151
|
Jack J, Havener TM, McLeod HL, Motsinger-Reif AA, Foster M. Evaluating the role of admixture in cancer therapy via in vitro drug response and multivariate genome-wide associations. Pharmacogenomics 2015; 16:1451-63. [PMID: 26314407 DOI: 10.2217/pgs.15.85] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
AIM We investigate the role of ethnicity and admixture in drug response across a broad group of chemotherapeutic drugs. Also, we generate hypotheses on the genetic variants driving differential drug response through multivariate genome-wide association studies. METHODS Immortalized lymphoblastoid cell lines from 589 individuals (Hispanic or non-Hispanic/Caucasian) were used to investigate dose-response for 28 chemotherapeutic compounds. Univariate and multivariate statistical models were used to elucidate associations between genetic variants and differential drug response as well as the role of ethnicity in drug potency and efficacy. RESULTS & CONCLUSION For many drugs, the variability in drug response appears to correlate with self-reported race and estimates of genetic ancestry. Additionally, multivariate genome-wide association analyses offered interesting hypotheses governing these differential responses.
Collapse
Affiliation(s)
- John Jack
- Department of Statistics, North Carolina State University, 2601 Stinson Drive, Raleigh, NC 27695, USA.,Bioinformatics Research Center, North Carolina State University, 2601 Stinson Drive, Raleigh, NC 27695, USA
| | - Tammy M Havener
- Center for Pharmacogenomics & Individualized Therapy, University of North Carolina, 120 Mason Farm Road, Chapel Hill, NC 27514, USA
| | - Howard L McLeod
- DeBartolo Family Personalized Medicine Institute, Moffitt Cancer Center, 12902 Magnolia Drive, Tampa, FL 33612, USA.,Pharmacogenetics for Every Nation Initiative, 1119 Oxbridge Drive, Tampa, FL 33549, USA
| | - Alison A Motsinger-Reif
- Department of Statistics, North Carolina State University, 2601 Stinson Drive, Raleigh, NC 27695, USA.,Bioinformatics Research Center, North Carolina State University, 2601 Stinson Drive, Raleigh, NC 27695, USA
| | - Matthew Foster
- Lineberger Comprehensive Cancer Center, University of North Carolina, 101 Manning Drive, Chapel Hill, NC 27514, USA
| |
Collapse
|
152
|
Iyengar SK, Sedor JR, Freedman BI, Kao WHL, Kretzler M, Keller BJ, Abboud HE, Adler SG, Best LG, Bowden DW, Burlock A, Chen YDI, Cole SA, Comeau ME, Curtis JM, Divers J, Drechsler C, Duggirala R, Elston RC, Guo X, Huang H, Hoffmann MM, Howard BV, Ipp E, Kimmel PL, Klag MJ, Knowler WC, Kohn OF, Leak TS, Leehey DJ, Li M, Malhotra A, März W, Nair V, Nelson RG, Nicholas SB, O’Brien SJ, Pahl MV, Parekh RS, Pezzolesi MG, Rasooly RS, Rotimi CN, Rotter JI, Schelling JR, Seldin MF, Shah VO, Smiles AM, Smith MW, Taylor KD, Thameem F, Thornley-Brown DP, Truitt BJ, Wanner C, Weil EJ, Winkler CA, Zager PG, Igo RP, Hanson RL, Langefeld CD. Genome-Wide Association and Trans-ethnic Meta-Analysis for Advanced Diabetic Kidney Disease: Family Investigation of Nephropathy and Diabetes (FIND). PLoS Genet 2015; 11:e1005352. [PMID: 26305897 PMCID: PMC4549309 DOI: 10.1371/journal.pgen.1005352] [Citation(s) in RCA: 96] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2014] [Accepted: 06/10/2015] [Indexed: 11/28/2022] Open
Abstract
Diabetic kidney disease (DKD) is the most common etiology of chronic kidney disease (CKD) in the industrialized world and accounts for much of the excess mortality in patients with diabetes mellitus. Approximately 45% of U.S. patients with incident end-stage kidney disease (ESKD) have DKD. Independent of glycemic control, DKD aggregates in families and has higher incidence rates in African, Mexican, and American Indian ancestral groups relative to European populations. The Family Investigation of Nephropathy and Diabetes (FIND) performed a genome-wide association study (GWAS) contrasting 6,197 unrelated individuals with advanced DKD with healthy and diabetic individuals lacking nephropathy of European American, African American, Mexican American, or American Indian ancestry. A large-scale replication and trans-ethnic meta-analysis included 7,539 additional European American, African American and American Indian DKD cases and non-nephropathy controls. Within ethnic group meta-analysis of discovery GWAS and replication set results identified genome-wide significant evidence for association between DKD and rs12523822 on chromosome 6q25.2 in American Indians (P = 5.74x10-9). The strongest signal of association in the trans-ethnic meta-analysis was with a SNP in strong linkage disequilibrium with rs12523822 (rs955333; P = 1.31x10-8), with directionally consistent results across ethnic groups. These 6q25.2 SNPs are located between the SCAF8 and CNKSR3 genes, a region with DKD relevant changes in gene expression and an eQTL with IPCEF1, a gene co-translated with CNKSR3. Several other SNPs demonstrated suggestive evidence of association with DKD, within and across populations. These data identify a novel DKD susceptibility locus with consistent directions of effect across diverse ancestral groups and provide insight into the genetic architecture of DKD. Type 2 diabetes is the most common cause of severe kidney disease worldwide and diabetic kidney disease (DKD) associates with premature death. Individuals of non-European ancestry have the highest burden of type 2 DKD; hence understanding the causes of DKD remains critical to reducing health disparities. Family studies demonstrate that genes regulate the onset and progression of DKD; however, identifying these genes has proven to be challenging. The Family Investigation of Diabetes and Nephropathy consortium (FIND) recruited a large multi-ethnic collection of individuals with type 2 diabetes with and without kidney disease in order to detect genes associated with DKD. FIND discovered and replicated a DKD-associated genetic locus on human chromosome 6q25.2 (rs955333) between the SCAF8 and CNKSR genes. Findings were supported by significantly different expression of genes in this region from kidney tissue of subjects with, versus without DKD. The present findings identify a novel kidney disease susceptibility locus in individuals with type 2 diabetes which is consistent across subjects of differing ancestries. In addition, FIND results provide a rich catalogue of genetic variation in DKD patients for future research on the genetic architecture regulating this common and devastating disease.
Collapse
Affiliation(s)
- Sudha K. Iyengar
- Department of Epidemiology & Biostatistics, Case Western Reserve University, Cleveland, Ohio, United States of America
- * E-mail: (SKI); (JRS); (BIF)
| | - John R. Sedor
- Departments of Medicine, Case Western Reserve University, Cleveland, Ohio, United States of America
- Departments of Physiology and Biophysics, Case Western Reserve University, Cleveland, Ohio, United States of America
- * E-mail: (SKI); (JRS); (BIF)
| | - Barry I. Freedman
- Department of Internal Medicine, Section on Nephrology, Wake Forest School of Medicine, Winston-Salem, North Carolina, United States of America
- * E-mail: (SKI); (JRS); (BIF)
| | - W. H. Linda Kao
- Department of Epidemiology and Medicine, John Hopkins University, Baltimore, Maryland, United States of America
| | - Matthias Kretzler
- Department of Internal Medicine/Nephrology, University of Michigan, Ann Arbor, Michigan, United States of America
| | - Benjamin J. Keller
- Department of Internal Medicine/Nephrology, University of Michigan, Ann Arbor, Michigan, United States of America
| | - Hanna E. Abboud
- Department of Medicine/Nephrology, The University of Texas Health Science Center, San Antonio, Texas, United States of America
| | - Sharon G. Adler
- Department of Medicine, Division of Nephrology and Hypertension, Harbor-UCLA Medical Center, Torrance, California, United States of America
| | - Lyle G. Best
- Missouri Breaks Industries Research, Timber Lake, South Dakota, United States of America
| | - Donald W. Bowden
- Department of Biochemistry, Center for Human Genomics, Wake Forest School of Medicine, Winston-Salem, North Carolina, United States of America
| | - Allison Burlock
- Department of Internal Medicine/Nephrology, University of Michigan, Ann Arbor, Michigan, United States of America
| | - Yii-Der Ida Chen
- The Institute for Translational Genomics and Population Sciences, Harbor-UCLA Medical Center, Torrance, California, United States of America
| | - Shelley A. Cole
- Department of Genetics, Texas Biomedical Research Institute, San Antonio, Texas, United States of America
| | - Mary E. Comeau
- Center for Public Health Genomics and Department of Biostatistical Sciences, Division of Public Health Sciences, Wake Forest School of Medicine, Winston-Salem, United States of America
| | - Jeffrey M. Curtis
- National Institutes of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Phoenix, Arizona, United States of America
| | - Jasmin Divers
- Center for Public Health Genomics and Department of Biostatistical Sciences, Division of Public Health Sciences, Wake Forest School of Medicine, Winston-Salem, United States of America
| | - Christiane Drechsler
- University Hospital Würzburg, Renal Division and Comprehensive Heart Failure Center, Würzburg, Germany
| | - Ravi Duggirala
- Department of Genetics, Texas Biomedical Research Institute, San Antonio, Texas, United States of America
| | - Robert C. Elston
- Department of Epidemiology & Biostatistics, Case Western Reserve University, Cleveland, Ohio, United States of America
| | - Xiuqing Guo
- The Institute for Translational Genomics and Population Sciences, Harbor-UCLA Medical Center, Torrance, California, United States of America
| | - Huateng Huang
- Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, Michigan, United States of America
| | | | - Barbara V. Howard
- MedStar Health Research Institute, Hyattsville, Maryland, United States of America
| | - Eli Ipp
- Department of Medicine, Section of Diabetes and Metabolism, Harbor-UCLA Medical Center, Torrance, California, United States of America
| | - Paul L. Kimmel
- Division of Kidney, Urologic, and Hematologic Diseases, National Institute of Diabetes and Digestive and Kidney Diseases, Bethesda, Maryland, United States of America
| | - Michael J. Klag
- Johns Hopkins Bloomberg School of Public Health, Johns Hopkins School of Medicine, Baltimore, Maryland, United States of America
| | - William C. Knowler
- National Institutes of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Phoenix, Arizona, United States of America
| | - Orly F. Kohn
- Department of Medicine, University of Chicago Medicine, Chicago, Illinois, United States of America
| | - Tennille S. Leak
- Department of Internal Medicine/Nephrology, University of Michigan, Ann Arbor, Michigan, United States of America
| | - David J. Leehey
- Department of Medicine, Loyola School of Medicine, Maywood, Illinois, United States of America
| | - Man Li
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland, United States of America
| | - Alka Malhotra
- National Institutes of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Phoenix, Arizona, United States of America
| | - Winfried März
- Heidelberg University and Synlab Academy, University of Graz, Graz, Austria
| | - Viji Nair
- Department of Internal Medicine/Nephrology, University of Michigan, Ann Arbor, Michigan, United States of America
| | - Robert G. Nelson
- National Institutes of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Phoenix, Arizona, United States of America
| | - Susanne B. Nicholas
- Department of Medicine, University of California, Los Angeles, Los Angeles, California, United States of America
| | - Stephen J. O’Brien
- Theodosius Dobzhansky Center for Genome Bioinformatics, St. Petersburg, Russia, and Oceanographic Center, Nova Southeastern University, Ft. Lauderdale, Florida, United States of America
| | - Madeleine V. Pahl
- Department of Medicine, University of California, Irvine, Irvine, California, United States of America
| | - Rulan S. Parekh
- Departments of Paediatrics and Medicine, Hospital for Sick Children, University Health Network and the University of Toronto, Toronto, Ontario, Canada
| | - Marcus G. Pezzolesi
- Department of Medicine, Joslin Diabetes Center, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Rebekah S. Rasooly
- National Institute of Diabetes and Digestive Disease, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Charles N. Rotimi
- Center for Research on Genomics and Global Health, Bethesda, Maryland, United States of America
| | - Jerome I. Rotter
- The Institute for Translational Genomics and Population Sciences, Harbor-UCLA Medical Center, Torrance, California, United States of America
| | - Jeffrey R. Schelling
- Departments of Medicine, Case Western Reserve University, Cleveland, Ohio, United States of America
| | - Michael F. Seldin
- Department of Biochemistry and Molecular Medicine, UC Davis School of Medicine, Davis, California, United States of America
| | - Vallabh O. Shah
- Department of Biochemistry & Molecular Biology, University of New Mexico, Albuquerque, New Mexico, United States of America
| | - Adam M. Smiles
- Joslin Diabetes Center, Section on Genetics and Epidemiology, Boston, Massachusetts, United States of America
| | - Michael W. Smith
- National Human Genome Research Institute, Rockville, Maryland, United States of America
| | - Kent D. Taylor
- The Institute for Translational Genomics and Population Sciences, Harbor-UCLA Medical Center, Torrance, California, United States of America
| | - Farook Thameem
- Department of Medicine, The University of Texas Health Science Center, San Antonio, Texas, United States of America
| | | | - Barbara J. Truitt
- Department of Epidemiology & Biostatistics, Case Western Reserve University, Cleveland, Ohio, United States of America
| | - Christoph Wanner
- Department of Medicine, Division of Nephrology, University Hospital Würzburg, Würzburg, Germany
| | - E. Jennifer Weil
- National Institutes of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Phoenix, Arizona, United States of America
| | - Cheryl A. Winkler
- Center for Cancer Research, National Cancer Institute, Frederick, Maryland, United States of America
| | - Philip G. Zager
- Department of Internal Medicine, University of New Mexico, Albuquerque, New Mexico, United States of America
| | - Robert P. Igo
- Department of Epidemiology & Biostatistics, Case Western Reserve University, Cleveland, Ohio, United States of America
| | - Robert L. Hanson
- National Institutes of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Phoenix, Arizona, United States of America
| | - Carl D. Langefeld
- The Institute for Translational Genomics and Population Sciences, Harbor-UCLA Medical Center, Torrance, California, United States of America
| | | |
Collapse
|
153
|
Sampson MG. Actualizing the Benefits of Genomic Discovery in Pediatric Nephrology. J Pediatr Genet 2015; 5:69-75. [PMID: 27617144 DOI: 10.1055/s-0035-1557113] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2014] [Accepted: 01/19/2015] [Indexed: 01/13/2023]
Abstract
The discovery of genetic variation associated with pediatric kidney disease has shed light on the biology underlying these conditions and, in some cases, has improved our clinical management of patients. We are challenged to continue the momentum of the genomic era in pediatric nephrology by identifying novel disease-associated genetic variation and translating these discoveries into clinical applications. This article reviews the diverse forms of genetic architecture that have been found to be associated with kidney diseases and traits. These include rare, fully penetrant variants responsible for Mendelian forms of disease, copy number variants, and more common variants associated with increased risk of disease. These discoveries have provided us with a greater understanding of the molecular mechanisms underlying these conditions and highlighted key pathways for potential intervention. In a number of areas, the identification of rare, fully penetrant variants is immediately clinically relevant, whether in regard to diagnostic testing, prediction of outcomes, or choice of therapies and interventions. This article discusses limitations in the deterministic view of rare, putatively causal mutations, a challenge increasing in importance as sequencing expands to many more genes and patients. This article also focusses on common genetic variants, using those found to be associated with focal segmental glomerulosclerosis in African-Americans, IgA nephropathy, chronic kidney disease (CKD), and estimated glomerular filtration rate (eGFR) as examples. Identifying common genetic variants associated with disease will complement other areas of genomic inquiry, lead to a greater biological understanding of disease, and will benefit pediatric nephrology patients.
