Genome-wide association studies (GWAS) have identified multiple, shared allelic associations with many autoimmune diseases. However, the pathogenic contributions of variants residing in risk loci remain unresolved. The location of the majority of shared disease-associated variants in noncoding regions suggests they contribute to risk of autoimmunity through effects on gene expression in the immune system. In the current study, we test this hypothesis by applying RNA sequencing to CD4⁺, CD8⁺, and CD19⁺ lymphocyte populations isolated from 81 subjects with type 1 diabetes (T1D). We characterize and compare the expression patterns across these cell types for three gene sets: all genes, the set of genes implicated in autoimmune disease risk by GWAS, and the subset of these genes specifically implicated in T1D. We performed RNA sequencing and aligned the reads to both the human reference genome and a catalog of all possible splicing events developed from the genome, thereby providing a comprehensive evaluation of the roles of gene expression and alternative splicing (AS) in autoimmunity. Autoimmune candidate genes displayed greater expression specificity in the three lymphocyte populations relative to other genes, with significantly increased levels of splicing events, particularly those predicted to have substantial effects on protein isoform structure and function (e.g., intron retention, exon skipping). The majority of single-nucleotide polymorphisms within T1D-associated loci were also associated with one or more cis-expression quantitative trait loci (cis-eQTLs) and/or splicing eQTLs. Our findings highlight a substantial, and previously underrecognized, role for AS in the pathogenesis of autoimmune disorders and particularly for T1D.

全基因组关联研究（GWAS）已确定与许多自身免疫性疾病有多个共享的等位基因关联。但是，仍未确定存在于风险基因座中的变体的致病作用。大多数共享的疾病相关变体在非编码区的位置表明，它们通过影响免疫系统中基因的表达而有助于自身免疫风险。在当前的研究中，我们通过将RNA测序应用于CD4 ⁺，CD8 ⁺和CD19 ⁺来检验这一假设。从81位1型糖尿病（T1D）受试者中分离出的淋巴细胞群。我们表征和比较了三种基因组在这些细胞类型中的表达模式：所有基因，GWAS牵涉自身免疫疾病风险的基因组以及这些基因在T1D中特异性涉及的子集。我们进行了RNA测序，并将读段与人类参考基因组和从基因组发展而来的所有可能的剪接事件的目录进行比对，从而对基因表达和选择性剪接（AS）在自身免疫中的作用提供了全面的评估。相对于其他基因，自身免疫候选基因在三个淋巴细胞群体中表现出更高的表达特异性，剪接事件的水平显着增加，特别是那些预测对蛋白质同工型结构和功能有实质性影响的物质（例如内含子保留，外显子跳跃）。T1D相关基因座中的大多数单核苷酸多态性也与一个或多个相关顺式表达定量性状基因座（顺式-eQTL）和/或剪接eQTL。我们的研究结果突显了AS在自身免疫性疾病的发病机制中，尤其是T1D的重要作用，而此前人们尚未得到充分认识。