Informatics methods for identifying breast cancer control genes and proteins

鉴定乳腺癌控制基因和蛋白质的信息学方法

• 批准号: 8248594
• 负责人: Umit V. Catalyurek
• 金额: $ 45.07万
• 依托单位: OHIO STATE UNIVERSITY
• 依托单位国家: 美国
• 财政年份: 2009
• 资助国家: 美国
• 起止时间: 2009-06-01 至 2014-04-30
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/8248594
• 关键词: Algorithms; Antibodies; BRCA1 gene; BRCA2 Protein; BRCA2 gene; Binding; Bioinformatics; Biological Assay; Biological Markers; Breast; Cancer Control; Candidate Disease Gene; Carcinogenicity Tests; Cell Extracts; Cell division; Cells; Centrosome; Clinical; Complex; Computers; DNA Double Strand Break; DNA Repair; Data; Data Set; Databases; Disease; Expression Library; Family; Gene Cluster; Gene Expression; Gene Expression Regulation; Gene Proteins; Gene Targeting; Genes; Group Identifications; Human; In Vitro; Individual; Informatics; Information Systems; Inherited; Label; Laboratories; Messenger RNA; Methods; Mining; Modality; Modeling; Mutate; Mutation; Oncogenes; Pathway interactions; Patients; Phenotype; Predictive Value; Predisposition; Process; Proteins; Public Domains; Publishing; RNA Interference; Regulation; Sampling; Screening procedure; System; Testing; Tissue Microarray; Tumor Suppressor Proteins; Western Blotting; base; breast cancer diagnosis; carcinogenesis; cell type; combinatorial; computer program; computerized tools; gene discovery; homologous recombination; malignant breast neoplasm; novel; protein complex; protein function; public health relevance; recombinational repair; success; tool

DESCRIPTION (provided by applicant): This project will develop a new framework for discovery of genes involved in the breast carcinogenesis process. Among families that have a predisposition to breast cancer, approximately 25% have inherited mutations in either breast cancer ("BRCA") genes BRCA1 or BRCA2, but the predisposing mutated genes in the majority of the families are unknown. BRCA1 and BRCA2 gene products both regulate cell division pathways that involve DNA repair and centrosome duplication, and their expression is correlated in microarray analyses in many cell types. We hypothesize that other unidentified BRCA genes may be involved in the same pathways that BRCA1 and BRCA2 regulate, and thus may be discovered by identifying genes whose expression also is correlated with that of BRCA1 and BRCA2. We will interrogate public-domain gene expression databases using newly developed computational tools that include combinatorial and algebraic clustering methods to identify genes whose expression correlates with these tumor suppressors. RNA interference will be used to disrupt the expression of the candidate BRCA gene products in two cell-based assays that are dependent on BRCA1 and BRCA2 expression. The first assay models the regulation of homology-directed recombination repair of double-strand DNA breaks, and the second assay tests the control of duplication of the centrosome. We will also perform a third test to determine whether the informatics-identified candidate BRCA gene product can form a protein complex with BRCA1 since several of the already identified co-expressed genes do form a complex with BRCA1. Candidate BRCA genes that are positive in the functional cell based assays will then be tested for changes in expression of their gene products in clinical samples, using an antibody-based, high-throughput tissue microarray system. In summary, this proposal outlines a novel experimental framework that will develop new bioinformatic tools for identifying candidate genes whose regulation suggests the potential for involvement in breast carcinogenesis, testing whether depletion of the proteins encoded by these candidate genes results in phenotypes in the laboratory that are consistent with breast cancer, and determining whether the expression of these candidate genes in clinical samples indicates their potential as biomarkers for breast carcinogenesis. This project defines a framework that may also be applicable to the identification of groups of genes involved in common pathways in other disease processes. PUBLIC HEALTH RELEVANCE: Among families that have a predisposition to breast cancer, approximately 25% have inherited mutations in either breast cancer ("BRCA") genes BRCA1 or BRCA2, but the predisposing mutated genes in the majority of the families are unknown. BRCA1 and BRCA2 gene products both regulate cell division pathways that involve DNA repair and centrosome duplication, and their expression is correlated in microarray analyses in many cell types. We hypothesize that other unidentified BRCA genes may be involved in the same pathways that BRCA1 and BRCA2 regulate, and thus may be discovered by identifying genes whose expression also is correlated with that of BRCA1 and BRCA2. These candidate BRCA genes will be identified through computer-program driven analyses of publicly available gene expression data. Candidate BRCA genes identified using these computer-based approaches will then be screened in laboratory tests using RNA interference assays to identify candidates that regulate homology-directed recombination repair of double-strand DNA breaks and/or centrosome duplication. Candidate BRCA genes that are validated in the laboratory will then be tested for changes in expression of their gene product using high-throughput labeled antibody assays in clinical samples. Thus, this proposal outlines a novel experimental framework that starts with a broad computer-based screen of gene expression libraries to identify initial candidates, performs a second screening using in vitro laboratory analyses of function, and then a third screen using expression in clinical samples. Genes that pass all three screens would be excellent candidates for genes that are responsible for breast cancer disposition in families, that may serve as biomarkers for the diagnosis of breast cancer, and that may contribute predictive value for the success of treatment modalities for an individual patient.

