Discovery and Functional Characterization of Two Regulatory Variants Underlying Lupus Susceptibility at 2p13.1.
Mehdi Fazel-NajafabadiHarikrishna-Reddy RallabandiManish K SinghGuru P MaitiJacqueline MorrisLoren L LoogerSwapan K NathPublished in: Genes (2022)
Genome-wide association studies have identified 2p13.1 as a prominent susceptibility locus for systemic lupus erythematosus (SLE)-a complex, multisystem autoimmune disease. However, the identity of underlying causal variant (s) and molecular mechanisms for increasing disease susceptibility are poorly understood. Using meta-analysis (cases = 10,252, controls = 21,604) followed by conditional analysis, bioinformatic annotation, and eQTL and 3D-chromatin interaction analyses, we computationally prioritized potential functional variants and subsequently experimentally validated their effects. Ethnicity-specific meta-analysis revealed striking allele frequency differences between Asian and European ancestries, but with similar odds ratios. We identified 20 genome-wide significant ( p < 5 × 10 -8 ) variants, and conditional analysis pinpointed two potential functional variants, rs6705628 and rs2272165, likely to explain the association. The two SNPs are near DGUOK , mitochondrial deoxyguanosine kinase, and its associated antisense RNA DGUOK-AS1 . Using luciferase reporter gene assays, we found significant cell type- and allele-specific promoter activity at rs6705628 and enhancer activity at rs2272165. This is supported by ChIP-qPCR showing allele-specific binding with three histone marks (H3K27ac, H3K4me3, and H3K4me1), RNA polymerase II (Pol II), transcriptional coactivator p300, CCCTC-binding factor (CTCF), and transcription factor ARID3A. Transcriptome data across 28 immune cell types from Asians showed both SNPs are cell-type-specific but only in B-cells. Splicing QTLs showed strong regulation of DGUOK-AS1 . Genotype-specific DGOUK protein levels are supported by Western blots. Promoter capture Hi-C data revealed long-range chromatin interactions between rs2272165 and several nearby promoters, including DGUOK . Taken together, we provide mechanistic insights into how two noncoding variants underlie SLE risk at the 2p13.1 locus.
Keyphrases
- genome wide
- transcription factor
- copy number
- systemic lupus erythematosus
- dna methylation
- systematic review
- gene expression
- disease activity
- dna binding
- genome wide association
- high throughput
- single cell
- electronic health record
- oxidative stress
- binding protein
- case control
- small molecule
- south africa
- rna seq
- rheumatoid arthritis
- big data
- genome wide identification
- data analysis
- protein kinase