1
|
Owiredu WKBA, Appiah M, Obirikorang C, Adu EA, Boima V, Amos-Abanyie EK, Akyaw PA, Owiredu EW, Acheampong E. Association of MYH9-rs3752462 polymorphisms with chronic kidney disease among clinically diagnosed hypertensive patients: a case-control study in a Ghanaian population. Clin Hypertens 2020; 26:15. [PMID: 32765897 PMCID: PMC7395421 DOI: 10.1186/s40885-020-00148-w] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2020] [Accepted: 06/03/2020] [Indexed: 12/19/2022] Open
Abstract
Background Chronic kidney disease (CKD) is a significant comorbidity among hypertensive patients. Polymorphisms in the non-muscle myosin heavy chain 9 gene (MYH9) have been demonstrated to be significantly associated with CKD, among African- and European-derived populations. We investigated the spectrum of MYH9-associated CKD among Ghanaian hypertensive patients. Methods The study constituted a total of 264 hypertensive patients. Hypertensive patients with glomerular filtration rate (eGFR) < 60 ml/min/1.73m2 (CKD-EPI formula) or clinically diagnosed were defined as case subjects (n = 132) while those with eGFR ≥60 ml/min/1.73m2 were classified as control subjects (n = 132). Demographic data were obtained with a questionnaire and anthropometric measurements were taken. Five (5) millilitres (ml) of venous blood was drawn from study subjects into gel and EDTA vacutainer tubes. Two (2) mL of EDTA anticoagulated blood was used for genomic DNA extraction while three (3) mL of blood was processed to obtain serum for biochemical measurements. Genotyping of MYH9 polymorphisms (rs3752462) was done employing Tetra primer Amplification Refractory Mutation System (T-ARMS) polymerase chain reaction (PCR). Spot urine samples were also collected for urinalysis. Hardy-Weinberg population was assessed. Logistic regression models were used to assess the associations between single nucleotide polymorphisms and CKD. Results The cases and control participants differed in terms of age, sex, family history, and duration of CKD (p-value < 0.001). The minor allele frequencies of rs3752462 SNP were 0.820 and 0.567 respectively among the control and case subjects. Patients with the heterozygote genotype of rs3752462 (CT) were more likely to develop CKD [aOR = 7.82 (3.81–16.04)] whereas those with homozygote recessive variant (TT) were protective [aOR = 0.12 (0.06–0.25)]. Single nucleotide polymorphism of rs3752462 (CT genotype) was associated with increased proteinuria, albuminuria, and reduced eGFR. Conclusions We have demonstrated that MYH9 polymorphisms exist among Ghanaian hypertensive patients and rs3752462 polymorphism of MYH9 is associated with CKD. This baseline indicates that further longitudinal and multi-institutional studies in larger cohorts in Ghana are warranted to evaluate MYH9 SNP as an independent predictor of CKD among hypertensive patients in Ghana.
Collapse
Affiliation(s)
- William K B A Owiredu
- Department of Molecular Medicine, School of Medicine and Dentistry, Kwame Nkrumah University of Science and Technology, Kumasi, Ghana
| | - Michael Appiah
- Department of Molecular Medicine, School of Medicine and Dentistry, Kwame Nkrumah University of Science and Technology, Kumasi, Ghana
| | - Christian Obirikorang
- Department of Molecular Medicine, School of Medicine and Dentistry, Kwame Nkrumah University of Science and Technology, Kumasi, Ghana
| | - Evans Asamoah Adu
- Department of Molecular Medicine, School of Medicine and Dentistry, Kwame Nkrumah University of Science and Technology, Kumasi, Ghana
| | - Vincent Boima
- Department of Medicine and Therapeutics, School of Medicine and Dentistry, College of Health Sciences, University of Ghana, Accra, Ghana
| | - Ernestine Kubi Amos-Abanyie
- H3Africa Kidney Disease Research Project, Noguchi Memorial Institute for Medical Research, University of Ghana, Accra, Ghana
| | - Priscilla Abena Akyaw
- H3Africa Kidney Disease Research Project, Noguchi Memorial Institute for Medical Research, University of Ghana, Accra, Ghana
| | - Eddie-Williams Owiredu
- Department of Molecular Medicine, School of Medicine and Dentistry, Kwame Nkrumah University of Science and Technology, Kumasi, Ghana
| | - Emmanuel Acheampong
- Department of Molecular Medicine, School of Medicine and Dentistry, Kwame Nkrumah University of Science and Technology, Kumasi, Ghana.,School of Medical and Health Science, Edith Cowan University, Joondalup, Australia
| |
Collapse
|
2
|
Adam KM, Mohammed AM, Elamin AA. Non-diabetic end-stage renal disease in Saudis associated with polymorphism of MYH9 gene but not UMOD gene. Medicine (Baltimore) 2020; 99:e18722. [PMID: 32011449 PMCID: PMC7220318 DOI: 10.1097/md.0000000000018722] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
The prevalence of risk factors of chronic kidney disease in Saudi Arabia has augmented an already serious public health problem, therefore, determination of genetic variants associated with the risk of the disease presents potential screening tools that help reducing the incidence rates and promote effective disease management.The aim of the present study is to determine the association of UMOD and MYH9 genetic variants with the risk of non-diabetic end-stage renal disease (ESRD) in the Saudi population.Two single nucleotide polymorphisms (SNP), rs12917707 in gene UMOD and rs4821480 in gene MYH9 were genotyped in 154 non-diabetic ESRD Saudi patients and 123 age-matched healthy controls using Primers and Polymerase chain reaction conditions (PCR), Sanger sequencing, and TaqMan Pre-designed SNP Genotyping Assay. The association of these genetic variants with the risk of the disease and other renal function determinants was assessed using statistical tools such as logistic regression and One-way Analysis of Variance tests.The genotypic frequency of the two SNPs showed no deviation from Hardy-Weinberg equilibrium, the minor allele frequency of UMOD SNP was 0.13 and MYH9 SNP was 0.08. rs4821480 in MYH9 was significantly associated with the risk of non-diabetic ESRD (OR = 3.86; 95%CI: 1.38-10.82, P value .010), while, rs12917707 showed lack of significant association with the disease, P value .380. and neither of the 2 SNPs showed any association with the renal function determinants, serum albumin, and alkaline phosphatase enzyme.
Collapse
|
3
|
Freedman BI, Limou S, Ma L, Kopp JB. APOL1-Associated Nephropathy: A Key Contributor to Racial Disparities in CKD. Am J Kidney Dis 2019; 72:S8-S16. [PMID: 30343724 DOI: 10.1053/j.ajkd.2018.06.020] [Citation(s) in RCA: 94] [Impact Index Per Article: 18.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2017] [Accepted: 06/25/2018] [Indexed: 01/09/2023]
Abstract
Genetic methodologies are improving our understanding of the pathophysiology in diverse diseases. Breakthroughs have been particularly impressive in nephrology, for which marked disparities exist in rates and etiologic classifications of end-stage kidney disease between African Americans and European Americans. Discovery of the apolipoprotein L1 gene (APOL1) association with focal segmental glomerulosclerosis, human immunodeficiency virus (HIV)-associated nephropathy, lupus nephritis, sickle cell nephropathy, and solidified glomerulosclerosis, as well as more rapid failure of transplanted kidneys from donors with APOL1 renal-risk genotypes, has improved our understanding of nondiabetic nephropathy. Environmental factors acting through natural selection in sub-Saharan African populations likely underlie this association. This article describes the discovery of chromosome 22q renal-risk variants and their worldwide distribution, reviews the epidemiology and pathology of APOL1-associated nephropathies, and explores several proposed mechanisms of kidney injury identified in cell culture and animal models. Detection of APOL1 associations with kidney diseases and delineation of injury pathways brings hope for effective treatment for these kidney diseases.