描述（由申请人提供）：该项目将开发一个新的框架，以发现与乳腺癌发生过程有关的基因。在患有乳腺癌易感性的家庭中，大约25％的乳腺癌（“ BRCA”）基因BRCA1或BRCA2具有遗传突变，但是大多数家族的诱发突变基因尚不清楚。 BRCA1和BRCA2基因产物都调节涉及DNA修复和中心体重复的细胞分裂途径，并且它们的表达在许多细胞类型的微阵列分析中相关。我们假设其他未识别的BRCA基因可能与BRCA1和BRCA2调节的途径有关，因此可以通过鉴定其表达也与BRCA1和BRCA2相关的基因来发现。我们将使用新开发的计算工具来询问公共域基因表达数据库，该工具包括组合和代数聚类方法，以识别其表达与这些肿瘤抑制器相关的基因。 RNA干扰将用于破坏候选BRCA基因产物在两个基于细胞的测定中取决于BRCA1和BRCA2表达的表达。第一个测定模拟了双链DNA断裂的同源指导重组修复的调节，第二个测定测试了中心体重复的控制。我们还将执行第三次测试，以确定信息鉴定的候选BRCA基因产物是否可以与BRCA1形成蛋白质复合物，因为一些已经鉴定的共表达基因确实与BRCA1形成了复合物。然后，将使用基于抗体的高通量组织微阵列系统的候选BRCA基因在基于功能细胞的测定中呈阳性的BRCA基因在临床样品中的基因产物表达变化。总而言之，该提议概述了一个新型的实验框架，该框架将开发新的生物信息学工具来识别候选基因的调节，其调节的潜力暗示了参与乳腺癌发生的潜力，测试了这些候选基因对这些候选基因所编码的蛋白质的耗尽，是否在实验室中表现出了这些候选者在乳腺癌中的表现是否一致，是否与这些候选者的表现相吻合，是否与乳腺癌相吻合，是否与乳腺癌相吻合。乳腺癌发生。该项目定义了一个框架，该框架也可能适用于识别其他疾病过程中常见途径中涉及的基因组。 公共卫生相关性：在对乳腺癌倾向的家庭中，大约25％的乳腺癌（“ BRCA”）基因BRCA1或BRCA2遗传了突变，但是大多数家族中易感性突变基因尚不清楚。 BRCA1和BRCA2基因产物都调节涉及DNA修复和中心体重复的细胞分裂途径，并且它们的表达在许多细胞类型的微阵列分析中相关。我们假设其他未识别的BRCA基因可能与BRCA1和BRCA2调节的途径有关，因此可以通过鉴定其表达也与BRCA1和BRCA2相关的基因来发现。这些候选BRCA基因将通过计算机程序驱动的公开基因表达数据的分析来识别。然后，使用这些基于计算机的方法鉴定的候选BRCA基因将在实验室测试中使用RNA干扰测定法进行筛选，以确定调节双链DNA断裂和/或中心体重复的同源指导重组修复的候选者。然后，在实验室中验证的候选BRCA基因将通过使用高通量标记的抗体测定在临床样品中测试其基因产物表达的变化。因此，该提案概述了一个新的实验框架，该框架从基于计算机的基因表达文库的广泛屏幕开始，以识别初始候选者，使用功能的体外实验室分析进行第二次筛选，然后使用临床样品中的表达进行第三个筛选。通过所有三个筛选的基因将是负责家庭乳腺癌处置的基因的出色候选者，这些基因可能是诊断乳腺癌的生物标志物，并且可能为单个患者的治疗方式成功贡献预测价值。