Clinical Research

APOL1 Risk Variants Are Strongly Associated with HIV-Associated Nephropathy in Black South Africans

Alex N. Kasembeli, Raquel Duarte, Michèle Ramsay, Pulane Mosiane, Caroline Dickens, Thérèse Dix-Peek, Sophie Limou, Efe Sezgin, George W. Nelson, Agnes B. Fogo, Stewart Goetsch, Jeffrey B. Kopp, Cheryl A. Winkler and Saraladevi Naicker
JASN November 2015, 26 (11) 2882-2890; DOI: https://doi.org/10.1681/ASN.2014050469

Abstract

APOL1 variants are associated with HIV-associated nephropathy and FSGS in African Americans. The prevalence of these variants in African populations with CKD in HIV-1 infection has not been investigated. We determined the role of APOL1 variants in 120 patients with HIV-associated nephropathy and CKD and 108 controls from a South-African black population. Patients with CKD were selected on the basis of histology. Genotypes were successfully determined for APOL1 G1 and G2 variants and 42 single nucleotide polymorphisms, including 18 ancestry informative markers, for 116 patients with CKD (96.7%; 38 patients with HIV-associated nephropathy, 39 patients with HIV-positive CKD, and 39 patients with HIV-negative CKD), and 108 controls (100%). Overall, 79% of patients with HIV-associated nephropathy and 2% of population controls carried two risk alleles. In a recessive model, individuals carrying any combination of two APOL1 risk alleles had 89-fold higher odds (95% confidence interval, 18 to 912; P<0.001) of developing HIV-associated nephropathy compared with HIV-positive controls. Population allele frequencies were 7.3% for G1 and 11.1% for G2. APOL1 risk alleles were not significantly associated with other forms of CKD. These results indicate HIV-positive, antiretroviral therapy–naïve South-African blacks with two APOL1 risk alleles are at very high risk for developing HIV-associated nephropathy. Further studies are required to determine the effect of APOL1 risk variants on kidney diseases in other regions of sub-Saharan Africa.

CKD is an important public health problem worldwide. African Americans experience high rates of CKD arising from diabetic nephropathy, hypertension-attributed CKD, FSGS, and HIV-associated nephropathy (HIVAN).1–3 HIV-positive individuals of African descent have an 18-fold to 50-fold increased risk of developing CKD4 and an 18-fold increased risk of developing HIVAN, suggesting that genetic factors play an important role in susceptibility for HIVAN.2

HIVAN is considered to be a morphologic variant of FSGS characterized by segmental and global glomerular collapse, hypertrophy and hyperplasia of visceral glomerular epithelial cells, and severe tubulointerstitial disease.5 In the absence of effective antiretroviral therapy (ART), approximately 50% of patients with HIVAN progress to ESRD within 2 years.6,7 The introduction of ART has led to a substantial decline in the incidence of HIVAN in the United States.6,7 In sub-Saharan Africa, HIVAN is the most common cause of kidney disease morbidity and mortality in HIV-positive ART-naïve patients.8,9

Mapping by admixture linkage disequilibrium studies for FSGS, HIVAN, and nondiabetic ESRD among African Americans led to the identification of a genomic region on chromosome 22q12 with very strong association with HIVAN, FSGS, and other forms of nondiabetic and hypertension-attributed ESRD.10,11 Further studies identified three codon-changing variants in the APOL1 gene, encoding ApoL1, with extremely strong associations with HIVAN (odds ratio [OR], 29; 95% CI, 13.1 to 68.5), FSGS (OR, 17; 95% CI, 11 to 26.5), and ESRD (OR, 7; 95% CI, 6 to 10) for homozygotes or compound heterozygotes carrying two risk alleles in Americans with African ancestry.12–14 APOL1 renal risk variants have been shown to increase the rate of progression to ESRD in persons with CKD, including FSGS, diabetic CKD, and hypertension-attributed CKD.13,15

The APOL1 risk alleles comprise two tightly linked missense variants G1 (rs73885319; p.S342G and rs60910145; p.I384M) and G2, a 6-bp in-frame deletion removing two amino acids (rs71785313; p.N388del:Y389del) in the last exon of the APOL1 gene.12 The G1 and G2 alleles range in frequency from 0% to approximately 45% for G1 and to approximately 20% for G2 in different geographical regions of sub-Saharan Africa with the lowest frequencies in East Africa and the highest frequencies observed in West Africa.13,16–19 The prevailing hypothesis is that the G1, and to a lesser extent G2, alleles have been under recent selection in West Africa by trypanosomes or other extracellular pathogens.12 This study aimed to determine the prevalence of APOL1 risk variants and the effect of these variants on HIVAN and CKD in black South Africans in a setting of high HIV-1 prevalence.

