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New computational, transcriptional, and genome editing approaches to the biology of inflammatory bowel disease

研究炎症性肠病生物学的新计算、转录和基因组编辑方法

基本信息

批准号：
9976502
负责人：
GREGORY C GIBSON
金额：
$ 17.39万
依托单位：
GEORGIA INSTITUTE OF TECHNOLOGY
依托单位国家：
美国
项目类别：
财政年份：
2018
资助国家：
美国
起止时间：
2018-09-19 至 2022-05-31
项目状态：
已结题

来源：
https://reporter.nih.gov/project-details/9976502
关键词：
Address Affect African American Alleles American Ancillary Study Architecture Area Award Bar Codes Biological Assay Biology Biopsy Blood CRISPR/Cas technology Categories Cells Clinical Clustered Regularly Interspaced Short Palindromic Repeats Complement Complex Crohn&apos s disease Cytokine Signaling DNA Data Data Coordinating Center Data Set Development Disease Disease Progression Drug Delivery Systems Epithelial Cells Ethnic Origin European Extracellular Matrix Foundations Functional disorder Gene Expression Genes Genetic Genetic Diseases Genetic Engineering Genetic Polymorphism Genetic Risk Genetic Transcription Genomic approach Genomics Guide RNA Human Immune Individual Inflammatory Bowel Diseases Intestines Knock-out Laboratories Location Mediating Messenger RNA Mitochondria Molecular National Institute of Diabetes and Digestive and Kidney Diseases Organ Culture Techniques Organoids Outcome Pathogenesis Pathology Patient-Focused Outcomes Patients Pharmacologic Substance Pharmacology Play Protocols documentation Quantitative Genetics Reagent Research Research Personnel Resources Risk Risk Assessment Role Side Signal Transduction Site Source Susceptibility Gene System Transcript Translating Ulcerative Colitis Variant aptamer base causal variant cell type gain of function gastrointestinal epithelium gene discovery gene therapy genetic analysis genetic approach genetic manipulation genetic profiling genome editing genome sequencing genome wide association study improved in silico in vivo intestinal epithelium knockout gene lipid nanoparticle mRNA delivery member nanoparticle nanoparticle delivery novel novel strategies patient response rectal response risk variant single-cell RNA sequencing therapeutic evaluation transcriptome transcriptomics treatment response whole genome

项目摘要

Project Summary Over the past decade, the NIDDK IBDGC (Inflammatory Bowel Disease Genetics Consortium) has generated extraordinary datasets in support of genetic analysis of the onset, progression, and therapeutic response to Crohn's disease and ulcerative colitis. This Ancillary project will complement ongoing IBDGC research by providing parallel statistical genetic analyses focused on transcriptomics, while also developing a novel strategy for genetic manipulation of patient-derived epithelial cells. There are four major biomedical genomics focus areas addressed by the research, namely fine mapping of loci influencing inflammatory bowel disease, elucidation of the cell and molecular function of causal genes, understanding how polymorphism influences pathology, and translating quantitative genetic discoveries into clinical outcomes. Specifically, integrative genomics expertise will be used to refine the credible intervals responsible for complex association signals at individual loci, enhance transcriptional risk scores (TRS) that have recently been shown to provide much greater prediction of disease and progression than genetic risk scores, and explore the potential of in silico predicted transcriptome-wide association studies in the context of IBD. These studies will utilize the IBDGC datasets through collaborative arrangements mediated by data coordinating center. In addition, proof of principle for the use of lipid nanoparticles as an efficient and specific delivery system for genome editing and/or pharmaceutical delivery to targeted cell types in gut- derived organoids will be demonstrated. Single cell RNA-Seq will be used to partition variability in gut epithelial gene expression in the half dozen most common organoid cell types into contributions of the ethnicity, location of the biopsy, type of disease, and source laboratory. This data will serve as a foundation for evaluating the effects of a half dozen gene knock-outs across cell types using the lipid nanoparticle delivery system. All analyses and reagents will be made available to consortium members as expected for collaborative IBDGC research.

项目摘要在过去的十年里，NIDDK IBDGC(炎症性肠病遗传学联合会) 生成了非凡的数据集，以支持对发病、进展和治疗的遗传分析对克罗恩病和溃疡性结肠炎的反应。这一辅助项目将补充正在进行的IBDGC 通过提供专注于转录组学的并行统计遗传分析进行的研究，同时也在开发患者来源的上皮细胞的基因操作的新策略。有四个主要的研究涉及的生物医学基因组学重点领域，即影响基因座的精细定位炎症性肠病，阐明致病基因的细胞和分子功能，了解多态如何影响病理学，以及如何将定量的基因发现转化为临床结果。具体地说，将使用综合基因组学专业知识来细化可信区间负责单个基因座上的复杂关联信号，提高转录风险分数(TRS)，最近被证明比遗传风险对疾病和进展的预测要好得多分数，并探索在电子预测转录组全关联研究中的潜力 IBD的症状。这些研究将通过以数据为中介的协作安排来利用IBDGC数据集协调中心。此外，使用脂质纳米粒作为一种有效和用于基因组编辑和/或药物递送到肠道中目标细胞类型的特定递送系统- 我们将展示衍生的有机化合物。单细胞RNA-Seq将用于划分肠道中的可变性上皮基因表达在六种最常见的器质性细胞类型中的贡献种族、活检地点、疾病类型和来源实验室。这些数据将作为基础使用脂质纳米颗粒评估六种不同细胞类型的基因敲除的效果传送系统。所有分析和试剂将按预期向财团成员提供合作的IBDGC研究。