Collapse
Affiliation(s)
- Matthew G Sampson
- Division of Pediatric Nephrology, Department of Pediatrics and Communicable Diseases, University of Michigan School of Medicine, Ann Arbor, Michigan, United States
| |
Collapse
|
154
|
Lewis EF, Claggett B, Parfrey PS, Burdmann EA, McMurray JJV, Solomon SD, Levey AS, Ivanovich P, Eckardt KU, Kewalramani R, Toto R, Pfeffer MA. Race and ethnicity influences on cardiovascular and renal events in patients with diabetes mellitus. Am Heart J 2015; 170:322-9. [PMID: 26299230 DOI: 10.1016/j.ahj.2015.05.008] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/07/2014] [Accepted: 05/10/2015] [Indexed: 11/17/2022]
Abstract
BACKGROUND The incidence of end-stage renal disease (ESRD) has been consistently shown to be higher among blacks and Hispanics compared to whites with unmeasured risk factors and access to care as suggested explanations. In a high-risk cohort with frequent protocol-directed follow-up, we evaluated the influence of race on cardiovascular (CV) outcomes and incidence of ESRD. METHODS TREAT was a randomized, double-blind, placebo-controlled study. This secondary analysis focused on role of race on outcomes. TREAT enrolled 4,038 patients with type 2 diabetes, chronic kidney disease (estimated glomerular filtration rate 20-60 mL/min per 1.73 m(2)), and anemia (hemoglobin level ≤11 g/dL) treated with either darbepoetin alfa or placebo. We compared self-described black and Hispanic patients to white patients with regard to baseline characteristics and outcomes, including mortality, CV outcomes (myocardial infarction, stroke, heart failure, resuscitated sudden death, and coronary revascularization), and incident ESRD. Multivariate adjusted Cox models were developed for these outcomes. RESULTS Black and Hispanic patients were younger, more likely women, had less prior CV disease, and higher blood pressure. During a mean follow-up of 2.4 years with comparable access to care, blacks and Hispanics had a greater risk of ESRD but a significant lower risk of myocardial infarction and coronary revascularization than whites. After adjusting for confounders, blacks remained at significantly greater risk of ESRD than whites (hazard ratio 1.53, 95% CI 1.26-1.85, P < .001), whereas this ESRD risk did not persist among Hispanics. CONCLUSION Despite similar access to care and lower CV event rates, the risk of ESRD was higher among blacks and Hispanics than whites. For blacks, but not Hispanics, this increase was independent of known attributable risk factors.
Collapse
Affiliation(s)
- Eldrin F Lewis
- Cardiovascular Division, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA.
| | - Brian Claggett
- Cardiovascular Division, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA
| | - Patrick S Parfrey
- Division of Nephrology, Health Sciences Center, St Johns, Newfoundland and Labrador, Canada
| | | | | | - Scott D Solomon
- Cardiovascular Division, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA
| | - Andrew S Levey
- Division of Nephrology, Tufts Medical Center, Boston, MA
| | - Peter Ivanovich
- Division of Nephrology/Hypertension, Department of Medicine, Feinberg School of Medicine, Northwestern University, Chicago, IL
| | - Kai-Uwe Eckardt
- Department of Nephrology and Hypertension, University of Erlangen-Nuremberg, Erlangen, Germany
| | | | - Robert Toto
- Department of Medicine, University of Texas SW, Dallas, TX
| | - Marc A Pfeffer
- Cardiovascular Division, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA
| |
Collapse
|
155
|
Regele F, Jelencsics K, Shiffman D, Paré G, McQueen MJ, Mann JF, Oberbauer R. Genome-wide studies to identify risk factors for kidney disease with a focus on patients with diabetes. Nephrol Dial Transplant 2015. [DOI: 10.1093/ndt/gfv087] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
|
156
|
Otero Gonzalez A, Prol MPB, Caride MJC, Nores JS, Novoa E, Melon CP, Macia P, Alves MT, Cid M, Osorio E, Coto E, Macias Nuñez JF. Estimated glomerular filtration rate (eGFR), 25(OH) D3, chronic kidney disease (CKD), the MYH9 (myosin heavy chain 9) gene in old and very elderly people. Int Urol Nephrol 2015; 47:1403-8. [PMID: 26152646 DOI: 10.1007/s11255-015-1041-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2014] [Accepted: 06/19/2015] [Indexed: 01/30/2023]
Abstract
It is known that the common physiological denominator of the ageing process is an attenuation of functional performance with respect to the situation of young people and adults. However, since the first cohort-based longitudinal studies, it has not been possible to establish a "linear" relationship between age and glomerular filtration in all cases. This does not mean that there is no physiological ageing process at all; in addition to those already elucidated, its mechanisms include cell senescence, podocyte dysfunction, a vitamin D deficiency, and homozygotic forms of the MYH9 gene. The aim of the present work was to analyse the prevalence of chronic kidney disease (CKD) and, where possible, the correlation between CKD, defined by an eGFR < 60 ml/min/1.73 m(2), plasma 25(OH)D3 levels and the MYH9 gene in a population of elderly and very elderly persons. These parameters have not been evaluated previously in populations of elderly and very elderly patients. It is concluded that a moderate decrease in the eGFR occurs with age. This does not imply the presence of CKD in elderly people, since in most individuals the reduced eGFR is not accompanied by anaemia, and no individuals show hypocalcaemia, hyperphosphataemia or a high Alb/Cr ratio. Here we observed a lower Hb level and an elevated Alb/Cr ratio in subjects heterozygotic for the MYH9 gene. This could be interpreted in the sense that the gene could exert some protective effect on renal function, whereas the heterozygotic form (allele A) of the MYH9 gene could be considered a very early marker, a new risk factor for the appearance of CKD, or a sign of renal frailty in elderly people.
Collapse
Affiliation(s)
- A Otero Gonzalez
- Servicio de Nefrología-Unidad Investigación, C.H Universitario de Ourense, Ourense, Spain
| | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
157
|
Anderson BR, Howell DN, Soldano K, Garrett ME, Katsanis N, Telen MJ, Davis EE, Ashley-Koch AE. In vivo Modeling Implicates APOL1 in Nephropathy: Evidence for Dominant Negative Effects and Epistasis under Anemic Stress. PLoS Genet 2015; 11:e1005349. [PMID: 26147622 PMCID: PMC4492502 DOI: 10.1371/journal.pgen.1005349] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2015] [Accepted: 06/09/2015] [Indexed: 01/13/2023] Open
Abstract
African Americans have a disproportionate risk for developing nephropathy. This disparity has been attributed to coding variants (G1 and G2) in apolipoprotein L1 (APOL1); however, there is little functional evidence supporting the role of this protein in renal function. Here, we combined genetics and in vivo modeling to examine the role of apol1 in glomerular development and pronephric filtration and to test the pathogenic potential of APOL1 G1 and G2. Translational suppression or CRISPR/Cas9 genome editing of apol1 in zebrafish embryos results in podocyte loss and glomerular filtration defects. Complementation of apol1 morphants with wild-type human APOL1 mRNA rescues these defects. However, the APOL1 G1 risk allele does not ameliorate defects caused by apol1 suppression and the pathogenicity is conferred by the cis effect of both individual variants of the G1 risk haplotype (I384M/S342G). In vivo complementation studies of the G2 risk allele also indicate that the variant is deleterious to protein function. Moreover, APOL1 G2, but not G1, expression alone promotes developmental kidney defects, suggesting a possible dominant-negative effect of the altered protein. In sickle cell disease (SCD) patients, we reported previously a genetic interaction between APOL1 and MYH9. Testing this interaction in vivo by co-suppressing both transcripts yielded no additive effects. However, upon genetic or chemical induction of anemia, we observed a significantly exacerbated nephropathy phenotype. Furthermore, concordant with the genetic interaction observed in SCD patients, APOL1 G2 reduces myh9 expression in vivo, suggesting a possible interaction between the altered APOL1 and myh9. Our data indicate a critical role for APOL1 in renal function that is compromised by nephropathy-risk encoding variants. Moreover, our interaction studies indicate that the MYH9 locus is also relevant to the phenotype in a stressed microenvironment and suggest that consideration of the context-dependent functions of both proteins will be required to develop therapeutic paradigms. African Americans have a disproportionate risk for developing chronic kidney disease compared to European Americans. Previous studies have identified a region on chromosome 22 containing two genes, MYH9 and APOL1, which likely accounts for nearly all of this difference. Previous reports provided strong statistical evidence implicating APOL1 as the major contributor to nephropathy risk in African Americans, driven by two coding variants, termed G1 and G2. However, other groups still report statistical evidence for MYH9 association in kidney disease, and animal models have demonstrated biological relevance for MYH9 function in the kidney. Here, we show that suppressing apol1 in zebrafish embryos results in perturbed kidney function. Importantly, using this in vivo assay, we show that the G1 variant appears to cause a loss of APOL1 function, while the G2 variant results in an altered protein that may be acting antagonistically in the presence of normal APOL1. We also report a genetic interaction between apol1 and myh9 under anemic stress, which is consistent with our previous findings in sickle cell disease (SCD) nephropathy patients. Finally, we provide functional evidence in vivo that the G2-altered APOL1 may be interacting with MYH9 to confer nephropathy risk.
Collapse
Affiliation(s)
- Blair R. Anderson
- Center for Human Disease Modeling, Duke University Medical Center, Durham, North Carolina, United States of America
| | - David N. Howell
- Department of Pathology, Division of Pathology Clinical Services, Duke University, Durham, North Carolina, United States of America
| | - Karen Soldano
- Center for Human Disease Modeling, Duke University Medical Center, Durham, North Carolina, United States of America
| | - Melanie E. Garrett
- Center for Human Disease Modeling, Duke University Medical Center, Durham, North Carolina, United States of America
| | - Nicholas Katsanis
- Center for Human Disease Modeling, Duke University Medical Center, Durham, North Carolina, United States of America
| | - Marilyn J. Telen
- Department of Medicine, Division of Hematology, Duke University Medical Center, Durham, North Carolina, United States of America
| | - Erica E. Davis
- Center for Human Disease Modeling, Duke University Medical Center, Durham, North Carolina, United States of America
| | - Allison E. Ashley-Koch
- Center for Human Disease Modeling, Duke University Medical Center, Durham, North Carolina, United States of America
- * E-mail:
| |
Collapse
|
158
|
Osafo C, Raji YR, Burke D, Tayo BO, Tiffin N, Moxey-Mims MM, Rasooly RS, Kimmel PL, Ojo A, Adu D, Parekh RS. Human Heredity and Health (H3) in Africa Kidney Disease Research Network: A Focus on Methods in Sub-Saharan Africa. Clin J Am Soc Nephrol 2015; 10:2279-87. [PMID: 26138261 DOI: 10.2215/cjn.11951214] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
CKD affects an estimated 14% of adults in sub-Saharan Africa, but very little research has been done on the cause, progression, and prevention of CKD there. As part of the Human Heredity and Health in Africa (H3Africa) Consortium, the H3Africa Kidney Disease Research Network was established to study prevalent forms of kidney disease in sub-Saharan Africa and increase the capacity for genetics and genomics research. The study is performing comprehensive phenotypic characterization and analyzing environmental and genetic factors from nine clinical centers in four African countries (Ghana, Nigeria, Ethiopia, and Kenya) over a 5-year period. Approximately 4000 participants with specified kidney disease diagnoses and 4000 control participants will be enrolled in the four African countries. In addition, approximately 50 families with hereditary glomerular disease will be enrolled. The study includes both pediatric and adult participants age <1 to 74 years across a broad spectrum of kidney diseases secondary to hypertension-attributed nephropathy, diabetes, HIV infection, sickle cell disease, biopsy-proven glomerular disease, and CKD of unknown origin. Clinical and demographic data with biospecimens are collected to assess clinical, biochemical, and genetic markers of kidney disease. As of March 2015, a total of 3499 patients and controls have been recruited and 1897 had complete entry data for analysis. Slightly more than half (50.2%) of the cohort is female. Initial quality control of clinical data collection and of biosample and DNA analysis is satisfactory, demonstrating that a clinical research infrastructure can be successfully established in Africa. This study will provide clinical, biochemical, and genotypic data that will greatly increase the understanding of CKD in sub-Saharan Africa.