Results

This study included 228 adult individuals of black African ancestry from Johannesburg, South Africa. Characteristics of the CKD patient groups, all of whom were verified by histology, and HIV-positive controls are presented in Table 1. HIVAN was distinguished from HIV-positive FSGS by the presence of glomerular capillary collapse and glomerular visceral epithelial cell proliferation affecting at least one glomerulus, together with microcystic tubular dilation and interstitial inflammation. Median eGFR was significantly lower in patients with HIVAN (11.9 ml/min per 1.73 m2) compared with all other patients with CKD (33.5 ml/min per 1.73 m2 and 56.6 ml/min per 1.73 m2 for HIV-positive and HIV-negative patients, respectively) and HIV-positive controls (P=0.001). Measures of kidney function were not available for the population control group; they were all apparently healthy individuals who gave consent to be enrolled for population genetic studies as control participants. The CKD patient groups and HIV-positive control group did not differ significantly by age (34.6, 36.1, 36.4, and 38.8 years, respectively) and sex at biopsy or study enrollment (P>0.05) (Table 1). All HIV-positive patients with CKD were ART naïve; however, 75% of the HIV-positive control group had been initiated on ART before recruitment into the study. Median viral load (log10 copies/ml) levels were highest in patients with HIVAN (5.1 log copies/ml) compared with HIV-positive patients with CKD (4.7 log copies/ml) and undetectable median levels in HIV-positive controls. Median CD4 counts were lowest in patients with HIVAN (92 cells/mm3) compared with HIV-positive patients with CKD (244.5 cells/mm3) and HIV-positive controls (371.0 cells/mm3) (Table 1). APOL1 genotypes were determined for 96.7% of patients with CKD (HIVAN, n=38; HIV-positive CKD, n=39; and HIV-negative CKD, n=39) and 100% of controls (HIV-positive controls, n=54; and population controls, n=54) (Table 2). Genotype distributions did not differ significantly from Hardy–Weinberg equilibrium expectations in HIV-positive and population control groups (P>0.05). Single nucleotide polymorphism (SNP) and haplotype frequencies are shown in Figure 1. Two infrequent haplotypes were observed for G1; these were confirmed by Sanger sequencing and by a repeat of the TaqMan assay. Because of the close proximity of the two G1 SNPs, recombination between them is a rare event. The haplotype G-G-I (G1GM), comprising the derived allele at both rs73885319 (p.S342G) and rs60910145 (p.I384M) and the ancestral insertion (I) allele at rs71785313, was the most frequent G1 configuration (6.4% in the population controls and 52.6% in the HIVAN group). A novel haplotype, G1+M (A-G-I), confirmed by Sanger sequencing of the PCR product, was observed as a compound heterozygote (G1+M/G1GM) in a single HIV-positive patient with FSGS. Although Kopp et al.13 showed that the effect size of the G1GM and G1G+ haplotypes are equivalent, the renal risk of G1+M cannot be determined; therefore, we excluded this individual from further analysis in this study.

View this table:
Table 1.

Characteristics of study participants and controls

View this table:
Table 2.

APOL1 genotype distribution among patients with HIVAN, HIV-positive patients with CKD, HIV-negative patients with CKD, and controls

Figure 1.
Figure 1.

Distribution of APOL1 haplotypes and risk alleles. Five APOL1 haplotypes are observed. The ancestral haplotype, denoted as G0, has three ancestral alleles. The G1GM haplotype has two missense alleles. The G1G+ haplotype has one missense risk allele at rs73885319. The G1+M has one missense variant at rs60910145. The G2 haplotype has the 6-bp deletion risk allele at rs71785313. The risk allele and haplotype frequencies are shown for patients with HIVAN, HIV-positive patients with CKD and HIV-negative patients with CKD, and HIV-positive controls and population controls (PCs).

In the population control group, the allele frequencies were 7.3% for the G1 risk allele for rs73885319 and 11.1% for the G2 deletion allele (Figure 1). The combined frequency of the G1 and G2 risk alleles was highly enriched in patients with HIVAN (90.6%) compared with HIV-positive controls (20.8%) (P=8.0×10−20) and the population control group (18.4%) (P=8.0×10−22) (Figure 1). Similar distortions were observed for carriage of two APOL1 risk alleles; 78.9% of the patients with HIVAN were homozygous (G1/G1 or G2/G2) or compound heterozygotes (G1/G2) compared with 3.7% of the HIV-positive controls (P=1.2×10−14) and 1.9% of the population controls (P=8.9×10−16) (Table 2). The distribution of G0, G1, and G2 genotypes and risk alleles among patients with CKD and controls are shown in Table 2. The distribution of genotypes was not statistically different when comparing the HIV-positive patients with CKD with HIV-positive controls or comparing HIV-negative patients with CKD with population controls (Table 2).

We explored the distribution of APOL1 G1 and G2 alleles among the histologically diagnosed HIV-positive and HIV-negative patients with CKD (Table 3, Supplemental Table 1). For the HIV-positive group, there was no significant association between APOL1 genotypes and HIV-positive patients with FSGS (OR, 2.13; 95% CI, 0.03 to 44.30; P=0.48) and HIV-associated immune complex kidney disease (HIVICK) (OR=5.60; 95% CI, 0.4 to 86; P=0.13) compared with HIV-positive controls. There was also no significant association for primary FSGS in the HIV-negative group (OR, 6.30; 95% CI, 0.04 to 248.70; P=0.26) compared with population controls (Tables 3 and 4). To increase statistical power, we combined HIV-positive patients with FSGS (n=13) and primary FSGS (n=9) and compared this with all controls (n=108) and still did not observe any significant association with APOL1 G1 and G2 alleles in a recessive model (P=0.20) (Table 4). Because the point ORs for APOL1 association with primary FSGS and HIVAN differed in this study from those reported by Kopp et al.,13 we used a Woolf test for homogeneity to determine whether the ORs were significantly different. Although the ORs in this study were higher for HIVAN and lower for FSGS compared with the ratios observed in African Americans, the differences were not statistically significant (P=0.56 and P=0.21 for FSGS and HIVAN, respectively). We also compared ORs for HIV-positive FSGS seen in this study with data from Fine et al.20 for African Americans with HIV-positive FSGS compared with a population control group from the study by Kopp et al.13 (OR, 24.5; 95% confidence interval [95% CI], 9.7 to 65.1); P=4.3×10−14); the Woolf test gave a P value of 0.07.

View this table:
Table 3.

Association between APOL1 risk alleles and various glomerular diseases

View this table:
Table 4.

APOL1 risk allele associations with HIVAN, HIV-associated FSGS, and HIV-negative FSGS (primary FSGS)

We assessed the effect size and statistical significance for carriage of one or two APOL1 risk variants by comparing the distribution of two versus one or zero copies of APOL1 G1 and G2 risk alleles in patients and controls in a recessive model (Table 4). Consistent with previous studies, the association of APOL1 genotypes with HIVAN best fits a recessive genetic model. Carriage of two copies of APOL1 renal risk alleles was a strong predictor of HIVAN (OR, 89.1; 95% CI, 17.68 to 911.72; P=1.24×10−14). The predictor was so strong that carriage of even one renal risk allele increased the risk of HIVAN with marginal statistical support (OR, 5.49; 95% CI, 0.87 to 61.14; P=0.05) (Table 4). The results for HIVAN remained highly significant after correcting for age, sex, and genetic ancestry (Table 4).

