■了解3D基因组对于阐明驱动自身免疫性疾病的遗传机制至关重要。每种细胞类型的3D基因组都是不同的,并且不确定细胞系是否忠实地概括了原代人类细胞的3D结构,或者儿科免疫系统的发育方面是否需要使用儿科样本。我们对B细胞和B细胞系进行了系统分析,以比较包括青少年特发性关节炎(JIA)风险位点的3D基因组特征,系统性狼疮(SLE),1型糖尿病(T1D)。
■我们从健康个体中分离出B细胞,年龄9-17使用CTCF抗体进行HiChIP,并鉴定了CTCF峰。将儿科中的CTCF循环与三个数据集进行了比较:1)儿科样本中自称为CTCF共识峰,2)ENCODE\'spublicavailableGM12878CTCFChIP-seq峰,和3)编码来自两名成年雌性的原代B细胞CTCFChIP-seq峰。在儿科样品和三个峰数据集中的每一个中评估差异循环。
■在儿科样本中调用的共有峰数量与ENCODE的GM12878和原代B细胞数据集中确定的相似。我们观察到<1%的环,其显示在儿科样品本身内调用的峰与当使用ENCODEGM12878峰调用时的峰之间的显著差异环。当比较儿科称为峰的环与ENCODE原代B细胞峰的环时,显着的循环差异甚至更小。当查询幼年特发性关节炎中发现的循环时,1型糖尿病,或系统性红斑狼疮风险单倍型,我们观察到只有2.2%的显著差异,1.0%,和1.3%的循环,分别,当比较儿科样本和ENCODEGM12878数据集中的峰值时。当与儿科和ENCODE成人原代B细胞峰值数据集进行比较时,差异甚至不那么明显。B细胞中的3D染色质结构在儿科中相似,成人,和EBV转化的细胞系。这种3D结构的保守性包括包含自身免疫风险单倍型的区域。
■因此,即使是儿科自身免疫性疾病,公开可用的成人B细胞和细胞系数据集可能足以评估在3D基因组空间中发挥的作用。
UNASSIGNED: Knowledge of the 3D genome is essential to elucidate genetic mechanisms driving autoimmune diseases. The 3D genome is distinct for each cell type, and it is uncertain whether cell lines faithfully recapitulate the 3D architecture of primary human cells or whether developmental aspects of the pediatric immune system require use of pediatric samples. We undertook a systematic analysis of B cells and B cell lines to compare 3D genomic features encompassing risk loci for juvenile idiopathic arthritis (JIA), systemic lupus (SLE), and type 1 diabetes (T1D).
UNASSIGNED: We isolated B cells from healthy individuals, ages 9-17. HiChIP was performed using CTCF antibody, and CTCF peaks were identified. CTCF loops within the pediatric were compared to three datasets: 1) self-called CTCF consensus peaks called within the pediatric samples, 2) ENCODE\'s publicly available GM12878 CTCF ChIP-seq peaks, and 3) ENCODE\'s primary B cell CTCF ChIPseq peaks from two adult females. Differential looping was assessed within the pediatric samples and each of the three peak datasets.
UNASSIGNED: The number of consensus peaks called in the pediatric samples was similar to that identified in ENCODE\'s GM12878 and primary B cell datasets. We observed <1% of loops that demonstrated significantly differential looping between peaks called within the pediatric samples themselves and when called using ENCODE GM12878 peaks . Significant looping differences were even less when comparing loops of the pediatric called peaks to those of the ENCODE primary B cell peaks. When querying loops found in juvenile idiopathic arthritis, type 1 diabetes, or systemic lupus erythematosus risk haplotypes, we observed significant differences in only 2.2%, 1.0%, and 1.3% loops, respectively, when comparing peaks called within the pediatric samples and ENCODE GM12878 dataset. The differences were even less apparent when comparing loops called with the pediatric vs ENCODE adult primary B cell peak datasets.The 3D chromatin architecture in B cells is similar across pediatric, adult, and EBVtransformed cell lines. This conservation of 3D structure includes regions encompassing autoimmune risk haplotypes.
UNASSIGNED: Thus, even for pediatric autoimmune diseases, publicly available adult B cell and cell line datasets may be sufficient for assessing effects exerted in the 3D genomic space.