Collapse
Affiliation(s)
- Charlotte Osafo
- Department of Medicine and Therapeutics, University of Ghana, Accra, Ghana
| | | | | | - Bamidele O Tayo
- Department of Public Health Sciences, Loyola University Chicago, Maywood, Illinois
| | - Nicki Tiffin
- South African National Bioinformatics Institute/Medical Research Council of South Africa Bioinformatics Unit, University of the Western Cape, Cape Town, South Africa
| | - Marva M Moxey-Mims
- National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland
| | - Rebekah S Rasooly
- National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland
| | - Paul L Kimmel
- National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland
| | - Akinlolu Ojo
- Department of Medicine, University of Michigan Medical School, Ann Arbor, Michigan
| | - Dwomoa Adu
- Department of Medicine and Therapeutics, University of Ghana, Accra, Ghana;
| | - Rulan S Parekh
- Departments of Pediatrics and Medicine, Hospital for Sick Children, University of Health Network, University of Toronto, Toronto, Ontario, Canada
| | | |
Collapse
|
159
|
Abstract
The global prevalence of diabetic nephropathy is rising in parallel with the increasing incidence of diabetes in most countries. Unfortunately, up to 40 % of persons diagnosed with diabetes may develop kidney complications. Diabetic nephropathy is associated with substantially increased risks of cardiovascular disease and premature mortality. An inherited susceptibility to diabetic nephropathy exists, and progress is being made unravelling the genetic basis for nephropathy thanks to international research collaborations, shared biological resources and new analytical approaches. Multiple epidemiological studies have highlighted the clinical heterogeneity of nephropathy and the need for better phenotyping to help define important subgroups for analysis and increase the power of genetic studies. Collaborative genome-wide association studies for nephropathy have reported unique genes, highlighted novel biological pathways and suggested new disease mechanisms, but progress towards clinically relevant risk prediction models for diabetic nephropathy has been slow. This review summarises the current status, recent developments and ongoing challenges elucidating the genetics of diabetic nephropathy.
Collapse
Affiliation(s)
- Amy Jayne McKnight
- Nephrology Research Group, Centre for Public Health, Queen's University Belfast, c/o Regional Genetics Centre, Level A, Tower Block, Belfast City Hospital, Lisburn Road, Belfast, BT9 7AB, UK,
| | | | | |
Collapse
|
160
|
Li H, Chen H, Liu F, Ren C, Wang S, Bo X, Shu W. Functional annotation of HOT regions in the human genome: implications for human disease and cancer. Sci Rep 2015; 5:11633. [PMID: 26113264 PMCID: PMC4481521 DOI: 10.1038/srep11633] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2015] [Accepted: 06/01/2015] [Indexed: 12/17/2022] Open
Abstract
Advances in genome-wide association studies (GWAS) and large-scale sequencing studies have resulted in an impressive and growing list of disease- and trait-associated genetic variants. Most studies have emphasised the discovery of genetic variation in coding sequences, however, the noncoding regulatory effects responsible for human disease and cancer biology have been substantially understudied. To better characterise the cis-regulatory effects of noncoding variation, we performed a comprehensive analysis of the genetic variants in HOT (high-occupancy target) regions, which are considered to be one of the most intriguing findings of recent large-scale sequencing studies. We observed that GWAS variants that map to HOT regions undergo a substantial net decrease and illustrate development-specific localisation during haematopoiesis. Additionally, genetic risk variants are disproportionally enriched in HOT regions compared with LOT (low-occupancy target) regions in both disease-relevant and cancer cells. Importantly, this enrichment is biased toward disease- or cancer-specific cell types. Furthermore, we observed that cancer cells generally acquire cancer-specific HOT regions at oncogenes through diverse mechanisms of cancer pathogenesis. Collectively, our findings demonstrate the key roles of HOT regions in human disease and cancer and represent a critical step toward further understanding disease biology, diagnosis, and therapy.
Collapse
Affiliation(s)
- Hao Li
- Department of Biotechnology, Beijing Institute of Radiation Medicine, Beijing 100850, China
| | - Hebing Chen
- Department of Biotechnology, Beijing Institute of Radiation Medicine, Beijing 100850, China
| | - Feng Liu
- Department of Biotechnology, Beijing Institute of Radiation Medicine, Beijing 100850, China
| | - Chao Ren
- Department of Biotechnology, Beijing Institute of Radiation Medicine, Beijing 100850, China
| | - Shengqi Wang
- Department of Biotechnology, Beijing Institute of Radiation Medicine, Beijing 100850, China
| | - Xiaochen Bo
- Department of Biotechnology, Beijing Institute of Radiation Medicine, Beijing 100850, China
| | - Wenjie Shu
- Department of Biotechnology, Beijing Institute of Radiation Medicine, Beijing 100850, China
| |
Collapse
|
161
|
Matsha TE, Kengne AP, Masconi KL, Yako YY, Erasmus RT. APOL1 genetic variants, chronic kidney diseases and hypertension in mixed ancestry South Africans. BMC Genet 2015; 16:69. [PMID: 26112018 PMCID: PMC4482162 DOI: 10.1186/s12863-015-0228-6] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2015] [Accepted: 06/10/2015] [Indexed: 01/07/2023] Open
Abstract
Background The frequencies of apolipoprotein L1 (APOL1) variants and their associations with chronic kidney disease (CKD) vary substantially in populations from Africa. Moreover, available studies have used very small sample sizes to provide reliable estimates of the frequencies of these variants in the general population. We determined the frequency of the two APOL1 risk alleles (G1 and G2) and investigated their association with renal traits in a relatively large sample of mixed-ancestry South Africans. APOL1 risk variants (G1: rs60910145 and rs73885319; G2: rs71785313) were genotyped in 859 African mixed ancestry individuals using allele-specific TaqMan technology. Glomerular filtration rate (eGFR) was estimated using the Modification of Diet in Renal Disease (MDRD) and Chronic Kidney Disease Epidemiology Collaboration (CKD-EPI) equations. Results The frequencies of rs73885319, rs60910145 and rs71785313 risk alleles were respectively, 3.6 %, 3.4 %, and 5.8 %, resulting in a 1.01 % frequency of the APOL1 two-risk allele (G1:G1 or G1:G2 or G2:G2). The presence of the two-risk allele increased serum creatinine with a corresponding reduction in eGFR (either MDRD or CKD-EPI based). In dominant and log-additive genetic models, significant associations were found between rs71785313 and systolic blood pressure (both p ≤ 0.025), with a significant statistical interaction by diabetes status, p = 0.022, reflecting a negative non-significant effect in nondiabetics and a positive effect in diabetics. Conclusions Although the APOL1 variants are not common in the mixed ancestry population of South Africa, the study does provide an indication that APOL1 variants may play a role in conferring an increased risk for renal and cardiovascular risk in this population.
Collapse
Affiliation(s)
- Tandi E Matsha
- Department of Biomedical Sciences, Faculty of Health and Wellness Science, Cape Peninsula University of Technology, PO Box 1906, Bellville, Cape Town, 7530, South Africa.
| | - Andre P Kengne
- Non-Communicable Diseases Research Unit, South African Medical Research Council & University of Cape Town, Cape Town, South Africa.
| | - Katya L Masconi
- Department of Surgery, Faculty of Health Sciences, University of Witwatersrand, Johannesburg, South Africa.
| | - Yandiswa Y Yako
- Department of Surgery, Faculty of Health Sciences, University of Witwatersrand, Johannesburg, South Africa.
| | - Rajiv T Erasmus
- Division of Chemical Pathology, Faculty of Health Sciences, National Health Laboratory Service (NHLS) and University of Stellenbosch, Cape Town, South Africa.
| |
Collapse
|
162
|
Jotwani V, Shlipak MG, Scherzer R, Parekh RS, Kao WHL, Bennett M, Cohen MH, Nowicki M, Sharma A, Young M, Tien PC, Parikh CR, Estrella MM. APOL1 Genotype and Glomerular and Tubular Kidney Injury in Women With HIV. Am J Kidney Dis 2015; 65:889-98. [PMID: 25921719 PMCID: PMC4615696 DOI: 10.1053/j.ajkd.2015.02.329] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2014] [Accepted: 02/15/2015] [Indexed: 12/17/2022]
Abstract
BACKGROUND APOL1 genotype is associated with advanced kidney disease in African Americans, but the pathogenic mechanisms are unclear. Here, associations of APOL1 genotype with urine biomarkers of glomerular and tubular injury and kidney function decline were evaluated. STUDY DESIGN Observational study. SETTING & PARTICIPANTS 431 human immunodeficiency virus (HIV)-infected African American women enrolled in Women's Interagency HIV Study (WIHS). PREDICTOR APOL1 genotype. OUTCOMES Albumin-creatinine ratio (ACR), 4 tubular injury biomarkers (interleukin 18 [IL-18], kidney injury molecule 1 [KIM-1], neutrophil gelatinase-associated lipocalin [NGAL], and α1-microglobulin [A1M]), and kidney function estimated using the CKD-EPI cystatin C equation. MEASUREMENTS Participants were genotyped for APOL1 single-nucleotide polymorphisms rs73885319 (G1 allele) and rs71785313 (G2 allele). Urine biomarkers were measured using stored samples from 1999-2000. Cystatin C was measured using serum collected at baseline and 4- and 8-year follow-ups. RESULTS At baseline, ACRs were higher among 47 women with 2 APOL1 risk alleles versus 384 women with 0/1 risk allele (median, 24 vs 11mg/g; P<0.001). Compared with women with 0/1 risk allele, women with 2 risk alleles had 104% higher ACRs (95% CI, 29-223mg/g) and 2-fold greater risk of ACR>30 (95% CI, 1.17-3.44) mg/g after multivariable adjustment. APOL1 genotype showed little association with urine IL-18:Cr ratio, KIM-1:Cr ratio, and NGAL:Cr ratio (estimates of -5% [95% CI, -24% to 18%], -20% [95% CI, -36% to -1%], and 10% [95% CI, -26% to 64%], respectively) or detectable urine A1M (prevalence ratio, 1.13; 95% CI, 0.65-1.97) in adjusted analyses. Compared with women with 0/1 allele, women with 2 risk alleles had faster eGFR decline, by 1.2 (95% CI, 0.2 to 2.2) mL/min/1.73m(2) per year, and 1.7- and 3.4-fold greater rates of incident chronic kidney disease (95% CI, 1.1 to 2.5) and 10% annual eGFR decline (95% CI, 1.7 to 6.7), respectively, with minimal attenuation after adjustment for glomerular and tubular injury biomarker levels. LIMITATIONS Results may not be generalizable to men. CONCLUSIONS Among HIV-infected African American women, APOL1-associated kidney injury appears to localize to the glomerulus, rather than the tubules.
Collapse
Affiliation(s)
- Vasantha Jotwani
- Department of Medicine, San Francisco VA Medical Center, San Francisco, CA; Department of Epidemiology and Biostatistics, University of California, San Francisco, CA.
| | - Michael G Shlipak
- Department of Medicine, San Francisco VA Medical Center, San Francisco, CA; Department of Epidemiology and Biostatistics, University of California, San Francisco, CA
| | - Rebecca Scherzer
- Department of Medicine, San Francisco VA Medical Center, San Francisco, CA; Department of Epidemiology and Biostatistics, University of California, San Francisco, CA
| | - Rulan S Parekh
- Hospital for Sick Children, University Healthy Network and University of Toronto, Toronto, Canada; Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD
| | - W H Linda Kao
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD
| | - Michael Bennett
- Division of Nephrology and Hypertension, Cincinnati Children's Hospital Medical Center, Cincinnati, OH
| | - Mardge H Cohen
- Department of Medicine, Stroger Hospital, Rush University, Chicago, IL; Department of Medicine, Rush University, Chicago, IL
| | - Marek Nowicki
- Department of Medicine, University of Southern California, Los Angeles, CA
| | - Anjali Sharma
- Division of Infectious Diseases, Department of Medicine, SUNY Downstate Medical Center, Brooklyn, NY
| | - Mary Young
- Division of Infectious Diseases and Travel Medicine, Department of Medicine, Georgetown University Medical Center, Washington, DC
| | - Phyllis C Tien
- Department of Medicine, San Francisco VA Medical Center, San Francisco, CA
| | - Chirag R Parikh
- Section of Nephrology, Department of Medicine, Yale University, New Haven, CT; Program of Applied Translational Research, Yale University, New Haven, CT
| | | |
Collapse
|
163
|
Bentley AR, Divers J, Shriner D, Doumatey AP, Gutiérrez OM, Adeyemo AA, Freedman BI, Rotimi CN. APOL1 G1 genotype modifies the association between HDLC and kidney function in African Americans. BMC Genomics 2015; 16:421. [PMID: 26025194 PMCID: PMC4448293 DOI: 10.1186/s12864-015-1645-7] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2015] [Accepted: 05/20/2015] [Indexed: 01/11/2023] Open
Abstract
Background Despite evidence of an association between variants at the apolipoprotein L1 gene (APOL1) locus and a spectrum of related kidney diseases, underlying biological mechanisms remain unknown. An earlier preliminary study published by our group showed that an APOL1 variant (rs73885319) modified the association between high-density lipoprotein cholesterol (HDLC) and estimated glomerular filtration rate (eGFR) in African Americans. To further understand this relationship, we evaluated the interaction in two additional large cohorts of African Americans for a total of 3,592 unrelated individuals from the Howard University Family Study (HUFS), the Natural History of APOL1-Associated Nephropathy Study (NHAAN), and the Atherosclerosis Risk in Communities Study (ARIC). The association between HDLC and eGFR was determined using linear mixed models, and the interaction between rs73885319 genotype and HDLC was evaluated using a multiplicative term. Results Among individuals homozygous for the risk genotype, a strong inverse HDLC-eGFR association was observed, with a positive association in others (p for the interaction of the rs73885319 × HDLC =0.0001). The interaction was similar in HUFS and NHAAN, and attenuated in ARIC. Given that ARIC participants were older, we investigated an age effect; age was a significant modifier of the observed interaction. When older individuals were excluded, the interaction in ARIC was similar to that in the other studies. Conclusions Based on these findings, it is clear that the relationship between HDLC and eGFR is strongly influenced by the APOL1 rs73885319 kidney risk genotype. Moreover, the degree to which this variant modifies the association may depend on the age of the individual. More detailed physiological studies are warranted to understand how rs73885319 may affect the relationship between HDLC and eGFR in individuals with and without disease and across the lifespan. Electronic supplementary material The online version of this article (doi:10.1186/s12864-015-1645-7) contains supplementary material, which is available to authorized users.
