Modulation of microbiome function by host-derived noncoding small RNA

宿主来源的非编码小 RNA 调节微生物组功能

• 批准号: 10317154
• 负责人: Christian Jobin
• 金额: $ 22.65万
• 依托单位: UNIVERSITY OF FLORIDA
• 依托单位国家: 美国
• 财政年份: 2021
• 资助国家: 美国
• 起止时间: 2021-06-01 至 2023-05-31
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/10317154
• 关键词: Address; Adhesions; Affect; Asthma; Bacteria; Bacterial Genes; Bacterial Infections; Bioinformatics; Campylobacter jejuni; Candidate Disease Gene; Carbohydrates; Cardiovascular Diseases; Clinical; Colitis associated colorectal cancer; Colorectal; Communication; Communities; Complex; Data; Development; Diet; Dietary Carbohydrates; Disease; Education; Epithelial Cells; Equilibrium; Escherichia coli; Flagellin; Gastroenterology; Gene Expression; Gene Expression Profile; Gene Expression Regulation; Generations; Genes; Gnotobiotic; Growth; Human; Hypertension; Immune response; Immune system; Immunoglobulins; Infection; Inflammation; Inflammatory Bowel Diseases; Intestines; Invaded; Invertebrates; Iron; Laboratories; Link; Malignant Neoplasms; Measures; Mediating; Membrane Proteins; Metabolic syndrome; MicroRNAs; Microbe; Modeling; Modification; Mucous body substance; Mus; Nutrient; Pathologic; Pharmaceutical Preparations; Pre-Clinical Model; Production; Recombinant DNA; Reporting; Reverse Transcriptase Polymerase Chain Reaction; Rheumatoid Arthritis; Ribosomal RNA; Role; Small Interfering RNA; Small RNA; Stress; Technology; Testing; The Sun; Therapeutic; Tissues; Toxin; Untranslated RNA; Virulence Factors; Vitamins; Western Blotting; antimicrobial peptide; bile acid metabolism; biological adaptation to stress; cell motility; cohort; cytolethal distending toxin; design; disease phenotype; enteric pathogen; exosome; extracellular vesicles; genetic manipulation; gut microbiota; host microbiota; in vivo; inflammatory disease of the intestine; inhibitor/antagonist; intestinal epithelium; knock-down; microbial; microbial community; microbial composition; microbial genomics; microbiome; microbiota; microorganism; prevent; siRNA delivery; therapeutic gene; transcriptome sequencing; transcriptomics

Summary: A number of studies have reported changes in the composition of microbiota in diseases such as metabolic syndrome, inflammatory bowel diseases, hypertension, Asthma, cardiovascular diseases, rheumatoid arthritis, cancer and infection. Some of these links have been shown to be causative of diseases by using specific bacteria introduced into pre-clinical models. For example, we showed that the human clinical isolate C. jejuni (C. jejuni) 81-176 promote development of colitis-associated colorectal cancer through the production of cytolethal distending toxin (cdt) (He Z et al. Gut. 2019; 68(2) 289-300). Importantly, mice colonized with C. jejuni 81-176 had a significantly different microbial gene expression profile compared to C. jejuni lacking the toxin cdtB group, and different microbial communities as measured by 16S rDNA sequencing (He Z et al. Gut. 2019; 68(2):289-300). In addition, we demonstrated that the intestinal microbiota prevents C. jejuni-induced intestinal inflammation in ex-GF Il10-/- mice, through bile acid metabolism (Sun X et al. Gastroenterology. 2018;154(6):1751-1763). Thus, disruption of microbial composition and function may be an important aspect of disease mediated by enteropathogenic microorganisms. The mechanism implicated in maintaining a healthy host-microbiota balance is complex and included production of host-derived anti-microbial peptides, mucus barrier and immunoglobulin secretion among others. Recent findings from our laboratory suggest that human intestinal microbiota obtained from healthy or colorectal tissues altered expression of mammalian-derived fecal small RNAs such as miRNA, with some miRNAs preferentially targeting bacteria genes as predicted by bioinformatic approach (Tomkovich S et al. mSystems. 2020; 5(1)). Many of these miRNAs were predicted to target bacterial genes implicated in regulating motility, secretion, outer membrane proteins, stress response, iron acquisition, and carbohydrate utilization/transport. Thus, host-derived production of small non-coding RNA may represent another mean by which the host regulate microbiota function. This exciting concept is supported by our preliminary data demonstrating gene knockdown in bacteria using mammalian extracellular vesicles (EVs) loaded with siRNA targeting prokaryotic genes. These findings suggest that bacteria differentially impact host- derived miRNA, which in turn could influence bacterial composition and gene expression. From these observations, we hypothesize that bacteria influence the production of miRNA, which in turn modified microbiota community function and consequently disease phenotype. We plan to test this hypothesis with the following two specific aims: Aim 1. Define the role of EV in bacteria-induced miRNA in Il10-/- mice. Aim 2. Define the impact of EV-mediated siRNA on microbial gene expression. This study will establish a proof of principal that enteric pathogens triggers selective EV-containing miRNA differently affecting microbiota. Our approach using microbial genomics, transcriptomic, genetic manipulation, and gnotobiotic technology represents a unique opportunity to address the interplay between host, microbiota activities, host response and inflammation. The findings generated from this project will provide a firm support for the existence of an interkingdom communication through small non-coding RNA and open new possibilities to exploit this discovery for microbial gene manipulation and therapeutic purpose.

