Omics/Clinical Core

组学/临床核心

基本信息

批准号：
10596511
负责人：
Jacques Ravel
金额：
$ 26.03万
依托单位：
UNIVERSITY OF MARYLAND BALTIMORE
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：
2021-04-20 至 2026-03-31
项目状态：
未结题

来源：
https://reporter.nih.gov/project-details/10596511
关键词：
3-Dimensional Automobile Driving Bacteria Base Sequence Bioinformatics Biological Biomimetics Biopsy Catalogs Cell Line Cells Cervical Chlamydia trachomatis Clinical Clinical Research Communities DNA Data Data Analyses Data Set Engineering Ensure Environment Exposure to Genes Genetic Genital Genitalia Genomics Goals Guidelines High-Throughput Nucleotide Sequencing Human Immune Immunity Infection Infrastructure Knowledge Laboratories Laboratory Research Laboratory Study Maintenance Maryland Metadata Modeling Modernization Mucous Membrane Neisseria gonorrhoeae Organ Protocols documentation Qualitative Evaluations RNA Reproducibility Research Resolution Resource Sharing Resources Rest Running Sampling Services Sexually Transmitted Diseases Specimen Structure Swab System Technology Testing Time Tissues Training United States National Institutes of Health Universities Vagina bacterial community cell type cervicovaginal chemokine cost cost effective cytokine data framework data sharing experience genome sciences host microbiota innovation medical schools metatranscriptomics microbiome microbiota novel open data pathogen programs response tool transcriptome transcriptome sequencing transcriptomics

项目摘要

PROJECT SUMMARY To support the goals of the SIM-STI Program, that aims at developing an innovative biomimetic model of the cervicovaginal environment comprising the microbiota to elucidate how the host-microbiota interactions are driving host functioning and response to infection by C. trachomatis or N. gonorrhoeae. To study these interactions requires technical approaches that describe the system from a broad perspective without prior knowledge to observe functioning of both the host, the microbiome and the pathogen(s), such as global transcriptomics (human host RNAseq and bacterial community transcriptomics [metatranscriptomics]), glycomics and in-depth immune cytokines and chemokines characterizations. Here we propose to apply these omics approaches to support Project 1, 2 and 3 of the SIM-STI program. Further, transferring our proposed 3D biomimetic models from the engineering laboratory to three research laboratories for the study of sexually transmitted infections requires consistent biological resources to insure reproducibility and comparability. Leveraging the expertise and experience of its PI and infrastructure of the Institute for Genome Sciences at the University fo Maryland School of Medicine, the Omics/Clinical Core C will support this goal and will assemble and distribute biological resources (primary cell lines and reconstructed microbiota) using consistent protocols and qualitative evaluation of the materials to Project 1, 2 and 3, as well as the Biomimetic Models Core B. The overall goal of the Omics/Clinical Core C is to 1/ apply high-throughput omics approaches to samples provided by each of the project; 2/ provide microbiological (reconstructed microbiota) and primary cell purchase, isolation and maintenance services; 3/ perform a clinical study to collect cervicovaginal specimens (swabs, secretion and biopsies) for microbiota characterization, bacterial isolation and primary cell lines isolation; and 4/ disseminate the data and resources to the rest of the team and ultimately the scientific community through the Open Science Data Framework (OSDF), an innovative and scalable platform to store data of different types along with their metadata and create relationships between the different datasets.

项目概要为了支持 SIM-STI 计划的目标，该计划旨在开发一种创新的仿生模型包含微生物群的子宫颈阴道环境，以阐明宿主与微生物群的相互作用驱动宿主功能和对沙眼衣原体或淋病奈瑟菌感染的反应。要研究这些交互需要从广泛的角度描述系统的技术方法，而无需先验观察宿主、微生物组和病原体功能的知识，例如全球转录组学（人类宿主 RNAseq 和细菌群落转录组学 [宏转录组学]），糖组学和深入的免疫细胞因子和趋化因子特征。在这里我们建议应用这些组学方法来支持 SIM-STI 计划的项目 1、2 和 3。此外，转移我们提出的 3D 仿生模型从工程实验室到三个研究实验室，用于性研究传播感染需要一致的生物资源以确保可重复性和可比性。利用其 PI 的专业知识和经验以及基因组科学研究所的基础设施马里兰大学医学院的组学/临床核心 C 将支持这一目标，并将聚集并使用一致的协议分配生物资源（原代细胞系和重建的微生物群）对项目 1、2 和 3 以及仿生模型核心 B 的材料进行定性评估。组学/临床核心 C 的总体目标是 1/ 对提供的样本应用高通量组学方法按每个项目； 2/提供微生物（重建微生物群）和原代细胞的购买、分离和维护服务； 3/ 进行临床研究，收集宫颈阴道样本（拭子、分泌物和活检）用于微生物群表征、细菌分离和原代细胞系分离； 4/传播通过开放科学向团队其他成员以及最终科学界提供数据和资源数据框架 (OSDF)，一个创新且可扩展的平台，用于存储不同类型的数据及其数据元数据并在不同数据集之间创建关系。