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初步数据，我们需要支持一系列的 涉及儿童自身免疫，特别是儿科系统性红斑狼疮（pSLE）的项目。 具体来说，我们需要在儿童的B细胞上生成3D染色质图谱，以便进行我们的工作 性新该项目还解决了对参考基因组数据集的严重需求，这些数据集可用于 广泛的研究旨在了解儿童发病，免疫驱动的疾病。 我们面临的问题是儿科中常见的问题，限制了我们严格追求遗传和 基因组翻译研究：关于是否公开可用的基因组数据集（例如，从 路线图表观基因组学）可以用作比较数据，以解释在儿童中产生的类似数据。的 因此，使用公共数据集的限制代表了儿科研究者研究的“税收”， 并不总是需要研究成人或成人发病疾病的研究人员，其中各种各样的基因组 已经有数据集，包括来自患病组织的数据集。在这个项目中，我们将制作一个 参考数据集，这将是有用的一系列调查免疫为基础的疾病发生在 孩子 我们在儿科自身免疫性疾病方面的工作旨在确定遗传风险单倍型的因果变异 以及受这些变异影响的基因。这些靶基因可能不是那些最接近的致病基因 变异，甚至是风险单倍型上的基因。它们几乎总是同一染色质内的基因 环或拓扑相关结构域，通过CCCT结合锚定的染色质环结构 因子（CTCF）和粘附素。因此，识别这些环结构是识别靶基因的关键步骤。 该项目的目的是在儿科样本中识别这些结构及其表达的基因。 我们的方法很简单。我们将使用CTCF切割和运行和HiChIP来识别CTCF锚定 健康儿童B细胞中的环状结构。我们还将对这些样本进行RNA测序 以鉴定环内表达的基因。在这个为期两年的项目完成后，我们将有 我获得了必要的数据，我们需要严格解释我们已经进行的pSLE研究 并将为该领域提供未来研究儿童自身免疫的基本工具。