KIR2DS5 allotypes that recognize the C2 epitope of HLA-C are common among Africans and absent from Europeans

Abstract

Introduction: KIR2DS5 is an activating human NK cell receptor of lineage III KIR. These include both inhibitory KIR2DL1, 2 and 3 and activating KIR2DS1 that recognize either the C1 or C2 epitope of HLA-C. In Europeans KIR2DS5 is essentially monomorphic, with KIR2DS5*002 being predominant. Pioneering investigations showed that KIR2DS5*002 has activating potential, but cannot recognize HLA-A, -B, or -C. Subsequent studies have shown that KIR2DS5 is highly polymorphic in Africans, and that KIR2DS5*006 protects pregnant Ugandan women from preeclampsia. Because inhibitory C2-specific KIR2DL1 correlates with preeclampsia, whereas activating C2-specific KIR2DS1 protects, this association pointed to KIR2DS5*006 being an activating C2-specific receptor. To test this hypothesis we made KIR-Fc fusion proteins from all ten KIR2DS5 allotypes and tested their binding to a representative set of HLA-A, -B and -C allotypes.

Results: Six African-specific KIR2DS5 bound to C2⁺ HLA-C but not to other HLA class I. Their avidity for C2 is ∼20% that of C2-specific KIR2DL1 and ∼40% that of C2-specific KIR2DS1. Among the African C2 receptors is KIR2DS5*006, which protected a cohort of pregnant Ugandans from pre-eclampsia. Three African KIR2DS5 allotypes and KIR2DS5*002, bound no HLA-A, -B or -C. As a group the C2-binding KIR2DS5 allotypes protect against pre-eclampsia compared to the non-binding KIR2DS5 allotypes. Natural substitutions that contribute to loss or reduction of C2 receptor function are at positions 127, 158, and 176 in the D2 domain.

Conclusions: KIR2DS5*005 has the KIR2DS5 consensus sequence, is the only allele found at both centromeric and telomeric locations of KIR2DS5, and is likely the common ancestor of all KIR2DS5 alleles. That KIR2DS5*005 has C2 receptor activity, points to KIR2DS5*002, and other allotypes lacking C2 receptor function, being products of attenuation, a characteristic feature of most KIR B haplotype genes. Alleles encoding attenuated and active KIR2DS5 are present in both centromeric and telomeric locations.

Keywords: Africa; HLA-C; KIR; NK cells; pregnancy.

Figure 1

KIR2DS5*006 specifically recognizes the C2 epitope of HLA‐C. (A) Comparison of the binding of KIR2DL1*003, 2DL3*001, 2DS5*002, and 2DS5*006 KIR‐Fc fusion proteins to nine C1⁺HLA‐C allotypes and two C1⁺HLA‐B allotypes (upper panel) and seven C2⁺HLA‐C allotypes (lower panel). Each data point represents the binding to a different HLA class I allotype. For each HLA‐coated bead, the binding data obtained with KIR‐Fc were normalized to that of the W6/32 antibody, which reacts equivalently with all HLA‐A, ‐B and ‐C allotypes (calculation detailed in Materials and Methods section). Four independent binding assays were performed for each KIR‐Fc and a representative experiment is shown. The mean binding value is indicated by the horizontal bar. The binding of KIR2DS5*006 to C2⁺HLA‐C is significantly higher than that of KIR2DS5*002 (two‐tailed paired Student's t‐test, p  = 0.0076). The statistical analysis used mean binding values from four independent assays (see Figure S1). (B) Binding of the KIR2DL3*001, 2DS5*002 and 2DS5*006‐Fc fusion proteins to each of the seven C2⁺HLA‐C allotypes is shown normalized to that of KIR2DL1*003. Values shown are representative of four independent binding experiments for each KIR‐Fc.

Figure 2

KIR2DS5 allotypes differ in their capacity to recognize C2⁺HLA‐C. Shown are the relative frequencies of the ten KIR2DS5 allotypes observed in the cohort of pre‐eclampsia patients studied by Nakimuli et al. 11, [Frequencies are calculated from KIR2DS5⁺ individuals only and are not the allele frequencies in the patient population, many of whom lack KIR2DS5]. Listed for each allotype are the amino‐acid substitutions that distinguish their extracellular domains (D1 and D2 and Stem) and the binding of their corresponding KIR‐Fc to seven C2⁺HLA‐C allotypes. KIR2DS5*005, the most frequent allotype in this cohort, is set as the consensus sequence with blank boxes indicating sequence identity to the consensus. Shown on the right is the mean binding of each KIR2DS5‐Fc to each C2⁺HLA‐C, normalized to that of 2DL1*003. The dashed vertical line shows KIR2DL3*001‐Fc binding to the same allotypes.

Figure 3

The majority of African KIR2DS5 allotypes recognize C2⁺HLA‐C. Shown are the relative frequencies of the KIR2DS5 allotypes that do, or do not, bind C2⁺HLA‐C. The frequencies are from the cohort studied by Nakimuli et al. 11 and represent relative frequencies of KIR2DS5 allotypes in KIR2DS5⁺ individuals in this population. The KIR2DS5 alleles distribute between locations in centromeric and telomeric regions of the KIR locus. Shown is the distribution between the centromeric and telomeric regions of the KIR locus of the alleles encoding KIR2DS5 allotypes that, do or do not, bind C2⁺HLA‐C. KIR2DS5*005 has the highest frequency and is the only allele found in both genomic regions.