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: 8053355
• 负责人: Umit V. Catalyurek
• 金额: $ 44.01万
• 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/8053355
• 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来发现参与乳腺癌发生过程的基因。在具有乳腺癌易感性的家庭中，大约25%的人遗传了乳腺癌（“BRCA”）基因BRCA1或BRCA2的突变，但大多数家庭中的易感突变基因尚不清楚。 BRCA1 和 BRCA2 基因产物均调节涉及 DNA 修复和中心体复制的细胞分裂途径，并且它们的表达在许多细胞类型的微阵列分析中具有相关性。我们假设其他未鉴定的 BRCA 基因可能参与 BRCA1 和 BRCA2 调节的相同途径，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（包括组合和代数聚类方法）查询公共领域的基因表达数据库，以识别其表达与这些肿瘤抑制因子相关的基因。 RNA 干扰将用于在两个依赖于 BRCA1 和 BRCA2 表达的细胞检测中破坏候选 BRCA 基因产物的表达。第一个测定模拟双链 DNA 断裂的同源定向重组修复的调节，第二个测定测试中心体复制的控制。我们还将进行第三次测试，以确定信息学鉴定的候选 BRCA 基因产物是否可以与 BRCA1 形成蛋白质复合物，因为一些已鉴定的共表达基因确实与 BRCA1 形成复合物。然后，将使用基于抗体的高通量组织微阵列系统，测试在基于功能细胞的检测中呈阳性的候选 BRCA 基因在临床样本中的基因产物表达的变化。总之，该提案概述了一个新颖的实验框架，该框架将开发新的生物信息学工具，用于识别候选基因，这些候选基因的调控表明可能参与乳腺癌发生，测试这些候选基因编码的蛋白质的耗尽是否会导致实验室中的表型与乳腺癌一致，并确定这些候选基因在临床样本中的表达是否表明它们作为乳腺癌生物标志物的潜力。该项目定义了一个框架，该框架也可能适用于识别参与其他疾病过程中常见途径的基因组。 公共健康相关性：在具有乳腺癌易感性的家庭中，大约 25% 的人患有乳腺癌 (“BRCA”) 基因 BRCA1 或 BRCA2 的遗传性突变，但大多数家庭中的易感突变基因尚不清楚。 BRCA1 和 BRCA2 基因产物均调节涉及 DNA 修复和中心体复制的细胞分裂途径，并且它们的表达在许多细胞类型的微阵列分析中具有相关性。我们假设其他未鉴定的 BRCA 基因可能参与 BRCA1 和 BRCA2 调节的相同途径，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对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识别出的候选 BRCA 基因将在实验室测试中使用 RNA 干扰测定进行筛选，以识别调节双链 DNA 断裂和/或中心体复制的同源定向重组修复的候选基因。然后，在实验室中验证的候选 BRCA 基因将使用临床样本中的高通量标记抗体检测来测试其基因产物表达的变化。因此，该提案概述了一个新颖的实验框架，该框架从基于计算机的基因表达库的广泛筛选开始，以识别初始候选者，使用体外实验室功能分析进行第二次筛选，然后使用临床样本中的表达进行第三次筛选。通过所有三项筛选的基因将是负责家族乳腺癌倾向的基因的优秀候选者，这些基因可以作为乳腺癌诊断的生物标志物，并且可以为个体患者的治疗方式的成功提供预测价值。