Deciphering the ancient and complex evolutionary history of human arylamine N-acetyltransferase genes

Abstract

The human N-acetyltransferase genes NAT1 and NAT2 encode two phase-II enzymes that metabolize various drugs and carcinogens. Functional variability at these genes has been associated with adverse drug reactions and cancer susceptibility. Mutations in NAT2 leading to the so-called slow-acetylation phenotype reach high frequencies worldwide, which questions the significance of altered acetylation in human adaptation. To investigate the role of population history and natural selection in shaping NATs variation, we characterized genetic diversity through the resequencing and genotyping of NAT1, NAT2, and the pseudogene NATP in a collection of 13 different populations with distinct ethnic backgrounds and demographic pasts. This combined study design allowed us to define a detailed map of linkage disequilibrium of the NATs region as well as to perform a number of sequence-based neutrality tests and the long-range haplotype (LRH) test. Our data revealed distinctive patterns of variability for the two genes: the reduced diversity observed at NAT1 is consistent with the action of purifying selection, whereas NAT2 functional variation contributes to high levels of diversity. In addition, the LRH test identified a particular NAT2 haplotype (NAT2*5B) under recent positive selection in western/central Eurasians. This haplotype harbors the mutation 341T-->C and encodes the "slowest-acetylator" NAT2 enzyme, suggesting a general selective advantage for the slow-acetylator phenotype. Interestingly, the NAT2*5B haplotype, which seems to have conferred a selective advantage during the past approximately 6,500 years, exhibits today the strongest association with susceptibility to bladder cancer and adverse drug reactions. On the whole, the patterns observed for NAT2 well illustrate how geographically and temporally fluctuating xenobiotic environments may have influenced not only our genome variability but also our present-day susceptibility to disease.

Figure 1

Schematic representation of the NATs region spanning >200 kb. Sequenced loci are represented by boxes (black boxes = coding regions; gray boxes = flanking regions; white boxes = intergenic regions), and arrows indicate the positions of genotyped SNPs.

Figure 2

NAT1 gene tree. Time is scaled in millions of years. Mutations are named for their physical positions along the NAT1 locus. Lineage absolute frequencies in Africa and western and eastern Eurasia are reported. Nonsynonymous mutations are highlighted in gray.

Figure 3

Proportion of SNP pairs in significant LD against physical distance in the NATs 200-kb region. In each population, genotyped SNPs were selected to have a MAF >10%. The Fisher’s exact test was used to assess LD significance, followed by Bonferroni corrections. SNP pairs were grouped into 20-kb bins.

Figure 4

REHH plotted against core haplotype frequencies. Circles represent NAT1 and NAT2 core haplotypes. The 95th and 99th percentiles were calculated from both simulated data (gray lines) and an empirical distribution obtained from the screening of the entire chromosome 8 (black lines). Circles above the 95th percentile of simulated and/or empirical distributions are blackened. A, NAT1 and NAT2 sub-Saharan African core haplotypes are plotted against both simulated data and the empirical distribution of ∼40,000 Yoruban core haplotypes from the HapMap. B, NAT1 and NAT2 core haplotypes in western/central and eastern Eurasian populations are plotted against both the simulated data and the empirical distribution of ∼40,000 European-descent core haplotypes from the HapMap. Numbers affiliated with significant core haplotypes refer to: (1) Moroccan NAT2*5B, (2) Swedish NAT2*5B, (3) Turkmen NAT1*4, (4) Moroccan NAT1*4, (5) Saami NAT1*4, and (6) Swedish NAT1*4.

Figure 5

Worldwide distribution of NAT2 acetylation phenotypes in healthy individuals. Each pie represents the population proportion of fast and slow acetylators. Populations numbered from 1 to 13 were analyzed in this study: (1) Bakola Pygmies, (2) Baka Pygmies, (3) Ateke Bantus, (4) Somali, (5) Morrocans, (6) Ashkenazi Jews, (7) Sardinians, (8) Swedes, (9) Saami, (10) Turkmen, (11) Gujarati, (12) Thai, and (13) Chinese. Numbers 14 to 36 refer to a reviewed population: (14) Yorubas (Jeyakumar and French 1981), (15) Zimbabweans (Nhachi 1988), (16) South Africans (Hodgkin et al. 1979), (17) Libyans (Karim et al. 1981), (18) Saudi Arabians (El-Yazigi et al. 1992), (19) Emiratis (Woolhouse et al. 1997), (20) Iranians (Sardas et al. 1993), (21) Jordanians (Irshaid et al. 1992), (22) Turkmen (Bozkurt et al. 1990), (23) Greeks (Asprodini et al. 1998), (24) Germans (Cascorbi et al. 1995), (25) Russians (Lil’in et al. 1984), (26) Pakistanis (Saleem et al. 1989), (27) Bangladeshi (Zaid et al. 2004), (28) Thai (Kukongviriyapan et al. 1984), (29) Malaysians (Ong et al. 1990), (30) Chinese (Zhao et al. 2000), (31) Koreans (Lee et al. 2002), (32) Japanese (Hashiguchi and Ebihara 1992), (33) Papua New Guineans (Hombhanje 1990), (34) Australian Aborigines (Ilett et al. 1993), (35) Eskimos (Eidus et al. 1974), and (36) Amerindians (Jorge-Nebert et al. 2002).