Diversity of KIR genes and their HLA-C ligands in Ugandan populations with historically varied malaria transmission intensity

Malaria is estimated to cause nearly half a million deaths each year worldwide [1]. Malaria is a known evolutionary driving force in the selection of several human genetic polymorphisms that protect against malaria. Red blood cell alterations are the most studied genetic abnormalities that impact on malaria [2]. These include mutations in the alpha- and beta-globin genes that lead to sickle cell anaemia or thalassemias, glucose-6-phosphate dehydrogenase (G6PD) deficiency and the Duffy antigen protein [3]. It has been suggested that many of these polymorphisms were selected in human populations due to their role in protection from the detrimental effects of Plasmodium falciparum infection [4]. It has been demonstrated that different populations have developed independent evolutionary responses to malaria [5]. For example, 3 haemoglobin variants (HbS, HbC, and HbE) appear to confer protection against malaria in different parts of the world [6]. The HbS allele is common in Africa, but rare in Southeast Asia, and the opposite is true for the HbE allele [7, 8].

A recent genome wide association study of 17,000 individuals in Africa reported that known genetic variants account for only 11% of the total genetic influence of malaria on the human genome [9]. Among other genes potentially influencing malaria responses are those mediating innate immunity, which is important in protection from P. falciparum infection. Natural killer (NK) cells play an important role in the innate immune response to malaria infection [10, 11]. NK cells are the first cells in peripheral blood to produce interferon gamma (IFN- γ) in response to P. falciparum infection [11], and they have also been shown to participate in adaptive immunity. Recent evidence indicates a role for NK cells in malaria infection in humans and in mouse models [10, 12]. It has been shown that copy number variation (CNV) in KIR genes influences immunity to infections [13] and plays an important role in NK cell education [14] through interactions with their HLA class I ligands. Hence, the expression of multiple copies of KIR genes could potentially lead to enhanced NK cell education, thereby strengthening immunity to pathogens. This has been well studied in viral infections, but not in malaria.

Some studies have demonstrated that individuals may vary in their ability to elicit an innate immune response to malaria infection, with clear implications for disease manifestations [15]. Heterogeneity in response could arise from variations in KIR and their major ligands, HLA-C molecules, that have a direct impact on NK cell functions [11, 16]. The frequencies of different KIR and HLA-C genes vary remarkably across world populations, which might reflect differential selection pressures as well as persistence of ancestral genotypes [17]. The KIR and HLA loci have been suggested to be fast evolving and under positive selection, with pathogen pressure as the driving force [18, 19]. Genetic variation of KIR and their HLA-C ligands across the African continent is not well documented. Several studies have linked high KIR and HLA genetic diversity in Africa to malaria pressure [20‐22]. However, there is limited data regarding the distribution of KIR and HLA variants in populations with varied malaria transmission intensity. Since interactions between the genetically diverse KIR and HLA molecules modulate the functionality of the NK cell response to malaria infections, a better understanding of the distribution of KIR and HLA genes in populations with varied malaria transmission intensity will be important in appreciating the impact of P. falciparum malaria on the evolution of KIR and HLA genes.

To date, there is limited data on the distribution of KIR and their HLA-C ligands in populations with varied malaria transmission intensity. This is partly due to the genotyping approaches that only reveal information about presence or absence of KIR and HLA genes. Furthermore, the few studies that have been carried out are case–control comparisons of severe versus uncomplicated malaria, with limited genetic information about KIR and HLA genes. As an alternative approach, more comprehensive genotyping techniques that provide additional information like copy number variation in these genes were used to evaluate the diversity of KIR genes and their HLA-C ligands in humans living in populations with historically varied malaria transmission intensity.

Most studies about genetic variation in KIR and HLA class I molecules and malaria have focused mainly on protection from severe malaria [33]. The aim of this study was to determine whether KIR and HLA-C genetic variants and CNV in KIR genes from 3 populations of Uganda with historically varied malaria transmission intensity have been shaped by selection pressure from falciparum malaria. Appreciation of malaria transmission prior to recent intensive control efforts and urbanization suggests a rank order for historical transmission intensity of Tororo > Jinja > Kanungu [31]. Thus, the measured prevalence of KIR genes and their HLA-C ligands in populations with historically varied malaria transmission was aimed at understanding impacts of malaria evolutionary pressure on KIR and HLA genes.

