3D Chromatin Studies in Pediatric B Cells To Study the Genetics of Autoimmunity

通过儿科 B 细胞的 3D 染色质研究来研究自身免疫的遗传学

• 批准号: 10514624
• 负责人: JAMES N JARVIS
• 金额: $ 7.98万
• 依托单位: STATE UNIVERSITY OF NEW YORK AT BUFFALO
• 依托单位国家: 美国
• 财政年份: 2021
• 资助国家: 美国
• 起止时间: 2021-11-01 至 2024-10-31
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/10514624
• 关键词: 3-Dimensional; ATAC-seq; Address; Adult; Affect; Area; Autoimmune Diseases; Autoimmunity; Automobile Driving; B-Lymphocytes; Binding; Binding Sites; Budgets; CD4 Positive T Lymphocytes; CRISPR interference; Cells; ChIP-seq; Child; Childhood; Childhood diabetes; Chromatin; Chromatin Loop; Chromatin Structure; Communities; Coupled; DNA Methylation; Data; Data Set; Deoxyribonucleases; Development; Disease; Enhancers; Face; Funding; Future; Gene Expression; Genes; Genetic; Genetic Risk; Genetic study; Genome; Genomics; Goals; Haplotypes; Hypersensitivity; Immune; Immune System Diseases; Immune system; Insulin-Dependent Diabetes Mellitus; Investigation; Lupus; Maps; Onset of illness; Pathologic; Pediatric Research; Pediatrics; Play; Research; Research Personnel; Resolution; Rheumatism; Risk; Role; Sampling; Site; Source; Structure; Systemic Lupus Erythematosus; Taxes; Time; Tissues; Uncertainty; Untranslated RNA; Variant; Work; body system; causal variant; cohesin; cost; disorder risk; endonuclease; epigenomics; genetic variant; genomic data; histone modification; neutrophil; novel; older patient; organ growth; prepuberty; promoter; three dimensional structure; tool; transcriptome sequencing; translational genomics; translational study

Abstract – The purpose of this small project is to gather preliminary data we need to support a range of projects relating to autoimmunity in children, and particularly to pediatric systemic lupus erythematosus (pSLE). Specifically, we need to generate 3D chromatin maps on B cells from children in order to carry our work forward. The project also addresses the serious need for reference genomic data sets that can be used in a broad spectrum of research aimed at understanding childhood-onset, immune-driven diseases. The problem we face is a common one in pediatrics and limits our ability to rigorously pursue genetic and genomic translational studies: the uncertainty as to whether publicly available genomic data sets (e.g., from Roadmap Epigenomics) can be used as comparison data to interpret similar data generated in children. The limitations in the use public data sets therefore represent a “tax” on the research of pediatric investigators that is not always required of investigators studying adult or adult-onset diseases, where a broad variety of genomic data sets are already available, including those from diseased tissues. In this project, we will produce an reference data set that will be useful to a range of investigations into immune-based diseases that occur in children. Our work in pediatric autoimmune diseases is aimed at identifying causal variants on genetic risk haplotypes as well as the genes impacted by those variants. These target genes may not be those nearest the causal variant, or even genes on the risk haplotype. They will almost invariably be genes within the same chromatin loop or topologically associated domains, chromatin loop structures that are anchored by the CCCT binding factor (CTCF) and cohesin. Identifying these loop structures is therefore a key step in identifying target genes. This project is aimed to identify these structures, and the genes expressed within them, in pediatric samples. Our approach is straightforward. We will use CTCF Cut-and-Run and HiChIP to identify CTCF-anchored loop structures in the B cells of healthy children. We will also perform RNA sequencing on these same samples in order to identify the genes expressed within loops. At the completion of this 2-year project, we will have obtained the essential data that we need to rigorously interpret the studies we already have under way in pSLE and will have provided the field with an essential tool for future investigations into autoimmunity in children.

摘要 - 这个小项目的目的是收集我们需要支持一系列范围的初步数据 与儿童自身免疫有关的项目，尤其是小儿全身性红斑狼疮（PSLE）。 具体而言，我们需要在儿童的B细胞上生成3D染色质图，以便携带我们的工作 向前。该项目还解决了可用于参考基因组数据集的严重需求 广泛的研究旨在了解儿童期为免疫驱动的疾病。 我们面临的问题是儿科中常见的问题，并限制了我们严格纯粹的遗传和 基因组转化研究：关于公开可用的基因组数据集的不确定性（例如 路线图表观基因组学）可以用作比较数​​据来解释儿童产生的类似数据。这 因此，使用公共数据集中的局限性代表了儿科研究人员研究的“税” 研究成人或成人发作疾病的调查人员并不总是需要，其中各种基因组 数据集已经可用，包括患病组织的数据集。在这个项目中，我们将产生一个 参考数据集将对发生在免疫疾病中的一系列研究中有用 孩子们。 我们在儿科自身免疫性疾病中的工作旨在识别遗传风险单倍型的因果变异 以及受这些变体影响的基因。这些靶基因可能不是最接近因果的基因 风险单倍型上的变体，甚至基因。它们几乎总是是同一染色质内的基因 循环或拓扑相关的结构域，由CCCT结合锚定的染色质循环结构 因子（CTCF）和粘着蛋白。因此，识别这些循环结构是识别靶基因的关键步骤。 该项目的目的是在小儿样本中识别这些结构，并在其中表达的基因。 我们的方法很简单。我们将使用CTCF剪切和HICHIP来识别CTCF锚定 健康儿童的B细胞中的循环结构。我们还将在这些相同样品上进行RNA测序 为了识别循环中表达的基因。在完成这个为期两年项目时，我们将拥有 获得了我们需要严格解释我们已经在PSLE中正在进行的研究的基本数据 并将为该领域提供一个必不可少的工具，以将来调查儿童自身免疫性。