Stimulatory state specific genetic regulatory signatures at diabetes GWAS signals

糖尿病 GWAS 信号的刺激状态特异性基因调控特征

• 批准号: 10678085
• 负责人: Christa Nicole Ventresca
• 金额: $ 4.05万
• 依托单位: UNIVERSITY OF MICHIGAN AT ANN ARBOR
• 依托单位国家: 美国
• 财政年份: 2023
• 资助国家: 美国
• 起止时间: 2023-05-01 至 2026-04-30
• 项目状态: 未结题
• 来源: https://reporter.nih.gov/project-details/10678085
• 关键词: Adipose tissue; Affect; Beta Cell; Binding; Biological; Biopsy; CRISPR-mediated transcriptional activation; Cell Line; Cell Nucleus; Cells; Chromatin; Chromatin Loop; Chromatin Structure; Clustered Regularly Interspaced Short Palindromic Repeats; Complex; Data; Data Set; Development; Diabetes Mellitus; Disease; Enhancers; Environment; Environmental Risk Factor; Exhibits; Exposure to; Follistatin; Functional disorder; Future; Gene Expression; Gene Expression Profiling; Gene Expression Regulation; Genes; Genetic; Genetic Predisposition to Disease; Genetic Structures; Genetic Transcription; Genetic study; Genome; Glucose; Goals; Growth; Individual; Inflammation; Insulin; Insulin Resistance; Islets of Langerhans; Knowledge; Link; Liver; Maps; Mesenchymal Differentiation; Mesenchymal Stem Cells; Metabolic; Methods; Minority; Molecular; Molecular Conformation; Multiomic Data; Muscle; Muscle Fibers; Non-Insulin-Dependent Diabetes Mellitus; Nucleic Acid Regulatory Sequences; Pathway interactions; Peripheral; Pluripotent Stem Cells; Predisposition; Property; Proteins; Regulation; Regulator Genes; Regulatory Element; Resolution; Role; Sampling; Signal Transduction; Single Nucleotide Polymorphism; Skeletal Muscle; Specificity; Statistical Data Interpretation; Stimulus; Tissue Sample; Tissues; Translating; Untranslated RNA; Up-Regulation; Validation; Variant; Work; activin A; adipocyte differentiation; cell type; diabetes risk; epigenome; falls; genetic signature; genome wide association study; genome-wide; human tissue; induced pluripotent stem cell; insight; interest; mTOR inhibition; metabolome; multimodality; multiple omics; novel; precursor cell; prevent; promoter; response; screening; stem cell biology; stem cell genes; transcription factor; transcriptome

Abstract Type 2 diabetes (T2D) is a complex disease that arises from a combination of genetic and environmental factors. Previous genome wide association studies (GWAS) of T2D have identified over 600 independent genetic signals, but most fall within non-coding regions of the genome, which makes identifying underlying mechanisms difficult. These signals can be cell-type specific, which adds another layer of complexity to nominating mechanisms. Recent work within the lab has identified skeletal muscle cell-type specific genetic regulators by investigating single-nucleus resolution chromatin structure across hundreds of samples. We observed several T2D GWAS signals colocalize specifically with mesenchymal stem cell (MSC) genetic regulators of chromatin structure, which represents a precursor cell stage that may reflect an early indicator of disease predisposition. Previous work within the lab has identified an ARL15 intronic T2D GWAS signal that is specific to MSCs. Chromatin looping analyses showed that this genetic regulatory region interacts with the follistatin (FST) promoter ~500kb away. The protein follistatin promotes muscle growth and affects insulin resistance by binding activin A and preventing it from inhibiting the mTOR pathway. Up-regulation of the FST pathway has been linked to increased T2D risk and impacts adipocyte differentiation. Follistatin is responsive to environmental stimulation, including inflammation, insulin, and glucose levels. These observations provide strong evidence that exploring the stimulatory state specific genetics of MSC chromatin structure, especially at FST and related pathway genes, will have implications for T2D. As a result, I am interested in studying the state-specific contexts which may influence T2D predisposition in MSCs, especially the state-specific genetic regulatory landscape of FST. Previous studies have shown that cellular state influences the genetic regulation of gene expression, where cells in a basal state display a “primed” chromatin conformation at response- specific differentially regulated genes. This primed state reflected a basal chromatin configuration that enabled the response-specific gene expression change. Therefore, the genetic signals of gene regulation vary across cell states within a cell type. To begin to investigate this within T2D, I will generate MSCs, induce different stimulatory states, and generate gene expression and chromatin structure data to establish genome-wide maps of FST pathway genes. Finally, I will investigate the FST gene pathway and select loci for validation with a novel inducible CRISPRi/a platform. Overall, I will generate MSC maps in different stimulatory states and use a multi-omics approach to compare the genetic control of gene expression and chromatin structure, focusing on the gene FST and related pathway genes, with the goal of nominating mechanisms at T2D GWAS signals.

摘要 2型糖尿病（T2 D）是一种复杂的疾病，由遗传和环境因素共同作用引起。 因素以前的T2 D全基因组关联研究（GWAS）已经确定了600多个独立的T2 D基因组。 遗传信号，但大多数属于基因组的非编码区，这使得识别潜在的 机制难。这些信号可以是特定于细胞类型的，这增加了另一层复杂性， 提名机制。实验室内最近的工作已经确定了骨骼肌细胞类型特异性遗传 通过研究数百个样本的单核分辨率染色质结构，我们 观察到几种T2 D GWAS信号与间充质干细胞（MSC）遗传共定位， 染色质结构的调节因子，其代表了可能反映细胞分化的早期指标的前体细胞阶段。 疾病易感性实验室内先前的工作已经确定了ARL 15内含子T2 D GWAS信号， 具体到MSC。染色质成环分析表明，这一基因调控区相互作用， 卵泡抑素（FST）启动子约500 kb。卵泡抑素蛋白促进肌肉生长和影响胰岛素 通过结合激活素A并阻止其抑制mTOR通路来抑制耐药性。FST上调 途径与T2 D风险增加有关并影响脂肪细胞分化。卵泡抑素对 环境刺激，包括炎症，胰岛素和葡萄糖水平。这些观察提供 强有力的证据表明，探索MSC染色质结构的刺激状态特异性遗传学，特别是在 FST和相关通路基因将对T2 D产生影响。因此，我有兴趣研究 可能影响MSC中T2 D易感性的状态特异性背景，特别是状态特异性遗传背景， FST的监管格局。以往的研究表明，细胞状态影响遗传调控 在基因表达的基础状态下，细胞在反应时显示出“启动”的染色质构象- 特异性差异调节基因这种引发状态反映了一种基础的染色质构型， 反应特异性基因表达的变化。因此，基因调控的遗传信号在不同的 细胞类型中的细胞状态。为了开始在T2 D中研究这一点，我将产生MSC，诱导不同的 刺激状态，并产生基因表达和染色质结构数据，以建立全基因组 FST途径基因的图谱。最后，我将研究FST基因通路，并选择位点进行验证， 一种新型的诱导型CRISPRi/a平台。总的来说，我将在不同的刺激状态下生成MSC图，并使用 一个多组学的方法来比较基因表达和染色质结构的遗传控制，重点 对基因FST和相关途径基因的研究，目标是T2 D GWAS信号的提名机制。