Collapse
Affiliation(s)
- Barry I Freedman
- Section on Nephrology, Department of Internal Medicine; Wake Forest School of Medicine, Winston-Salem, NC.
| | - Sophie Limou
- Centre de Recherche en Transplantation et Immunologie (CRTI) UMR1064, INSERM, Université de Nantes, Nantes, France; Institut de Transplantation Urologie et Néphrologie (ITUN), CHU Nantes, Nantes, France; Ecole Centrale de Nantes, Nantes, France
| | - Lijun Ma
- Section on Nephrology, Department of Internal Medicine; Wake Forest School of Medicine, Winston-Salem, NC
| | - Jeffrey B Kopp
- Kidney Disease Section, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD.
| |
Collapse
|
4
|
Mehta RS, Feder AF, Boca SM, Rosenberg NA. The Relationship Between Haplotype-Based FST and Haplotype Length. Genetics 2019; 213:281-295. [PMID: 31285255 PMCID: PMC6727796 DOI: 10.1534/genetics.119.302430] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2019] [Accepted: 06/29/2019] [Indexed: 11/18/2022] Open
Abstract
The population-genetic statistic [Formula: see text] is used widely to describe allele frequency distributions in subdivided populations. The increasing availability of DNA sequence data has recently enabled computations of [Formula: see text] from sequence-based "haplotype loci." At the same time, theoretical work has revealed that [Formula: see text] has a strong dependence on the underlying genetic diversity of a locus from which it is computed, with high diversity constraining values of [Formula: see text] to be low. In the case of haplotype loci, for which two haplotypes that are distinct over a specified length along a chromosome are treated as distinct alleles, genetic diversity is influenced by haplotype length: longer haplotype loci have the potential for greater genetic diversity. Here, we study the dependence of [Formula: see text] on haplotype length. Using a model in which a haplotype locus is sequentially incremented by one biallelic locus at a time, we show that increasing the length of the haplotype locus can either increase or decrease the value of [Formula: see text], and usually decreases it. We compute [Formula: see text] on haplotype loci in human populations, finding a close correspondence between the observed values and our theoretical predictions. We conclude that effects of haplotype length are valuable to consider when interpreting [Formula: see text] calculated on haplotypic data.
Collapse
Affiliation(s)
- Rohan S Mehta
- Department of Biology, Stanford University, Stanford, California 94305
| | - Alison F Feder
- Department of Biology, Stanford University, Stanford, California 94305
- Department of Integrative Biology, University of California, Berkeley, California 94720
| | - Simina M Boca
- Innovation Center for Biomedical Informatics, Georgetown University, Washington, DC 20007
| | - Noah A Rosenberg
- Department of Biology, Stanford University, Stanford, California 94305
| |
Collapse
|
5
|
Cyrus C, Chathoth S, Vatte C, Alrubaish N, Almuhanna O, Borgio JF, Al-Mueilo S, Al Muhanna F, Al Ali AK. Novel Haplotype Indicator for End-Stage Renal Disease Progression among Saudi Patients. Int J Nephrol 2019; 2019:1095215. [PMID: 31534799 PMCID: PMC6724424 DOI: 10.1155/2019/1095215] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2019] [Revised: 07/16/2019] [Accepted: 07/17/2019] [Indexed: 12/21/2022] Open
Abstract
BACKGROUND End-stage renal disease (ESRD) is the result of hypertensive nephrosclerosis and chronic glomerular diseases and is associated with high morbidity and mortality. There are strong heritable components in the manifestation of the disease with a genetic predisposition to renal disorders, including focal segmental glomerulosclerosis and arterionephrosclerosis. Recent studies in genetics have examined modifiable risk factors that contribute to renal disease, and this has provided a deep insight into progressive kidney disease. Single-nucleotide polymorphisms at the proximity of SHROOM3, CST3, SLC7A9, and MYH9 genes have been associated with an increased risk of developing CKD and ESRD. METHODS A total of 160 CKD patients and 189 control subjects of Saudi origin participated in the study. Eight polymorphisms (SHROOM3-rs9992101, rs17319721; SLC7A9-rs4805834; MYH9-rs4821480, rs4821481, rs2032487, rs3752462; CST3-rs13038305) were genotyped using TaqMan assay, and the haplotype analysis was done using the HaploView 4.2 software. RESULTS Haplotype analysis revealed a novel haplotype "E6"-GTTT to be associated significantly with an increased risk for ESRD (p=0.0001) and CKD (p=0.03). CONCLUSION CKD is often silent until symptomatic uremia during the advanced stages of the disease. The newly identified haplotype will help recognize patients at risk for a rapid progression of CKD to ESRD. Accurate detection and mapping of the genetic variants facilitates improved risk stratification and development of improved and targeted therapeutic management for CKD.
Collapse
Affiliation(s)
- Cyril Cyrus
- Department of Biochemistry, College of Medicine, Imam Abdulrahman Bin Faisal University, Dammam, Saudi Arabia
| | - Shahanas Chathoth
- Department of Biochemistry, College of Medicine, Imam Abdulrahman Bin Faisal University, Dammam, Saudi Arabia
| | - Chittibabu Vatte
- Department of Biochemistry, College of Medicine, Imam Abdulrahman Bin Faisal University, Dammam, Saudi Arabia
| | - Nafie Alrubaish
- Department of Internal Medicine, King Fahd Hospital of the University, Imam Abdulrahman Bin Faisal University, Al-Khobar, Saudi Arabia
| | - Othman Almuhanna
- Department of Internal Medicine, King Fahd Hospital of the University, Imam Abdulrahman Bin Faisal University, Al-Khobar, Saudi Arabia
| | - J. Francis Borgio
- Institute for Research and Medical Consultation, Imam Abdulrahman Bin Faisal University, Dammam, Saudi Arabia
| | - Samir Al-Mueilo
- Department of Internal Medicine, King Fahd Hospital of the University, Imam Abdulrahman Bin Faisal University, Al-Khobar, Saudi Arabia
| | - Fahd Al Muhanna
- Department of Internal Medicine, King Fahd Hospital of the University, Imam Abdulrahman Bin Faisal University, Al-Khobar, Saudi Arabia
| | - Amein K. Al Ali
- Department of Biochemistry, College of Medicine, Imam Abdulrahman Bin Faisal University, Dammam, Saudi Arabia
| |
Collapse
|
6
|
Shah S, Shapiro R, Murphy B, Menon MC. APOL1 high-risk genotypes and renal transplantation. Clin Transplant 2019; 33:e13582. [PMID: 31050035 DOI: 10.1111/ctr.13582] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2018] [Revised: 04/02/2019] [Accepted: 04/25/2019] [Indexed: 01/11/2023]
Abstract
The discovery of apolipoprotein L1 (APOL1) gene variants and its association with kidney disease in African-Americans represent a significant breakthrough in understanding the genetic basis of ancestry-based differences in a public health problem. The role these variants play in renal transplantation is still incompletely understood. This article reviews the epidemiologic data and current reports of APOL1 variant pathogenesis in transplantation. We examine existing data on outcomes in APOL1 high-risk kidneys, high-risk APOL1 recipients, live donors with high-risk mutations and non-renal transplantation of high-risk APOL1 organs. We discuss the rapidly evolving role and potential pros and cons of APOL1 genotyping of donors and recipients in transplantation. Finally, we highlight the ongoing nationwide National Institutes of Health-sponsored "APOL1 Long-term Kidney Transplantation Outcomes (APOLLO)" study, which will quantify outcomes and "second hits" in pertinent to APOL1 high-risk variants in renal transplantation.
