Association of trypanolytic ApoL1 variants with kidney disease in African Americans

Abstract

African Americans have higher rates of kidney disease than European Americans. Here, we show that, in African Americans, focal segmental glomerulosclerosis (FSGS) and hypertension-attributed end-stage kidney disease (H-ESKD) are associated with two independent sequence variants in the APOL1 gene on chromosome 22 {FSGS odds ratio = 10.5 [95% confidence interval (CI) 6.0 to 18.4]; H-ESKD odds ratio = 7.3 (95% CI 5.6 to 9.5)}. The two APOL1 variants are common in African chromosomes but absent from European chromosomes, and both reside within haplotypes that harbor signatures of positive selection. ApoL1 (apolipoprotein L-1) is a serum factor that lyses trypanosomes. In vitro assays revealed that only the kidney disease-associated ApoL1 variants lysed Trypanosoma brucei rhodesiense. We speculate that evolution of a critical survival factor in Africa may have contributed to the high rates of renal disease in African Americans.

Figure 1

Association analysis in FSGS cohorts with logistic regression for alleles G1 and G2. (A) Results of association beween 205 idiopathic biopsy-proven African American FSGS cases and 180 African American controls using Fisher’s exact test. On the x-axis and y-axis, genomic position and −log10 of the p-values are shown. Also highlighted are SNPs rs4821481 and rs3752462 whose combined risk alleles define the E-1 haplotype(5). (B) SNP associations after conditioning on allele G1 using logistic regression. (C) SNP associations after conditioning on alleles G1 and G2 using logistic regression.

Figure 2

Natural selection analysis for the Yoruba population. (A) Extended haplotype homozygosity (EHH) values for the three APOL1 alleles (G1, G2, and WT). We computed EHH after combining Hapmap3 genotype data with our genotype data for alleles G1 and G2 (Supplementary Table 3), shown together with recombination hotspots around APOL1. Although APOL1 and MYH9 are in close physical proximity (20kb apart), they are separated by a recombination hotspot, giving a genetic distance (0.2cM), equivalent to a physical distance of approximately 200kb. (B) Distribution of iHS values in Yoruba, highlighting the iHS value for the SNPs defining G1 (iHS=−2.45). The iHS scores are distributed as a standard normal random variable. Therefore values for which |iHS|>2 are considered suggestive of selection. (C) Distribution of ΔiHH values highlighting the SNPs defining allele G1 and allele G2 (for G1, ΔiHH=0.471 cM, and for G2, ΔiHH=0.275 cM). Values are measured in centimorgans (cM). Raw data are available in Table S4.

Figure 3

G1 and G2 alleles of ApoL1 kill T.b. rhodesiense. Trypanolytic potential of ApoL1 variants on normal human serum-resistant (SRA+) and normal human serum-sensitive (SRA−) T. b. rhodesiense ETat 1.2 clones. ETat 1.2R is resistant to normal human serum, and ETat 1.2S is sensitive to normal human serum. (A) Titration of trypanolytic activity in human plasma samples after overnight incubation, expressed as % survival compared to fetal calf serum control. (hom, het=homozygous and heterozygous mutations, respectively). (B) ApoL1 content of various plasma samples before and after affinity chromatography through SRA column (NHS=normal human serum; WT=wild type ApoL1; S=serine 342; G=glycine 342; I=isoleucine 384; M=methionine 384; i=insertion of N388/Y389; d=deletion of N388/Y389). (C) Trypanolytic activity of various recombinant ApoL1 variants after overnight incubation, expressed as % survival compared to fetal calf serum (FCS) control. (D) Kinetics of trypanolysis by 20 μg/ml recombinant ApoL1 variants, in the presence or absence of 25 μM chloroquine (clq). (E) Phenotype of ETat1.2R trypanosomes incubated with various recombinant ApoL1 (20 μg/ml; 1h30 and 6h incubation, for G1 and G2 respectively; the arrows point to the swelling lysosome).