Examination of the independent effect sizes (ORs) of the G1 and G2 alleles (Figure 2) indicated that the effect size of G2 was weaker than G1; however, it is worth noting that G1/G2 compound heterozygotes are equivalent in effect size to G1/G1.

Figure 2.
Figure 2.

ORs for the effect sizes for HIVAN with different combination of APOL1 G1 and G2 alleles. ORs with CIs for association of different strata of G1–G2 genotypes with HIVAN patients compared with participants carrying no G1 or G2 risk alleles (+/+). For G1/G1 and G1/G2, the OR is infinity, because these genotypes were only observed in patients.

Population stratification analyses using a principal components analysis (PCA) showed that the distribution of patients with HIVAN and HIV-positive control groups was not significantly different along the top-two eigen axes (P>0.05), confirming that the high association observed is not due to an undetected population substructure that might cause false positive associations (Supplemental Figure 1).

Discussion

This is the first study that correlates genotypic information with phenotypes in HIV-associated CKD in Africa, a region with the highest prevalence of HIV-1 infection.21 The study shows an extremely strong association between APOL1 variants, found only on African chromosomes, and biopsy-confirmed HIVAN, an aggressive form of kidney disease that rapidly progresses to ESRD if untreated. Among the patients with HIVAN, 79% carried two copies of APOL1 risk alleles compared with 2% in the general population. Notably, the effect size of APOL1 risk alleles for HIVAN in black South Africans (OR, 89.1; 95% CI, 17.8 to 911.72; P=1.24×10−14) was numerically higher than in African Americans (OR, 29.2; 95% CI, 13.1 to 68.5; P=6.0×10−22), although the CIs overlapped.13 To our knowledge, this is the strongest effect size ever reported for common variants with complex diseases.22

Although there is no statistical difference between effect sizes in South Africans with HIVAN compared with African Americans with HIVAN,13 both the frequency of APOL1 risk alleles (79% versus 72%) and ORs (89 versus 29) are elevated in South Africa. Although these differences may reflect statistical fluctuation, APOL1 may also have a stronger gene–environment interaction in this setting, which warrants further investigation. First, this strong effect might be related to HIV-1 subtype C. HIV-1 subtype C is the dominant strain in Southern and Eastern Africa and South Asia, whereas HIV-1 subtype A is common in West Africa and subtype B is dominant in Europe, Australia, and the Americas.23 HIV-1 subtype C is highly virulent and accounts for approximately 50% of all HIV infections worldwide and 98% of HIV infections in South Africa, with corresponding higher viral loads.23,24 High HIV RNA levels are correlated with a decline in CD4 T cells and with the development of HIVAN in individuals of African ancestry.25 Second, in resource-limited settings, late initiation of ART may predispose at-risk individuals to HIVAN; several studies have shown that effective rollout of ART can reduce the occurrence of HIVAN.6,7,9 Furthermore, all of the HIV-positive patients with CKD in this study were ART naïve. Third, there are regional differences in nutrition, environmental exposures, and other viral infections that may modify the effects of APOL1 variants on the kidney. Fourth, there might be other genetic variants unique to or more common in this population that interacts with APOL1-driven susceptibility to HIVAN.

This study also showed a weak effect with one APOL1 risk allele in HIVAN (OR, 5.49; 95% CI, 0.87 to 61.14; P=0.05), consistent with previous studies.12,13,26 An effect from one risk allele would be consistent with a gain of injury and/or toxicity of these variants in kidney cells that manifests with a strong environmental insult, such as HIV infection, as opposed to a purely recessive effect that might suggest a loss of function.

There was little or no significant APOL1 association with multiple histologic phenotypes of HIV-positive patients with CKD and HIV-negative patients with CKD. Previous studies in African Americans have reported ORs for primary FSGS with two APOL1 risk alleles as 10.5 (95% CI, 6.0 to 18.1) and 17 (95% CI, 11 to 26.5; P=1.3×10−48).12,13 In addition, other studies also demonstrated higher association of APOL1 risk alleles with FSGS.20,27 It is possible that HIV infection is an incidental finding to primary FSGS in black South Africans, with FSGS being the commonest histology reported in children and adults worldwide.28,29 However, others have suggested that FSGS may be part of the spectrum of histology in response to HIV infection.30 It is also possible that due to the high HIV prevalence in South Africa, susceptible HIV-infected individuals who are ART naïve may develop HIVAN and not FSGS. In addition, we found that APOL1 risk allele status was not associated with HIVICK, a result in concordance with that of a study in African Americans that observed two APOL1 risk alleles in only 1 of 31 patients with HIVICK.31

HIV is a powerful driver of APOL1 nephropathy, as seen by the large proportion of individuals with HIVAN who carry two risk allele genotypes and the strong effect sizes observed. Furthermore, the frequencies were similar for two risk allele genotypes in HIVAN (79% in this study and 72% in Kopp et al.13 study), although the two risk allele genotype frequencies are markedly lower in the South-African (2%–4%) compared with the African-American general population (12%–14%).13 It was previously estimated that 50% of HIV-positive patients with two APOL1 risk alleles who do not receive ART will develop HIVAN in their lifetime, suggesting the magnitude of the interaction.13 Nevertheless, it is worth noting that HIV-positive patients with two risk alleles do not necessarily develop HIVAN and that approximately 20% of patients with HIVAN carry one or no APOL1 risk allele, suggesting that there are more factors to be considered. Clearly, HIV infection interacts strongly with APOL1 variants, although the molecular mechanism is largely unknown, and this interaction is similar in South Africa and the United States.

