PgmNr P2098: IRF4 haplotype diversity and associations with hair, eye and skin pigmentation in a Brazilian admixed population.

Authors:
C. T. Mendes-Junior 1 ; A. L. E. Pereira 1 ; N. C. A. Fracasso 2 ; L. Marcorin 1 ; G. Debortoli 2 ; J. D. Massaro 3 ; A. L. Simões 2 ; E. A. Donadi 3 ; E. C. Castelli 4 ; M. L. G. Oliveira 2


Institutes
1) Universidade de São Paulo (Departamento de Química, FFCLRP-USP), Ribeirão Preto, SP, Brazil; 2) Universidade de São Paulo (Departamento de Genética, FMRP-USP), Ribeirão Preto, SP, Brazil; 3) Universidade de São Paulo (Departamento de Clinica Médica, FMRP-USP), Ribeirão Preto, SP, Brazil; 4) Universidade Estadual Paulista (Departamento de Patologia, FMB-UNESP), Botucatu, SP, Brazil.


Abstract:

The Interferon Regulatory Factor 4 gene, located at chromosomal region 6p25-p23, encodes a DNA-binding transcription factor, expressed exclusively in immune system cells and melanocytic lineages. The rs12203592 SNP (intron 4) has been associated with presence of freckles, hair, eye and skin color. Functional studies in human and mice melanin-containing cells revealed that this SNP is directly involved in the regulation of IRF4 expression, suggesting a clear role in melanocyte pigmentation. In spite of these findings, the IRF4 diversity in admixed populations has not been evaluated so far. In order to verify if other variation sites spread across the IRF4 gene may be associated with human pigmentation, the regulatory and coding (9 exons and part of their flanking introns) regions were analyzed by next-generation sequencing in a Brazilian admixed population sample. The population sample was composed of 228 unrelated individuals from São Paulo State, which were stratified according to eye (blue, green, hazel, light-brown, and dark-brown), hair (red, blond, dark-blond, light-brown, dark-brown and black) and skin (light, intermediate and dark) pigmentation, as well as regarding the presence of freckles and intensity of hair greying. DNA libraries, including other pigmentation genes, were prepared using the Haloplex Target Enrichment System (Agilent) and sequenced at the MiSeq platform (Illumina). CutAdapt, BWA and GATK packages were used for trimming adaptor sequences, alignment and genotype calling, respectively. Missing alleles and haplotypes were inferred by using the PHASE method. A total of 105 variation sites were identified. Eighteen of these SNPs presented strong association (OR > 10) with at least one pigmentation feature. However, if the Bonferroni correction for multiple tests is taken into account, only two associations, both of them involving the rs12203592 SNP, remain significant: allele T associated with light skin and blue eyes. This result is in agreement with previous reports that the rs12203592*T allele leads to reduced IRF4 activation and reduced tyrosinase expression, leading to sun sensitivity and blue eyes. A total of 101 different haplotypes were inferred. When haplotypes were subdivided in promoter, coding and 3’UTR haplotypes, 17, 29 and 37 different haplotypes were observed, respectively. Various associations were identified, particularly involving the most frequent promoter haplotype, the two most frequent coding (only one of them with allele rs12203592*T) and the most frequent 3’UTR, all of them with light skin, blue eyes, brown hair and hair greying. These results suggest that other variation sites besides rs12203592, when considered in a haplotype background, are associated with human pigmentation. Financial Support: CAPES, CNPq (309572/2014­2 and 448242/2014-1) and FAPESP (2013/15447-0).