摘要： 一些研究已经报道了代谢等疾病中微生物区系组成的变化 综合征、炎症性肠病、高血压、哮喘、心血管疾病、类风湿性关节炎、 癌症和感染。这些联系中的一些已经被证明是疾病的原因，通过使用特定的 将细菌引入临床前模型。例如，我们证明了人类临床分离的空肠弯曲菌 (空肠)81-176促进结肠炎相关性结直肠癌的发生 细胞致死性膨胀毒素(CDT)(何智等)肠胃。2019年；68(2)289-300)。重要的是，携带空肠弯曲菌的小鼠 81-176的微生物基因表达谱与缺乏CDtB毒素的空肠弯曲菌显著不同 通过16S rDNA测序测定不同微生物群落(He Z et al.肠胃。2019年； 68(2)：289-300)。此外，我们还证明了肠道微生物区系可以阻止空肠弯曲菌诱导的肠道。 前GF Il10-/-小鼠的炎症，通过胆汁酸代谢(Sun X等人)。胃肠病学。 2018年；154(6)：1751-1763)。因此，微生物组成和功能的破坏可能是 由肠道致病微生物引起的疾病。维持身体健康的机制 宿主-微生物区系平衡是复杂的，包括宿主衍生的抗菌肽、粘液的产生 屏障和免疫球蛋白分泌等。我们实验室的最新发现表明，人类 从健康或结直肠组织获得的肠道微生物群改变了哺乳动物来源的粪便的表达 小RNA，如miRNA，其中一些miRNAs优先针对细菌基因，如 生物信息学方法(Tomkovich，S等人)。M系统公司。2020年；5(1))。其中许多miRNA被预测为 涉及调节运动、分泌、外膜蛋白、应激反应、铁的靶细菌基因 以及碳水化合物的利用/运输。因此，宿主衍生的小的非编码RNA的生产可以 代表寄主调节微生物区系功能的另一种方式。这一令人兴奋的概念得到了 我们的初步数据显示，利用哺乳动物细胞外小泡(EVS)在细菌中敲除了基因 携带靶向原核基因的siRNA。这些发现表明细菌对宿主的影响是不同的 衍生的miRNA，这反过来又可以影响细菌组成和基因表达。从这些 根据观察，我们假设细菌影响miRNA的产生，而miRNA反过来又改变了微生物区系 社区功能，因此疾病表型。我们计划用以下两种方法来检验这一假设 具体目标： 目的1.明确EV在细菌诱导的IL10-/-小鼠miRNA中的作用。 目的2.明确EV介导的siRNA对微生物基因表达的影响。 这项研究将确立肠道病原体触发选择性含EV的miRNA的原理证据。 以不同的方式影响微生物区系。我们的方法使用微生物基因组学，转录，基因操作， 而灵知生物技术代表着一个独特的机会来解决宿主、微生物群之间的相互作用 活动、宿主反应和炎症。本项目所产生的结果将提供有力的支持 为跨王国通信的存在通过小分子非编码RNA打开了新的可能性 将这一发现用于微生物基因操作和治疗目的。