The APOL1 G1 and G2 alleles show distinct distributions among various African and African-derived populations. With a robust population sample comprising 216 chromosomes (including HIV-positive controls), we were able to establish that the G1 allele (rs73885319) frequency is approximately 7.3%, much lower than reported in West Africa (Yoruba and Igbo from Nigeria), in whom the frequencies are approximately 45% and 30%, respectively, or in African Americans where the G1 frequency is approximately 20%.13,17 This may be as a result of relaxation of selection pressures exerted by trypanosomiasis or other pathogens in regions inhabited by ancestors of this South-African population or may represent introgression of the variant alleles into southern African populations as a result of gene flow from the Bantu expansion.32,33 In this study, G1 and G2 alleles have a combined allele frequency of 18.4%, indicating that in the general black population, 32% of individuals carry one risk allele and 2% carry two risk alleles. The risk of developing HIVAN is substantial for individuals living with HIV infection and possessing two APOL1 risk alleles.13,27 We also detected a rare, recombinant haplotype, G1+M (A-G-I), in the heterozygous state (G1GM/G1+M), in a single individual with HIV-positive CKD, which has not been previously reported in the 1000 Genomes Project or in previous studies of African populations, summarized by Thomson et al.33 and Limou et al.34

The molecular mechanisms by which APOL1 variants cause kidney disease remain unclear. This protein is expressed in podocytes and proximal tubular epithelial cells in normal kidneys and arteriolar endothelial cells and in vascular smooth muscle cells in HIVAN and FSGS biopsies.35 The G1 and G2 variant proteins, respectively, have altered and deleted amino acids in the APOL1-binding region of the trypanosomal serum resistance–associated (SRA) protein.12 By so doing, the trypanosomal SRA is not able to bind APOL1, and hence is exposed to the trypanolytic activity of ApoL1. This suggests that the risk variants in the SRA domain of APOL1 act by a gain of injury or a toxicity mechanism on podocytes or vascular cells.

A study by Nichols et al.36 showed that despite the recessive mode of inheritance observed in APOL1 kidney disease, there is evidence suggesting that APOL1 risk variants act as toxic gain-of-function mutations and that HIV triggers the immune system by activating exogenous IFNs that in turn increase ApoL1 expression in cells, leading to the development of kidney disease.36 Having carried out our study in a high HIV prevalence setting, with predominantly HIV-1 subtype C, puts HIV as an important environmental factor inducing APOL1-mediated kidney disease, supporting a two-hit model for APOL1-associated disease expression.37 This study highlights the need to consider gene–environment interaction in the interpretation of genome-wide association studies for other common diseases.

Our study also highlights the need for HIV screening, surveillance, and implementation of World Health Organization (WHO) recommendations for earlier ART initiation to reduce the burden of HIVAN and other forms of HIV-related kidney disease in Africa. At present, guidelines for the treatment of HIV infection in South Africa suggest that ART be instituted for individuals with WHO clinical stage 3 and 4 disease and HIV-specific manifestations (e.g., HIV-related malignancies, kidney or other organ involvement, and hepatitis B and C infection) and in all HIV-positive individuals with CD4 counts <350 cells/µl.38

There are several limitations to our study. We lacked sufficient numbers of primary or HIV-positive patients with FSGS to detect the effects of the G1 and G2 risk alleles (a sample size of 95 patients with FSGS and 95 controls would be required for 80% power to detect an OR of 5, α 0.05). Our control group comprised healthy population controls who were assumed to have normal kidney function; however, kidney function was not assessed. Although it is theoretically possible that undetected renal disease could reduce power, random controls are commonly used in genetic studies and it is unlikely that healthy individuals in this group had undetected glomerulopathy particularly given the low frequency of individuals carrying two APOL1 renal risk alleles in our control group.

In conclusion, this study shows an extremely strong association between APOL1 variants and biopsy-confirmed HIVAN driven by interaction between APOL1 and untreated HIV infection, the first such study in Southern Africa.

Concise Methods

Study Participants

Archived kidney biopsies obtained from patients aged >18 years were retrieved from the Division of Anatomic Pathology at the University of the Witwatersrand, according to their histologic diagnosis and HIV status (Table 1). Renal histologic diagnoses were made on the basis of standard diagnostic criteria. Histology was confirmed by an independent pathologist (A.B.F.). HIVAN was defined by the presence of glomerular capillary collapse and glomerular visceral epithelial cell proliferation affecting at least one glomerulus, together with microcystic tubular dilation and interstitial inflammation. HIVICK was defined by the presence of glomerular endocapillary cell proliferation together with an increased deposition of at least one Ig, thus including HIV-positive IgA nephropathy. Other histopathologic groups included the following: HIV-positive and HIV-negative FSGS, other GN (which included membranoproliferative GN and membranoproliferative GN consistent with C3 glomerulopathy, membranous GN, HIV-negative IgA nephropathy, and lupus nephritis,) and other kidney disease (which included thrombotic microangiopathy, nodular glomerulosclerosis, minimal change disease, arterionephrosclerosis and benign nephrosclerosis, oxalosis, and global glomerulosclerosis).

Blood samples were collected prospectively from 54 volunteers of black ethnicity and of similar age and sex to the patients with CKD for each of the two control groups: a control group (HIV-positive controls) comprising HIV-positive individuals with no clinical evidence of CKD (normal renal function; no proteinuria) from Charlotte Maxeke Johannesburg Academic Hospital and a population control group from the National Health Laboratory Service who were all apparently healthy individuals who gave consent to be enrolled for population genetic studies as control participants. All HIV-positive individuals with CKD were ART naïve and 75% of the HIV-positive control group was receiving ART. Exclusion criteria included patients aged <18 years, patients with a history of diabetes, and persons who were nonblack South Africans. This study was approved by the University of the Witwatersrand Human Research Ethics Committee (medical; approval numbers M111185 and M10745). All prospective participants (controls) provided signed informed consent.

Genomic DNA Extraction from Formalin-Fixed Paraffin-Embedded Kidney Tissue and Peripheral Blood Samples

The All Prep QIAamp DNA formalin-fixed paraffin-embedded tissue kit (Qiagen, Chatsworth, CA) was used to purify genomic DNA from formalin-fixed paraffin-embedded kidney samples, and a modified in-house salting-out procedure39 was used to extract genomic DNA from peripheral blood samples.