Collapse
Affiliation(s)
- Amy R Bentley
- Center for Research on Genomics and Global Health, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA.
| | - Jasmin Divers
- Department of Biostatistical Sciences, Wake Forest School of Medicine, Winston-Salem, NC, USA.
| | - Daniel Shriner
- Center for Research on Genomics and Global Health, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA.
| | - Ayo P Doumatey
- Center for Research on Genomics and Global Health, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA.
| | - Orlando M Gutiérrez
- Division of Nephrology, University of Alabama at Birmingham, Birmingham, AL, USA.
| | - Adebowale A Adeyemo
- Center for Research on Genomics and Global Health, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA.
| | - Barry I Freedman
- Department of Internal Medicine/Nephrology, Wake Forest School of Medicine, Winston-Salem, NC, USA.
| | - Charles N Rotimi
- Center for Research on Genomics and Global Health, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA.
| |
Collapse
|
164
|
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
|
165
|
Liu R, Lee K, He JC. Genetics and Epigenetics of Diabetic Nephropathy. KIDNEY DISEASES (BASEL, SWITZERLAND) 2015; 1:42-51. [PMID: 27536664 PMCID: PMC4934801 DOI: 10.1159/000381796] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/08/2015] [Revised: 03/20/2015] [Indexed: 12/21/2022]
Abstract
BACKGROUND Diabetic nephropathy (DN) is the most common cause of end-stage renal disease (ESRD) in the USA and worldwide, contributing to significant morbidity and mortality in diabetic patients. A genetic factor for the development of DN is strongly implicated, as only one third of diabetic patients eventually develop kidney disease. Growing evidence also supports an important role of epigenetic modifications in DN. SUMMARY Multiple studies have been performed to identify risk genes and loci associated with DN. So far, only several genes and loci have been identified, none of which showed a strong association with DN. Therefore, a better study design with a larger sample size to identify rare variants and a clinically defined patient population to identify genes and loci associated with progressive DN are still needed. In addition to genetic factors, epigenetic modifications, such as DNA methylation, histone modifications and microRNAs, also play a major role in the pathogenesis of DN through a second layer of gene regulation. Although a major progress has been made in this field, epigenetic studies in DN are still in the early phase and have been limited mostly due to the heterogeneity of kidney tissue samples with multiple cells. However, rapid development of high-throughput genome-wide techniques will help us to better identify genetic variants and epigenetic changes in DN. KEY MESSAGE Understanding of genetic and epigenetic changes in DN is needed for the development of new biomarkers and better drug targets against DN. Summarized in this review are important recent findings on genetic and epigenetic studies in the field of DN.
Collapse
Affiliation(s)
- Ruijie Liu
- Division of Nephrology, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, N.Y., USA
- Renal Section, James J. Peters VAMC, New York, N.Y., USA
| | - Kyung Lee
- Division of Nephrology, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, N.Y., USA
| | - John Cijiang He
- Division of Nephrology, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, N.Y., USA
- Renal Section, James J. Peters VAMC, New York, N.Y., USA
| |
Collapse
|
166
|
Fox CS, Hall JL, Arnett DK, Ashley EA, Delles C, Engler MB, Freeman MW, Johnson JA, Lanfear DE, Liggett SB, Lusis AJ, Loscalzo J, MacRae CA, Musunuru K, Newby LK, O'Donnell CJ, Rich SS, Terzic A. Future translational applications from the contemporary genomics era: a scientific statement from the American Heart Association. Circulation 2015; 131:1715-36. [PMID: 25882488 DOI: 10.1161/cir.0000000000000211] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
The field of genetics and genomics has advanced considerably with the achievement of recent milestones encompassing the identification of many loci for cardiovascular disease and variable drug responses. Despite this achievement, a gap exists in the understanding and advancement to meaningful translation that directly affects disease prevention and clinical care. The purpose of this scientific statement is to address the gap between genetic discoveries and their practical application to cardiovascular clinical care. In brief, this scientific statement assesses the current timeline for effective translation of basic discoveries to clinical advances, highlighting past successes. Current discoveries in the area of genetics and genomics are covered next, followed by future expectations, tools, and competencies for achieving the goal of improving clinical care.
Collapse
|
167
|
The Role of Systemic Blood Pressure in the Progression of Chronic Kidney Disease. CURRENT CARDIOVASCULAR RISK REPORTS 2015. [DOI: 10.1007/s12170-015-0450-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
|
168
|
Sortica DA, Buffon MP, Souza BM, Nicoletto BB, Santer A, Assmann TS, Crispim D, Canani LH. Association between the ENPP1 K121Q polymorphism and risk of diabetic kidney disease: a systematic review and meta-analysis. PLoS One 2015; 10:e0118416. [PMID: 25794151 PMCID: PMC4368055 DOI: 10.1371/journal.pone.0118416] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2014] [Accepted: 01/16/2015] [Indexed: 01/05/2023] Open
Abstract
The potential association between the K121Q (A/C, rs1044498) polymorphism in the ectonucleotide pyrophosphatase/phosphodiesterase (ENPP1) gene and risk of diabetic kidney disease (DKD) has been investigated. Nevertheless, the effect of this variant on DKD risk is still under debate, and conflicting results have been reported. To this date, no meta-analysis has evaluated the association of the K121Q polymorphism with DKD. This paper describes the first meta-analysis conducted to evaluate whether the ENPP1K121Q polymorphism is associated with DKD. A literature search was conducted to identify all case-control or cross-sectional studies that evaluated associations between the ENPP1K121Q polymorphism and DKD. Pooled odds ratios (OR) and 95% confidence intervals (95% CI) were calculated for allele contrast, additive, dominant and recessive inheritance models. Seven studies were eligible for inclusion in the meta-analysis, providing data on 3571 type 1 or type 2 diabetic patients (1606 cases with DKD and 1965 diabetic controls without this complication). No significant heterogeneity was observed among the studies included in the meta-analysis when assuming different inheritance models (I² < 50% or P > 0.10 for the entire sample and after stratification by ethnicity). Meta-analysis results revealed significant associations between the K121Q polymorphism and risk of DKD in Asians and Europeans when assuming the different inheritance models analyzed. The most powerful association was observed for the additive model (OR = 1.74, 95% CI 1.27-2.38 for the total sample). In conclusion, the present meta-analysis detected a significant association between the ENPP1K121Q polymorphism and increased susceptibility of DKD in European and Asian populations.
Collapse
Affiliation(s)
- Denise Alves Sortica
- Endocrine Division, Hospital de Clínicas de Porto Alegre, Porto Alegre, RS, Brazil
- Postgraduate Program in Medical Sciences: Endocrinology, Universidade Federal do Rio Grande do Sul, Porto Alegre, RS, Brazil
| | - Marjorie Piucco Buffon
- Endocrine Division, Hospital de Clínicas de Porto Alegre, Porto Alegre, RS, Brazil
- Postgraduate Program in Medical Sciences: Endocrinology, Universidade Federal do Rio Grande do Sul, Porto Alegre, RS, Brazil
| | - Bianca Marmontel Souza
- Endocrine Division, Hospital de Clínicas de Porto Alegre, Porto Alegre, RS, Brazil
- Postgraduate Program in Medical Sciences: Endocrinology, Universidade Federal do Rio Grande do Sul, Porto Alegre, RS, Brazil
| | - Bruna Bellicanta Nicoletto
- Endocrine Division, Hospital de Clínicas de Porto Alegre, Porto Alegre, RS, Brazil
- Postgraduate Program in Medical Sciences: Endocrinology, Universidade Federal do Rio Grande do Sul, Porto Alegre, RS, Brazil
| | - Andressa Santer
- Endocrine Division, Hospital de Clínicas de Porto Alegre, Porto Alegre, RS, Brazil
| | - Tais Silveira Assmann
- Endocrine Division, Hospital de Clínicas de Porto Alegre, Porto Alegre, RS, Brazil
- Postgraduate Program in Medical Sciences: Endocrinology, Universidade Federal do Rio Grande do Sul, Porto Alegre, RS, Brazil
| | - Daisy Crispim
- Endocrine Division, Hospital de Clínicas de Porto Alegre, Porto Alegre, RS, Brazil
- Postgraduate Program in Medical Sciences: Endocrinology, Universidade Federal do Rio Grande do Sul, Porto Alegre, RS, Brazil
| | - Luis Henrique Canani
- Endocrine Division, Hospital de Clínicas de Porto Alegre, Porto Alegre, RS, Brazil
- Postgraduate Program in Medical Sciences: Endocrinology, Universidade Federal do Rio Grande do Sul, Porto Alegre, RS, Brazil
- * E-mail:
| |
Collapse
|
169
|
Yamada Y, Matsui K, Takeuchi I, Fujimaki T. Association of genetic variants with dyslipidemia and chronic kidney disease in a longitudinal population-based genetic epidemiological study. Int J Mol Med 2015; 35:1290-300. [PMID: 25813695 PMCID: PMC4380205 DOI: 10.3892/ijmm.2015.2152] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2015] [Accepted: 03/20/2015] [Indexed: 12/21/2022] Open
Abstract
We previously identified 9 genes and chromosomal region 3q28 as susceptibility loci for myocardial infarction, ischemic stroke, or chronic kidney disease (CKD) in Japanese individuals by genome-wide or candidate gene association studies. In the present study, we examined the association of 13 polymorphisms at these 10 loci with the prevalence of hypertriglyceridemia, hyper-low-density lipoprotein (LDL) cholesterolemia, hypo-high-density lipoprotein (HDL) cholesterolemia, or CKD in community-dwelling Japanese individuals. The study subjects comprised 6,027 individuals who were recruited to the Inabe Health and Longevity Study, a longitudinal genetic epidemiological study of atherosclerotic, cardiovascular and metabolic diseases. The subjects were recruited from individuals who visited the Health Care Center at Inabe General Hospital for an annual health checkup, and they were followed up each year (mean follow‑up period, 5 years). Longitudinal analysis with a generalized estimating equation and with adjustment for covariates revealed that rs6929846 of butyrophilin, subfamily 2, member A1 gene (BTN2A1) was significantly associated with the prevalence of hypertriglyceridemia (P=0.0001), hyper-LDL cholesterolemia (P=0.0004), and CKD (P=0.0007); rs2569512 of interleukin enhancer binding factor 3 (ILF3) was associated with hyper-LDL cholesterolemia (P=0.0029); and rs2074379 (P=0.0019) and rs2074388 (P=0.0029) of alpha-kinase 1 (ALPK1) were associated with CKD. Longitudinal analysis with a generalized linear mixed-effect model and with adjustment for covariates among all individuals revealed that rs6929846 of BTN2A1 was significantly associated with the serum concentrations of triglycerides (P=0.0011), LDL cholesterol (P=3.3 x 10(-5)), and creatinine (P=0.0006), as well as with the estimated glomerular filtration rate (eGFR) (P=0.0004); rs2569512 of ILF3 was shown to be associated with the serum concentration of LDL cholesterol (P=0.0221); and rs2074379 (P=0.0302) and rs2074388 (P=0.0336) of ALPK1 were shown to be associated with the serum concentration of creatinine. Similar analysis among individuals not taking any anti‑dyslipidemic medication revealed that rs6929846 of BTN2A1 was significantly associated with the serum concentrations of triglycerides (P=8.3 x 10‑5) and LDL cholesterol (P=0.0004), and that rs2569512 of ILF3 was associated with the serum concentration of LDL cholesterol (P=0.0010). BTN2A1 may thus be a susceptibility gene for hypertriglyceridemia, hyper‑LDL cholesterolemia and CKD in Japanese individuals.
