Comparative functional genomics for lung cancer gene discovery

肺癌基因发现的比较功能基因组学

• 批准号: 8303011
• 负责人: ATUL J BUTTE
• 金额: $ 52.11万
• 依托单位: STANFORD UNIVERSITY
• 依托单位国家: 美国
• 财政年份: 2008
• 资助国家: 美国
• 起止时间: 2008-09-23 至 2014-07-31
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/8303011
• 关键词: Accounting; American; Bioinformatics; Biological; Biological Testing; Cancer Patient; Cancer cell line; Carcinogens; Cells; Cessation of life; Clinical; Communities; Complex; Computer Simulation; Critical Pathways; DNA-Protein Interaction; Data; Data Set; Development; Diagnosis; Diagnostic; Disease; Drug Delivery Systems; Event; Exposure to; Foundations; Gene Expression; Gene Expression Profile; Gene Expression Profiling; Gene Targeting; Genes; Genetic; Genetic Variation; Genetically Engineered Mouse; Genomics; Genotype; Goals; Human; Individual; Induced Mutation; Knowledge; Link; Lung; Lung Adenocarcinoma; Lung Neoplasms; Malignant Neoplasms; Malignant neoplasm of lung; Mediating; Mediator of activation protein; Molecular; Molecular Profiling; Mus; Mutant Strains Mice; Mutate; Mutation; Non-Small-Cell Lung Carcinoma; Nucleic Acid Regulatory Sequences; Oncogenes; Oncogenic; Pathogenesis; Pathway interactions; Patients; Pattern; Plant Roots; Prognostic Factor; Prognostic Marker; Proteins; Protocols documentation; RNA Interference; Regulator Genes; Research; Role; Screening procedure; Source; Staging; System; Techniques; Testing; Therapeutic; Tissue Microarray; Tissues; Tumor Cell Line; United States; Validation; Woman; Work; abstracting; anticancer research; base; cancer gene expression; cigarette smoking; comparative; design; functional genomics; gene discovery; genetic profiling; genome-wide; high throughput screening; human data; human tissue; improved; in vivo; lung tumorigenesis; men; mortality; mouse model; neoplastic cell; novel; novel strategies; outcome forecast; prevent; prognostic; public health relevance; research study; therapeutic development; tool; treatment strategy; trend; tumor; tumorigenesis

DESCRIPTION (provided by applicant): Abstract Since the mid-1990s, approximately 150,000 Americans have died of lung cancer every year, and the upward trend in total cancer deaths is largely due to the increasing rate of lung cancer mortality. Even if we could prevent cigarette smoking and exposure to other carcinogens today, hundreds of thousands of lung cancer cases would still need to be treated in the next decades. A major current effort in the lung cancer field is to detect and treat lung cancer at earlier stages to improve the survival of patients. In addition, identifying novel drug targets would allow for the development of more efficacious therapeutic strategies against lung tumors. Finally, lung cancer patients are treated following well-established protocols that most often do not take into account the genetic diversity of their tumors, and very little is known about prognostic factors for individual lung cancer patients. A better knowledge of the molecular events in lung cancer development would help to identify diagnostic and prognostic markers in lung cancer patients. Rb, p53 and Kras are among the most frequently mutated genes in human cancer. In particular, combinations of mutations in these three genes are often found in human lung cancer and define important clinical subtypes. Using advanced gene-targeting approaches, we and others have generated genetically engineered mice with mutations in these genes. These mutant mice develop tumors that closely resemble human lung tumors and provide a genetically tractable system to study lung tumorigenesis in vivo. Here, we propose to use comparative gene expression analysis to define genotype-specific oncogenic signatures using these mouse models of lung cancer. Our specific goals are: - To develop gene expression signatures from mouse tumors and compare them to human data to identify new human lung cancer subtypes. The validation of subtype-specific genes from these signatures will be performed using human tissue arrays. - To identify key regulators and "drivers" of these gene expression signatures using conventional bioinformatics approaches as well as a novel "event" centered gene network that we will develop. In particular, we will introduce the notion of ordered, causal events in lung cancer gene networks to identify key nodes in these gene networks. - To functionally analyze potential key regulators of these lung cancer gene expression signatures. To this end, we will first use gene expression-based high throughput screening to identify such regulators and we will then test their functional role in lung cancer development in vivo. The overall goal of our work is to begin to define critical pathways that are required for genotype-specific oncogenesis. Characterization of these pathways may provide a useful approach for identification of new approaches for diagnosis, prognosis, and targeted therapy in lung cancer patients. PUBLIC HEALTH RELEVANCE: We propose to use a novel gene network to identify molecular events downstream of key oncogenic "driver" mutations for lung cancer by comparing gene expression profiles in lung tumors from genetically defined mouse models to gene expression profiles from human lung tumors. We will test the functional role of candidate regulators of lung cancer in mouse models and human tumor cell lines and tissues. Our experiments will lay the foundation needed for the development of novel strategies to detect and treat lung cancer, the number one cancer killer in both men and women in the United States.