SNP Genotyping

The APOL1 SNPs G1 (rs73885319 and rs60910145) and the G2 indel (rs71785313) were genotyped using the TaqMan SNP genotyping system (Applied Biosystems, Foster City, CA), whereas 42 SNPs (18 ancestry informative markers and 24 other SNPs from chromosome 22 not in linkage disequilibrium with the risk variants) were genotyped using the Illumina BeadXpress SNP system (Illumina Inc., San Diego, CA). Sanger sequencing was used to confirm unusual haplotype configurations. Each SNP was tested for deviation from Hardy–Weinberg equilibrium using a chi-squared goodness-of-fit test in the population control group.

Population Stratification

Population stratification was assessed based on 42 SNPs distributed throughout the genome including chromosome 22 using the PCA module of Eigensoft software.40 For these analyses, chromosome 22 SNPs were limited to r2<0.05 with each other. SNPs defining the APOL1 risk genotypes were excluded from the population stratification analyses.

Terminology

For APOL1 haplotypes, we used the terms G1G+ (carrying the derived risk allele at S342G only), G1GM (containing the derived risk alleles at S342G and I384M), and G1+M (containing only the derived allele at I384M). It has not been determined whether I384M confers risk in the absence of S342G.13 For APOL1 alleles, we use the terms G0 for the ancestral, nonrisk (+/+) allele, G1 for the risk allele of S342G that occurs on two G1 haplotypes (G1G+ and G1GM), and G2 for the deletion allele (Figure 1).

Statistical Analyses

The effect of APOL1 risk genotypes on kidney disease was tested by using the Fisher’s exact test, and by logistic regression adjusting for age, sex, and the first two eigen values obtained from a PCA of genetic ancestry. Informed by previous association results, we primarily tested recessive models (comparing individuals with two risk alleles, i.e., G1/G1, G1/G2, or G2/G2, against all others), but also tested other models (dominant; and one versus zero, two versus zero, two versus one, and two versus one or zero risk alleles). Comparisons were made between HIV-positive patients and HIV-positive controls and between HIV-negative patients and population controls, comparing the distribution of two risk alleles (explanatory exposure) to zero or two risk alleles (no exposure). The Woolf test was used to test for homogeneity of the ORs in South-African and African-American FSGS populations.

Disclosures

None.

Acknowledgments

The authors thank Dr. Nadia Carstens and Angela Hobbs Steyn (University of the Witwatersrand) and Victor David and Elizabeth Binns-Roemer (Frederick National Laboratory) for excellent technical support, as well as Dr. Francois Venter for access to the HIV clinic at Charlotte Maxeke Johannesburg Academic Hospital.

This project was funded by the National Institutes of Health (NIH) Fogarty International Center (Grant 1D43TW008330-01A1 [July 1, 2010– June 30, 2015] Millennium Promise Award), the National Institute of Diabetes and Digestive and Kidney Diseases Intramural Research Programs, the Non-communicable Chronic Diseases Leadership Training Program, the Medical Research Council of South Africa, the National Research Foundation of South Africa, the National Health Laboratory Service Research Trust, the Columbia University–South Africa Training Program for Research on AIDS-Related Malignancies, the NIH National Cancer Institute (Grant 1D43CA153715-03), the Division of Nephrology of University of the Witwatersrand and the Faculty Research Committee individual grant, University of the Witwatersrand. This project was also funded in part with federal funds from the NIH National Cancer Institute (Contract HHSN26120080001E), and was supported in part by the Intramural Research Program of the NIH National Cancer Institute Center for Cancer Research.

The content of this publication does not necessarily reflect the views or policies of the US Department of Health and Human Services, nor does mention of trade names, commercial products, or organizations imply endorsement by the US Government.

