Meta-transcriptomic analysis of host-microbiota interactions in a longitudinal study in CF patients

CF 患者纵向研究中宿主-微生物群相互作用的宏转录组分析

• 批准号: 432969571
• 负责人: Dr. Sébastien Boutin, Ph.D.
• 金额: --
• 依托单位: Abteilung Medizinische Mikrobiologie und Hygiene
• 依托单位国家: 德国
• 项目类别: Research Grants
• 财政年份: 2020
• 资助国家: 德国
• 起止时间: 2019-12-31 至 2021-12-31
• 项目状态: 已结题
• 来源: https://gepris.dfg.de/gepris/projekt/432969571?language=en
• 关键词: Meta; transcriptomic; analysis; host; microbiota

Patients suffering from cystic fibrosis (CF) develop polymicrobial infections of the lower airways as well as a chronic inflammatory host response resulting in a steady decline in lung function. Next generation sequencing has deciphered the composition of the airways’ microbiota. However, many studies have only been done in cross-sectional designs, yet longitudinal studies are needed to understand the role of the altered microbiome in the evolution of the disease. We are currently analyzing the microbiome evolution via 16S rRNA sequencing in a large cohort of cystic fibrosis patients in the framework of a project funded by the German Center for Lung Reasearch (DZL). Since 2013, we have included 318 patients in a longitudinal study with meanwhile over 6,500 samples at the translational lung research center (TLRC) in Heidelberg. During the study it has now turned out that microbiome evolution and host immune responses are closely linked. An unbiased study of the functional interrelation of host and microbiota requires a meta-transcriptomic approach which is not in the scope of the running study. A pilot dual RNAseq study was performed by us and shows the feasibility of meta-transcriptomic analysis with sputum sample to study the functional input from both, host and microbiota. We would now like to focus on a well-defined subset of patients to analyze in depth the interplay of microbiome evolution and host response over time. Patients within our cohort are sampled regularly every 3-4 months as well as when they suffer from exacerbation. On each of those visits, sputum samples will be taken for dual RNAseq meta-transcriptomic analysis. Based on the previous analysis we can define subgroups that differ in clinical disease development therefore allowing an informative study design. A special focus will be the function of commensal bacteria which is actually controversially discussed.The objective of this add-on project proposal therefore is to use meta-transcriptomics in our already established CF cohort to analyze the functional interrelation of host and microbiota. The following questions will be approached: How stable are the microbial transcriptome and the host transcriptome over a year? How does the microbial transcriptome correlate with the host transcriptome? What is the impact of microbial dominance on the stability of the active microbiota and does it modify the human transcriptome? What is the impact of exacerbation on short term and long term functional changes of the microbiome and of the host? How do microbial and host transcriptome correlate to the clinical outcome?

患有囊性纤维化（CF）的患者发生下呼吸道的多微生物感染以及慢性炎症宿主反应，导致肺功能的稳定下降。下一代测序已经破译了气道微生物群的组成。然而，许多研究仅在横断面设计中进行，但需要进行纵向研究以了解改变的微生物组在疾病演变中的作用。我们目前正在德国肺疾病中心（DZL）资助的一个项目框架内，通过16 S rRNA测序分析一个大型囊性纤维化患者队列中的微生物组进化。自2013年以来，我们在海德堡的转化肺研究中心（TLRC）进行了一项纵向研究，纳入了318名患者，同时收集了6,500多份样本。在研究过程中，现在已经证明微生物组进化和宿主免疫反应密切相关。对宿主和微生物群的功能相互关系的无偏见研究需要元转录组学方法，这不在正在进行的研究范围内。我们进行了一项试点双重RNAseq研究，显示了用痰液样品进行元转录组学分析以研究来自宿主和微生物群两者的功能输入的可行性。现在，我们将重点关注一个明确定义的患者子集，以深入分析微生物组进化和宿主反应随时间的相互作用。我们队列中的患者每3-4个月定期采样一次，以及当他们患有急性加重时。在每次访视时，将采集痰液样本进行双重RNAseq元转录组学分析。基于之前的分析，我们可以定义临床疾病发展不同的亚组，因此可以进行信息丰富的研究设计。一个特别的焦点将是肠道细菌的功能，这实际上是有争议的讨论。因此，这个附加项目提案的目标是在我们已经建立的CF队列中使用元转录组学来分析宿主和微生物群的功能相互关系。将探讨以下问题：微生物转录组和宿主转录组在一年内的稳定性如何？微生物的转录组与宿主的转录组有何关联？微生物优势对活跃微生物群的稳定性有什么影响，它是否会改变人类的转录组？急性加重对微生物组和宿主的短期和长期功能变化有何影响？微生物和宿主转录组与临床结果如何相关？