加和丢失）。我们将使用 100在第一阶段的发现步骤中，我们使用冷冻 PCA 样本和 25 配对良性前列腺组织来初步发现 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)）。将对肿瘤进行已知的 ETS 基因融合评估（例如，TMPRSS2- ERG、SLC45A3- ETV1 等）。我们还将尝试根据当前的基因融合知识来平衡基于已知融合和无融合的样本。第一阶段的验证步骤将进行。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，以确定超过 200 个 PCA 样本和 400 个良性组织的组织微阵列上的 PCA 特异性，我们还将探索从男性中收集的 100 个尿液样本中的 PCA 特异性。在没有 PCA 的情况下，将使用 mRNA 对本地样本使用严格的 RT-PCR 检测融合基因以及体细胞改变基因的过度或表达不足进行测试。 PSA 作为内部对照，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 名候选人交给哈佛/密歇根/威尔康奈尔大学的 EDRN 临床验证中心进行正式的 2 期验证（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。