Footnotes

References

  1. ↵
    1. Kitiyakara C,
    2. Kopp JB,
    3. Eggers P
    : Trends in the epidemiology of focal segmental glomerulosclerosis. Semin Nephrol 23: 172–182, 2003pmid:12704577
    OpenUrlCrossRefPubMed
  2. ↵
    1. Kopp JB,
    2. Winkler C
    : HIV-associated nephropathy in African Americans. Kidney Int Suppl 83: S43–S49, 2003pmid:12864874
    OpenUrlPubMed
  3. ↵
    1. Mohanram A,
    2. Zhang Z,
    3. Shahinfar S,
    4. Keane WF,
    5. Brenner BM,
    6. Toto RD
    : Anemia and end-stage renal disease in patients with type 2 diabetes and nephropathy. Kidney Int 66: 1131–1138, 2004pmid:15327408
    OpenUrlCrossRefPubMed
  4. ↵
    1. Collins AJ,
    2. Foley RN,
    3. Chavers B,
    4. Gilbertson D,
    5. Herzog C,
    6. Johansen K,
    7. Kasiske B,
    8. Kutner N,
    9. Liu J,
    10. St Peter W,
    11. Guo H,
    12. Gustafson S,
    13. Heubner B,
    14. Lamb K,
    15. Li S,
    16. Li S,
    17. Peng Y,
    18. Qiu Y,
    19. Roberts T,
    20. Skeans M,
    21. Snyder J,
    22. Solid C,
    23. Thompson B,
    24. Wang C,
    25. Weinhandl E,
    26. Zaun D,
    27. Arko C,
    28. Chen SC,
    29. Daniels F,
    30. Ebben J,
    31. Frazier E,
    32. Hanzlik C,
    33. Johnson R,
    34. Sheets D,
    35. Wang X,
    36. Forrest B,
    37. Constantini E,
    38. Everson S,
    39. Eggers P,
    40. Agodoa L
    : United States Renal Data System 2011 Annual Data Report: Atlas of chronic kidney disease and end-stage renal disease in the United States. Am J Kidney Dis 59[Suppl 1]: A7, e1–e420, 2012
    OpenUrl
  5. ↵
    1. Laurinavicius A,
    2. Hurwitz S,
    3. Rennke HG
    : Collapsing glomerulopathy in HIV and non-HIV patients: A clinicopathological and follow-up study. Kidney Int 56: 2203–2213, 1999pmid:10594796
    OpenUrlCrossRefPubMed
  6. ↵
    1. Kalayjian RC
    : The treatment of HIV-associated nephropathy. Adv Chronic Kidney Dis 17: 59–71, 2010pmid:20005490
    OpenUrlCrossRefPubMed
  7. ↵
    1. Hays T,
    2. Wyatt CM
    : APOL1 variants in HIV-associated nephropathy: Just one piece of the puzzle. Kidney Int 82: 259–260, 2012pmid:22791322
    OpenUrlCrossRefPubMed
  8. ↵
    1. Han TM,
    2. Naicker S,
    3. Ramdial PK,
    4. Assounga AG
    : A cross-sectional study of HIV-seropositive patients with varying degrees of proteinuria in South Africa. Kidney Int 69: 2243–2250, 2006pmid:16672914
    OpenUrlCrossRefPubMed
  9. ↵
    1. Wearne N,
    2. Swanepoel CR,
    3. Boulle A,
    4. Duffield MS,
    5. Rayner BL
    : The spectrum of renal histologies seen in HIV with outcomes, prognostic indicators and clinical correlations. Nephrol Dial Transplant 27: 4109–4118, 2012pmid:22200584
    OpenUrlAbstract/FREE Full Text
  10. ↵
    1. Kopp JB,
    2. Smith MW,
    3. Nelson GW,
    4. Johnson RC,
    5. Freedman BI,
    6. Bowden DW,
    7. Oleksyk T,
    8. McKenzie LM,
    9. Kajiyama H,
    10. Ahuja TS,
    11. Berns JS,
    12. Briggs W,
    13. Cho ME,
    14. Dart RA,
    15. Kimmel PL,
    16. Korbet SM,
    17. Michel DM,
    18. Mokrzycki MH,
    19. Schelling JR,
    20. Simon E,
    21. Trachtman H,
    22. Vlahov D,
    23. Winkler CA
    : MYH9 is a major-effect risk gene for focal segmental glomerulosclerosis. Nat Genet 40: 1175–1184, 2008pmid:18794856
    OpenUrlCrossRefPubMed
  11. ↵
    1. Kao WH,
    2. Klag MJ,
    3. Meoni LA,
    4. Reich D,
    5. Berthier-Schaad Y,
    6. Li M,
    7. Coresh J,
    8. Patterson N,
    9. Tandon A,
    10. Powe NR,
    11. Fink NE,
    12. Sadler JH,
    13. Weir MR,
    14. Abboud HE,
    15. Adler SG,
    16. Divers J,
    17. Iyengar SK,
    18. Freedman BI,
    19. Kimmel PL,
    20. Knowler WC,
    21. Kohn OF,
    22. Kramp K,
    23. Leehey DJ,
    24. Nicholas SB,
    25. Pahl MV,
    26. Schelling JR,
    27. Sedor JR,
    28. Thornley-Brown D,
    29. Winkler CA,
    30. Smith MW,
    31. Parekh RS,
    32. Family Investigation of Nephropathy and Diabetes Research Group
    : MYH9 is associated with nondiabetic end-stage renal disease in African Americans. Nat Genet 40: 1185–1192, 2008pmid:18794854
    OpenUrlCrossRefPubMed
  12. ↵
    1. Genovese G,
    2. Friedman DJ,
    3. Ross MD,
    4. Lecordier L,
    5. Uzureau P,
    6. Freedman BI,
    7. Bowden DW,
    8. Langefeld CD,
    9. Oleksyk TK,
    10. Uscinski Knob AL,
    11. Bernhardy AJ,
    12. Hicks PJ,
    13. Nelson GW,
    14. Vanhollebeke B,
    15. Winkler CA,
    16. Kopp JB,
    17. Pays E,
    18. Pollak MR
    : Association of trypanolytic ApoL1 variants with kidney disease in African Americans. Science 329: 841–845, 2010pmid:20647424
    OpenUrlAbstract/FREE Full Text
  13. ↵
    1. Kopp JB,
    2. Nelson GW,
    3. Sampath K,
    4. Johnson RC,
    5. Genovese G,
    6. An P,
    7. Friedman D,
    8. Briggs W,
    9. Dart R,
    10. Korbet S,
    11. Mokrzycki MH,
    12. Kimmel PL,
    13. Limou S,
    14. Ahuja TS,
    15. Berns JS,
    16. Fryc J,
    17. Simon EE,
    18. Smith MC,
    19. Trachtman H,
    20. Michel DM,
    21. Schelling JR,
    22. Vlahov D,
    23. Pollak M,
    24. Winkler CA
    : APOL1 genetic variants in focal segmental glomerulosclerosis and HIV-associated nephropathy. J Am Soc Nephrol 22: 2129–2137, 2011pmid:21997394
