HLA-C Level Is Regulated by a Polymorphic Oct1 Binding Site in the HLA-C Promoter Region

Abstract

Differential HLA-C levels influence several human diseases, but the mechanisms responsible are incompletely characterized. Using a validated prediction algorithm, we imputed HLA-C cell surface levels in 228 individuals from the 1000 Genomes dataset. We tested 68,726 SNPs within the MHC for association with HLA-C level. The HLA-C promoter region variant, rs2395471, 800 bp upstream of the transcription start site, gave the most significant association with HLA-C levels (p = 4.2 × 10). This imputed expression quantitative trait locus, termed impeQTL, was also shown to associate with HLA-C expression in a genome-wide association study of 273 donors in which HLA-C mRNA expression levels were determined by quantitative PCR (qPCR) (p = 1.8 × 10) and in two cohorts where HLA-C cell surface levels were determined directly by flow cytometry (n = 369 combined, p < 10). rs2395471 is located in an Oct1 transcription factor consensus binding site motif where the A allele is predicted to have higher affinity for Oct1 than the G allele. Mobility shift electrophoresis demonstrated that Oct1 binds to both alleles in vitro, but decreased HLA-C promoter activity was observed in a luciferase reporter assay for rs2395471_G relative to rs2395471_A on a fixed promoter background. The rs2395471 variant accounts for up to 36% of the explained variation of HLA-C level. These data strengthen our understanding of HLA-C transcriptional regulation and provide a basis for understanding the potential consequences of manipulating HLA-C levels therapeutically.

Molecular evolution of elements controlling HLA‐C expression: Adaptation to a role as a killer‐cell immunoglobulin‐like receptor ligand regulating natural killer cell function

“…The presence of an A nucleotide in place of a G at this position was associated with higher Oct‐1 binding and transcriptional activity. This association was confirmed in a genome‐wide expression quantitative trait analysis of HLA‐C mRNA levels determined by qPCR of peripheral blood mononuclear cell RNA from 273 individuals . Interestingly, the group of HLA‐C alleles that have the highest level of expression ( HLA‐C*01 , *04 , *06 , *12 , and *14 ), all possess the A residue associated with higher promoter activity .…”

“…A study of SNPs associated with the level of HLA-C mRNA expression identified an SNP in a predicted Oct-binding site 800 bp upstream of the transcription start site as being highly associated with differences in HLA-C expression between alleles. 37 The presence of an A nucleotide in place of a G at this position was associated with higher Oct-1 binding and transcriptional activity. This association was confirmed in a genome-wide expression quantitative trait analysis of HLA-C mRNA levels determined by qPCR of peripheral blood mononuclear cell RNA from 273 individuals.…”

“…This association was confirmed in a genome-wide expression quantitative trait analysis of HLA-C mRNA levels determined by qPCR of peripheral blood mononuclear cell RNA from 273 individuals. 37,40 Interestingly, the group of HLA-C alleles that have the highest level of expression (HLA-C*01, *04, *06, *12, and *14), all possess the A residue associated with higher promoter activity. 30,32 Furthermore, a second SNP located 20 bp upstream of the Oct-1 site was also significantly associated with HLA-C transcript levels, and this SNP is located within a putative NFAT-AP1 binding site, 52 suggesting the presence of an enhancer element in this region.…”

Posttranscriptional Regulation of HLA-A Protein Expression by Alternative Polyadenylation Signals Involving the RNA-Binding Protein Syncrip

“…We have shown previously that a polymorphic microRNA (miRNA) binding site in the 3’UTR of HLA-C contributes to allele-specific variation in expression levels and associates with both human immunodeficiency virus (HIV) viral control and risk of Crohn’s disease independently of individual HLA allelic effects(1). More recently, a variant in an Oct1 binding site 800bp upstream of the HLA-C coding region was also shown to regulate HLA-C expression levels(2), and this variant along with the polymorphic miRNA binding site account for 40% of the differential cell surface expression levels of HLA-C. Thus, variation in regulatory regions of the HLA class I loci that affect their expression levels may influence the immune response and disease susceptibility.…”

Endoplasmic reticulum aminopeptidase 1 polymorphism Ile276Met is associated with atopic dermatitis and affects the generation of an HLA‐C associated antigenic epitope in vitro

“…On the other hand, it contains a rs2395471G allele which leads to low expression. 26 Nevertheless, the net result of these three polymorphisms is rather high expression on the cell surface. 24,25 Therefore, HLA-C*05:01 has a potential for efficient presentation of bound peptides.…”