Collapse
Affiliation(s)
- Sapna Shah
- Nephrology, Medicine and Recanati-Miller Transplant Institute at Mount Sinai, New York, New York
| | - Ron Shapiro
- Nephrology, Medicine and Recanati-Miller Transplant Institute at Mount Sinai, New York, New York
| | - Barbara Murphy
- Nephrology, Medicine and Recanati-Miller Transplant Institute at Mount Sinai, New York, New York
| | - Madhav C Menon
- Nephrology, Medicine and Recanati-Miller Transplant Institute at Mount Sinai, New York, New York
| |
Collapse
|
7
|
Boronat M, Tugores A, Saavedra P, Garay P, Bosch E, Lorenzo D, García-Cantón C. Association between polymorphism rs2032487 in the non-muscle myosin heavy chain IIA gene (MHY9) and chronic kidney disease secondary to type 2 diabetes mellitus in a population of the Canary Islands. ACTA ACUST UNITED AC 2019; 66:639-646. [PMID: 30954444 DOI: 10.1016/j.endinu.2019.01.006] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2018] [Revised: 12/03/2018] [Accepted: 01/17/2019] [Indexed: 01/22/2023]
Abstract
INTRODUCTION Certain polymorphisms in the non-muscle myosin IIA (MYH9) and apolipoprotein L1 (APOL1) genes have been associated to chronic kidney disease (CKD) in different populations. This study examined the association between the MHY9 rs2032487 and APOL1 rs73885319 polymorphisms and advanced CKD related to type 2 diabetes mellitus (T2DM) in a population of Gran Canaria (Canary Islands, Spain). PATIENTS AND METHODS Polymorphisms were genotyped in 152 patients with advanced CKD (estimated glomerular filtration rate [eGFR]<30mL/min/1.73 m2) secondary to T2DM, 110 patients with T2DM onset ≥ 20 years before without advanced CKD (eGFR ≥ 45mL/min/1.73 m2 and no proteinuria), and 292 healthy blood donors over 50 years of age without CKD or diabetes. RESULTS The frequency of the risk allele for rs2032487 was 10.7% in patients with diabetes and advanced CKD, 7.1% in those with diabetes but without advanced CKD, and 6.1% in healthy subjects, with significant differences between the first and third groups (P=.015). Among subjects with advanced CKD, 78.5% were homozygous for the protective allele, as compared to 87.9% in the other two groups (P=.015 and P=.016 respectively). The frequency of the risk allele for the rs73885319 polymorphism did not exceed 0.5% in any of the three groups. CONCLUSIONS These data suggest that polymorphism rs2032487 is associated to advanced CKD related to T2DM in the population of Gran Canaria.
Collapse
Affiliation(s)
- Mauro Boronat
- Sección de Endocrinología y Nutrición, Hospital Universitario Insular, Las Palmas de Gran Canaria, España; Instituto de Investigaciones Biomédicas y Sanitarias, Universidad de Las Palmas de Gran Canaria, Las Palmas de Gran Canaria, España.
| | - Antonio Tugores
- Unidad de Investigación, Complejo Hospitalario Universitario Insular Materno-Infantil, Las Palmas de Gran Canaria, España
| | - Pedro Saavedra
- Departamento de Matemáticas, Universidad de Las Palmas de Gran Canaria, Las Palmas de Gran Canaria, España
| | - Paloma Garay
- Unidad de Investigación, Complejo Hospitalario Universitario Insular Materno-Infantil, Las Palmas de Gran Canaria, España
| | - Elvira Bosch
- Servicio de Nefrología, Hospital Universitario Insular, Las Palmas de Gran Canaria, España
| | - Dionisio Lorenzo
- Universidad Fernando Pessoa Canarias, Santa María de Guía, Las Palmas, España
| | - César García-Cantón
- Servicio de Nefrología, Hospital Universitario Insular, Las Palmas de Gran Canaria, España
| |
Collapse
|
8
|
Non-Muscle Myosin Heavy Chain 9 Gene (MYH9) Polymorphism (rs4821481) is Associated with Urinary Albumin Excretion in Iranian Diabetic Patients. IRANIAN RED CRESCENT MEDICAL JOURNAL 2016. [DOI: 10.5812/ircmj.40076] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
|
9
|
Kasembeli AN, Duarte R, Ramsay M, Naicker S. African origins and chronic kidney disease susceptibility in the human immunodeficiency virus era. World J Nephrol 2015; 4:295-306. [PMID: 25949944 PMCID: PMC4419140 DOI: 10.5527/wjn.v4.i2.295] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/09/2014] [Revised: 01/06/2015] [Accepted: 01/18/2015] [Indexed: 02/06/2023] Open
Abstract
Chronic kidney disease (CKD) is a major public health problem worldwide with the estimated incidence growing by approximately 6% annually. There are striking ethnic differences in the prevalence of CKD such that, in the United States, African Americans have the highest prevalence of CKD, four times the incidence of end stage renal disease when compared to Americans of European ancestry suggestive of genetic predisposition. Diabetes mellitus, hypertension and human immunodeficiency virus (HIV) infection are the major causes of CKD. HIV-associated nephropathy (HIVAN) is an irreversible form of CKD with considerable morbidity and mortality and is present predominantly in people of African ancestry. The APOL1 G1 and G2 alleles were more strongly associated with the risk for CKD than the previously examined MYH9 E1 risk haplotype in individuals of African ancestry. A strong association was reported in HIVAN, suggesting that 50% of African Americans with two APOL1 risk alleles, if untreated, would develop HIVAN. However these two variants are not enough to cause disease. The prevailing belief is that modifying factors or second hits (including genetic hits) underlie the pathogenesis of kidney disease. This work reviews the history of genetic susceptibility of CKD and outlines current theories regarding the role for APOL1 in CKD in the HIV era.
Collapse
|
10
|
Abstract
With the recent massive scale-up of access to antiretroviral therapy (ART) in resource-limited countries, HIV has become a chronic disease with new challenges. There is mounting evidence of an increased burden of renal and genitourinary diseases among HIV-infected persons caused by direct HIV viral effects and/or indirectly through the development of opportunistic infections, ART medication-related toxicities, and other noncommunicable diseases (NCDs). We review the epidemiology of HIV-associated renal and urogenital diseases, including interactions with kidney-related NCDs such as hypertension, diabetes mellitus, and cardiovascular disease. We also examine the current evidence regarding the impact of HIV infection on the development of urogenital diseases. Highly advisable in sub-Saharan Africa are the establishment of renal disease registries, reviews of existing clinical practice including cost-effectiveness studies, and the adoption and use of HIV-related NCD management, with training for different cadres of health providers. Epidemiological research priorities include prospective studies to evaluate the true prevalence and spectrum of HIV-related renal disease and their progression. Simple diagnostics tools should be evaluated, including urinary dipsticks and point-of-care urea and creatinine tests to screen for kidney injury in primary care settings. Study of urological manifestations of HIV can help determine the extent of disease and outcomes. As patients live longer on ART, the burden of renal and genitourological complications of HIV and of ART can be expected to increase with a commensurate urgency in both discovery and evidence-based improvements in clinical management.
