Omics/Clinical Core

组学/临床核心

• 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
• 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

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.

项目摘要 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， 包括微生物群的宫颈阴道环境，以阐明宿主-微生物群相互作用是如何 驱动宿主功能和对C.感染的反应。trachomatis或N.淋病研究这些 交互需要从广泛的角度描述系统的技术方法，而不需要事先考虑 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[元转录组学]）， 糖组学和深入的免疫细胞因子和趋化因子表征。在这里，我们建议应用这些 组学方法，以支持SIM-STI计划的项目1，2和3。此外，将我们提出的3D 从工程实验室到三个研究实验室的仿生模型， 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 马里兰州大学医学院的组学/临床核心C将支持这一目标，并将组装 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的材料以及仿生模型核心B进行定性评价。的 组学/临床核心C的总体目标是1/将高通量组学方法应用于提供的样本 2/提供微生物（重建的微生物群）和原代细胞购买、分离 3/进行临床研究，收集宫颈阴道标本（拭子、分泌物和 活组织检查）用于微生物群表征、细菌分离和原代细胞系分离;以及4/播散 将数据和资源提供给团队的其他成员，并最终通过开放科学提供给科学界。 数据框架（OSDF），一个创新的和可扩展的平台，用于存储不同类型的数据及其 元数据并在不同数据集之间创建关系。