    OpenUrlAbstract/FREE Full Text
  14. ↵
    1. Tzur S,
    2. Rosset S,
    3. Shemer R,
    4. Yudkovsky G,
    5. Selig S,
    6. Tarekegn A,
    7. Bekele E,
    8. Bradman N,
    9. Wasser WG,
    10. Behar DM,
    11. Skorecki K
    : Missense mutations in the APOL1 gene are highly associated with end stage kidney disease risk previously attributed to the MYH9 gene. Hum Genet 128: 345–350, 2010pmid:20635188
    OpenUrlCrossRefPubMed
  15. ↵
    1. Parsa A,
    2. Kao WH,
    3. Xie D,
    4. Astor BC,
    5. Li M,
    6. Hsu CY,
    7. Feldman HI,
    8. Parekh RS,
    9. Kusek JW,
    10. Greene TH,
    11. Fink JC,
    12. Anderson AH,
    13. Choi MJ,
    14. Wright JT Jr,
    15. Lash JP,
    16. Freedman BI,
    17. Ojo A,
    18. Winkler CA,
    19. Raj DS,
    20. Kopp JB,
    21. He J,
    22. Jensvold NG,
    23. Tao K,
    24. Lipkowitz MS,
    25. Appel LJ,
    26. AASK Study Investigators,
    27. CRIC Study Investigators
    : APOL1 risk variants, race, and progression of chronic kidney disease. N Engl J Med 369: 2183–2196, 2013pmid:24206458
    OpenUrlCrossRefPubMed
  16. ↵
    1. Ko WY,
    2. Rajan P,
    3. Gomez F,
    4. Scheinfeldt L,
    5. An P,
    6. Winkler CA,
    7. Froment A,
    8. Nyambo TB,
    9. Omar SA,
    10. Wambebe C,
    11. Ranciaro A,
    12. Hirbo JB,
    13. Tishkoff SA
    : Identifying Darwinian selection acting on different human APOL1 variants among diverse African populations. Am J Hum Genet 93: 54–66, 2013pmid:23768513
    OpenUrlCrossRefPubMed
  17. ↵
    1. Ulasi II,
    2. Tzur S,
    3. Wasser WG,
    4. Shemer R,
    5. Kruzel E,
    6. Feigin E,
    7. Ijoma CK,
    8. Onodugo OD,
    9. Okoye JU,
    10. Arodiwe EB,
    11. Ifebunandu NA,
    12. Chukwuka CJ,
    13. Onyedum CC,
    14. Ijoma UN,
    15. Nna E,
    16. Onuigbo M,
    17. Rosset S,
    18. Skorecki K
    : High population frequencies of APOL1 risk variants are associated with increased prevalence of non-diabetic chronic kidney disease in the Igbo people from south-eastern Nigeria. Nephron Clin Pract 123: 123–128, 2013pmid:23860441
    OpenUrlCrossRefPubMed
    1. Tzur S,
    2. Rosset S,
    3. Skorecki K,
    4. Wasser WG
    : APOL1 allelic variants are associated with lower age of dialysis initiation and thereby increased dialysis vintage in African and Hispanic Americans with non-diabetic end-stage kidney disease. Nephrol Dial Transplant 27: 1498–1505, 2012pmid:22357707
    OpenUrlAbstract/FREE Full Text
  19. ↵
    1. Behar DM,
    2. Kedem E,
    3. Rosset S,
    4. Haileselassie Y,
    5. Tzur S,
    6. Kra-Oz Z,
    7. Wasser WG,
    8. Shenhar Y,
    9. Shahar E,
    10. Hassoun G,
    11. Maor C,
    12. Wolday D,
    13. Pollack S,
    14. Skorecki K
    : Absence of APOL1 risk variants protects against HIV-associated nephropathy in the Ethiopian population. Am J Nephrol 34: 452–459, 2011pmid:21968148
    OpenUrlCrossRefPubMed
  20. ↵
    1. Fine DM,
    2. Wasser WG,
    3. Estrella MM,
    4. Atta MG,
    5. Kuperman M,
    6. Shemer R,
    7. Rajasekaran A,
    8. Tzur S,
    9. Racusen LC,
    10. Skorecki K
    : APOL1 risk variants predict histopathology and progression to ESRD in HIV-related kidney disease. J Am Soc Nephrol 23: 343–350, 2012pmid:22135313
    OpenUrlAbstract/FREE Full Text
  21. ↵
    World Health Organization, Joint United Nations Programme on HIV/AIDS, United Nations Children’s Fund: Global HIV/AIDS Response: Epidemic Update and Health Sector Progress Towards Universal Access, Geneva, Switzerland, World Health Organization, 2011
  22. ↵
    1. Hindorff LA,
    2. Sethupathy P,
    3. Junkins HA,
    4. Ramos EM,
    5. Mehta JP,
    6. Collins FS,
    7. Manolio TA
    : Potential etiologic and functional implications of genome-wide association loci for human diseases and traits. Proc Natl Acad Sci U S A 106: 9362–9367, 2009pmid:19474294
    OpenUrlAbstract/FREE Full Text
  23. ↵
    1. Hemelaar J,
    2. Gouws E,
    3. Ghys PD,
    4. Osmanov S
    : Global and regional distribution of HIV-1 genetic subtypes and recombinants in 2004. AIDS 20: W13–W23, 2006pmid:17053344
    OpenUrlCrossRefPubMed
  24. ↵
    1. Novitsky V,
    2. Ndung’u T,
    3. Wang R,
    4. Bussmann H,
    5. Chonco F,
    6. Makhema J,
    7. De Gruttola V,
    8. Walker BD,
    9. Essex M
    : Extended high viremics: A substantial fraction of individuals maintain high plasma viral RNA levels after acute HIV-1 subtype C infection. AIDS 25: 1515–1522, 2011pmid:21505307
    OpenUrlCrossRefPubMed
  25. ↵
    1. Izzedine H,
    2. Wirden M,
    3. Launay-Vacher V
    : Viral load and HIV-associated nephropathy. N Engl J Med 353: 1072–1074, 2005pmid:16148301
    OpenUrlCrossRefPubMed
  26. ↵
    1. Kanji Z,
    2. Powe CE,
    3. Wenger JB,
    4. Huang C,
    5. Ankers E,
    6. Sullivan DA,
    7. Collerone G,
    8. Powe NR,
    9. Tonelli M,
    10. Bhan I,
    11. Bernhardy AJ,
    12. Dibartolo S,
    13. Friedman D,
    14. Genovese G,
    15. Pollak MR,
    16. Thadhani R
    : Genetic variation in APOL1 associates with younger age at hemodialysis initiation. J Am Soc Nephrol 22: 2091–2097, 2011pmid:21997398
    OpenUrlAbstract/FREE Full Text
  27. ↵
    1. Papeta N,
