Fazel-Najafabadi Mehdi, Looger Loren L, Rallabandi Harikrishna Reddy, Nath Swapan K
Oklahoma Medical Research Foundation, Oklahoma City.
University of California, San Diego, La Jolla.
Arthritis Rheumatol. 2024 Jul;76(7):1071-1084. doi: 10.1002/art.42829. Epub 2024 Mar 26.
Systemic lupus erythematosus (SLE), an autoimmune disease with incompletely understood etiology, has a strong genetic component. Although genome-wide association studies (GWASs) have revealed multiple SLE susceptibility loci and associated single-nucleotide polymorphisms (SNPs), the precise causal variants, target genes, cell types, tissues, and mechanisms of action remain largely unknown.
Here, we report a comprehensive post-GWAS analysis using extensive bioinformatics, molecular modeling, and integrative functional genomic and epigenomic analyses to optimize fine-mapping. We compile and cross-reference immune cell-specific expression quantitative trait loci (cis- and trans-expression quantitative trait loci) with promoter capture high-throughput capture chromatin conformation (PCHi-C), allele-specific chromatin accessibility, and massively parallel reporter assay data to define predisposing variants and target genes. We experimentally validate a predicted locus using CRISPR/Cas9 genome editing, quantitative polymerase chain reaction, and Western blot.
Anchoring on 452 index SNPs, we selected 9,931 high linkage disequilibrium (r > 0.8) SNPs and defined 182 independent non-human leukocyte antigen (HLA) SLE loci. The 3,746 SNPs from 143 loci were identified as regulating 564 unique genes. Target genes are enriched in lupus-related tissues and associated with other autoimmune diseases. Of these, 329 SNPs (106 loci) showed significant allele-specific chromatin accessibility and/or enhancer activity, indicating regulatory potential. Using CRISPR/Cas9, we validated reference SNP identifier 57668933 (rs57668933) as a functional variant regulating multiple targets, including SLE-risk gene ELF1 in B cells.
We demonstrate and validate post-GWAS strategies for using multidimensional data to prioritize likely causal variants with cognate gene targets underlying SLE pathogenesis. Our results provide a catalog of significantly SLE-associated SNPs and loci, target genes, and likely biochemical mechanisms to guide experimental characterization.
系统性红斑狼疮（SLE）是一种病因尚不完全清楚的自身免疫性疾病，具有很强的遗传成分。尽管全基因组关联研究（GWAS）已经揭示了多个SLE易感位点以及相关的单核苷酸多态性（SNP），但确切的因果变异、靶基因、细胞类型、组织和作用机制仍 largely未知。
在此，我们报告了一项全面的GWAS后分析，使用广泛的生物信息学、分子建模以及综合功能基因组和表观基因组分析来优化精细定位。我们将免疫细胞特异性表达定量性状位点（顺式和反式表达定量性状位点）与启动子捕获高通量捕获染色质构象（PCHi-C）、等位基因特异性染色质可及性和大规模平行报告基因检测数据进行汇编和交叉引用，以确定易感变异和靶基因。我们使用CRISPR/Cas9基因组编辑、定量聚合酶链反应和蛋白质免疫印迹对一个预测位点进行实验验证。
基于452个索引SNP，我们选择了9931个高连锁不平衡（r>0.8）的SNP，并定义了182个独立的非人类白细胞抗原（HLA）SLE位点。来自143个位点的3的3746个SNP被确定为调控564个独特基因。靶基因在狼疮相关组织中富集，并与其他自身免疫性疾病相关。其中，329个SNP（106个位点）显示出显著的等位基因特异性染色质可及性和/或增强子活性，表明具有调控潜力。使用CRISPR/Cas9，我们验证了参考SNP标识符57668933（rs57668933）是一个调控多个靶标的功能变异，包括B细胞中的SLE风险基因ELF1。
我们展示并验证了GWAS后策略，即使用多维数据对SLE发病机制中潜在的因果变异及其同源基因靶标进行优先级排序。我们的结果提供了一份与SLE显著相关的SNP和位点、靶基因以及可能的生化机制目录，以指导实验表征。
