An in-depth characterization of the major psoriasis susceptibility locus identifies candidate susceptibility alleles within an HLA-C enhancer element

PLoS One. 2013 Aug 19;8(8):e71690. doi: 10.1371/journal.pone.0071690. eCollection 2013.

Abstract

Psoriasis is an immune-mediated skin disorder that is inherited as a complex genetic trait. Although genome-wide association scans (GWAS) have identified 36 disease susceptibility regions, more than 50% of the genetic variance can be attributed to a single Major Histocompatibility Complex (MHC) locus, known as PSORS1. Genetic studies indicate that HLA-C is the strongest PSORS1 candidate gene, since markers tagging HLA-Cw*0602 consistently generate the most significant association signals in GWAS. However, it is unclear whether HLA-Cw*0602 is itself the causal PSORS1 allele, especially as the role of SNPs that may affect its expression has not been investigated. Here, we have undertaken an in-depth molecular characterization of the PSORS1 interval, with a view to identifying regulatory variants that may contribute to disease susceptibility. By analysing high-density SNP data, we refined PSORS1 to a 179 kb region encompassing HLA-C and the neighbouring HCG27 pseudogene. We compared multiple MHC sequences spanning this refined locus and identified 144 candidate susceptibility variants, which are unique to chromosomes bearing HLA-Cw*0602. In parallel, we investigated the epigenetic profile of the critical PSORS1 interval and uncovered three enhancer elements likely to be active in T lymphocytes. Finally we showed that nine candidate susceptibility SNPs map within a HLA-C enhancer and that three of these variants co-localise with binding sites for immune-related transcription factors. These data indicate that SNPs affecting HLA-Cw*0602 expression are likely to contribute to psoriasis susceptibility and highlight the importance of integrating multiple experimental approaches in the investigation of complex genomic regions such as the MHC.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Alleles
  • Chromosome Mapping / methods
  • Chromosomes, Human, Pair 6 / genetics
  • Enhancer Elements, Genetic / genetics*
  • Epigenesis, Genetic
  • Genetic Loci / genetics
  • Genetic Predisposition to Disease / genetics*
  • Genome-Wide Association Study
  • HLA-C Antigens / genetics*
  • Haplotypes
  • Humans
  • Linkage Disequilibrium
  • Molecular Sequence Data
  • Polymorphism, Single Nucleotide
  • Proteins / genetics
  • Psoriasis / genetics*
  • Sequence Analysis, DNA
  • T-Lymphocytes / metabolism

Substances

  • HLA-C Antigens
  • HLA-C*06:02 antigen
  • PSORS1C1 protein, human
  • PSORS1C3 lncRNA, human
  • Proteins

Associated data

  • GENBANK/KC312698