Collapse
|
11
|
Limou S, Nelson GW, Kopp JB, Winkler CA. APOL1 kidney risk alleles: population genetics and disease associations. Adv Chronic Kidney Dis 2014; 21:426-33. [PMID: 25168832 DOI: 10.1053/j.ackd.2014.06.005] [Citation(s) in RCA: 135] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2014] [Revised: 06/09/2014] [Accepted: 06/09/2014] [Indexed: 01/13/2023]
Abstract
APOL1 kidney disease is a unique case in the field of the genetics of common disease: 2 variants (termed G1 and G2) with high population frequency have been repeatedly associated with nondiabetic CKDs, with very strong effect size (odds ratios 3-29) in populations of sub-Saharan African descent. This review provides an update on the spectrum of APOL1 kidney disease and on the worldwide distribution of these kidney risk variants. We also summarize the proper way to run a recessive analysis on joint and independent effects of APOL1 G1 and G2 kidney risk variants.
Collapse
|
12
|
Gomez F, Hirbo J, Tishkoff SA. Genetic variation and adaptation in Africa: implications for human evolution and disease. Cold Spring Harb Perspect Biol 2014; 6:a008524. [PMID: 24984772 DOI: 10.1101/cshperspect.a008524] [Citation(s) in RCA: 83] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Because modern humans originated in Africa and have adapted to diverse environments, African populations have high levels of genetic and phenotypic diversity. Thus, genomic studies of diverse African ethnic groups are essential for understanding human evolutionary history and how this leads to differential disease risk in all humans. Comparative studies of genetic diversity within and between African ethnic groups creates an opportunity to reconstruct some of the earliest events in human population history and are useful for identifying patterns of genetic variation that have been influenced by recent natural selection. Here we describe what is currently known about genetic variation and evolutionary history of diverse African ethnic groups. We also describe examples of recent natural selection in African genomes and how these data are informative for understanding the frequency of many genetic traits, including those that cause disease susceptibility in African populations and populations of recent African descent.
Collapse
Affiliation(s)
- Felicia Gomez
- Department of Genetics and Biology, School of Medicine and School of Arts and Sciences, University of Pennsylvania, Philadelphia, Pennsylvania 19104 Hominid Paleobiology Doctoral Program and The Center for the Advanced Study of Hominid Paleobiology, Department of Anthropology, The George Washington University, Washington, D.C. 20052
| | - Jibril Hirbo
- Department of Genetics and Biology, School of Medicine and School of Arts and Sciences, University of Pennsylvania, Philadelphia, Pennsylvania 19104
| | - Sarah A Tishkoff
- Department of Genetics and Biology, School of Medicine and School of Arts and Sciences, University of Pennsylvania, Philadelphia, Pennsylvania 19104
| |
Collapse
|
13
|
Abstract
Type 2 diabetes remains an important cause of morbidity and mortality. The metabolic syndrome affects 25% of the adult US population based on the Third Report of the Expert Panel on Detection, Evaluation and Treatment of High Blood Cholesterol in Adults from the National Cholesterol Education Program. Knowledge on the impact of obesity on metabolic health parameters has increased greatly over the past decade. This review discusses the limitations of the National Cholesterol Education Program metabolic syndrome definition and the racial disparities in the clinical presentation of the insulin resistance syndrome. We also examine the current literature with particular emphasis on albuminuria, nonalcoholic fatty liver disease, and intramyocellular lipid content. This review explores potential environmental and genetic reasons for differences in the manifestation of insulin resistance across racial/ethnic groups and highlights several promising areas for further study.
Collapse
Affiliation(s)
- Holly Kramer
- Departments of Public Health Sciences and Medicine, Division of Nephrology and Hypertension, Loyola University Chicago Health Sciences Campus, Maywood, IL.
| | | | | |
Collapse
|
14
|
Ding WY, Koziell A, McCarthy HJ, Bierzynska A, Bhagavatula MK, Dudley JA, Inward CD, Coward RJ, Tizard J, Reid C, Antignac C, Boyer O, Saleem MA. Initial steroid sensitivity in children with steroid-resistant nephrotic syndrome predicts post-transplant recurrence. J Am Soc Nephrol 2014; 25:1342-8. [PMID: 24511128 DOI: 10.1681/asn.2013080852] [Citation(s) in RCA: 74] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022] Open
Abstract
Of children with idiopathic nephrotic syndrome, 10%-20% fail to respond to steroids or develop secondary steroid resistance (termed initial steroid sensitivity) and the majority progress to transplantation. Although 30%-50% of these patients suffer disease recurrence after transplantation, with poor long-term outcome, no reliable indicator of recurrence has yet been identified. Notably, the incidence of recurrence after transplantation appears reduced in patients with steroid-resistant nephrotic syndrome (SRNS) due to monogenic disorders. We reviewed 150 transplanted patients with SRNS to identify biomarkers that consistently predict outcome of SRNS after transplantation. In all, 25 children had genetic or familial SRNS and did not experience post-transplant recurrence. We reviewed phenotypic factors, including initial steroid sensitivity, donor type, age, ethnicity, time to ESRD, and time on dialysis, in the remaining 125 children. Of these patients, 57 (45.6%) developed post-transplant recurrence; 26 of 28 (92.9%) patients with initial steroid sensitivity recurred after transplantation, whereas only 26 of 86 (30.2%) patients resistant from the outset recurred (odds ratio, 30; 95% confidence interval, 6.62 to 135.86; P<0.001). We were unable to determine recurrence in two patients (one with initial steroid sensitivity), and nine patients did not receive initial steroids. Our data show that initial steroid sensitivity is highly predictive of post-transplant disease recurrence in this pediatric patient population. Because a pathogenic circulating permeability factor in nephrotic syndrome remains to be confirmed, we propose initial steroid sensitivity as a surrogate marker for post-transplant recurrence.
