A Systems Biology Approach to the Model Apicomplexan Toxoplasma gondii

描述（由申请人提供）：本申请的重点是发展中国家许多疾病的病原，与全球健康相关（专题领域4）。它使用基因组学和其他高通量技术（专题领域1），对大型数据集进行系统级集成、分析和挖掘，其总体目标是将我们的发现转化为治疗和疾病预防的新见解（专题领域2）。为了实现我们的目标，我们组建了一个多学科合作团队，具有传染病，糖尿病，代谢，病理学，分子生物学，动物模型和病理生理学方面的专业知识，在具有挑战性的生物医学领域进行创新研究（专题领域5）。作为主要的新出现和再出现的病原体，顶复合体寄生虫感染了世界上三分之一以上的人口。这些专性细胞内寄生虫包括刚地弓形虫、疟原虫和隐孢子虫。刚地弓形虫是艾滋病流行的一种主要机会性病原体，是造成出生缺陷的一种原因，由于与水传播疾病暴发有关，它也是B类优先病原体。疟原虫是疟疾的病原体，每年感染超过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，因此需要新的治疗和预防疾病的战略。人们对顶复合体如何调节毒力性状和对环境变化作出反应知之甚少。新的高通量技术的发展使大型基因组和蛋白质组学数据集的收集成为可能。这些可以用来发展真核细胞如何调节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，以促进综合系统方法来理解模型顶复合体弓形虫的基因表达调控和表观遗传学。我们将测试的必要性染色质重塑和候选转录因子使用适度的通量基因破坏策略。使用表位标记的染色质重塑子和转录因子，我们将使用染色质免疫沉淀和表达微阵列的高通量测序来鉴定共调节基因组。最后，我们将进行高通量蛋白质组学来表征参与基因表达调控的大分子复合物的成分。这些表观基因组学、转录组学和蛋白质组学数据集将促进计算方法来模拟顶复合体的表观遗传和遗传因素如何在基因网络中相互作用。这项工作将创造重要的社区资源，使系统生物学的方法来理解毒力性状的表达和鉴定新的药物靶点顶复合体寄生虫。

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.