HLA-E polymorphisms in an Afro-descendant Southern Brazilian population

Abstract

HLA-E is a non-classical I (Ib) gene which has limited polymorphism and low levels of tissue expression. Currently, 11 alleles are described in the literature with only three protein products. In the present study we investigated HLA-E gene variations at exons 2 and 3 and calculated allele, genotype and haplotype frequencies in a sample of 152 individuals who reported themselves as being Afro-descendants and who are voluntary bone marrow donors living in the state of Paraná, Brazil. The most frequent allele in the sample analyzed was the E(∗)01:01 (59.21%). The presence of the E(∗)01:04 allele was not detected suggesting that it has a very low worldwide frequency or that this allele may be an artifact of sequencing. We reported the most frequent alleles found as well as genotypes and haplotypes and compared our results with the few other studies found in the literature. This study is the first to investigate Afro-descendants from the South of Brazil.

HLA-E coding and 3′ untranslated region variability determined by next-generation sequencing in two West-African population samples

“…Regarding the coding region, E ⁄ 01:01 and E ⁄ 01:03 were found to account for 94% of all HLA-E alleles [18]. Similar results were found in Brazilian Afro-descendants [17], four Chinese Han populations [15], Amerindians from Mexico, Colombia and Chile [14] and different European populations [22].…”

“…Together, these molecules account for more than 98% of all HLA-E encoded molecules in the present series (Africans pooled together) and more than 90% in worldwide populations [14][15][16][17][18]22]. The frequency of alleles encoding for the E ⁄ 01:03 protein is higher in Lobi as compared to Susu (60.34% and 46.00%, respectively), which is probably due to the different genetic background that characterizes these populations.…”

“…Previous data regarding HLA-E variation demonstrated that we usually find HLA-E coding sequences encoding two main molecules, named E ⁄ 01:01 and E ⁄ 01:03, differing by a single amino acid at codon 107, related to the non-synonymous mutation at the HLA-E position +756 or the genomic position 6:30.458.064 (Table 1) [14,15,17,18]. The first HLA-E protein, E ⁄ 01:01, is characterized by the presence of an Arginine at position 107 and it is encoded by alleles carrying an Adenine at position +756.…”

“…To date, only 17 alleles and six full-length protein variants have been recognized by the IMGT/HLA (http://www.ebi.ac.uk/ipd/imgt/hla/stats.html, database version 3.20.0). Two major allele groups -HLA-E ⁄ 01:01 and E ⁄ 01:03 -account for most of the HLA-E molecules found in the different populations investigated so far [14][15][16][17][18]. The molecules encoded by these groups differ by a single amino acid substitution, encoded at codon 107 (exon 3), in which E ⁄ 01:01 presents an Arginine and E ⁄ 01:03 presents a Glycine.…”

“…A major limitation of previous studies is that they sequenced only a few exons or used genotyping methods to detect known HLA-E polymorphisms [14,17,18,[23][24][25][26][27][28][29][30]. Even in the Brazilian population [18], which represents the most comprehensively studied sample for HLA-E at the moment, only exons 1-4, in addition to the 3 0 UTR were sequenced.…”