A Systems Biology Approach to the Model Apicomplexan Toxoplasma gondii

描述(由申请人提供)：本申请侧重于复合体，这是发展中国家许多疾病的病原体，与全球卫生有关(专题领域4)。它使用基因组学和其他高通量技术(主题领域1)，对大型数据集进行系统级的集成、分析和挖掘，总体目标是将我们的发现转化为对治疗和疾病预防的新见解(主题领域2)。为了实现我们的目标，我们组建了一个拥有传染病、糖尿病、新陈代谢、病理学、分子生物学、动物模型和病理生理学专业知识的多学科协作团队，在具有挑战性的生物医学领域进行创新研究(主题领域5)。作为主要的新出现和再次出现的病原体，Apicomplexan寄生虫感染了世界三分之一以上的人口。这些专性胞内寄生虫包括弓形虫、疟原虫和隐孢子虫。弓形虫是艾滋病流行的主要机会性病原体，是导致出生缺陷的原因之一，也是B类优先病原体，因为它与水传播的暴发有关。疟疾的病原体--疟原虫每年感染2.67亿人，每年造成近100万人死亡。尽管这些寄生虫在人类疾病中很重要，但目前还没有针对这些病原体的有效疫苗，需要新的治疗和预防疾病的策略。人们对Apicomplexa如何调节毒力特征以及对环境变化的反应知之甚少。新的高通量技术的发展使收集大型基因组和蛋白质组数据集成为可能。这些可以用来发展对真核细胞如何调控基因表达的综合理解。我们将利用基因组操作、全基因组阵列、高通量测序和蛋白质组学来开发数据集，这些数据集将有助于采用集成的系统方法来了解模型顶端复合体弓形虫的基因表达调控和表观遗传学。我们将使用适度的吞吐量基因中断策略来测试染色质重构体和候选转录因子的重要性。利用表位标记的染色质重构体和转录因子，我们将使用染色质免疫沉淀物和表达微阵列的高通量测序来识别共调控基因组。最后，我们将进行高通量蛋白质组学，以确定参与基因表达调控的大分子复合体的成分。这些表观基因组、转录组和蛋白质组数据集将有助于计算方法来模拟表观遗传和遗传因素如何在基因网络中相互作用。这一努力将创造重要的社区资源，使系统生物学方法能够理解毒力特征的表达和识别顶复合体寄生虫的新药物靶点。 与公共卫生相关：弓形虫是一种寄生性病原体，会在包括艾滋病患者在内的免疫功能受损的人中引起严重疾病，导致出生缺陷，由于与水传播疫情有关，因此是生物防御性B类病原体。最后，它是其他寄生虫的模型系统，比如导致人类疟疾的疟原虫。这些寄生虫影响着世界上三分之一以上的人口。我们正在努力生成大型数据集，帮助我们了解这些寄生性病原体如何随着与人类宿主的互动而变化，以及它们如何调控导致疾病的基因。这些数据利用了基因组测序项目，并将使用新的强大的高通量技术。收集这些数据对于开发新的治疗方法、防止弓形虫在感染者身上持续存在以及了解Apicomplexan寄生虫如何致病将是重要的。

DESCRIPTION (provided by applicant): This application focuses upon the Apicomplexa, etiologic agents of many diseases in the developing world and relevant to global health (thematic area 4). It uses genomics and other high throughput technologies (thematic area 1) with a systems-level integration, analysis and mining of large datasets with the overarching goal of translating our discoveries into new insights into therapy and disease prevention (thematic area 2). To accomplish our goals, we have assembled a multidisciplinary collaborative team with expertise in infectious diseases, diabetes, metabolism, pathology, molecular biology, animal models and pathophysiology to conduct an innovative study in challenging biomedical areas (thematic area 5). As major emerging and reemerging pathogens, Apicomplexan parasites infect more than a third of the world's population. These obligate intracellular parasites include Toxoplasma gondii, Plasmodium species and Cryptosporidium. Toxoplasma gondii is a major opportunistic pathogen of the AIDS epidemic, a cause of birth defects and is also a Category B priority agent due to its association with waterborne outbreaks. Plasmodium species, the agents of malaria, infect over 267 million people per year and cause nearly 1 million deaths per year. Despite the importance of these parasites in human disease, there are no effective vaccines for these pathogens, and new strategies for treatment and prevention of disease are needed. Very little is understood how the Apicomplexa regulate virulence traits and respond to changes in their environment. The development of new high-throughput technologies has enabled collection of large genomic and proteomics datasets. These can be used to develop an integrated understanding of how eukaryotic cells regulate gene expression. We will take advantage of genome manipulation, genome-wide arrays, high throughput sequencing, and proteomics to develop datasets that will facilitate an integrated systems approach to understanding regulation of gene expression and epigenetics in the model apicomplexan T.gondii. We will test the essentiality of chromatin remodellers and candidate transcription factors using a moderate through-put gene disruption strategy. Using epitope tagged chromatin remodelers and transcription factors, we will use high throughput sequencing of chromatin immunoprecipitates and expression microarrays to identify groups of co-regulated genes. Finally, we will perform high-throughput proteomics to characterize the constituents of macromolecular complexes involved in regulation of gene expression. These epigenomic, transcriptome, and proteomic datasets will facilitate computational approaches to model how epigenetic and genetic factors in the Apicomplexa interact within gene networks. This effort will create important community resources to enable a systems biology approach toward understanding expression of virulence traits and identification of novel drug targets for apicomplexan parasites. PUBLIC HEALTH RELEVANCE: Toxoplasma gondii is a parasitic pathogen that causes severe disease in immunocompromised individuals including people with AIDS, causes birth defects, and is a Biodefense Category B pathogen due to its association with waterborne outbreaks. Finally it is a model system for other parasites like Plasmodium, which cause human malaria. These parasites affect over a third of the world's population. We are trying to generate large datasets that will help us understand how these parasitic pathogens change in response to interaction with human hosts and how they regulate genes that cause disease. These data take advantage of genome sequencing projects and will use new powerful high throughput technologies. Gathering these data will be important for developing new treatments that will prevent T. gondii from persisting in infected people, and understanding how Apicomplexan parasites cause disease.