Collapse
Affiliation(s)
- Wen Y Ding
- Department of Paediatric Nephrology, Bristol Royal Hospital for Children, Bristol, United Kingdom; Academic Renal Unit, University of Bristol, Southmead Hospital, Bristol, United Kingdom
| | - Ania Koziell
- Department of Paediatric Nephrology, Evelina Children's Hospital, London, United Kingdom; Department of Experimental Immunobiology, King's College London, Guy's Hospital, London, United Kingdom
| | - Hugh J McCarthy
- Department of Paediatric Nephrology, Bristol Royal Hospital for Children, Bristol, United Kingdom; Academic Renal Unit, University of Bristol, Southmead Hospital, Bristol, United Kingdom
| | - Agnieszka Bierzynska
- Academic Renal Unit, University of Bristol, Southmead Hospital, Bristol, United Kingdom
| | | | - Jan A Dudley
- Department of Paediatric Nephrology, Bristol Royal Hospital for Children, Bristol, United Kingdom
| | - Carol D Inward
- Department of Paediatric Nephrology, Bristol Royal Hospital for Children, Bristol, United Kingdom
| | - Richard J Coward
- Department of Paediatric Nephrology, Bristol Royal Hospital for Children, Bristol, United Kingdom; Academic Renal Unit, University of Bristol, Southmead Hospital, Bristol, United Kingdom
| | - Jane Tizard
- Department of Paediatric Nephrology, Bristol Royal Hospital for Children, Bristol, United Kingdom
| | - Christopher Reid
- Department of Paediatric Nephrology, Evelina Children's Hospital, London, United Kingdom
| | - Corinne Antignac
- Pediatric Nephrology, French Institute of Health and Medical Research Unit 983, Necker Hospital for Sick Children, Paris, France
| | - Olivia Boyer
- Pediatric Nephrology, French Institute of Health and Medical Research Unit 983, Necker Hospital for Sick Children, Paris, France
| | - Moin A Saleem
- Department of Paediatric Nephrology, Bristol Royal Hospital for Children, Bristol, United Kingdom; Academic Renal Unit, University of Bristol, Southmead Hospital, Bristol, United Kingdom;
| |
Collapse
|
15
|
Tayo BO, Kramer H, Salako BL, Gottesman O, McKenzie CA, Ogunniyi A, Bottinger EP, Cooper RS. Genetic variation in APOL1 and MYH9 genes is associated with chronic kidney disease among Nigerians. Int Urol Nephrol 2013; 45:485-94. [PMID: 22956460 PMCID: PMC3599169 DOI: 10.1007/s11255-012-0263-4] [Citation(s) in RCA: 46] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2012] [Accepted: 08/07/2012] [Indexed: 01/13/2023]
Abstract
PURPOSE A region of chromosome 22 which includes APOL1 and MYH9 genes was recently identified as a risk locus for non-diabetic forms of kidney disease, including idiopathic and HIV-associated focal segmental glomerular sclerosis and kidney disease clinically attributed to hypertension among African Americans. The purposes of the current study were, therefore, to examine the frequency of these variants and to determine whether they are associated with chronic kidney disease (CKD) among native Africans. METHODS To investigate the possible evidence of association between variants in these genes and non-diabetic CKD among West Africans, we performed a case/control analysis in a sample of 166 Nigerians without history of European admixture. Our study included a total of 9 variants on APOL1 (n = 4) and MYH9 (n = 5) genes. RESULTS We observed significantly strong associations with previously reported APOL1 variants rs73885319 and rs60910145, and their two-allele "G1" haplotype (P < 0.005). We did not observe significant evidence of association between non-diabetic CKD and any of the MYH9 variants or haplotypes after accounting for multiple testing in our sample. CONCLUSIONS In conclusion, APOL1 risk variants are associated with non-diabetic forms of CKD among Nigerians of Yoruba ethnicity. Further information on APOL1/MYH9 variants may lead to screening programs, which could lead to earlier detection and interventions for non-diabetic kidney disease.
Collapse
Affiliation(s)
- Bamidele O Tayo
- Department of Preventive Medicine and Epidemiology, Loyola University Chicago Stritch School of Medicine, 2160 S. First Ave., Maywood, IL, USA.
| | | | | | | | | | | | | | | |
Collapse
|
16
|
Tavira B, Coto E, Gómez J, Tranche S, Miguélez K, Ortega F, Díez B, Sánchez E, Marín R, Arenas J, Alvarez V. Association between a MYH9 polymorphism (rs3752462) and renal function in the Spanish RENASTUR cohort. Gene 2013; 520:73-6. [PMID: 23470845 DOI: 10.1016/j.gene.2013.02.024] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2012] [Revised: 02/12/2013] [Accepted: 02/13/2013] [Indexed: 11/25/2022]
Abstract
The MYH9 gene encodes a protein that is expressed in the kidney glomerular podocytes. MYH9 single nucleotide polymorphisms (SNPs) have been linked to the risk for chronic kidney disease (CKD) and end stage renal disease. Our aim was to determine whether MYH9 SNPs were associated with renal disease in Spanish Caucasians. The RENASTUR cohort consisted of 592 Spanish Caucasians, aged 55-85 years. They were genotyped for SNPs rs3752462 and rs4821480, which tagged haplotype E. The main values between individuals with a glomerular filtration rate (eGFR) <60 and ≥ 60 ml/min/1.73 m(2) were statistically compared. The next variables were significantly associated with the eGFR in the univariate analysis: age, gender, type 2 diabetes, total cholesterol, total LDL-cholesterol, and the MYH9 rs3752462 (TC+TT genotypes; p=0.003). This SNP remained significantly associated with the eGFR in the multivariate analysis. In conclusion, SNP rs3752462 was an independent predictor of reduced eGFR in the Spanish RENASTUR population. The genotyping of this MYH9 SNP could help to identify individuals at risk of developing CKD.
Collapse
Affiliation(s)
- Beatriz Tavira
- Genética Molecular-Laboratorio Medicina, HUCA, Oviedo, Spain
| | | | | | | | | | | | | | | | | | | | | |
Collapse
|
17
|
Hussain N, Zello JA, Vasilevska-Ristovska J, Banh TM, Patel VP, Patel P, Battiston CD, Hebert D, Licht CPB, Piscione TD, Parekh RS. The rationale and design of Insight into Nephrotic Syndrome: Investigating Genes, Health and Therapeutics (INSIGHT): a prospective cohort study of childhood nephrotic syndrome. BMC Nephrol 2013; 14:25. [PMID: 23351121 PMCID: PMC3608224 DOI: 10.1186/1471-2369-14-25] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2012] [Accepted: 01/10/2013] [Indexed: 01/10/2023] Open
Abstract
BACKGROUND Nephrotic syndrome is one of the most commonly diagnosed kidney diseases in childhood and its progressive forms can lead to chronic kidney disease (CKD) and/or end-stage renal disease (ESRD). There have been few longitudinal studies among a multi-ethnic cohort to determine potential risk factors influencing disease susceptibility, treatment response, and progression of nephrotic syndrome. Temporal relationships cannot be studied through cross-sectional study design. Understanding the interaction between various factors is critical to developing new strategies for treating children with kidney disease. We present the rationale and the study design of a longitudinal cohort study of children with nephrotic syndrome, the Insight into Nephrotic Syndrome: Investigating Genes, Health and Therapeutics (INSIGHT) study. The specific aims are to determine: 1) socio-demographic, environmental, and genetic factors that influence disease susceptibility; 2) rates of steroid treatment resistance and steroid treatment dependence, and identify factors that may modify treatment response; 3) clinical and genetic factors that influence disease susceptibility and progression to CKD and ESRD; and 4) the interaction between the course of illness and socio-demographic, environmental, and clinical risk factors. METHODS/DESIGN INSIGHT is a disease-based observational longitudinal cohort study of children with nephrotic syndrome. At baseline, participants complete questionnaires and provide biological specimen samples (blood, urine, and toenail clippings). Follow-up questionnaires and repeat biological specimen collections are performed annually for up to five years. DISCUSSION The proposed cohort will provide the structure to test various risk factors predicting or influencing disease susceptibility, treatment response, and progression to CKD among children with nephrotic syndrome. TRIAL REGISTRATION ClinicalTrials.gov Identifier NCT01605266.