    2. Kiryluk K,
    3. Patel A,
    4. Sterken R,
    5. Kacak N,
    6. Snyder HJ,
    7. Imus PH,
    8. Mhatre AN,
    9. Lawani AK,
    10. Julian BA,
    11. Wyatt RJ,
    12. Novak J,
    13. Wyatt CM,
    14. Ross MJ,
    15. Winston JA,
    16. Klotman ME,
    17. Cohen DJ,
    18. Appel GB,
    19. D’Agati VD,
    20. Klotman PE,
    21. Gharavi AG
    : APOL1 variants increase risk for FSGS and HIVAN but not IgA nephropathy. J Am Soc Nephrol 22: 1991–1996, 2011pmid:21997397
    OpenUrlAbstract/FREE Full Text
  28. ↵
    1. Adhikari M,
    2. Bhimma R,
    3. Coovadia HM
    : Focal segmental glomerulosclerosis in children from KwaZulu/Natal, South Africa. Clin Nephrol 55: 16–24, 2001pmid:11200863
    OpenUrlPubMed
  29. ↵
    1. Chou YH,
    2. Lien YC,
    3. Hu FC,
    4. Lin WC,
    5. Kao CC,
    6. Lai CF,
    7. Chiang WC,
    8. Lin SL,
    9. Tsai TJ,
    10. Wu KD,
    11. Chen YM
    : Clinical outcomes and predictors for ESRD and mortality in primary GN. Clin J Am Soc Nephrol 7: 1401–1408, 2012pmid:22798538
    OpenUrlAbstract/FREE Full Text
  30. ↵
    1. Meehan SM,
    2. Kim L,
    3. Chang A
    : A spectrum of morphologic lesions of focal segmental glomerulosclerosis by Columbia criteria in human immunodeficiency virus infection. Virchows Arch 460: 429–435, 2012
    OpenUrlCrossRefPubMed
  31. ↵
    1. Foy MC,
    2. Estrella MM,
    3. Lucas GM,
    4. Tahir F,
    5. Fine DM,
    6. Moore RD,
    7. Atta MG
    : Comparison of risk factors and outcomes in HIV immune complex kidney disease and HIV-associated nephropathy. Clin J Am Soc Nephrol 8: 1524–1532, 2013pmid:23685946
    OpenUrlAbstract/FREE Full Text
  32. ↵
    1. de Filippo C,
    2. Barbieri C,
    3. Whitten M,
    4. Mpoloka SW,
    5. Gunnarsdóttir ED,
    6. Bostoen K,
    7. Nyambe T,
    8. Beyer K,
    9. Schreiber H,
    10. de Knijff P,
    11. Luiselli D,
    12. Stoneking M,
    13. Pakendorf B
    : Y-chromosomal variation in sub-Saharan Africa: Insights into the history of Niger-Congo groups. Mol Biol Evol 28: 1255–1269, 2011pmid:21109585
    OpenUrlCrossRefPubMed
  33. ↵
    1. Thomson R,
    2. Genovese G,
    3. Canon C,
    4. Kovacsics D,
    5. Higgins MK,
    6. Carrington M,
    7. Winkler CA,
    8. Kopp J,
    9. Rotimi C,
    10. Adeyemo A,
    11. Doumatey A,
    12. Ayodo G,
    13. Alper SL,
    14. Pollak MR,
    15. Friedman DJ,
    16. Raper J
    : Evolution of the primate trypanolytic factor APOL1. Proc Natl Acad Sci U S A 111: E2130–E2139, 2014pmid:24808134
    OpenUrlAbstract/FREE Full Text
  34. ↵
    1. Limou S,
    2. Nelson GW,
    3. Kopp JB,
    4. Winkler CA
    : APOL1 kidney risk alleles: Population genetics and disease associations. Adv Chronic Kidney Dis 21: 426–433, 2014pmid:25168832
    OpenUrlCrossRefPubMed
  35. ↵
    1. Madhavan SM,
    2. O’Toole JF,
    3. Konieczkowski M,
    4. Ganesan S,
    5. Bruggeman LA,
    6. Sedor JR
    : APOL1 localization in normal kidney and nondiabetic kidney disease. J Am Soc Nephrol 22: 2119–2128, 2011pmid:21997392
    OpenUrlAbstract/FREE Full Text
  36. ↵
    1. Nichols B,
    2. Jog P,
    3. Lee JH,
    4. Blackler D,
    5. Wilmot M,
    6. D’Agati V,
    7. Markowitz G,
    8. Kopp JB,
    9. Alper SL,
    10. Pollak MR,
    11. Friedman DJ
    : Innate immunity pathways regulate the nephropathy gene Apolipoprotein L1 [published online ahead of print August 6, 2014]. Kidney Int doi:10.1038/ki.2014.270pmid:25100047
    OpenUrlCrossRefPubMed
  37. ↵
    1. Freedman BI,
    2. Skorecki K
    : Gene-gene and gene-environment interactions in apolipoprotein L1 gene-associated nephropathy. Clin J Am Soc Nephrol 9: 2006–2013, 2014pmid:24903390
    OpenUrlAbstract/FREE Full Text
  38. ↵
    1. Meintjes G,
    2. Maartens G,
    3. Southern African HIV Clinicians Society
    : Guidelines for antiretroviral therapy in adults. S Afr J HIV Med 13: 114–133, 2012
    OpenUrl
  39. ↵
    1. Nasiri H,
    2. Forouzandeh M,
    3. Rasaee MJ,
    4. Rahbarizadeh F
    : Modified salting-out method: High-yield, high-quality genomic DNA extraction from whole blood using laundry detergent. J Clin Lab Anal 19: 229–232, 2005pmid:16302208
    OpenUrlCrossRefPubMed
  40. ↵
    1. Price AL,
    2. Patterson NJ,
    3. Plenge RM,
    4. Weinblatt ME,
    5. Shadick NA,
    6. Reich D
    : Principal components analysis corrects for stratification in genome-wide association studies. Nat Genet 38: 904–909, 2006pmid:16862161
    OpenUrlCrossRefPubMed
View Abstract
Back to top

In this issue

View Selected Citations (0)
Print
Download PDF
Article Alerts
Email Article
Citation Tools
Request Permissions
APOL1 Risk Variants Are Strongly Associated with HIV-Associated Nephropathy in Black South Africans
Alex N. Kasembeli, Raquel Duarte, Michèle Ramsay, Pulane Mosiane, Caroline Dickens, Thérèse Dix-Peek, Sophie Limou, Efe Sezgin, George W. Nelson, Agnes B. Fogo, Stewart Goetsch, Jeffrey B. Kopp, Cheryl A. Winkler, Saraladevi Naicker
JASN Nov 2015, 26 (11) 2882-2890; DOI: 10.1681/ASN.2014050469
del.icio.us logo Digg logo Reddit logo Twitter logo CiteULike logo Facebook logo Google logo Mendeley logo

Jump to section

More in this TOC Section

Cited By...

Similar Articles

Related Articles

Keywords