Functional Genomics Study and Database for Tuberculosis

项目描述（申请人提供）：研究结核分枝杆菌的功能基因组学，建立科学和临床应用数据库。该项目代表了微生物学和基因组学领域的一项新努力，在耐多药结核病日益成为公共卫生威胁、科学家正在寻找具有新作用机制的新药之际，具有重要意义。鉴于微阵列技术对基因组学的巨大影响，该数据库将存储在各种设计实验条件下产生的微阵列基因表达数据，并提供基于表达和调控谱的基因功能注释。将获得符合实验标准的对药物敏感和耐药的结核分枝杆菌临床分离株。将开发一个基于web的SQL Server关系数据库来实现功能基因组数据库，通过基于web的图形界面提供查询和分析功能。数据库中的每个基因将根据其表达特征、共调控基因和相关调控通路或网络以及临床意义（如果合适）进行注释。此外，该数据库将每个基因链接到主要的生物信息学和基因组学数据库，以产生一个集成的检索报告。所有功能基因组学数据和分析将被置于公共领域。该数据库与其他联邦资助的资源中心协同工作，旨在允许其他研究人员存储微阵列数据，进行数据分析，并获得内部系统的程序代码。在本项目中，将进行一系列差异和协调的全基因组基因表达研究，以探索药物靶点，耐药性和生物学。重要的抗结核药物和有希望的新候选药物将通过药物挑战基因表达研究来评估，以诱导药物作用引起的药物特异性基因表达模式。研究人员将利用同步结核分枝杆菌体外诱导的非复制持久性培养来研究细胞生物学，从而鉴定周期依赖基因和相关调控机制，并研究从非复制状态到复制状态转变过程中伴随代谢重编程的基因表达。这些研究将揭示许多共调控的基因家族，并允许基于与已知功能基因的共表达推断未表征基因的功能。结合聚类分析、顺式调控元件的上游搜索和转录因子数据库的使用，将揭示基因调控网络，并能够推断生物学途径和发现新的药物靶点。确定的重要调控基因将进行进一步分析，以确认其使用敲除菌株的调控作用。部分耐药和细菌持久性是结核病中经常遇到的两个重要临床情况，将使用功能基因组学研究进行分析。所提出的方法的潜在价值已经得到证明，并且与以前的技术相比具有优势。研究成果将促进分子生物学知识的发展，并有利于结核病的公共卫生管理。

DESCRIPTION (provided by applicant): The functional genomics of Mycobacterium tuberculosis will be studied and a database will be constructed for both scientific and clinical applications. Representing a new endeavor in microbiology and genomics, this project is important at this time when multidrug-resistant tuberculosis is increasingly a public-health threat and scientists are seeking new drugs with novel mechanisms of action. In light of the tremendous impact of the microarray technology on genomics, the database will store the microarray gene expression data engendered under various designed experimental conditions as well as provides functional annotations of genes based on expression and regulation profiling. M. tuberculosis clinical isolates both drug-sensitive and -resistant that meet experimental criteria will be obtained. A web-based SQL Server relational database will be developed to implement the functional genomics database, providing query and analysis capabilities via a web-based graphical interface. Each gene in the database will be annotated by its expression characteristics, co-regulated genes and associated regulated pathways or networks, and its clinical significance, if appropriate. Furthermore, the database links each gene to major bioinformatics and genomics databases to produce an integrated retrieved report. All functional genomics data and analyses will be placed in the public domain. Working synergistically with other federally funded resource centers, the database is designed to allow other researchers to deposit microarray data, conduct data analysis, and obtain program code for making in-house systems. In this project, a set of differential and coordinated genome-wide gene expression studies will be performed to explore drug targets, drug resistance, and biology. Important anti-tubercular drugs and promising new drug candidates will be assessed using drug-challenged gene expression studies to induce drug-specific gene-expression patterns resulting from drug action. Cell biology will be investigated using synchronized M. tuberculosis culture based on in vitro induced non-replicating persistence so that cycle-dependent genes and pertinent regulatory mechanisms will be identified and gene expression accompanying metabolic reprogramming that occurs during shift from non-replicating to replicating states will be studied. These studies will uncover many co-regulated families of genes and allow the functions of uncharacterized genes to be deduced based on co-expression with genes of known function. Combining cluster analysis, search of cis-regulatory elements upstream of regulons, and use of transcription factor databases will unravel gene regulatory networks and enable inferences about biological pathways and discovery of novel drug targets. Important regulatory genes identified will be subjected to further analysis for confirming their regulatory roles using knockout strains. Partial drug resistance and bacterial persistence, which are two important clinical circumstances often encountered in tuberculosis, will be analyzed using functional-genomics studies. The potential value of the proposed methods has been demonstrated and advantages over previous technology been recognized. Research results will advance molecular biological knowledge and benefit public health management in tuberculosis.