Dissecting transcriptomics and epigenomic signatures of immune cells in type 1 diabetes

剖析 1 型糖尿病免疫细胞的转录组学和表观基因组特征

• 批准号: 10658838
• 负责人: Golnaz Vahedi
• 金额: $ 51.07万
• 依托单位: UNIVERSITY OF PENNSYLVANIA
• 依托单位国家: 美国
• 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/10658838
• 关键词: 3-Dimensional; Autoantibodies; Autoimmune Diseases; Autoimmunity; Beta Cell; Biological Assay; Biological Markers; Blood; Blood Circulation; Cells; Clinical; Clone Cells; Cytotoxic T-Lymphocytes; Data; Development; Disease; Endocrine; Event; Family; Flow Cytometry; Frequencies; Gene Expression; Gene Expression Profile; Gene Expression Regulation; Generations; Genes; Genetic; Genetic Transcription; Genetic Variation; Genome; Genome engineering; Genomic Segment; Genomics; Goals; Human; Image; Immune; Immunologics; Infiltration; Insulin; Insulin-Dependent Diabetes Mellitus; Islets of Langerhans; Knowledge; Libraries; Link; Manuscripts; Measurement; Measures; Methods; Modality; Molecular; Molecular Profiling; Mutate; Nature; Needles; Nuclear; Organ Donor; Outcome; Output; Pancreas; Pathogenicity; Phase; Population; Process; Production; Proteins; Resolution; Role; Science; Single Nucleotide Polymorphism; Structure; Structure of beta Cell of islet; T-Lymphocyte; T-cell receptor repertoire; Techniques; Testing; TimeLine; Tissues; Tumor-infiltrating immune cells; Untranslated RNA; Validation; Variant; base; cell injury; cell type; chronic autoimmune disease; clinical diagnosis; computerized tools; data integration; diabetic; epigenomics; experimental study; genetic signature; genome wide association study; knowledge integration; non-diabetic; novel; peripheral blood; single cell proteins; single-cell RNA sequencing; transcriptomics; web portal

T1D is an autoimmune disease in which cytotoxic T cells attack and destroy insulin-secreting pancreatic beta cells. The role of genetics in T1D development is evident from its clustering in families. Although genome-wide association studies uncovered the T1D-associated single-nucleotide-polymorphisms, currently there is a large gap in knowledge regarding the molecular processes through which genetics contributes to autoimmunity. Specifically, because most disease-associated SNPs have been found in non-coding genomic regions, they are thought to impact gene regulation rather than causing production of mutated proteins. Recent advances in our understanding of nuclear organization indicate that genetic variation may impact gene regulation through altered 3D genomic structure and reorganization of large transcriptionally coordinated regions of the genome in the disease relevant cell type(s). However, the link between sequence variation, cellular context, 3D genome organization, and aberrant gene expression in T1D remains largely unknown. Our overall objective is to define the molecular hallmark of T1D-associated immune cells from human pancreatic tissues and study the utility of such deep profiling in detecting early T1D processes. Our latest results provide the first-ever evidence of early transcriptomics and 3D epigenomic alterations in T1D. Our hypothesis is that pathogenic immune cell subtypes residing in pancreatic tissues in asymptomatic and clinically diagnosed phases of T1D share transcriptional and 3D epigenomic signatures. We propose to generate the deepest-possible molecular profiling of immune cell populations in pancreatic tissues and peripheral blood in clinically well-characterized human organ donors collected by HPAP. Since the most accessible entity for biomarker testing, i.e. blood, is the conduit by which major immunological traffic occurs, we will examine if immunological features of beta cell destruction can be found in peripheral blood at asymptomatic stages of T1D. Once the molecule and epigenomic signatures of T1D are precisely defined in pancreatic tissues, they can be used as a powerful magnet to look for the needle in the haystack of circulating cells. Our single-cell resolution experiments will identify T1D-associated immune cells and deregulated genes in pancreatic tissues (Aim 1). Our state-of-the-art epigenomics, imaging, and genome engineering techniques will determine 3D genome misfolding events associated with T1D (Aim 2). The outcomes of each Aim can dramatically expand our understanding of early disease processes. The integration of knowledge gained in two Aims can elucidate detailed molecular mechanisms of pathogenic gene regulation in T1D.

T1D是一种自身免疫性疾病，其中细胞毒性T细胞攻击并破坏分泌胰岛素的胰腺β 细胞。遗传学在T1D发展中的作用从其在家庭中的聚类中很明显。虽然全基因组 协会研究发现了与T1D相关的单核苷酸 - 多态性，目前有一个很大的 关于遗传学有助于自身免疫性的分子过程的知识差距。 具体而言，由于在非编码基因组区域中发现了大多数与疾病相关的SNP，所以它们 被认为会影响基因调节，而不是引起突变蛋白的产生。最近的进步 我们对核组织的理解表明，遗传变异可能会通过 改变了3D基因组结构和基因组的大型转录协调区域的重组 疾病相关的细胞类型。但是，序列变化，细胞环境，3D基因组之间的联系 T1D中的组织和异常基因表达仍然在很大程度上未知。我们的总体目标是定义 T1D与人类胰腺组织的T1D相关免疫细胞的分子标志，并研究了 在检测早期T1D过程时进行了如此深刻的分析。我们的最新结果提供了有史以来早期的证据 T1D中的转录组学和3D表观基因组改变。我们的假设是致病性免疫细胞亚型 居住在无症状和临床诊断的T1D共享转录阶段中的胰组织中 和3D表观基因组特征。我们建议生成免疫的最深分子分析 胰腺组织中的细胞群和临床表征良好的人体器官捐献者的外周血 由HPAP收集。由于生物标志物测试最容易获得的实体，即血液，是渠道 发生重大免疫学交通，我们将检查β细胞破坏的免疫学特征是否可以 在T1D的无症状阶段发现了外周血。一旦分子和表观基因组特征 T1D精确定义在胰腺组织中，它们可以用作强大的磁铁来寻找针头 在循环细胞的干草堆中。我们的单细胞分辨率实验将鉴定与T1D相关的免疫 细胞和胰腺组织中失调的基因（AIM 1）。我们最先进的表观基因组学，成像和 基因组工程技术将确定与T1D相关的3D基因组错误折叠事件（AIM 2）。 每个目标的结果可以大大扩展我们对早期疾病过程的理解。这 在两个目标中获得的知识的整合可以阐明致病基因的详细分子机制 T1D中的调节。