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

摘要-这个小项目的目的是收集我们需要的初步数据，以支持一系列 与儿童自身免疫，特别是儿童系统性红斑狼疮(PSLE)有关的项目。 具体地说，我们需要在儿童的B细胞上生成3D染色质图，以便进行我们的工作 往前走。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 旨在了解儿童期发病的免疫驱动疾病的广泛研究。 我们面临的问题是儿科常见的问题，限制了我们严格追求基因和 基因组翻译研究：关于公开可获得的基因组数据集(例如，来自 路线图表观基因组学)可以作为比较数据来解释在儿童中产生的类似数据。这个 因此，公共数据集的使用限制对儿科研究人员的研究构成了一种“负担”， 研究成人或成人发病疾病的研究人员并不总是需要的，在这些疾病中，各种各样的基因组 已经有了数据集，包括那些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，这将有助于对发生在 孩子们。 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最接近因果关系的基因 变异，甚至风险单倍型上的基因。它们几乎都是同一染色质内的基因 由CCCT结合锚定的环或拓扑相关结构域、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。 这个项目的目的是在儿科样本中识别这些结构以及其中表达的基因。 我们的方法很直截了当。我们将使用CTCF切入并运行和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 以确定循环中表达的基因。在这个为期两年的项目完成后，我们将拥有 获得了我们需要的基本数据，以严格解释我们在pSLE中已经进行的研究 并将为该领域未来对儿童自身免疫的调查提供必要的工具。

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.