Collapse
Affiliation(s)
- Yoshiji Yamada
- Department of Human Functional Genomics, Life Science Research Center, Mie University, Tsu, Mie 514‑8507, Japan
| | - Kota Matsui
- Core Research for Evolutionary Science and Technology (CREST), Japan Science and Technology Agency, Tokyo 102‑0076, Japan
| | - Ichiro Takeuchi
- Core Research for Evolutionary Science and Technology (CREST), Japan Science and Technology Agency, Tokyo 102‑0076, Japan
| | - Tetsuo Fujimaki
- Department of Cardiovascular Medicine, Inabe General Hospital, Inabe, Mie 511‑0428, Japan
| |
Collapse
|
170
|
Horowitz B, Miskulin D, Zager P. Epidemiology of hypertension in CKD. Adv Chronic Kidney Dis 2015; 22:88-95. [PMID: 25704344 DOI: 10.1053/j.ackd.2014.09.004] [Citation(s) in RCA: 102] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2014] [Revised: 08/25/2014] [Accepted: 09/10/2014] [Indexed: 01/13/2023]
Abstract
Both hypertension (HTN) and CKD are serious interrelated global public health problems. Nearly 30% and 15% of US adults have HTN and CKD, respectively. Because HTN may cause or result from CKD, HTN prevalence is higher and control more difficult with worse kidney function. Etiology of CKD, presence and degree of albuminuria, and genetic factors all influence HTN severity and prevalence. In addition, socioeconomic and lifestyle factors influence HTN prevalence and control. There are racial and ethnic disparities in the prevalence, treatment, risks, and outcomes of HTN in patients with CKD. Control of blood pressure (BP) in Hispanic and African Americans with CKD is worse than it is whites. There are disparities in the patterns of treatment and rates of progression of CKD in patients with HTN. The presence and severity of CKD increase treatment resistance. HTN is also extremely prevalent in patients receiving hemodialysis, and optimal targets for BP control are being elucidated. Although the awareness, treatment, and control of HTN in CKD patients is improving, control of BP in patients at all stages of CKD remains suboptimal.
Collapse
|
171
|
Duster T. A post-genomic surprise. The molecular reinscription of race in science, law and medicine. THE BRITISH JOURNAL OF SOCIOLOGY 2015; 66:1-27. [PMID: 25789799 DOI: 10.1111/1468-4446.12118] [Citation(s) in RCA: 58] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/14/2023]
Abstract
The completion of the first draft of the Human Genome Map in 2000 was widely heralded as the promise and future of genetics-based medicines and therapies - so much so that pundits began referring to the new century as 'The Century of Genetics'. Moreover, definitive assertions about the overwhelming similarities of all humans' DNA (99.9 per cent) by the leaders of the Human Genome Project were trumpeted as the end of racial thinking about racial taxonomies of human genetic differences. But the first decade of the new century brought unwelcomed surprises. First, gene therapies turned out to be far more complicated than any had anticipated - and instead the pharmaceutical industry turned to a focus on drugs that might be 'related' to population differences based upon genetic markers. While the language of 'personalized medicine' dominated this frame, research on racially and ethnically designated populations differential responsiveness to drugs dominated the empirical work in the field. Ancestry testing and 'admixture research' would play an important role in a new kind of molecular reification of racial categories. Moreover, the capacity of the super-computer to map differences reverberated into personal identification that would affect both the criminal justice system and forensic science, and generate new levels of concern about personal privacy. Social scientists in general, and sociologists in particular, have been caught short by these developments - relying mainly on assertions that racial categories are socially constructed, regionally and historically contingent, and politically arbitrary. While these assertions are true, the imprimatur of scientific legitimacy has shifted the burden, since now 'admixture research' can claim that its results get at the 'reality' of human differentiation, not the admittedly flawed social constructions of racial categories. Yet what was missing from this framing of the problem: 'admixture research' is itself based upon socially constructed categories of race.
Collapse
Affiliation(s)
- Troy Duster
- Warren Institute on Law and Social Policy, University of California; Berkeley and Department of Sociology, New York University
| |
Collapse
|
172
|
Franceschini N, Chasman DI, Cooper-DeHoff RM, Arnett DK. Genetics, ancestry, and hypertension: implications for targeted antihypertensive therapies. Curr Hypertens Rep 2015; 16:461. [PMID: 24903233 DOI: 10.1007/s11906-014-0461-9] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Hypertension is the most common chronic condition seen by physicians in ambulatory care and a condition for which life-long medications are commonly prescribed. There is evidence for genetic factors influencing blood pressure variation in populations and response to medications. This review summarizes recent genetic discoveries that surround blood pressure, hypertension, and antihypertensive drug response from genome-wide association studies, while highlighting ancestry-specific findings and any potential implication for drug therapy targets. Genome-wide association studies have identified several novel loci for inter-individual variation of blood pressure and hypertension risk in the general population. Evidence from pharmacogenetic studies suggests that genes influence the blood pressure response to antihypertensive drugs, although results are somewhat inconsistent across studies. There is still much work that remains to be done to identify genes both for efficacy and adverse events of antihypertensive medications.
Collapse
Affiliation(s)
- Nora Franceschini
- Department of Epidemiology, University of North Carolina Gillings School of Global Public Health, 137 E. Franklin St., Suite 306, Chapel Hill, NC, USA,
| | | | | | | |
Collapse
|
173
|
Genetic causes of proteinuria and nephrotic syndrome: impact on podocyte pathobiology. Pediatr Nephrol 2015; 30:221-33. [PMID: 24584664 PMCID: PMC4262721 DOI: 10.1007/s00467-014-2753-3] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/02/2013] [Revised: 12/31/2013] [Accepted: 01/02/2014] [Indexed: 12/11/2022]
Abstract
In the past 20 years, multiple genetic mutations have been identified in patients with congenital nephrotic syndrome (CNS) and both familial and sporadic focal segmental glomerulosclerosis (FSGS). Characterization of the genetic basis of CNS and FSGS has led to the recognition of the importance of podocyte injury to the development of glomerulosclerosis. Genetic mutations induce injury due to effects on the podocyte's structure, actin cytoskeleton, calcium signaling, and lysosomal and mitochondrial function. Transgenic animal studies have contributed to our understanding of podocyte pathobiology. Podocyte endoplasmic reticulum stress response, cell polarity, and autophagy play a role in maintenance of podocyte health. Further investigations related to the effects of genetic mutations on podocytes may identify new pathways for targeting therapeutics for nephrotic syndrome.
Collapse
|
174
|
Almeida FAD, Ciambelli GS, Bertoco AL, Jurado MM, Siqueira GV, Bernardo EA, Pavan MV, Gianini RJ. Agregação familiar da doença renal crônica secundária à hipertensão arterial ou diabetes mellitus: estudo caso-controle. CIENCIA & SAUDE COLETIVA 2015; 20:471-8. [DOI: 10.1590/1413-81232015202.03572014] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2014] [Accepted: 06/19/2014] [Indexed: 11/22/2022] Open
Abstract
No Brasil, a hipertensão e o diabetes mellitus tipo 2 são responsáveis por 60% dos casos de doença renal crônica terminal em terapia renal substitutiva. Estudos americanos identificaram agregação familiar da doença renal crônica, predominante em afrodescendentes. Um único estudo brasileiro observou agregação familiar entre portadores de doença renal crônica quando comparados a indivíduos internados com função renal normal. O objetivo deste artigo é avaliar se existe agregação familiar da doença renal crônica em familiares de indivíduos em terapia renal substitutiva causada por hipertensão e/ou diabetes mellitus. Estudo caso-controle tendo como casos 336 pacientes em terapia renal substitutiva portadores de diabetes mellitus ou hipertensão há pelo menos 5 anos e controles amostra pareada de indivíduos com hipertensão ou diabetes mellitus e função renal normal (n = 389). Os indivíduos em terapia renal substitutiva (casos) apresentaram razão de chance de 2,35 (IC95% 1,42-3,89; p < 0,001) versus controles de terem familiares com doença renal crônica terminal, independente da raça ou doença de base. Existe agregação familiar da doença renal crônica na amostra estudada e esta predisposição independe da raça e da doença de base (hipertensão ou diabetes mellitus).
Collapse
|
175
|
Kruzel-Davila E, Wasser WG, Aviram S, Skorecki K. APOL1 nephropathy: from gene to mechanisms of kidney injury. Nephrol Dial Transplant 2015; 31:349-58. [PMID: 25561578 DOI: 10.1093/ndt/gfu391] [Citation(s) in RCA: 71] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2014] [Accepted: 11/22/2014] [Indexed: 12/22/2022] Open
Abstract
The contribution of African ancestry to the risk of focal segmental glomerulosclerosis and chronic kidney disease has been partially explained by the recently described chromosome 22q variants in the gene apolipoprotein L1 (APOL1). The APOL1 variants appear at a high allele frequency in populations of West African ancestry as a result of apparent adaptive selection of the heterozygous state. Heterozygosity protects from infection with Trypanosoma brucei rhodesiense. This review will describe the role of the approaches in population genetics for the description of APOL1-associated nephropathies and draw inferences as to the biologic mechanisms from genetic epidemiology findings to date. Modifier loci can influence APOL1 risk for the development of kidney disease. 'Second hits', both viral and non-viral, may explain the discrepancy between the remarkably high odds ratios and the low lifetime risks of kidney disease in two allele carriers of APOL1 risk variants. Therapeutic strategies for APOL1-associated nephropathies will require the prevention and treatment of these 'second hits' and the development of drugs to protect the APOL1 downstream renal injury pathways.
Collapse
Affiliation(s)
- Etty Kruzel-Davila
- Rappaport Faculty of Medicine and Research Institute, Technion-Israel Institute of Technology, Rambam Health Care Campus, Haifa 3109601, Israel Rambam Health Care Campus, Haifa 3109601, Israel
| | - Walter G Wasser
- Rambam Health Care Campus, Haifa 3109601, Israel Mayanei HaYeshua Medical Center, Bnei Brak 51544, Israel
| | - Sharon Aviram
- Rappaport Faculty of Medicine and Research Institute, Technion-Israel Institute of Technology, Rambam Health Care Campus, Haifa 3109601, Israel
| | - Karl Skorecki
- Rappaport Faculty of Medicine and Research Institute, Technion-Israel Institute of Technology, Rambam Health Care Campus, Haifa 3109601, Israel Rambam Health Care Campus, Haifa 3109601, Israel
| |
Collapse
|
176
|
Freedman BI, Langefeld CD, Lu L, Palmer ND, Smith SC, Bagwell BM, Hicks PJ, Xu J, Wagenknecht LE, Raffield LM, Register TC, Carr JJ, Bowden DW, Divers J. APOL1 associations with nephropathy, atherosclerosis, and all-cause mortality in African Americans with type 2 diabetes. Kidney Int 2015; 87:176-81. [PMID: 25054777 PMCID: PMC4281283 DOI: 10.1038/ki.2014.255] [Citation(s) in RCA: 66] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2014] [Revised: 05/30/2014] [Accepted: 06/05/2014] [Indexed: 12/30/2022]
Abstract
Albuminuria and reduced estimated glomerular filtration rate (eGFR) associate with two apolipoprotein L1 gene (APOL1) variants in nondiabetic African Americans (AAs). Whether APOL1 associates with subclinical atherosclerosis and survival remains unclear. To determine this, 717 African American-Diabetes Heart Study participants underwent computed tomography to determine coronary artery-, carotid artery-, and aorta-calcified atherosclerotic plaque mass scores in addition to the urine albumin:creatinine ratio (UACR), eGFR, and C-reactive protein (CRP). Associations between mass scores and APOL1 were assessed adjusting for age, gender, African ancestry, body mass index (BMI), hemoglobin A1c, smoking, hypertension, use of statins and angiotensin-converting enzyme inhibitors, albuminuria, and eGFR. Participants were 58.9% female with mean age 56.5 years, eGFR 89.5 ml/min per 1.73 m(2), UACR 169.6 mg/g, and coronary artery-, carotid artery-, and aorta-calcified plaque mass scores of 610, 171, and 5378, respectively. In fully adjusted models, APOL1 risk variants were significantly associated with lower levels of carotid artery-calcified plaque (β=-0.42, s.e. 0.18; dominant model) and marginally lower coronary artery plaque (β=-0.36, s.e. 0.21; dominant model), but not with aorta-calcified plaque, CRP, UACR, or eGFR. By the end of a mean follow-up of 5.0 years, 89 participants had died. APOL1 nephropathy risk variants were significantly associated with improved survival (hazard ratio 0.67 for one copy; 0.44 for two copies). Thus, APOL1 nephropathy variants associate with lower levels of subclinical atherosclerosis and reduced risk of death in AAs with type 2 diabetes mellitus.
