Enhancer-based Immune and Beta Cell Dysregulation Underlying T1D Risk

基于增强剂的免疫和 β 细胞失调是 T1D 风险的基础

基本信息

批准号：
10263319
负责人：
Dieter Meinrad Egli
金额：
$ 111.5万
依托单位：
COLUMBIA UNIVERSITY HEALTH SCIENCES
依托单位国家：
美国
项目类别：
财政年份：
2020
资助国家：
美国
起止时间：
2020-09-15 至 2024-06-30
项目状态：
已结题

来源：
https://reporter.nih.gov/project-details/10263319
关键词：
Affect Alleles Area Autoimmune Diseases Base Pairing Beta Cell Binding Biological Assay Biology CRISPR/Cas technology Cell Nucleus Cells Chromatin Clinical Research Communities Computing Methodologies Coupled Data Data Set Defect Detection Development Disease Enhancers Event Gene Expression Genes Genetic Risk Genetic Transcription Genomic Segment Genomics Homeostasis Immune Individual Differences Inflammation Inflammatory Insulin Insulin-Dependent Diabetes Mellitus Islets of Langerhans Lead Maps Measures Mediating Molecular Mutation Organ Output Pancreas Pathologic Patients Phenotype Play Point Mutation Predisposition Preventive RNA Regulator Genes Regulatory Element Research Research Design Resolution Resources Response Elements Role Seminal Signal Pathway Signal Transduction System T-Lymphocyte Technology Therapeutic Transcription Initiation Site Translating Ultrafine Untranslated RNA Validation Variant base causal variant cell type clinical application cytokine diabetes risk genetic association genome editing genome wide association study genome-wide monocyte promoter response risk variant skills stem cells transcription factor transcriptome sequencing

项目摘要

Abstract Type 1 diabetes (T1D) is an organ-specific autoimmune disease, whereby immune cell-mediated and inflammatory cytokines lead to loss of the insulin-producing β cells in the pancreas. Genome-wide association studies (GWAS) have identified ~60 genomic regions associated with T1D risk. The vast majority of GWAS risk variants associated with T1D reside in non-coding regions, particularly enhancers, suggesting that gene regulatory changes substantially contribute to inter-individual differences in susceptibility to T1D. Driven by our T1D GWAS annotation data, highlighting the importance of a systematic analysis of both immune and β cell systems of both T1D patients and controls, we propose to identify causal enhancer variants and causal target genes using contemporary computational methods and cutting-edge global genomics. We will perform our PRO-cap and PRO-seq assays to comprehensively identify active enhancers harboring T1D-associated variants in T cells, monocytes and stem cell derived β cells (sc-β cells) from T1D patients and controls, followed by validation of active enhancers harboring T1D-associated variants using our eSTARR-seq assays (Aim 1). We will perform our Tri-HiC assays to profile the enhancer-promoter interactomes at unprecedented high resolution in primary T cells, primary monocytes and sc-β cells from T1D patients and controls as well as pancreatic islets to comprehensively identify target genes of T1D-associated variants, and refine targets of T1D-associated variants with T1D-sepcific alteration in target gene expression in each cell type using our coupled single cell nucleus (sn) RNA-seq and snATAC-seq assays (Aim 2). We will validate targets of T1D-associated variants in T cells, monocytes and β cells using CRISPR/Cas9 endogenous enhancer mutational strategies in the context of the endogenous chromatin landscape in each cell type. Our analytical and experimental framework represents an exciting new paradigm for studying T1D, and the subsequent clinical research based on our results has the potential to develop preventive and therapeutic strategies against T1D. The data sets generated by these studies will represent important, but currently lacking, resources for the T1D research community.

抽象的 1 型糖尿病 (T1D) 是一种器官特异性自身免疫性疾病，因此由免疫细胞介导和炎症细胞因子导致全基因组胰腺中产生胰岛素的 β 细胞丧失。研究 (GWAS) 已确定约 60 个与 T1D 风险相关的基因组区域。与 T1D 相关的变异存在于非编码区，特别是增强子，这表明基因监管变化极大地导致了 T1D 易感性的个体差异。 T1D GWAS 注释数据，强调了免疫和β系统分析的重要性通过对 T1D 患者和对照的细胞系统进行分析，我们建议识别因果增强子变异和因果增强子变异我们将使用当代计算方法和尖端的全球基因组学来执行我们的目标基因。 PRO-cap 和 PRO-seq 检测可全面识别含有 T1D 相关变异的活性增强子来自 T1D 患者和对照的 T 细胞、单核细胞和干细胞衍生的 β 细胞（sc-β 细胞），然后使用我们的 eSTARR-seq 检测验证含有 T1D 相关变异的活性增强子（目标 1）。将进行我们的 Tri-HiC 检测，以前所未有的高分辨率分析增强子-启动子相互作用组来自 T1D 患者和对照以及胰岛的原代 T 细胞、原代单核细胞和 sc-β 细胞全面鉴定T1D相关变异的靶基因，并细化T1D相关靶点使用我们的偶联单细胞在每种细胞类型中靶基因表达具有 T1D 特异性改变的变体核 (sn) RNA-seq 和 snATAC-seq 检测（目标 2）将验证 T1D 相关变异的靶点。 T细胞、单核细胞和β细胞在背景下使用CRISPR/Cas9内源增强子突变策略我们的分析和实验框架代表了每种细胞类型的内源染色质景观。一个令人兴奋的 T1D 研究新范式，以及基于我们结果的后续临床研究这些研究生成的数据集有可能制定针对 T1D 的预防和治疗策略。将为 T1D 研究界提供重要但目前缺乏的资源。