Omics/Clinical Core

组学/临床核心

• 批准号: 10190233
• 负责人: Jacques Ravel
• 金额: $ 22.15万
• 依托单位: UNIVERSITY OF MARYLAND BALTIMORE
• 依托单位国家: 美国
• 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/10190233
• 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; Data Store; Engineering; Ensure; Environment; Exposure to; Genes; Genetic; Genital; Genitalia; Genomics; Goals; Guidelines; High-Throughput Nucleotide Sequencing; Human; Human Microbiome; Immune; Immunity; Infection; Infrastructure; Institutes; Knowledge; Laboratories; Laboratory Research; Laboratory Study; Maintenance; Maryland; Metadata; Microbiology; Modeling; Modernization; Mucous Membrane; Neisseria gonorrhoeae; 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; body system; cell type; cervicovaginal; chemokine; cost; cost effective; cytokine; data framework; data resource; data sharing; experience; genome sciences; host microbiome; host microbiota; innovation; medical schools; metatranscriptomics; microbiome; microbiota; novel; open data; pathogen; programs; response; tool; transcriptome; transcriptome sequencing; transcriptomics

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.

项目总结 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 包括微生物区系的宫颈阴道环境，以阐明宿主-微生物区系如何相互作用 驱动宿主功能和对沙眼衣原体或淋病奈瑟菌感染的反应。为了研究这些 交互需要从广泛的角度描述系统的技术方法，而不需要事先 观察寄主、微生物群和病原体的功能(S)的知识，如全球 转录组学(人类宿主RNAseq和细菌群落转录组学[后转录组学])， 糖类和深入免疫细胞因子和趋化因子的表征。在这里，我们建议应用这些 支持SIM-STI计划项目1、2和3的组学方法。此外，将我们提议的3D 从工程实验室到三个研究实验室的仿生模型研究 传播感染需要一致的生物资源，以确保重复性和可比性。 利用其PI的专业知识和经验以及基因组科学研究所在 在马里兰医学院，Omics/临床核心C将支持这一目标，并将组装 并使用一致的方案分配生物资源(原代细胞系和重建的微生物区系) 以及对项目1、2和3的材料以及仿生模型Core B的定性评估。 OMICS/临床核心C的总体目标是将高通量组学方法应用于所提供的样本 通过每个项目；2/提供微生物(重建的微生物区系)和原代细胞购买、分离 和维护服务；3/进行临床研究以收集宫颈阴道标本(拭子、分泌物和 活组织检查)，用于微生物区系鉴定、细菌分离和原代细胞系分离；以及4/传播 通过Open Science将数据和资源提供给团队其他成员，并最终提供给科学界 数据框架(OSDF)，这是一个创新且可扩展的平台，用于存储不同类型的数据及其 元数据，并在不同的数据集之间创建关系。