Collapse
Affiliation(s)
- Barry I. Freedman
- Department of Internal Medicine–Section on Nephrology, Wake Forest School of Medicine, Winston-Salem, North Carolina
- Center for Genomics and Personalized Medicine Research, Wake Forest School of Medicine, Winston-Salem, North Carolina
- Center for Diabetes Research, Wake Forest School of Medicine, Winston-Salem, North Carolina
- Center for Public Health Genomics, Wake Forest School of Medicine, Winston-Salem, North Carolina
| | - Carl D. Langefeld
- Center for Genomics and Personalized Medicine Research, Wake Forest School of Medicine, Winston-Salem, North Carolina
- Center for Diabetes Research, Wake Forest School of Medicine, Winston-Salem, North Carolina
- Center for Public Health Genomics, Wake Forest School of Medicine, Winston-Salem, North Carolina
- Division of Public Health Sciences-Department of Biostatistical Sciences, Wake Forest School of Medicine, Winston-Salem, North Carolina
| | - Lingyi Lu
- Center for Public Health Genomics, Wake Forest School of Medicine, Winston-Salem, North Carolina
- Division of Public Health Sciences-Department of Biostatistical Sciences, Wake Forest School of Medicine, Winston-Salem, North Carolina
| | - Nicholette D. Palmer
- Center for Genomics and Personalized Medicine Research, Wake Forest School of Medicine, Winston-Salem, North Carolina
- Center for Diabetes Research, Wake Forest School of Medicine, Winston-Salem, North Carolina
- Center for Public Health Genomics, Wake Forest School of Medicine, Winston-Salem, North Carolina
- Division of Public Health Sciences-Department of Biostatistical Sciences, Wake Forest School of Medicine, Winston-Salem, North Carolina
- Department of Biochemistry, Wake Forest School of Medicine, Winston-Salem, North Carolina
| | - S. Carrie Smith
- Department of Internal Medicine–Section on Nephrology, Wake Forest School of Medicine, Winston-Salem, North Carolina
| | - Benjamin M. Bagwell
- Department of Internal Medicine–Section on Nephrology, Wake Forest School of Medicine, Winston-Salem, North Carolina
| | - Pamela J. Hicks
- Department of Biochemistry, Wake Forest School of Medicine, Winston-Salem, North Carolina
| | - Jianzhao Xu
- Center for Genomics and Personalized Medicine Research, Wake Forest School of Medicine, Winston-Salem, North Carolina
- Center for Diabetes Research, Wake Forest School of Medicine, Winston-Salem, North Carolina
- Department of Biochemistry, Wake Forest School of Medicine, Winston-Salem, North Carolina
| | - Lynne E. Wagenknecht
- Division of Public Health Sciences-Department of Biostatistical Sciences, Wake Forest School of Medicine, Winston-Salem, North Carolina
| | - Laura M. Raffield
- Center for Genomics and Personalized Medicine Research, Wake Forest School of Medicine, Winston-Salem, North Carolina
- Center for Diabetes Research, Wake Forest School of Medicine, Winston-Salem, North Carolina
| | - Thomas C. Register
- Department of Pathology, Wake Forest School of Medicine, Winston-Salem, North Carolina
| | - J. Jeffrey Carr
- Department of Radiology; Vanderbilt University School of Medicine, Nashville, Tennessee
| | - Donald W. Bowden
- Center for Genomics and Personalized Medicine Research, Wake Forest School of Medicine, Winston-Salem, North Carolina
- Center for Public Health Genomics, Wake Forest School of Medicine, Winston-Salem, North Carolina
| | - Jasmin Divers
- Center for Genomics and Personalized Medicine Research, Wake Forest School of Medicine, Winston-Salem, North Carolina
- Center for Diabetes Research, Wake Forest School of Medicine, Winston-Salem, North Carolina
- Center for Public Health Genomics, Wake Forest School of Medicine, Winston-Salem, North Carolina
- Division of Public Health Sciences-Department of Biostatistical Sciences, Wake Forest School of Medicine, Winston-Salem, North Carolina
| |
Collapse
|
177
|
Bruce MA, Griffith DM, Thorpe RJ. Stress and the kidney. Adv Chronic Kidney Dis 2015; 22:46-53. [PMID: 25573512 DOI: 10.1053/j.ackd.2014.06.008] [Citation(s) in RCA: 50] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2014] [Revised: 06/19/2014] [Accepted: 06/30/2014] [Indexed: 12/30/2022]
Abstract
The prevalence of CKD has increased considerably over the past 2 decades. The rising rates of CKD have been attributed to known comorbidities such as diabetes, hypertension, and obesity; however, recent research has begun to explore the degree to which social, economic, and psychological factors have implications for the prevalence and progression of CKD, especially among high-risk populations such as African Americans. It has been suggested that stress can have implications for CKD, but this area of research has been largely unexplored. One contributing factor associated with the paucity of research on CKD is that many of the social, psychological, and environmental stressors cannot be recreated or simulated in a laboratory setting. Social science has established that stress can have implications for health, and we believe that stress is an important determinant of the development and progression of CKD. We draw heavily from the social scientific and social epidemiologic literature to present an intersectional conceptual frame specifying how stress can have implications for kidney disease, its progression, and its complications through multiple stressors and pathways.
Collapse
|
178
|
Madhavan SM, O'Toole JF. The biology of APOL1 with insights into the association between APOL1 variants and chronic kidney disease. Clin Exp Nephrol 2014; 18:238-42. [PMID: 24233469 DOI: 10.1007/s10157-013-0907-4] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2013] [Accepted: 10/29/2013] [Indexed: 12/15/2022]
Abstract
Recent studies have identified genetic variants in APOL1 that may contribute to the increased incidence of kidney disease in populations with African ancestry. Here, we review the biology of APOL1 present in the circulation and localized to the kidney as it may contribute to the pathogenesis of APOL1-associated kidney disease.
Collapse
|
179
|
Braun MC, Herring SM, Gokul N, Monita M, Bell R, Zhu Y, Gonzalez-Garay ML, Wenderfer SE, Doris PA. Hypertensive renal injury is associated with gene variation affecting immune signaling. ACTA ACUST UNITED AC 2014; 7:903-10. [PMID: 25366137 DOI: 10.1161/circgenetics.114.000533] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
BACKGROUND The spontaneously hypertensive rat (SHR) strain exists in lines that contrast strongly in susceptibility to renal injury in hypertension. These inbred lines share common ancestry, and only 13% of their genomes arise from different ancestors. METHODS AND RESULTS We used next gen sequencing to detect natural allelic variation in 5 genes of the immunoreceptor signaling pathway (IgH, Dok3, Src, Syk, and JunD) that arise from different ancestors in the injury-prone SHR-A3 and the resistant SHR-B2 lines. We created an intercross between these lines, and in the F2 progeny, we observed that the inheritance of haplotype blocks containing the SHR-A3 alleles of these 5 genes correlated with increased albuminuria and histological measures of renal injury. To test whether accumulated genetic variation in this pathway may create a therapeutic target in hypertensive renal injury, rats of both lines were treated with the immunosuppressant mycophenolate mofetil (MMF). MMF reduced proteinuria (albumin to creatinine ratio) from 6.6 to 1.2 mg/mg (P<0.001) in SHR-A3. Glomerular injury scores were reduced in MMF-treated SHR-A3 from 1.6 to 1.4 (P<0.002). Tubulo-interstitial injury was reduced in MMF-treated SHR-A3 from 2.62 to 2.0 (P=0.001). MMF treatment also reduced renal fibrosis in SHR-A3 (3.9 versus 2.0; P<0.001). CONCLUSIONS Polygenic susceptibility to renal injury in hypertension arises in association with genetic variation in genes that participate in immune responses and is dramatically improved by reduction of immune system activity.
Collapse
Affiliation(s)
- Michael C Braun
- From the Department of Pediatrics, Baylor College of Medicine (M.C.B., S.E.W.), and Institute of Molecular Medicine (S.M.H., N.G., M.M., R.B., Y.Z., M.L.G.-G., P.A.D.), University of Texas Health Science Center at Houston
| | - Stacy M Herring
- From the Department of Pediatrics, Baylor College of Medicine (M.C.B., S.E.W.), and Institute of Molecular Medicine (S.M.H., N.G., M.M., R.B., Y.Z., M.L.G.-G., P.A.D.), University of Texas Health Science Center at Houston
| | - Nisha Gokul
- From the Department of Pediatrics, Baylor College of Medicine (M.C.B., S.E.W.), and Institute of Molecular Medicine (S.M.H., N.G., M.M., R.B., Y.Z., M.L.G.-G., P.A.D.), University of Texas Health Science Center at Houston
| | - Monique Monita
- From the Department of Pediatrics, Baylor College of Medicine (M.C.B., S.E.W.), and Institute of Molecular Medicine (S.M.H., N.G., M.M., R.B., Y.Z., M.L.G.-G., P.A.D.), University of Texas Health Science Center at Houston
| | - Rebecca Bell
- From the Department of Pediatrics, Baylor College of Medicine (M.C.B., S.E.W.), and Institute of Molecular Medicine (S.M.H., N.G., M.M., R.B., Y.Z., M.L.G.-G., P.A.D.), University of Texas Health Science Center at Houston
| | - Yaming Zhu
- From the Department of Pediatrics, Baylor College of Medicine (M.C.B., S.E.W.), and Institute of Molecular Medicine (S.M.H., N.G., M.M., R.B., Y.Z., M.L.G.-G., P.A.D.), University of Texas Health Science Center at Houston
| | - Manuel L Gonzalez-Garay
- From the Department of Pediatrics, Baylor College of Medicine (M.C.B., S.E.W.), and Institute of Molecular Medicine (S.M.H., N.G., M.M., R.B., Y.Z., M.L.G.-G., P.A.D.), University of Texas Health Science Center at Houston
| | - Scott E Wenderfer
- From the Department of Pediatrics, Baylor College of Medicine (M.C.B., S.E.W.), and Institute of Molecular Medicine (S.M.H., N.G., M.M., R.B., Y.Z., M.L.G.-G., P.A.D.), University of Texas Health Science Center at Houston
| | - Peter A Doris
- From the Department of Pediatrics, Baylor College of Medicine (M.C.B., S.E.W.), and Institute of Molecular Medicine (S.M.H., N.G., M.M., R.B., Y.Z., M.L.G.-G., P.A.D.), University of Texas Health Science Center at Houston.
| |
Collapse
|
180
|
Lucas GM, Ross MJ, Stock PG, Shlipak MG, Wyatt CM, Gupta SK, Atta MG, Wools-Kaloustian KK, Pham PA, Bruggeman LA, Lennox JL, Ray PE, Kalayjian RC. Clinical practice guideline for the management of chronic kidney disease in patients infected with HIV: 2014 update by the HIV Medicine Association of the Infectious Diseases Society of America. Clin Infect Dis 2014; 59:e96-138. [PMID: 25234519 PMCID: PMC4271038 DOI: 10.1093/cid/ciu617] [Citation(s) in RCA: 205] [Impact Index Per Article: 20.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2014] [Accepted: 07/25/2014] [Indexed: 12/15/2022] Open
Abstract
It is important to realize that guidelines cannot always account for individual variation among patients. They are not intended to supplant physician judgment with respect to particular patients or special clinical situations. IDSA considers adherence to these guidelines to be voluntary, with the ultimate determination regarding their application to be made by the physician in the light of each patient's individual circumstances.
Collapse
Affiliation(s)
| | | | | | | | | | | | | | | | - Paul A. Pham
- Johns HopkinsSchool of Medicine, Baltimore, Maryland
| | - Leslie A. Bruggeman
- MetroHealth Medical Center, Case Western Reserve University, Cleveland, Ohio
| | | | | | - Robert C. Kalayjian
- MetroHealth Medical Center, Case Western Reserve University, Cleveland, Ohio
| |
Collapse
|
181
|
Udler MS, Nadkarni GN, Belbin G, Lotay V, Wyatt C, Gottesman O, Bottinger EP, Kenny EE, Peter I. Effect of Genetic African Ancestry on eGFR and Kidney Disease. J Am Soc Nephrol 2014; 26:1682-92. [PMID: 25349204 DOI: 10.1681/asn.2014050474] [Citation(s) in RCA: 72] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2014] [Accepted: 09/02/2014] [Indexed: 01/08/2023] Open
Abstract
Self-reported ancestry, genetically determined ancestry, and APOL1 polymorphisms are associated with variation in kidney function and related disease risk, but the relative importance of these factors remains unclear. We estimated the global proportion of African ancestry for 9048 individuals at Mount Sinai Medical Center in Manhattan (3189 African Americans, 1721 European Americans, and 4138 Hispanic/Latino Americans by self-report) using genome-wide genotype data. CKD-EPI eGFR and genotypes of three APOL1 coding variants were available. In admixed African Americans and Hispanic/Latino Americans, serum creatinine values increased as African ancestry increased (per 10% increase in African ancestry, creatinine values increased 1% in African Americans and 0.9% in Hispanic/Latino Americans; P≤1x10(-7)). eGFR was likewise significantly associated with African genetic ancestry in both populations. In contrast, APOL1 risk haplotypes were significantly associated with CKD, eGFR<45 ml/min per 1.73 m(2), and ESRD, with effects increasing with worsening disease states and the contribution of genetic African ancestry decreasing in parallel. Using genetic ancestry in the eGFR equation to reclassify patients as black on the basis of ≥50% African ancestry resulted in higher eGFR for 14.7% of Hispanic/Latino Americans and lower eGFR for 4.1% of African Americans, affecting CKD staging in 4.3% and 1% of participants, respectively. Reclassified individuals had electrolyte values consistent with their newly assigned CKD stage. In summary, proportion of African ancestry was significantly associated with normal-range creatinine and eGFR, whereas APOL1 risk haplotypes drove the associations with CKD. Recalculation of eGFR on the basis of genetic ancestry affected CKD staging and warrants additional investigation.
