HLA-DQA1 and HLA-DQB1 alleles and haplotypes in two Brazilian Indian tribes: Evidence of conservative evolution of HLA-DQ

V.S. SOTOMAIOR, F.R. FAUCZ, C. SCHAFHAUSER,I M. JANZEN-DUCK, A.B.W. BOLDT, AND M.L. PETZL-ERLER

Abstract Nucleotide sequence polymorphism of the HLA-DQAI and HLA-DQBI class II genes was analyzed in the Kaingang and Guarani Amerindians from southern Brazil using PCR sequence-specific oligonucleotide typing methods. Four different DQAI-DQBI haplotypes were found: DQAl*-DQBI*0402 (associated with DRBI*0802, DRBI *08041, and DRB] *0807, DQA] *0501-DQBI*0301 (associated with DRBI*1602, DRB]*1413, and DRBI*1402), DQAI*03DQB]*0302 (associated with DRBI*0404 and DRB]*0411), and DQA1*03-DQBI*03032 (associated with DRB]*09012). These HLADQAI and HLA-DQBI alleles and haplotypes are common in many other populations of all major ethnic groups. Alleles and haplotypes introduced into the populations by post-Columbian admixture were seen at low frequency both in the Kaingang (3.2%) and in the Guarani (3.8%). No novel HLA-DQAI and HLA-DQBI alleles have thus far been identified in Amerindians. This differs from previous results for HLA-DRB], another class II locus presenting novel alleles (i.e., alleles not found in other ethnic groups and probably generated after migration of paleo-Indians to the Americas) in the Guarani and in other South American Indian populations. The distribution of the HLA-DQ alleles and haplotypes in Amerindians indicates a weaker diversifying selective pressure on the HLADQ genes compared with HLA-DRB] and HLA-B. The more conservative evolution of HLA-DQA] and HLA-DQB1 compared with HLA-DRB] is strong evidence of (still not well-defined) functional differences of these class II genes.

KEY WORDS: AMERINDIANS, MHC, HLA-DQ, DQAI, DQBI, POLYMORPHISM

The Guarani and the Kaingang are two anthropologically well-defined and genetically distinct endogamous Amerindian tribes. The Guarani belong to the Tupi linguistic group, and the Kaingang are a Ge-speaking people. Despite living side by side for many centuries, these populations still differ in many aspects of their culture. The study of their HLA genes has contributed new insights into the mechanisms of generation and maintenance of the HLA polymorphism (Belich et al. 1992; Petzl-Erler et al. 1993; Petzl-Erler and McDevitt 1994; Pando et al. 1994; Parham et al. 1997). The two populations exhibit great differences regarding the sets of alleles and allele frequencies at almost all thus far examined MHC loci (Guerra et al. 1992; Petzl-Erler et al. 1993; Messias et al. 1993; Petzl-Erler and McDevitt 1994; Weg-Remers et al. 1997; Petzl-Erler et al. 1997). Thus the clear cultural and linguistic distinctiveness of these two populations is paralleled by great genetic distance between them (Petzl-Erler et al. 1993; Salzano et al. 1997).

The class II region of the human major histocompatibility complex (MHC) consists of a series of closely linked genes mapped to chromosome 6p21.3. Although some MHC class II loci are essentially monomorphic or bear few common alleles, most are highly polymorphic. The HLA-DQAJ and HLA-DQB] genes, which encode the a and the i chains, respectively, of the HLA-DQ molecule, are among the polyallelic and polymorphic genes. Twenty DQAJ and 35 DQBI alleles had been identified up to 1997. Variability of the HLA-DQ molecule is increased further, because aft heterodimers can result from the chains encoded by HLA-DQA1 and HLA-DQBI alleles in both cis and trans positions (Kwok et al. 1993).

The genetic diversity of the MHC genes is of interest for its functional and evolutionary significance. The analysis of these genes has been useful in unraveling the historical relationships between distinct ethnic groups. Furthermore and equally important, the population studies are giving important insights into the microevolution of the MHC itself. The relative contribution of point mutation and interallelic gene conversion as mechanisms of generation of new HLA alleles and of different forms of selection and genetic drift in shaping the diversity of these genes at the population level are subjects of controversy. In searching for evidence of the evolutionary mechanisms acting on HLA-DQ diversity, we studied the second exon nucleotide sequence polymorphism of the HLA-DQA1 and HLA-DQBJ genes in the two major Amerindian tribes of southern Brazil, the Kaingang and the Guarani. All examined individuals belong to the population samples investigated by Petzl-Erler et al. (1993) and were typed serologically for HLA-A, -B, -C, -DR, and -DQ. A subgroup was typed for HLA-DRB by direct DNA analysis (Petzl-Erler and McDevitt 1994; Probst and Petzl-Erler, unpublished data, 1997). The population sample analyzed in this study was 200 individuals (92 Guarani and 108 Kaingang).

Standard methods were used for DNA purification and PCR sequencespecific oligonucleotide typing. The sequences of the primers and probes correspond to those recommended by the 1I th and 12th International Histocompatibility Workshops (Kimura and Sasazuki 1992; Fernandez-Vina and Bignon 1997). Twenty-one and 36 different sequence-specific oligonucleotides were used for HLA-DQAI and HLA-DQBI typing, respectively. Positive and negative controls for the several probes were International Histocompatibility Workshop reference cell lines and individuals from the local cell panel. Allele frequencies were obtained by direct counting. Genotype frequencies, also obtained by direct counting, were tested for Hardy-Weinberg equilibrium fit. The statistical significance of all deviations was verified by chisquare tests with a Yates correction, if pertinent. The DRB]-DQA]-DQB] haplotypes were identified by analysis of homozygous individuals and by segregation analysis in families. Information on the HLA-DRBI alleles of these populations was available from our previous studies (Petzl-Erler and McDevitt 1994; Probst and Petzl-Erler, unpublished data, 1997).