There was high KIR diversity in the 3 studied populations, as has been seen in previous studies in Uganda [20] and in other African populations [34]. Generally, the frequency of KIR3DS1 was low across the 3 populations, similar to that reported in previous studies from other African populations [35]. The frequency of KIR3DS1 was significantly lower in Kanungu compared to Tororo and Jinja, implying that KIR3DS1 could have been positively selected for in Tororo and Jinja to offer some advantage against malaria. The prevalence of KIR2DS5 and KIR2DL5 genes was significantly lower in Kanungu. Interestingly, results from a previous study in Nigeria demonstrated that KIR2DS5 and KIR2DL5 genes were associated with reduced parasitaemia [36]. The KIR3DS1, KIR2DL5, KIR2DS5 and KIR2DS1 genes can be present together on a particular haplotype in sub-Saharan Africans [37]. Differences in the prevalence of this haplotype across the three sites could potentially be explained by the selective pressure imposed by malaria. If so, the responsible gene or genes on the haplotype are not known, but KIR3DS1 has a low frequency and is present on few other haplotypes in Ugandans [38]. This gene is more prevalent in other populations, including Europeans [39], suggesting that it is selected against in Uganda or it evolved outside Africa [35]. The observed differences may be due, in part, to genetic differences between the ethnic groups principally inhabiting these populations. Indeed, in the previous study from these cohorts, it was observed that the populations of Tororo and Kanungu were homogeneous, based on language groups, but the Jinja population had ethnic groups from all over Uganda [40]. Although the specific ligands and expression details for KIR2DS3 and KIR2DS5 are yet to be defined, it is speculated that under functionally relevant combinations these activating genes, in conjunction with their putative ligands, may increase the threshold of NK cell activation and subsequent recruitment of other immune factors that mediate protection against malaria.

Although there was no significant difference in KIR/HLA-C combinations across the three sites in Uganda, it should be noted that, interactions between KIR and their HLA-C ligands within an individual play a key role in modulating the activity of NK cells [41]. For instance, the presence of particular HLA-C allotypes and inhibitory KIR2DL1, KIR2DL2 and KIR2DL3 genes determines the strength of NK cell inhibition during malaria infection [33]. The best characterized KIR-HLA ligand interactions are KIR2DL1 with the HLA-C2 subgroup and KIR2DL2/L3 with the HLA-C1 subgroup. Generally, KIR2DL1/HLA-C2 provides the strongest inhibition, followed by KIR2DL2/HLAC1, and KIR2DL3/HLA-C1 [42, 43]. HLA-C1/C1 individuals are only able to receive inhibitory signals via KIR2DL2 and KIR2DL3, whereas HLA-C2/C2 individuals receive inhibitory signals predominantly via KIR2DL1, and heterozygous individuals have the ligand for all three of these KIR genes [44]. Lower KIR inhibition may allow unrestrained NK cell activation that could contribute to immune-mediated pathology. This would be consistent with the theory that mechanisms that prevent malaria infection and those that prevent severe disease are distinct and may have a balancing effect on the maintenance of different KIR and their HLA ligands in malaria-endemic populations.

The role of KIR/HLA compound genotypes during falciparum malaria requires more attention given that malaria parasites spend most of the life cycle outside of HLA-expressing cells. Sporozoites infect hepatocytes after injection by mosquitoes. This is the only stage in the parasite replicative life cycle which is within an HLA-expressing host cell (39). Because erythrocyte membranes contain little to no HLA (42), it is postulated that the influence of KIR on cell-mediated anti-parasite immunity may occur primarily during the liver stage. This implies that cellular immune responses play an important role in restricting P. falciparum infection. During the blood stage, KIR-expressing effector cells may respond more strongly to an HLA-devoid cell due to the loss of inhibitory signalling via inhibitory KIR (43). KIR inhibition may also influence the clearance of parasites through antibody-dependent cellular cytotoxity (44, 45).

Previous studies have indicated that variation in KIR copy number, which leads to expression differences [14], may be important for susceptibility to some diseases. For example, CNV of KIR3DL1/S1 influences HIV control [45] and expression differences of KIR2DL3, interacting with HLA-C, may have a profound effect on resolution of hepatitis C virus infection [46]. However, there was no significant difference between KIR CNV across the three populations of Uganda.

Although different KIR and HLA variants may have been selected in different populations primarily due to differential risk of malaria, the role of other infectious pathogens that are prevalent in these malaria-endemic populations should not be overlooked, as they may also have exerted selective pressure on the evolution of KIR and HLA. Therefore, the role of other co-infections should be considered in future studies involving KIR and malaria, especially in populations affected by many infectious pathogens.

This study had some limitations. First, the genotyping technique for both KIR and HLA-C could not give detailed information up to the allele level. Second, other HLA class I genes, for instance HLA-B (e.g., HLA Bw4 and HLA Bw6 allotypes), which may play a role in malaria risk were not looked at. Nevertheless, analysis for HLA-C allotypes, which are the major ligands for KIR genes, was done. Third, the status of KIR genes and their HLA-C ligands remain unknown in a larger part of Uganda that was not covered in this study given its limited coverage. Despite these limitations, description of the genetic diversity of KIR and their HLA-C ligands in populations with historically varied malaria transmission intensity offered an opportunity to identify KIR and HLA-C genetic variants that are under positive selection and are potentially important in protection against malaria.

This study has provided baseline information about differences in the prevalence KIR genes and their HLA-C ligands in populations of Uganda with historically varied malaria transmission intensity. The KIR3DS1, KIR2DL5, KIR2DS5, and KIR2DS1 genes may partly explain differences in transmission intensity of malaria since these genes have been positively selected for in places with historically high malaria transmission intensity. This is the largest cohort ever studied investigating KIR, HLA-C and malaria risk. A new high-throughput real-time PCR assay for HLA-C genotyping has been developed from this study. This will be useful in disease association studies that involve larger cohorts.