Metatramscriptome of the Oral Microbiome During Periodontal Disease Progression

牙周病进展过程中口腔微生物组的宏转录组

• 批准号: 8137671
• 负责人: Jorge Frias-Lopez
• 金额: $ 40.25万
• 依托单位: ADA FORSYTH INSTITUTE, INC.
• 依托单位国家: 美国
• 财政年份: 2010
• 资助国家: 美国
• 起止时间: 2010-09-03 至 2014-08-31
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/8137671
• 关键词: Adult; Affect; American; Bioinformatics; Biometry; Cardiovascular Diseases; Censuses; Chronic; Clinic; Clinical; Clinical Research; Cloning; Communities; Compassion; Complementary DNA; Complex; Conduct Clinical Trials; DNA; Data Set; Databases; Development; Diabetes Mellitus; Diagnosis; Diagnostic; Disease; Disease Progression; Disorder by Site; Gene Expression; Genes; Genome; Goals; Health; In Situ; Individual; Inflammation; Institutes; Lesion; Lung diseases; Measures; Messenger RNA; Metabolic; Metagenomics; Methods; Microbial Biofilms; Molecular; Molecular Profiling; Monitor; Nucleotides; Oral; Organism; Outcome; Pathogenesis; Patients; Pattern; Periodontal Diseases; Periodontal Infection; Periodontitis; Physiological; Polymerase Chain Reaction; Population; Prevalence; Prevention; Proteins; Public Health Schools; RNA; Relative (related person); Research; Research Personnel; Resources; Risk; Sampling; Site; Staging; Techniques; Tissues; Tooth Loss; Tooth structure; Translational Research; United States; Work; microbial; microbial community; microorganism; next generation; novel; oral biofilm; oral microbiome; prevent; programs; public health relevance; reproductive; subgingival biofilm

DESCRIPTION (provided by applicant): Periodontitis is a polymicrobial disease caused by the coordinated action of a complex microbial community, which results in inflammation of tissues that support the teeth. Periodontitis is a widespread and serious health condition that occurs in moderate form in 30% to 50% of American adults and in severe form in 10% of adults. The goal of this research program is to identify in situ the molecular mechanisms of pathogenesis by which periodontitis progress in some sites while in others the disease remains latent. Metagenomic and metatranscriptomic analysis (gene expression analysis of entire complex bacterial communities in situ) provides the information required to understand the activity and relative importance of the constituents in the pathogenic biofilm during periodontal infection. To this end we propose the following Specific Aims: Aim 1. Determine differences in prevalence and relative abundance of species in microbial communities from progressing and non-progressing periodontal sites. Aim 2. Identify in situ genes that are differentially expressed in microbial communities from progressing and non-progressing periodontal sites. We have successfully applied metatranscriptomic techniques to the study of environmental samples. The key step of the method to assess expression analysis in whole microbial communities is the linear amplification of small quantities of RNA extracted from the bacterial assemblages. The final amplified RNA is a direct representation of the relative abundance of mRNA in the original sample. The second aspect that facilitates metatranscriptomic analysis of whole bacterial communities is that pyrosequencing techniques allow now to sequence large amounts of DNA avoiding cloning biases associated with classical techniques. The target subject population will consist of 20 chronic periodontitis individuals. This subject population was chosen because chronic periodontitis is the most commonly encountered type of periodontitis and thus, the microbial changes observed will be relevant to a large proportion of subjects with periodontal disease. The patients will be followed monthly for a period of 6 months, during which they will undergo clinical monitoring to determine which samples will be used for compassion of progressing and non-progressing sites by metagenomic and metatranscriptomic analysis. Identification of critical genes that are required for pathogenesis and information about their differential expression can be used to develop novel targeted approaches to early-stage diagnosis, treatment, monitoring and prevention. Moreover, the potential impact extends beyond the study of periodontitis because the same principles and methods potentially can be applied to other polymicrobial diseases. We believe that the team we have assembled for this project (Forsyth Institute with help of Broad Institute and the Department of Biostatistics at Harvard School of Public Health) has all the qualifications to accomplish successfully the goals proposed in the present application. PUBLIC HEALTH RELEVANCE: Periodontitis is a polymicrobial disease caused by complex microbial community, which could result in the loss of teeth. The goal of this project is to understand which organisms are active and what they are doing during periodontitis progression to develop specific treatments against them.

描述（由申请人提供）：牙周炎是一种由复杂微生物群落协调作用引起的多种微生物疾病，导致支持牙齿的组织发炎。牙周炎是一种广泛而严重的健康状况，30% 至 50% 的美国成年人患有中度牙周炎，10% 的成年人患有严重牙周炎。该研究计划的目标是原位确定牙周炎在某些部位进展而在其他部位疾病仍然潜伏的发病机制的分子机制。宏基因组和宏转录组分析（整个复杂细菌群落的原位基因表达分析）提供了了解牙周感染期间致病生物膜中成分的活性和相对重要性所需的信息。为此，我们提出以下具体目标： 目标 1. 确定进展和非进展牙周部位微生物群落中物种的流行率和相对丰度的差异。目标 2. 鉴定在进展和非进展牙周部位微生物群落中差异表达的原位基因。我们已成功地将宏转录组技术应用于环境样本的研究。评估整个微生物群落表达分析的方法的关键步骤是对从细菌组合中提取的少量 RNA 进行线性扩增。最终扩增的 RNA 直接代表原始样品中 mRNA 的相对丰度。促进整个细菌群落宏转录组分析的第二个方面是焦磷酸测序技术现在可以对大量 DNA 进行测序，避免与经典技术相关的克隆偏差。目标受试者群体将包括 20 名慢性牙周炎个体。选择该受试者群体是因为慢性牙周炎是最常见的牙周炎类型，因此观察到的微生物变化将与大部分患有牙周病的受试者相关。患者将每月接受一次为期 6 个月的随访，在此期间他们将接受临床监测，以确定哪些样本将用于通过宏基因组和宏转录组分析来同情进展和非进展部位。鉴定发病机制所需的关键基因及其差异表达信息可用于开发新的有针对性的早期诊断、治疗、监测和预防方法。此外，潜在的影响超出了牙周炎的研究范围，因为相同的原理和方法可能适用于其他多种微生物疾病。我们相信，我们为该项目组建的团队（福赛斯研究所在布罗德研究所和哈佛大学公共卫生学院生物统计系的帮助下）拥有成功实现本申请中提出的目标的所有资格。 公共卫生相关性：牙周炎是一种由复杂微生物群落引起的多种微生物疾病，可能导致牙齿脱落。该项目的目标是了解哪些生物体是活跃的以及它们在牙周炎进展过程中正在做什么，以开发针对它们的具体治疗方法。