Collapse
Affiliation(s)
- Miriam S Udler
- Departments of Medicine and Genetics and Genomic Sciences, The Charles Bronfman Institute for Personalized Medicine,
| | - Girish N Nadkarni
- Departments of Medicine and The Charles Bronfman Institute for Personalized Medicine, Division of Nephrology
| | - Gillian Belbin
- Genetics and Genomic Sciences, The Charles Bronfman Institute for Personalized Medicine
| | - Vaneet Lotay
- The Charles Bronfman Institute for Personalized Medicine
| | | | - Omri Gottesman
- Departments of Medicine and The Charles Bronfman Institute for Personalized Medicine
| | - Erwin P Bottinger
- Departments of Medicine and The Charles Bronfman Institute for Personalized Medicine, Division of Nephrology
| | - Eimear E Kenny
- Genetics and Genomic Sciences, The Charles Bronfman Institute for Personalized Medicine, The Center for Statistical Genetics, and The Institute for Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Inga Peter
- Genetics and Genomic Sciences, The Charles Bronfman Institute for Personalized Medicine, The Institute for Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, New York
| |
Collapse
|
182
|
Gbadegesin RA, Adeyemo A, Webb NJA, Greenbaum LA, Abeyagunawardena A, Thalgahagoda S, Kale A, Gipson D, Srivastava T, Lin JJ, Chand D, Hunley TE, Brophy PD, Bagga A, Sinha A, Rheault MN, Ghali J, Nicholls K, Abraham E, Janjua HS, Omoloja A, Barletta GM, Cai Y, Milford DD, O'Brien C, Awan A, Belostotsky V, Smoyer WE, Homstad A, Hall G, Wu G, Nagaraj S, Wigfall D, Foreman J, Winn MP. HLA-DQA1 and PLCG2 Are Candidate Risk Loci for Childhood-Onset Steroid-Sensitive Nephrotic Syndrome. J Am Soc Nephrol 2014; 26:1701-10. [PMID: 25349203 DOI: 10.1681/asn.2014030247] [Citation(s) in RCA: 91] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2014] [Accepted: 09/09/2014] [Indexed: 12/11/2022] Open
Abstract
Steroid-sensitive nephrotic syndrome (SSNS) accounts for >80% of cases of nephrotic syndrome in childhood. However, the etiology and pathogenesis of SSNS remain obscure. Hypothesizing that coding variation may underlie SSNS risk, we conducted an exome array association study of SSNS. We enrolled a discovery set of 363 persons (214 South Asian children with SSNS and 149 controls) and genotyped them using the Illumina HumanExome Beadchip. Four common single nucleotide polymorphisms (SNPs) in HLA-DQA1 and HLA-DQB1 (rs1129740, rs9273349, rs1071630, and rs1140343) were significantly associated with SSNS at or near the Bonferroni-adjusted P value for the number of single variants that were tested (odds ratio, 2.11; 95% confidence interval, 1.56 to 2.86; P=1.68×10(-6) (Fisher exact test). Two of these SNPs-the missense variants C34Y (rs1129740) and F41S (rs1071630) in HLA-DQA1-were replicated in an independent cohort of children of white European ancestry with SSNS (100 cases and ≤589 controls; P=1.42×10(-17)). In the rare variant gene set-based analysis, the best signal was found in PLCG2 (P=7.825×10(-5)). In conclusion, this exome array study identified HLA-DQA1 and PLCG2 missense coding variants as candidate loci for SSNS. The finding of a MHC class II locus underlying SSNS risk suggests a major role for immune response in the pathogenesis of SSNS.
Collapse
Affiliation(s)
- Rasheed A Gbadegesin
- Department of Pediatrics, Division of Nephrology and Center for Human Genetics, Duke University Medical Center, Durham, North Carolina
| | - Adebowale Adeyemo
- Center for Research on Genomics and Global Health, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland;
| | - Nicholas J A Webb
- Department of Pediatric Nephrology and NIHR/Wellcome Trust Children's Clinical Research Facility, The University of Manchester, Manchester Academic Health Science Centre, Royal Manchester Children's Hospital, Manchester, United Kingdom
| | - Larry A Greenbaum
- Division of Pediatric Nephrology, Emory University School of Medicine and Children's Healthcare of Atlanta, Georgia
| | | | | | - Arundhati Kale
- Division of Nephrology, Baylor College of Medicine and Texas Children's Hospital, Houston, Texas
| | - Debbie Gipson
- Department of Pediatrics, Division of Nephrology, University of Michigan, Ann Arbor, Michigan
| | - Tarak Srivastava
- Division of Nephrology, Children's Mercy Hospital, Kansas City, Missouri
| | - Jen-Jar Lin
- Department of Pediatrics, Division of Nephrology, Wake Forest University Baptist Medical Center, Winston-Salem, North Carolina
| | - Deepa Chand
- Department of Pediatrics, Division of Nephrology, Rush University, Chicago, Illinois
| | - Tracy E Hunley
- Department of Pediatrics, Division of Nephrology, Vanderbilt University, Nashville, Tennessee
| | - Patrick D Brophy
- Department of Pediatrics, Division of Nephrology, University of Iowa, Iowa City, Iowa
| | - Arvind Bagga
- Department of Pediatrics, Division of Nephrology, All India Institute of Medical Science, Ansari Nagar, New Delhi, India
| | - Aditi Sinha
- Department of Pediatrics, Division of Nephrology, All India Institute of Medical Science, Ansari Nagar, New Delhi, India
| | - Michelle N Rheault
- Department of Pediatrics, Division of Nephrology, University of Minnesota Amplatz Children's Hospital, Minneapolis, Minnesota
| | - Joanna Ghali
- Department of Nephrology, Royal Melbourne Hospital, Parkville, Australia
| | - Kathy Nicholls
- Department of Nephrology, Royal Melbourne Hospital, Parkville, Australia
| | - Elizabeth Abraham
- Department of Pediatrics, Division of Nephrology, St. Louis University, St. Louis, Missouri
| | - Halima S Janjua
- Pediatric Institute, Center for Pediatric Nephrology, Cleveland Clinic, Cleveland, Ohio
| | - Abiodun Omoloja
- Division of Nephrology, Dayton Children's Hospital, Dayton, Ohio
| | | | - Yi Cai
- Division of Nephrology, Helen Devos Children's Hospital, Grand Rapids, Michigan
| | | | | | - Atif Awan
- Division of Nephrology, The Children's University Hospital, Dublin, Ireland
| | - Vladimir Belostotsky
- Department of Pediatrics, Division of Nephrology, Leeds Teaching Hospital, Leeds, United Kingdom
| | - William E Smoyer
- Center for Clinical and Translational Research, Research Institute at Nationwide Children's Hospital, Columbus, Ohio; and
| | - Alison Homstad
- Department of Pediatrics, Division of Nephrology and Center for Human Genetics, Duke University Medical Center, Durham, North Carolina
| | - Gentzon Hall
- Department of Medicine, Division of Nephrology and Center for Human Genetics, Duke University Medical Center, Durham, North Carolina
| | - Guanghong Wu
- Department of Medicine, Division of Nephrology and Center for Human Genetics, Duke University Medical Center, Durham, North Carolina
| | - Shashi Nagaraj
- Department of Pediatrics, Division of Nephrology and Center for Human Genetics, Duke University Medical Center, Durham, North Carolina
| | - Delbert Wigfall
- Department of Pediatrics, Division of Nephrology and Center for Human Genetics, Duke University Medical Center, Durham, North Carolina
| | - John Foreman
- Department of Pediatrics, Division of Nephrology and Center for Human Genetics, Duke University Medical Center, Durham, North Carolina
| | - Michelle P Winn
- Department of Medicine, Division of Nephrology and Center for Human Genetics, Duke University Medical Center, Durham, North Carolina
| | | |
Collapse
|
183
|
Smyth LJ, Duffy S, Maxwell AP, McKnight AJ. Genetic and epigenetic factors influencing chronic kidney disease. Am J Physiol Renal Physiol 2014; 307:F757-76. [PMID: 25080522 DOI: 10.1152/ajprenal.00306.2014] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
Chronic kidney disease (CKD) has become a serious public health problem because of its associated morbidity, premature mortality, and attendant healthcare costs. The rising number of persons with CKD is linked with the aging population structure and an increased prevalence of diabetes, hypertension, and obesity. There is an inherited risk associated with developing CKD, as evidenced by familial clustering and differing prevalence rates across ethnic groups. Previous studies to determine the inherited risk factors for CKD rarely identified genetic variants that were robustly replicated. However, improvements in genotyping technologies and analytic methods are now helping to identify promising genetic loci aided by international collaboration and multiconsortia efforts. More recently, epigenetic modifications have been proposed to play a role in both the inherited susceptibility to CKD and, importantly, to explain how the environment dynamically interacts with the genome to alter an individual's disease risk. Genome-wide, epigenome-wide, and whole transcriptome studies have been performed, and optimal approaches for integrative analysis are being developed. This review summarizes recent research and the current status of genetic and epigenetic risk factors influencing CKD using population-based information.
Collapse
Affiliation(s)
- L J Smyth
- Nephrology Research, Centre for Public Health, Queen's University of Belfast, Belfast, Northern Ireland
| | - S Duffy
- Nephrology Research, Centre for Public Health, Queen's University of Belfast, Belfast, Northern Ireland
| | - A P Maxwell
- Nephrology Research, Centre for Public Health, Queen's University of Belfast, Belfast, Northern Ireland
| | - A J McKnight
- Nephrology Research, Centre for Public Health, Queen's University of Belfast, Belfast, Northern Ireland
| |
Collapse
|
184
|
Pollak MR. Familial FSGS. Adv Chronic Kidney Dis 2014; 21:422-5. [PMID: 25168831 DOI: 10.1053/j.ackd.2014.06.001] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2014] [Revised: 05/31/2014] [Accepted: 06/02/2014] [Indexed: 12/12/2022]
Abstract
Focal segmental glomerulosclerosis (FSGS) and nephrotic syndrome can be caused by rare highly penetrant mutations in number of genes. FSGS can follow both recessive and dominant inheritance patterns. In general, recessive forms present early, whereas the autosomal dominant forms present in adolescence or adulthood. Many of the genes found to be mutated in FSGS and nephrotic syndrome patients encode proteins essential for normal podocyte structure and/or function. An exception appears to be APOL1, which harbors common variants responsible for the high rate of FSGS and other nephropathies in people of recent African ancestry. Familial FSGS should be regarded as part of a spectrum of inherited glomerulopathies where the precise histologic presentation may depend on the age of onset, function of the responsible gene and gene products, and other factors.
Collapse
|
185
|
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
|
186
|
Padullés A, Rama I, Llaudó I, Lloberas N. Developments in renal pharmacogenomics and applications in chronic kidney disease. PHARMACOGENOMICS & PERSONALIZED MEDICINE 2014; 7:251-66. [PMID: 25206311 PMCID: PMC4157401 DOI: 10.2147/pgpm.s52763] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Chronic kidney disease (CKD) has shown an increasing prevalence in the last century. CKD encompasses a poor prognosis related to a remarkable number of comorbidities, and many patients suffer from this disease progression. Once the factors linked with CKD evolution are distinguished, it will be possible to provide and enhance a more intensive treatment to high-risk patients. In this review, we focus on the emerging markers that might be predictive or related to CKD progression physiopathology as well as those related to a different pattern of response to treatment, such as inhibitors of the renin–angiotensin system (including angiotensin-converting enzyme inhibitors and angiotensin II receptor blockers; the vitamin D receptor agonist; salt sensitivity hypertension; and progressive kidney-disease markers with identified genetic polymorphisms). Candidate-gene association studies and genome-wide association studies have analyzed the genetic basis for common renal diseases, including CKD and related factors such as diabetes and hypertension. This review will, in brief, consider genotype-based pharmacotherapy, risk prediction, drug target recognition, and personalized treatments, and will mainly focus on findings in CKD patients. An improved understanding will smooth the progress of switching from classical clinical medicine to gene-based medicine.
Collapse
Affiliation(s)
- Ariadna Padullés
- Pharmacy Department, IDIBELL-Hospital Universitari Bellvitge, L'Hospitalet de Llobregat, Barcelona, Spain
| | - Inés Rama
- Nephrology Department, IDIBELL-Hospital Universitari Bellvitge, L'Hospitalet de Llobregat, Barcelona, Spain
| | - Inés Llaudó
- Nephrology Department, IDIBELL-Hospital Universitari Bellvitge, L'Hospitalet de Llobregat, Barcelona, Spain
| | - Núria Lloberas
- Nephrology Department, IDIBELL-Hospital Universitari Bellvitge, L'Hospitalet de Llobregat, Barcelona, Spain
| |
Collapse
|
187
|
Recuenco MC, Ohmori T, Tanigawa S, Taguchi A, Fujimura S, Conti MA, Wei Q, Kiyonari H, Abe T, Adelstein RS, Nishinakamura R. Nonmuscle Myosin II Regulates the Morphogenesis of Metanephric Mesenchyme-Derived Immature Nephrons. J Am Soc Nephrol 2014; 26:1081-91. [PMID: 25168025 DOI: 10.1681/asn.2014030281] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2014] [Accepted: 07/14/2014] [Indexed: 12/21/2022] Open
Abstract
The kidney develops from reciprocal interactions between the metanephric mesenchyme and ureteric bud. The mesenchyme transforms into epithelia and forms complicated nephron structures, whereas the ureteric bud extends its pre-existing epithelial ducts. Although the roles are well established for extracellular stimuli, such as Wnt and Notch, it is unclear how the intracellular cytoskeleton regulates these morphogenetic processes. Myh9 and Myh10 encode nonmuscle myosin II heavy chains, and Myh9 mutations in humans are implicated in congenital kidney diseases and focal segmental glomerulosclerosis in adults. Here, we analyzed the roles of Myh9 and Myh10 in the developing kidney. Ureteric bud-specific depletion of Myh9 resulted in no apparent phenotypes, whereas mesenchyme-specific Myh9 deletion caused proximal tubule dilations and renal failure. Mesenchyme-specific Myh9/Myh10 mutant mice died shortly after birth and showed a severe defect in nephron formation. The nascent mutant nephrons failed to form a continuous lumen, which likely resulted from impaired apical constriction of the elongating tubules. In addition, nephron progenitors lacking Myh9/Myh10 or the possible interactor Kif26b were less condensed at midgestation and reduced at birth. Taken together, nonmuscle myosin II regulates the morphogenesis of immature nephrons derived from the metanephric mesenchyme and the maintenance of nephron progenitors. Our data also suggest that Myh9 deletion in mice results in failure to maintain renal tubules but not in glomerulosclerosis.
