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存在多个共享的等位基因关联。然而，存在于风险位点的变异的致病作用仍未解决。大多数与疾病相关的共有变异位于非编码区，表明它们通过影响免疫系统中的基因表达而增加自身免疫的风险。^{在当前的研究中，我们通过对从 81 名 1 型糖尿病 (T1D) 受试者中分离的 CD4 +}、 CD8 ⁺和 CD19 ⁺淋巴细胞群应用 RNA 测序来检验这一假设。我们表征并比较了这些细胞类型中三个基因组的表达模式：所有基因、GWAS 与自身免疫性疾病风险相关的基因组，以及这些基因中与 T1D 特别相关的子集。我们进行了 RNA 测序，并将读数与人类参考基因组和从基因组开发的所有可能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进行全面评估。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大的表达特异性，剪接事件水平显着增加，特别是那些预计对蛋白质异构体结构和功能有重大影响的基因（例如内含子保留、外显子跳跃）。T1D 相关基因座内的大多数单核苷酸多态性也与一个或多个顺式表达数量性状基因座 ( cis -eQTL) 和/或剪接 eQTL 相关。我们的研究结果强调了 AS 在自身免疫性疾病，特别是 T1D 发病机制中的重要作用，但之前并未得到充分认识。