Collapse
Affiliation(s)
- Neesha Hussain
- Division of Nephrology, The Hospital for Sick Children, and University of Toronto, Dalla Lana School of Public Health, 555 University Avenue, M5G 1X8, Toronto, ON, Canada
| | | | | | | | | | | | | | | | | | | | | |
Collapse
|
18
|
APOL1 null alleles from a rural village in India do not correlate with glomerulosclerosis. PLoS One 2012; 7:e51546. [PMID: 23300552 PMCID: PMC3530541 DOI: 10.1371/journal.pone.0051546] [Citation(s) in RCA: 64] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2012] [Accepted: 11/02/2012] [Indexed: 11/19/2022] Open
Abstract
BACKGROUND Among African-Americans, genome wide association revealed a strong correlation between the G1 and G2 alleles of APOL1 (apolipoproteinL1, also called trypanolytic factor) and kidney diseases including focal and segmental glomerulosclerosis, HIV-associated nephropathy and hypertensive nephrosclerosis. In the prevailing hypothesis, heterozygous APOL1 G1 and G2 alleles increase resistance against Trypanosoma that cause African sleeping sickness, resulting in positive selection of these alleles, but when homozygous the G1 and G2 alleles predispose to glomerulosclerosis. While efforts are underway to screen patients for G1 and G2 alleles and to better understand "APOL1 glomerulopathy," no data prove that these APOL1 sequence variants cause glomerulosclerosis. G1 and G2 correlate best with glomerulosclerosis as recessive alleles, which suggests a loss of function mutation for which proof of causality is commonly tested with homozygous null alleles. This test cannot be performed in rodents as the APOL gene cluster evolved only in primates. However, there is a homozygous APOL1 null human being who lives in a village in rural India. This individual and his family offer a unique opportunity to test causality between APOL1 null alleles and glomerulosclerosis. METHODS AND FINDINGS We obtained clinical data, blood and urine from this APOL1 null patient and 50 related villagers. Based on measurements of blood pressure, BUN, creatinine, albuminuria, genotyping and immunoblotting, this APOL1 null individual does not have glomerulosclerosis, nor do his relatives who carry APOL1 null alleles. CONCLUSIONS This small study cannot provide definitive conclusions but the absence of glomerulosclerosis in this unique population is consistent with the possibility that African-American glomerulosclerosis is caused, not by loss of APOL1 function, but by other mechanisms including a subtle gain of function or by the "genetic hitchhiking" of deleterious mutations in a gene linked to APOL1 G1 and G2.
Collapse
|
19
|
Matsha TE, Masconi K, Yako YY, Hassan MS, Macharia M, Erasmus RT, Kengne AP. Polymorphisms in the non-muscle myosin heavy chain gene (MYH9) are associated with lower glomerular filtration rate in mixed ancestry diabetic subjects from South Africa. PLoS One 2012; 7:e52529. [PMID: 23285077 PMCID: PMC3527551 DOI: 10.1371/journal.pone.0052529] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2012] [Accepted: 11/16/2012] [Indexed: 01/03/2023] Open
Abstract
Objective Though single nucleotide polymorphisms (SNPs) in the non-muscle myosin gene (MYH9) have been reported to explain most of the excess risk of nondiabetic chronic kidney disease (CKD), in African-Americans, some studies have also shown associations with diabetic end-stage renal disease. We investigated the association of MYH9 SNPs with renal traits in a mixed-ancestry South African population prone to diabetes. Research Design and Methods Three SNPs known to be associated with CKD (rs4821480, rs5756152 and rs12107) were genotyped using Taqman assay in 716 adults (198 with diabetes) from the Bellville-South community, Cape Town. Glomerular filtration rate was estimated (eGFR) and urinary albumin/creatinine ratio (ACR) assessed. Multivariable regressions were used to relate the SNPs with renal traits. Results Mean age was 53.6 years, with the expected differences observed in characteristics by diabetic status. Significant associations were found between rs575152 and serum creatinine, and eGFR in the total population, and in diabetic participants (all p≤0.003), but not in non-diabetics (all p≥0.16), with significant interactions by diabetes status (interaction-p≤0.009). The association with ACR was borderline in diabetic participants (p = 0.05) and non-significant in non-diabetics (p = 0.85), with significant interaction (interaction p = 0.02). rs12107 was associated with fasting-, 2-hour glucose and HbA1c in diabetic participants only (interaction-p≤0.003), but not with renal traits. Conclusion MYH9 SNPs were associated with renal traits only in diabetic participants in this population. Our findings and other studies suggest that MYH9 may have a broader genetic risk effect on kidney diseases.
Collapse
Affiliation(s)
- Tandi Edith Matsha
- Department of Biomedical Sciences, Faculty of Health and Wellness Science, Cape Peninsula University of Technology, Cape Town, South Africa
| | - Katya Masconi
- Division of Chemical Pathology, Faculty of Health Sciences, National Health Laboratory Service and University of Stellenbosch, Cape Town, South Africa
| | - Yandiswa Yolanda Yako
- Division of Chemical Pathology, Faculty of Health Sciences, National Health Laboratory Service and University of Stellenbosch, Cape Town, South Africa
| | - Mogamat Shafick Hassan
- Division of Chemical Pathology, Faculty of Health Sciences, National Health Laboratory Service and University of Stellenbosch, Cape Town, South Africa
- Department of Nursing and Radiography, Faculty of Health and Wellness Science, Cape Peninsula University of Technology, Cape Town, South Africa
| | - Muiriri Macharia
- Division of Chemical Pathology, Faculty of Health Sciences, National Health Laboratory Service and University of Stellenbosch, Cape Town, South Africa
| | - Rajiv Timothy Erasmus
- Division of Chemical Pathology, Faculty of Health Sciences, National Health Laboratory Service and University of Stellenbosch, Cape Town, South Africa
| | - Andre Pascal Kengne
- NCRP for Cardiovascular and Metabolic Diseases, South African Medical Research Council & University of Cape Town, Cape Town, South Africa
- * E-mail:
| |
Collapse
|
20
|
Abstract
Apolipoprotein L1 (APOL1) gene association studies and results of the African American Study of Kidney Disease and Hypertension are disproving the longstanding concept that mild to moderate essential hypertension contributes substantially to end-stage renal disease susceptibility in African Americans. APOL1 coding variants underlie a spectrum of kidney diseases, including that attributed to hypertension (labeled arteriolar or hypertensive nephrosclerosis), focal segmental glomerulosclerosis, and HIV-associated nephropathy. APOL1 nephropathy risk variants persist because of protection afforded from the parasite that causes African sleeping sickness. This breakthrough will lead to novel treatments for hypertensive African Americans with low-level proteinuria, for whom effective therapies are lacking. Furthermore, APOL1 nephropathy risk variants contribute to racially variable allograft survival rates after kidney transplantation and assist in detecting nondiabetic forms of nephropathy in African Americans with diabetes. Discovery of APOL1-associated nephropathy was a major success of the genetics revolution, demonstrating that secondary hypertension is typically present in nondiabetic African Americans with nephropathy.
Collapse
|
21
|
O'Seaghdha CM, Fox CS. Genome-wide association studies of chronic kidney disease: what have we learned? Nat Rev Nephrol 2011; 8:89-99. [PMID: 22143329 DOI: 10.1038/nrneph.2011.189] [Citation(s) in RCA: 57] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
The past 3 years have witnessed a dramatic expansion in our knowledge of the genetic determinants of estimated glomerular filtration rate (eGFR) and chronic kidney disease (CKD). However, heritability estimates of eGFR indicate that we have only identified a small proportion of the total heritable contribution to the phenotypic variation. The majority of associations reported from genome-wide association studies identify genomic regions of interest and further work will be required to identify the causal variants responsible for a specific phenotype. Progress in this area is likely to stem from the identification of novel risk genotypes, which will offer insight into the pathogenesis of disease and potential novel therapeutic targets. Follow-up studies stimulated by findings from genome-wide association studies of kidney disease are already yielding promising results, such as the identification of an association between urinary uromodulin levels and incident CKD. Although this work is at an early stage, prospects for progress in our understanding of CKD and its treatment look more promising now than at any point in the past.
