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

基本信息

批准号：
10415206
负责人：
Christian Jobin
金额：
$ 18.84万
依托单位：
UNIVERSITY OF FLORIDA
依托单位国家：
美国
项目类别：
财政年份：
2021
资助国家：
美国
起止时间：
2021-06-01 至 2023-11-30
项目状态：
已结题

来源：
https://reporter.nih.gov/project-details/10415206
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 Reporting Reverse Transcriptase Polymerase Chain Reaction Rheumatoid Arthritis Ribosomal DNA 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 inflammation gut microbiota host microbiota in vivo inhibitor intestinal epithelium knock-down microbial microbial community microbial composition microbial genomics microbiome microbiota microorganism prevent siRNA delivery therapeutic gene transcriptome sequencing transcriptomics

项目摘要

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.

概括：许多研究报告了代谢等疾病中微生物群组成的变化综合症、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。通过使用特定的方法，其中一些联系已被证明是导致疾病的原因。将细菌引入临床前模型。例如，我们表明人类临床分离空肠弯曲菌（空肠弯曲菌）81-176 通过产生以下物质促进结肠炎相关结直肠癌的发展细胞致死膨胀毒素 (cdt) (He Z et al. Gut. 2019; 68(2) 289-300)。重要的是，小鼠被空肠弯曲菌定殖与缺乏毒素 cdtB 的空肠弯曲菌相比，81-176 具有显着不同的微生物基因表达谱通过 16S rDNA 测序测量不同的微生物群落（He Z et al. Gut. 2019； 68（2）：289-300）。此外，我们证明肠道微生物群可以预防空肠弯曲菌诱导的肠道微生物群 ex-GF Il10-/- 小鼠通过胆汁酸代谢产生炎症（Sun X 等人，胃肠病学。 2018；154(6):1751-1763）。因此，破坏微生物的组成和功能可能是由肠道病原微生物介导的疾病。维持健康的机制宿主-微生物群平衡是复杂的，包括宿主衍生的抗微生物肽、粘液的产生屏障和免疫球蛋白分泌等。我们实验室的最新研究结果表明，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粪便的表达小RNA，例如miRNA，其中一些miRNA优先针对细菌基因，正如预测的那样生物信息学方法（Tomkovich S 等人 mSystems.2020；5(1)）。许多这些 miRNA 被预测涉及调节运动、分泌、外膜蛋白、应激反应、铁的目标细菌基因获取和碳水化合物利用/运输。因此，源自宿主的小非编码RNA的产生可能代表宿主调节微生物群功能的另一种方式。这个令人兴奋的概念得到了支持我们的初步数据证明使用哺乳动物细胞外囊泡（EV）对细菌进行基因敲除装载有针对原核基因的 siRNA。这些发现表明细菌对宿主的影响不同衍生的 miRNA，进而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，进而改变微生物群群落功能以及由此产生的疾病表型。我们计划用以下两个方法来检验这个假设具体目标：目标 1. 明确 EV 在 Il10-/- 小鼠细菌诱导的 miRNA 中的作用。目标 2. 确定 EV 介导的 siRNA 对微生物基因表达的影响。这项研究将建立肠道病原体触发选择性含有 EV 的 miRNA 的原理证明对微生物群产生不同的影响。我们的方法使用微生物基因组学、转录组学、基因操作、限菌技术为解决宿主、微生物群之间的相互作用提供了独特的机会活动、宿主反应和炎症。该项目的研究结果将为通过小非编码RNA存在王国间交流并开启新的可能性利用这一发现进行微生物基因操作和治疗目的。