Longitudinal and functional dynamics of autoimmune gut microbiomes

描述(由申请人提供)：自身免疫性疾病是一种使人虚弱并常常危及生命的疾病，折磨着相当少数的人类人口。除了一些已知的基因变异外，自身免疫的原因尚不清楚，西方国家疾病流行率上升的原因也是如此。最近对人类微生物组的研究表明，各种微生物和微生物蛋白与自身免疫性疾病的发生和反应有关。我们建议通过研究微生物组在疾病发生和发展过程中如何与宿主相互作用来提高对微生物组与自身免疫性疾病之间关系的理解。这些研究将使用炎症性肠病(IBD)的小鼠模型，其中TFGb信号被转基因表达的显性阴性形式的TGFbRII(DNR)阻断在T细胞上。这个系统使我们能够进行仔细的受控实验，并探索早期的症状前时间点，这些时间点在人类临床研究中不易获得。我们的第一个目标是表征DNR小鼠从出生到严重IBD期间的体重变化和免疫标记物，并使用这些数据来识别疾病检查点(启动、激活前、激活后严重疾病)。为了探索肠道微生物群落和自身免疫性疾病之间的关系，我们的第二个目标将使用鸟枪元基因组测序和尖端生物信息学工具来描述DNR小鼠和健康野生型(WT)小鼠在每个疾病检查点的微生物组蛋白质谱。我们将把元基因组测序读数映射到蛋白质家族和途径中，然后使用广义线性模型来测试不同品系之间这些生理图谱的显著差异。这些检测将确定预测IBD发病或进展的候选生物标记物。我们的第三个目标是确定IBD的时间生物标记物、微生物蛋白质和具有不同纵向轨迹的途径。我们将对从出生到严重IBD的其他时间点的元基因组进行排序，并使用混合效应模型来识别与宿主免疫学变化相关的微生物生物标记物，并区分DNR和WT小鼠。然后，我们的发现将与人类IBD的元基因组学研究相关联，以开发关于疾病诱导机制的可测试假说，并从我们的研究中识别也可能用作人类IBD的廉价、早期和临时诊断的基因和途径。本研究的总体目标是阐明IBD与哺乳动物肠道微生物群的关系。这项研究将建立使用小鼠模型来研究微生物组在人类自身免疫性疾病中的作用的可行性，并最终开发基于微生物组的治疗方法。

DESCRIPTION (provided by applicant): Autoimmune diseases are debilitating and often life-threatening conditions that afflict a substantial minority of the human population. Aside from some known genetic variations, the causes of autoimmunity remain unclear, as does the reason for the rise in disease prevalence in Western countries. Recent studies of the human microbiome implicate various microbes and microbial proteins in the development of and response to autoimmune diseases. We propose to improve understanding of the relationship between the microbiome and autoimmune disease by investigating how the microbiome interacts with its host over the time course of disease onset and progression. These studies will use a mouse model of inflammatory bowel disease (IBD) where TFGb signaling is blocked on T cells by transgenic expression of a dominant negative form of TGFbRII (DNR). This system enables us to conduct carefully controlled experiments and to probe early, pre- symptomatic time points that are not easily accessible in human clinical studies. Our first aim is to characterize weight change and immunological markers from birth through severe IBD in DNR mice and use this data to identify disease checkpoints (initiation, pre-activation, post-activation severe disease). To explore the relationship between gut microbial communities and autoimmune disease, our second aim will use shotgun metagenomic sequencing and cutting-edge bioinformatics tools to profile the microbiome's protein repertoire at each disease checkpoint in DNR mice versus healthy wildtype (WT) littermates. We will map metagenomic sequencing reads into protein families and pathways and then use generalized linear models to test for significant differences in these physiological profiles between lines. These tests will identify candidate biomarkers that predict IBD onset or progression. Our third aim is to identify temporal biomarkers for IBD, microbial proteins and pathways that have different longitudinal trajectories. We will sequence metagenomes from additional time points¿from birth through severe IBD¿and use mixed effects models to identify microbial biomarkers that correlate with changes in host immunology and also distinguish DNR and WT mice. Our findings will then be related to metagenomic studies of IBD in humans to develop testable hypotheses about mechanisms of disease induction and to identify genes and pathways from our study that might also serve as inexpensive, early-onset and temporal diagnostics of IBD in humans. The overall goal of this study is to clarify the relationship between IBD and the mammalian gut microbiome. This study will establish the feasibility of using mouse models to study the role of the microbiome in human autoimmune disease and ultimately to develop microbiome-based therapeutics.