Collapse
Affiliation(s)
- Conall M O'Seaghdha
- National Heart, Lung and Blood Institute's Framingham Heart Study and the Center for Population Studies, 73 Mount Wayte Avenue, Suite 2, Framingham, MA 01702, USA
| | | |
Collapse
|
22
|
Kopp JB, Nelson GW, Sampath K, Johnson RC, Genovese G, An P, Friedman D, Briggs W, Dart R, Korbet S, Mokrzycki MH, Kimmel PL, Limou S, Ahuja TS, Berns JS, Fryc J, Simon EE, Smith MC, Trachtman H, Michel DM, Schelling JR, Vlahov D, Pollak M, Winkler CA. APOL1 genetic variants in focal segmental glomerulosclerosis and HIV-associated nephropathy. J Am Soc Nephrol 2011; 22:2129-37. [PMID: 21997394 PMCID: PMC3231787 DOI: 10.1681/asn.2011040388] [Citation(s) in RCA: 618] [Impact Index Per Article: 47.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2011] [Accepted: 08/04/2011] [Indexed: 12/13/2022] Open
Abstract
Trypanolytic variants in APOL1, which encodes apolipoprotein L1, associate with kidney disease in African Americans, but whether APOL1-associated glomerular disease has a distinct clinical phenotype is unknown. Here we determined APOL1 genotypes for 271 African American cases, 168 European American cases, and 939 control subjects. In a recessive model, APOL1 variants conferred seventeenfold higher odds (95% CI 11 to 26) for focal segmental glomerulosclerosis (FSGS) and twenty-nine-fold higher odds (95% CI 13 to 68) for HIV-associated nephropathy (HIVAN). FSGS associated with two APOL1 risk alleles associated with earlier age of onset (P = 0.01) and faster progression to ESRD (P < 0.01) but similar sensitivity to steroids compared with other subjects. Individuals with two APOL1 risk alleles have an estimated 4% lifetime risk for developing FSGS, and untreated HIV-infected individuals have a 50% risk for developing HIVAN. The effect of carrying two APOL1 risk alleles explains 18% of FSGS and 35% of HIVAN; alternatively, eliminating this effect would reduce FSGS and HIVAN by 67%. A survey of world populations indicated that the APOL1 kidney risk alleles are present only on African chromosomes. In summary, African Americans carrying two APOL1 risk alleles have a greatly increased risk for glomerular disease, and APOL1-associated FSGS occurs earlier and progresses to ESRD more rapidly. These data add to the evidence base required to determine whether genetic testing for APOL1 has a use in clinical practice.
Collapse
Affiliation(s)
- Jeffrey B Kopp
- Kidney Disease Section, National Institute of Diabetes and Digestive and Kidney Disease, National Institutes of Health, Bethesda, Maryland, USA.
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
23
|
Abstract
The successes of genome-wide association (GWA) studies have mainly come from studies performed in populations of European descent. Since complex traits are characterized by marked genetic heterogeneity, the findings so far may provide an incomplete picture of the genetic architecture of complex traits. However, the recent GWA studies performed on East Asian populations now allow us to globally assess the heterogeneity of association signals between populations of European ancestry and East Asians, and the possible obstacles for multi-ethnic GWA studies. We focused on four different traits that represent a broad range of complex phenotypes, which have been studied in both Europeans and East Asians: type 2 diabetes, systemic lupus erythematosus, ulcerative colitis and height. For each trait, we observed that most of the risk loci identified in East Asians were shared with Europeans. However, we also observed that a significant part of the association signals at these shared loci seems to be independent between populations. This suggests that disease aetiology is common between populations, but that risk variants are often population specific. These variants could be truly population specific and result from natural selection, genetic drift and recent mutations, or they could be spurious, caused by the limitations of the method of analysis employed in the GWA studies. We therefore propose a three-stage framework for multi-ethnic GWA analyses, starting with the commonly used single-nucleotide polymorphism-based analysis, and followed by a gene-based approach and a pathway-based analysis, which will take into account the heterogeneity of association between populations at different levels.
Collapse
Affiliation(s)
- Jingyuan Fu
- Department of Genetics, University Medical Centre and University of Groningen, Groningen, The Netherlands
| | | | | |
Collapse
|
24
|
Rosset S, Tzur S, Behar DM, Wasser WG, Skorecki K. The population genetics of chronic kidney disease: insights from the MYH9-APOL1 locus. Nat Rev Nephrol 2011; 7:313-26. [PMID: 21537348 DOI: 10.1038/nrneph.2011.52] [Citation(s) in RCA: 53] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Many rare kidney disorders exhibit a monogenic, Mendelian pattern of inheritance. Population-based genetic studies have identified many genetic variants associated with an increased risk of developing common kidney diseases. Strongly associated variants have potential clinical uses as predictive markers and may advance our understanding of disease pathogenesis. These principles are elegantly illustrated by a region within chromosome 22q12 that has a strong association with common forms of kidney disease. Researchers had identified DNA sequence variants in this locus that were highly associated with an increased prevalence of common chronic kidney diseases in people of African ancestry. Initial research concentrated on MYH9 as the most likely candidate gene; however, population-based whole-genome analysis enabled two independent research teams to discover more strongly associated mutations in the neighboring APOL1 gene. The powerful evolutionary selection pressure of an infectious pathogen in West Africa favored the spread of APOL1 variants that protect against a lethal form of African sleeping sickness but are highly associated with an increased risk of kidney disease. We describe the data sources, process of discovery, and reasons for initial misidentification of the candidate gene, as well as the lessons that can be learned for future population genetics research.
Collapse
Affiliation(s)
- Saharon Rosset
- Department of Statistics and Operations Research, Tel Aviv University, Tel Aviv 69978, Israel
| | | | | | | | | |
Collapse
|
25
|
O'Seaghdha CM, Parekh RS, Hwang SJ, Li M, Köttgen A, Coresh J, Yang Q, Fox CS, Kao WHL. The MYH9/APOL1 region and chronic kidney disease in European-Americans. Hum Mol Genet 2011; 20:2450-6. [PMID: 21429915 DOI: 10.1093/hmg/ddr118] [Citation(s) in RCA: 77] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023] Open
Abstract
Polymorphisms in the MYH9 and adjacent APOL1 gene region demonstrate a strong association with non-diabetic kidney disease in African-Americans. However, it is not known to what extent these polymorphisms are present in other ethnic groups. To examine the association of genetic polymorphisms in this region with chronic kidney disease (CKD; estimated glomerular filtration rate <60 ml/min/1.73 m(2)) in individuals of European ancestry, we examined rs4821480, an MYH9 single-nucleotide polymorphism (SNP) recently identified as associated with kidney disease in African-Americans, in 13 133 participants from the Framingham Heart Study (FHS) and Atherosclerosis Risk in Communities (ARIC) Study. In addition, we further interrogated the MYH9/APOL1 gene region using 282 SNPs for association with CKD using age-, sex- and center-adjusted models and performed a meta-analysis of the results from both studies. Because of prior data linking rs4821480 and kidney disease, we used a P-value of <0.05 to test the association with CKD. In the meta-analysis, rs4821480 (minor allele frequency 4.45 and 3.96% in FHS and ARIC, respectively) was associated with higher CKD prevalence in participants free of diabetes (odds ratio 1.44; 95% confidence interval 1.15-1.80; P = 0.001). No other SNPs achieved significance after adjusting for multiple testing. Results utilizing directly genotyped data confirmed the results of the primary analysis. Recently identified APOL1 risk variants were also directly genotyped, but did not account for the observed MYH9 signal. These data suggest that the MYH9 polymorphism rs4821480 is associated with an increased risk of non-diabetic CKD in individuals of European ancestry.
