Functional Genomics Study and Database for Tuberculosis

描述(申请人提供)：将研究结核分枝杆菌的功能基因组学，并将建立一个数据库，用于科学和临床应用。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健康威胁、科学家正在寻找具有新作用机制的新药之际，该项目具有重要意义。鉴于微阵列技术对基因组学的巨大影响，数据库将存储在各种设计的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图谱的基因功能注释。将获得符合实验标准的结核分枝杆菌临床分离株，包括药物敏感和耐药。将开发一个基于网络的SQL Server关系数据库，以实施功能基因组学数据库，通过基于网络的图形界面提供查询和分析能力。如果合适的话，数据库中的每个基因都将通过其表达特征、共同调节的基因和相关的调节途径或网络以及其临床意义进行注释。此外，该数据库将每个基因与主要的生物信息学和基因组学数据库联系起来，以产生一个综合的检索报告。所有功能基因组数据和分析都将被置于公共领域。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，并获得用于制造内部系统的程序代码。在这个项目中，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药候选将通过药物挑战的基因表达研究进行评估，以诱导药物作用产生的药物特有的基因表达模式。将使用体外诱导的非复制持久性的同步结核分枝杆菌培养来研究细胞生物学，以便识别周期依赖的基因和相关的调控机制，并研究在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。这些研究将发现许多共同调节的基因家族，并允许根据与已知功能基因的共表达来推断未表征基因的功能。结合聚类分析，搜索调节子上游的顺式调控元件，以及使用转录因子数据库，将揭开基因调控网络，并能够推断生物途径和发现新的药物靶点。已确定的重要调控基因将接受进一步分析，以利用基因敲除菌株确认它们的调控作用。部分耐药性和细菌持久性是结核病经常遇到的两种重要临床情况，将使用功能基因组学研究进行分析。提出的方法的潜在价值已经被证明，并认识到相对于以前的技术的优势。研究成果将促进分子生物学知识的发展，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.