摘要自20世纪90年代中期以来，每年约有15万美国人死于肺癌，癌症死亡总数的上升趋势主要是由于肺癌死亡率的增加。即使我们今天能够防止吸烟和接触其他致癌物质，在未来几十年内仍有数十万肺癌病例需要治疗。目前在肺癌领域的主要努力是在早期阶段检测和治疗肺癌，以提高患者的生存率。此外，确定新的药物靶点将允许开发针对肺肿瘤的更有效的治疗策略。最后，肺癌患者的治疗遵循完善的方案，这些方案通常不考虑其肿瘤的遗传多样性，并且对个体肺癌患者的预后因素知之甚少。更好地了解肺癌发展中的分子事件将有助于确定肺癌患者的诊断和预后标志物。Rb、p53和Kras是人类癌症中最常见的突变基因。特别是，这三个基因的突变组合经常在人类肺癌中发现，并定义了重要的临床亚型。使用先进的基因靶向方法，我们和其他人已经产生了这些基因突变的基因工程小鼠。这些突变小鼠产生的肿瘤与人类肺肿瘤非常相似，并提供了一个遗传学上易于处理的系统来研究体内肺肿瘤发生。在这里，我们建议使用比较基因表达分析来定义基因型特异性致癌签名使用这些小鼠肺癌模型。我们的具体目标是：从小鼠肿瘤中开发基因表达特征，并将其与人类数据进行比较，以识别新的人类肺癌亚型。将使用人体组织阵列对来自这些特征的亚型特异性基因进行验证。- 使用传统的生物信息学方法以及我们将开发的新的以“事件”为中心的基因网络来识别这些基因表达特征的关键调控因子和“驱动因子”。特别是，我们将引入肺癌基因网络中有序因果事件的概念，以识别这些基因网络中的关键节点。- 功能分析这些肺癌基因表达特征的潜在关键调控因子。为此，我们将首先使用基于基因表达的高通量筛选来鉴定这些调节剂，然后我们将测试它们在体内肺癌发展中的功能作用。我们工作的总体目标是开始确定基因型特异性肿瘤发生所需的关键途径。这些途径的表征可能为肺癌患者的诊断、预后和靶向治疗的新方法的鉴定提供有用的方法。 公共卫生关系：我们建议使用一种新的基因网络，以确定关键致癌“驱动”突变的肺癌下游的分子事件，通过比较基因表达谱在肺肿瘤从遗传定义的小鼠模型，从人类肺肿瘤的基因表达谱。我们将在小鼠模型和人类肿瘤细胞系和组织中测试肺癌候选调节因子的功能作用。我们的实验将为开发检测和治疗肺癌的新策略奠定基础，肺癌是美国男性和女性的头号癌症杀手。

项目成果

A common rejection module (CRM) for acute rejection across multiple organs identifies novel therapeutics for organ transplantation.

• DOI: 10.1084/jem.20122709
• 发表时间: 2013-10-21
• 期刊: The Journal of experimental medicine
• 作者: Khatri P;Roedder S;Kimura N;De Vusser K;Morgan AA;Gong Y;Fischbein MP;Robbins RC;Naesens M;Butte AJ;Sarwal MM
• 通讯作者: Sarwal MM

Systematic pan-cancer analysis of tumour purity.

肿瘤纯度的系统泛滥分析。

• DOI: 10.1038/ncomms9971
• 发表时间: 2015-12-04
• 期刊: Nature communications
• 影响因子: 16.6
• 作者: Aran D;Sirota M;Butte AJ
• 通讯作者: Butte AJ

A drug repositioning approach identifies tricyclic antidepressants as inhibitors of small cell lung cancer and other neuroendocrine tumors.

• DOI: 10.1158/2159-8290.cd-13-0183
• 发表时间: 2013-12
• 期刊: Cancer discovery
• 影响因子: 28.2
• 作者: Jahchan NS;Dudley JT;Mazur PK;Flores N;Yang D;Palmerton A;Zmoos AF;Vaka D;Tran KQ;Zhou M;Krasinska K;Riess JW;Neal JW;Khatri P;Park KS;Butte AJ;Sage J
• 通讯作者: Sage J

Computational repositioning of the anticonvulsant topiramate for inflammatory bowel disease.

• DOI: 10.1126/scitranslmed.3002648
• 发表时间: 2011-08-17
• 期刊: Science translational medicine
• 影响因子: 17.1
• 作者: Dudley JT;Sirota M;Shenoy M;Pai RK;Roedder S;Chiang AP;Morgan AA;Sarwal MM;Pasricha PJ;Butte AJ
• 通讯作者: Butte AJ