Haptoglobin Gene Promoter Polymorphism and Haplotypes Are Unique in Different Populations

Human Biology, Feb 2006 by Teye, Kwesi, Soejima, Mikiko, Quaye, Isaac K E, Pang, Hao, Et al

Abstract

We investigated the distribution of haptoglobin (HP) alleles and haplotypes among Africans (Ghanaians), Europeans (from South Africa), and Chinese. HP*1F was present only in Africans and Europeans, whereas HP*del was unique to Chinese. Six base substitutions at the promoter region were population specific. Only 3 out of 18 haplotypes were shared among the populations. A probable application of HP in human population genetics appears legitimate.

KEY WORDS: HP HAPLOTYPES, HAPTOGLOBIN, HP, HP PROMOTER POLYMORPHISM, SOUTH AFRICAN EUROPEANS, GHANAIANS, CHINESE.

Haptoglobin (Hp) is an acute phase hemoglobin binding protein consisting of 2α and 2β chains (Giblett 1968). Humans are unique in having a genetic polymorphism of the α protein because of two codominant alleles, HP*1 and HP*2 (Smithies 1955). Two variants of HP*1, HP*1F and HP*1S, have been described (Black and Dixon 1968; Maeda 1991). These alleles give rise to three major phenotypes: HP 1,1, HP 2,2, and HP 2,1. A fourth phenotype, HP 0,0, has been characterized in Asian populations as being due to homozygosity of the HP*del allele (Koda et al. 1998, 2000).

The HP phenotype determines the serum levels of the protein. In all populations studied the serum levels are generally in the order HP 1,1 > HP 2,1 > HP 2,2 (Langlois and Delanghe 1996; Kasvosve et al. 2000). Although the reasons for these differences are unknown, there is evidence that they are associated with polymorphism in the HP promoter (Maeda 1991; Teye et al. 2003). Maeda (1991) described an association between HP promoter polymorphism and HP gene expression in the HP 2,1 mod phenotype, which leads to a lower serum reference value than in an HP 2,1 individual. We also have reported an association between HP promoter polymorphism and HP gene expression (Teye et al. 2003). A - 61A -rarr; C substitution, first described by Maeda (1991) and located in one of three interleukin 6 responsive elements (Oliviero and Cortese 1989), and a novel - 101 C -[arrow right] G substitution were found to be strongly associated with ahaptoglobinemia and hypohaptoglobinemia, respectively (Teye et al. 2003). Significant geographic variations exist in the distribution of HP phenotypes and the range of Hp serum levels. In the present paper we compare the distribution of HP alleles, HP gene promoter polymorphism, and haplotypes among Africans from Ghana, Europeans from South Africa, and Chinese to determine the differences that characterize the phenotypes in each population, for use as probable markers for anthropologic studies.

Materials and Methods

Populations. Genomic DNA was isolated from Ghanaians, Europeans of South Africa, and Chinese as described in previous studies (Liu et al. 1998,1999; Teye et al. 2003). The Kurume University ethical committee approved the study.

PCR Amplification and DNA Sequencing. We performed PCR amplification to determine HP genotypes and the presence of the HP*del allele, as described previously (Koda et al. 1998, 2000). We also examined HP*1 variants by amplifying HP exons 2 to 4 (Koda et al. 1998). Using restriction digests with XbaI, we were able to differentiate the HP*1S and HP*1F alleles (Maeda et al. 1984). The promoter region of HP was amplified using PCR, purified, and sequenced directly with an ABI Prism dye terminator cycle sequencing ready reaction kit (Applied Biosystems, Tokyo, Japan).

Haplotype Determination and Statistics. Allele and single nucleotide polymorphism (SNP) frequencies were determined using gene counting. Maximum likelihood haplotypes were estimated using Arlequin software (Schneider et al. 2000). Variations in HP alleles and SNPs were evaluated using Fischer's exact test. FST values were estimated using DnaSP software (Rozas and Rozas 1999).

Results

We evaluated the distribution of HP alleles and base substitutions at the promoter region among Africans (Ghana), Europeans (South Africa), and Chinese to determine the population differences and associations. The distribution of the four HP alleles among the study populations showed marked geographic differences (Table 1). The HP*2 allele was the most prevalent in all three populations but was significantly higher in the Chinese population (P

There was distinct variation in the distribution of HP promoter SNPs (- 55A [arrow right] G, - 61A [arrow right] C, 0 - 101C [arrow right] G, - 104T [arrow right] A, - 191T- [arrow right] G, and - 242C [arrow right] T) across the study populations (Table T). Strikingly, the - 61C and - 101G substitutions were found only in the African population (Table 2). The - 242T substitution was generally high in Europeans (P

The most likely haplotypes determined by Arlequin software are shown in Table 3. We found that the -61C and - 101G substitutions were strongly in linkage disequilibrium with the HP*2 and HP*1S alleles, respectively. The - 55G and - 104A substitutions are almost always associated with the HP*1F allele in both the African and European populations. The - 55G substitution was found associated with HP*2 in all populations, with frequencies that varied extensively according to the population. The - 55G, - 104A, HP*2 haplotype was found only in the African population, which also had a high frequency of the - 55G, - 104A, HP*1F haplotype. Overall, 18 haplotypes were observed among the study populations. Of this number, only three haplotypes were shared among all three populations. With the exception of the - 55G, HP*2 haplotype, all the shared haplotypes were of the wild-type allele, and even then visible variations existed between the frequency distributions (Table 3).