Collapse
Affiliation(s)
- Conall M O'Seaghdha
- National Heart, Lung and Blood Institute's Framingham Heart Study and Center for Population Studies, Framingham, MA, USA
| | | | | | | | | | | | | | | | | |
Collapse
|
26
|
Zenker M, Mertens PR. Arrest of the true culprit and acquittal of the innocent? Genetic revelations charge APOL1 variants with kidney disease susceptibility. Int Urol Nephrol 2010; 42:1131-4. [PMID: 21080072 DOI: 10.1007/s11255-010-9863-z] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2010] [Accepted: 10/15/2010] [Indexed: 12/11/2022]
Affiliation(s)
- Martin Zenker
- Institute of Human Genetics, Otto-von-Guericke-University Magdeburg, Leipziger Strasse 40, 39120, Magdeburg, Germany.
| | | |
Collapse
|
27
|
Henn BM, Gravel S, Moreno-Estrada A, Acevedo-Acevedo S, Bustamante CD. Fine-scale population structure and the era of next-generation sequencing. Hum Mol Genet 2010; 19:R221-6. [PMID: 20876616 DOI: 10.1093/hmg/ddq403] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Fine-scale population structure characterizes most continents and is especially pronounced in non-cosmopolitan populations. Roughly half of the world's population remains non-cosmopolitan and even populations within cities often assort along ethnic and linguistic categories. Barriers to random mating can be ecologically extreme, such as the Sahara Desert, or cultural, such as the Indian caste system. In either case, subpopulations accumulate genetic differences if the barrier is maintained over multiple generations. Genome-wide polymorphism data, initially with only a few hundred autosomal microsatellites, have clearly established differences in allele frequency not only among continental regions, but also within continents and within countries. We review recent evidence from the analysis of genome-wide polymorphism data for genetic boundaries delineating human population structure and the main demographic and genomic processes shaping variation, and discuss the implications of population structure for the distribution and discovery of disease-causing genetic variants, in the light of the imminent availability of sequencing data for a multitude of diverse human genomes.
Collapse
Affiliation(s)
- Brenna M Henn
- Department of Genetics, Stanford University School of Medicine, 300 Pasteur Drive, Stanford, CA 94305, USA
| | | | | | | | | |
Collapse
|
28
|
Freedman BI, Kopp JB, Langefeld CD, Genovese G, Friedman DJ, Nelson GW, Winkler CA, Bowden DW, Pollak MR. The apolipoprotein L1 (APOL1) gene and nondiabetic nephropathy in African Americans. J Am Soc Nephrol 2010; 21:1422-6. [PMID: 20688934 PMCID: PMC7391383 DOI: 10.1681/asn.2010070730] [Citation(s) in RCA: 208] [Impact Index Per Article: 14.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023] Open
Abstract
Mapping by admixture linkage disequilibrium (LD) detected strong association between nonmuscle myosin heavy chain 9 gene (MYH9) variants on chromosome 22 and nondiabetic nephropathy in African Americans. MYH9-related variants were posited to be the probable, but not necessarily the definitive, causal variants as a result of impressive statistical evidence of association, renal expression, and a role in autosomal dominant MYH9 disorders characterized by progressive glomerulosclerosis (Epstein and Fechtner syndromes). Dense mapping within MYH9 revealed striking LD patterns and racial variation in risk allele frequencies, suggesting population genetic factors such as selection may be operative in this region. Genovese and colleagues examined large chromosomal regions adjacent to MYH9 using genome-wide association methods and non-HapMap single nucleotide polymorphisms identified in Yoruba from the 1000 Genomes project. Statistically stronger associations were detected between two independent sequence variants in the Apolipoprotein L1 gene (APOL1) and nondiabetic nephropathy in African Americans, with odds ratios of 10.5 in idiopathic FSGS and 7.3 in hypertension-attributed ESRD. These kidney disease risk variants likely rose to high frequency in Africa because they confer resistance to trypanosomal infection and protect from African sleeping sickness. Risk variants in MYH9 and APOL1 are in strong LD, and the genetic risk that was previously attributed to MYH9 may reside, in part or in whole, in APOL1, although more complex models of risk cannot be excluded. This association likely explains racial disparities in nondiabetic nephropathy as a result of the high prevalence of risk alleles in individuals of African ancestry.
Collapse
Affiliation(s)
| | - Jeffrey B. Kopp
- Kidney Disease Section, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland
| | | | - Giulio Genovese
- Department of Internal Medicine/Nephrology, Beth Israel Deaconess Medical Center and Harvard Medical School, Boston, Massachusetts
| | - David J. Friedman
- Department of Internal Medicine/Nephrology, Beth Israel Deaconess Medical Center and Harvard Medical School, Boston, Massachusetts
| | - George W. Nelson
- SAIC-National Cancer Institute, National Institutes of Health–Frederick, Frederick, Maryland; and
| | | | - Donald W. Bowden
- Department of Biochemistry and Centers for Diabetes Research and Human Genomics, Wake Forest University School of Medicine, Winston-Salem, North Carolina
| | - Martin R. Pollak
- Department of Internal Medicine/Nephrology, Beth Israel Deaconess Medical Center and Harvard Medical School, Boston, Massachusetts
- Broad Institute of Harvard and Massachusetts Institute of Technology, Cambridge, Massachusetts
| |
Collapse
|
29
|
Genovese G, Friedman DJ, Ross MD, Lecordier L, Uzureau P, Freedman BI, Bowden DW, Langefeld CD, Oleksyk TK, Uscinski Knob AL, Bernhardy AJ, Hicks PJ, Nelson GW, Vanhollebeke B, Winkler CA, Kopp JB, Pays E, Pollak MR. Association of trypanolytic ApoL1 variants with kidney disease in African Americans. Science 2010; 329:841-5. [PMID: 20647424 PMCID: PMC2980843 DOI: 10.1126/science.1193032] [Citation(s) in RCA: 1443] [Impact Index Per Article: 103.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
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.
Collapse
MESH Headings
- Africa
- Black or African American/genetics
- Alleles
- Apolipoprotein L1
- Apolipoproteins/blood
- Apolipoproteins/genetics
- Apolipoproteins/metabolism
- Case-Control Studies
- Cohort Studies
- Gene Frequency
- Genetic Association Studies
- Genetic Predisposition to Disease
- Glomerulosclerosis, Focal Segmental/ethnology
- Glomerulosclerosis, Focal Segmental/genetics
- Haplotypes
- Humans
- Hypertension/complications
- Immunity, Innate
- Kidney Failure, Chronic/ethnology
- Kidney Failure, Chronic/etiology
- Kidney Failure, Chronic/genetics
- Linkage Disequilibrium
- Lipoproteins, HDL/blood
- Lipoproteins, HDL/genetics
- Lipoproteins, HDL/metabolism
- Logistic Models
- Molecular Motor Proteins/genetics
- Myosin Heavy Chains/genetics
- Polymorphism, Single Nucleotide
- Recombinant Proteins/metabolism
- Selection, Genetic
- Sequence Deletion
- Trypanosoma brucei rhodesiense/metabolism
- Trypanosomiasis, African/genetics
- Trypanosomiasis, African/parasitology
Collapse
Affiliation(s)
- Giulio Genovese
- Division of Nephrology, Department of Medicine, Beth Israel Deaconess Medical Center and Harvard Medical School, Boston, MA 02215, USA
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|