Collapse
Affiliation(s)
| | | | | | | | - Sayoko Fujimura
- Liaison Laboratory Research Promotion Center, Institute of Molecular Embryology and Genetics, Kumamoto University, Kumamoto, Japan
| | - Mary Anne Conti
- Laboratory of Molecular Cardiology, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, Maryland; and
| | - Qize Wei
- Laboratory of Molecular Cardiology, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, Maryland; and
| | - Hiroshi Kiyonari
- Laboratory for Animal Resources and Genetic Engineering, RIKEN Center for Developmental Biology, Kobe, Japan
| | - Takaya Abe
- Laboratory for Animal Resources and Genetic Engineering, RIKEN Center for Developmental Biology, Kobe, Japan
| | - Robert S Adelstein
- Laboratory of Molecular Cardiology, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, Maryland; and
| | | |
Collapse
|
188
|
Parker MM, Foreman MG, Abel HJ, Mathias RA, Hetmanski JB, Crapo JD, Silverman EK, Beaty TH. Admixture mapping identifies a quantitative trait locus associated with FEV1/FVC in the COPDGene Study. Genet Epidemiol 2014; 38:652-9. [PMID: 25112515 DOI: 10.1002/gepi.21847] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2013] [Revised: 06/30/2014] [Accepted: 07/03/2014] [Indexed: 12/31/2022]
Abstract
African Americans are admixed with genetic contributions from European and African ancestral populations. Admixture mapping leverages this information to map genes influencing differential disease risk across populations. We performed admixture and association mapping in 3,300 African American current or former smokers from the COPDGene Study. We analyzed estimated local ancestry and SNP genotype information to identify regions associated with FEV1 /FVC, the ratio of forced expiratory volume in one second to forced vital capacity, measured by spirometry performed after bronchodilator administration. Global African ancestry inversely associated with FEV1 /FVC (P = 0.035). Genome-wide admixture analysis, controlling for age, gender, body mass index, current smoking status, pack-years smoked, and four principal components summarizing the genetic background of African Americans in the COPDGene Study, identified a region on chromosome 12q14.1 associated with FEV1 /FVC (P = 2.1 × 10(-6) ) when regressed on local ancestry. Allelic association in this region of chromosome 12 identified an intronic variant in FAM19A2 (rs348644) as associated with FEV1 /FVC (P = 1.76 × 10(-6) ). By combining admixture and association mapping, a marker on chromosome 12q14.1 was identified as being associated with reduced FEV1 /FVC ratio among African Americans in the COPDGene Study.
Collapse
Affiliation(s)
- Margaret M Parker
- Department of Epidemiology, Bloomberg School of Public Health, The Johns Hopkins University, Baltimore, Maryland, United States of America
| | | | | | | | | | | | | | | |
Collapse
|
189
|
Chen SY, Chen CH, Huang YC, Chan CJ, Chen DC, Tsai FJ. Genetic susceptibility to idiopathic membranous nephropathy in high-prevalence Area, Taiwan. Biomedicine (Taipei) 2014; 4:9. [PMID: 25520922 PMCID: PMC4265015 DOI: 10.7603/s40681-014-0009-y] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2014] [Accepted: 05/04/2014] [Indexed: 12/24/2022] Open
Abstract
Idiopathic membranous nephropathy (MN) is one common cause of idiopathic nephrotic syndrome in adults; 25% of MN patients proceed to end-stage renal disease. In adults, membranous nephropathy is a lead cause of nephrotic syndrome, with about 75% of the cases idiopathic. Secondary causes include autoimmune disease, infection, drugs and malignancy. Three hypotheses about pathogenesis have surfaced: preformed immune complex, in situ immune complex formation, and auto-antibody against podocyte membrane antigen. Pathogenesis does involve immune complex formation with later deposition in sub-epithelial sites, but definite mechanism is still unknown. Several genes were recently proven associated with primary membranous nephropathy in Taiwan: IL-6, NPHS1, TLR-4, TLR-9, STAT4, and MYH9 . These may provide a useful tool for diagnosis and prognosis. This article reviews epidemiology and lends new information on KIRREL2 (rs443186 and rs447707) polymorphisms as underlying causes of MN; polymorphisms revealed by this study warrant further investigation.
Collapse
Affiliation(s)
- Shih-Yin Chen
- Genetics Center, Department of Medical Research, China Medical University Hospital, Taichung, Taiwan ; Graduate Institute of Chinese Medical Science, China Medical University, Taichung, Taiwan ; Department of Biotechnology and Bioinformatics, Asia University, Taichung, Taiwan
| | - Cheng-Hsu Chen
- Division of Nephrology, Department of Internal Medicine, Taichung Veterans General Hospital, Taichung, Taiwan
| | - Yu-Chuen Huang
- Genetics Center, Department of Medical Research, China Medical University Hospital, Taichung, Taiwan ; Graduate Institute of Chinese Medical Science, China Medical University, Taichung, Taiwan
| | - Chia-Jung Chan
- Genetics Center, Department of Medical Research, China Medical University Hospital, Taichung, Taiwan
| | - Da-Chung Chen
- Taiwan LandSeed Hospital, Pingjen City, Taoyuan, Taiwan ; Department of Chemical and Materials Engineering, National Central University, Taoyuan, Taiwan
| | - Fuu-Jen Tsai
- Department of Pediatrics, China Medical University Hospital, Taichung, Taiwan ; Department of Medical Genetics, China Medical University Hospital, No. 2, Yuh Der Road, 404, Taichung, Taiwan ; Department of Biotechnology and Bioinformatics, Asia University, Taichung, Taiwan
| |
Collapse
|
190
|
Galanter JM, Gignoux CR, Torgerson DG, Roth LA, Eng C, Oh SS, Nguyen EA, Drake KA, Huntsman S, Hu D, Sen S, Davis A, Farber HJ, Avila PC, Brigino-Buenaventura E, LeNoir MA, Meade K, Serebrisky D, Borrell LN, Rodríguez-Cintrón W, Estrada AM, Mendoza KS, Winkler CA, Klitz W, Romieu I, London SJ, Gilliland F, Martinez F, Bustamante C, Williams LK, Kumar R, Rodríguez-Santana JR, Burchard EG. Genome-wide association study and admixture mapping identify different asthma-associated loci in Latinos: the Genes-environments & Admixture in Latino Americans study. J Allergy Clin Immunol 2014; 134:295-305. [PMID: 24406073 PMCID: PMC4085159 DOI: 10.1016/j.jaci.2013.08.055] [Citation(s) in RCA: 88] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2013] [Revised: 08/27/2013] [Accepted: 08/27/2013] [Indexed: 02/06/2023]
Abstract
BACKGROUND Asthma is a complex disease with both genetic and environmental causes. Genome-wide association studies of asthma have mostly involved European populations, and replication of positive associations has been inconsistent. OBJECTIVE We sought to identify asthma-associated genes in a large Latino population with genome-wide association analysis and admixture mapping. METHODS Latino children with asthma (n = 1893) and healthy control subjects (n = 1881) were recruited from 5 sites in the United States: Puerto Rico, New York, Chicago, Houston, and the San Francisco Bay Area. Subjects were genotyped on an Affymetrix World Array IV chip. We performed genome-wide association and admixture mapping to identify asthma-associated loci. RESULTS We identified a significant association between ancestry and asthma at 6p21 (lowest P value: rs2523924, P < 5 × 10(-6)). This association replicates in a meta-analysis of the EVE Asthma Consortium (P = .01). Fine mapping of the region in this study and the EVE Asthma Consortium suggests an association between PSORS1C1 and asthma. We confirmed the strong allelic association between SNPs in the 17q21 region and asthma in Latinos (IKZF3, lowest P value: rs90792, odds ratio, 0.67; 95% CI, 0.61-0.75; P = 6 × 10(-13)) and replicated associations in several genes that had previously been associated with asthma in genome-wide association studies. CONCLUSIONS Admixture mapping and genome-wide association are complementary techniques that provide evidence for multiple asthma-associated loci in Latinos. Admixture mapping identifies a novel locus on 6p21 that replicates in a meta-analysis of several Latino populations, whereas genome-wide association confirms the previously identified locus on 17q21.
Collapse
Affiliation(s)
- Joshua M Galanter
- Department of Medicine, University of California, San Francisco, Calif; Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, Calif.
| | - Christopher R Gignoux
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, Calif
| | - Dara G Torgerson
- Department of Medicine, University of California, San Francisco, Calif
| | - Lindsey A Roth
- Department of Medicine, University of California, San Francisco, Calif
| | - Celeste Eng
- Department of Medicine, University of California, San Francisco, Calif
| | - Sam S Oh
- Department of Medicine, University of California, San Francisco, Calif
| | | | - Katherine A Drake
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, Calif
| | - Scott Huntsman
- Department of Medicine, University of California, San Francisco, Calif
| | - Donglei Hu
- Department of Medicine, University of California, San Francisco, Calif
| | - Saunak Sen
- Department of Epidemiology & Biostatistics, University of California, San Francisco, Calif
| | - Adam Davis
- Children's Hospital and Research Center Oakland, Oakland, Calif
| | - Harold J Farber
- Department of Pediatrics, Section of Pulmonology, Baylor College of Medicine and Texas Children's Hospital, Houston, Tex
| | - Pedro C Avila
- Division of Allergy-Immunology, Feinberg School of Medicine, Northwestern University, Chicago, Ill
| | | | | | - Kelley Meade
- Children's Hospital and Research Center Oakland, Oakland, Calif
| | | | - Luisa N Borrell
- Department of Health Sciences, Graduate Program in Public Health, Lehman College, City University of New York, Bronx, NY
| | | | | | | | - Cheryl A Winkler
- Frederick National Laboratory for Cancer Research, National Institutes of Health, Frederick, Md
| | - William Klitz
- School of Public Health, University of California, Berkeley, Calif
| | | | - Stephanie J London
- National Institute of Environmental Health Sciences, National Institutes of Health, Dept of Health and Human Services, Research Triangle Park, NC
| | - Frank Gilliland
- Department of Preventive Medicine, University of Southern California, Los Angeles, Calif
| | | | | | - L Keoki Williams
- Department of Internal Medicine, Henry Ford Health System, Detroit, Mich
| | - Rajesh Kumar
- Ann and Robert H. Lurie Children's Hospital of Chicago, Chicago, Ill
| | | | - Esteban G Burchard
- Department of Medicine, University of California, San Francisco, Calif; Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, Calif
| |
Collapse
|
191
|
De S, Kuwahara S, Saito A. The endocytic receptor megalin and its associated proteins in proximal tubule epithelial cells. MEMBRANES 2014; 4:333-55. [PMID: 25019425 PMCID: PMC4194038 DOI: 10.3390/membranes4030333] [Citation(s) in RCA: 70] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/31/2014] [Revised: 06/23/2014] [Accepted: 07/01/2014] [Indexed: 02/08/2023]
Abstract
Receptor-mediated endocytosis in renal proximal tubule epithelial cells (PTECs) is important for the reabsorption and metabolization of proteins and other substances, including carrier-bound vitamins and trace elements, in glomerular filtrates. Impairment of this endocytic process results in the loss of such substances and development of proteinuria, which is an important clinical indicator of kidney diseases and is also a risk marker for cardiovascular disease. Megalin, a member of the low-density lipoprotein receptor gene family, is a multiligand receptor expressed in the apical membrane of PTECs and plays a central role in the endocytic process. Megalin interacts with various intracellular adaptor proteins for intracellular trafficking and cooperatively functions with other membrane molecules, including the cubilin-amnionless complex. Evidence suggests that megalin and the cubilin-amnionless complex are involved in the uptake of toxic substances into PTECs, which leads to the development of kidney disease. Studies of megalin and its associated molecules will be useful for future development of novel strategies for the diagnosis and treatment of kidney diseases.
Collapse
Affiliation(s)
- Shankhajit De
- Division of Clinical Nephrology and Rheumatology, Niigata University Graduate School of Medical and Dental Sciences, 1-757 Asahimachi-dori, Chuo-ku, Niigata 951-8510, Japan.
| | - Shoji Kuwahara
- Department of Applied Molecular Medicine, Niigata University Graduate School of Medical and Dental Sciences, 1-757 Asahimachi-dori, Chuo-ku, Niigata 951-8510, Japan.
| | - Akihiko Saito
- Department of Applied Molecular Medicine, Niigata University Graduate School of Medical and Dental Sciences, 1-757 Asahimachi-dori, Chuo-ku, Niigata 951-8510, Japan.
| |
Collapse
|
192
|
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
|
193
|
Abstract
Marked familial aggregation of chronic kidney disease suggests that inherited factors play a major role in nephropathy susceptibility. Molecular genetics analyses have identified a number of genes reproducibly associated with a broad range of renal phenotypes. Most associations show polygenic inheritance patterns with limited effect size. In contrast, genetic association between the apolipoprotein L1 (APOL1) gene and several severe nondiabetic forms of kidney disease in African Americans approach Mendelian inheritance patterns and account for a large proportion of glomerulosclerosis in populations of African ancestry. Emerging data support an important role for APOL1 in the progression of diverse etiologies of kidney disease, in concert with requisite environmental (gene*environment) and inherited (gene*gene) interactions. This article reviews the current status of APOL1-associated nephropathy and discusses research questions under active investigation in the search for a cure for these severe and often progressive kidney diseases.
Collapse
|
194
|
Hays T, Ma’ayan A, Clark NR, Tan CM, Teixeira A, Teixeira A, Choi JW, Burdis N, Jung SY, Bajaj AO, O’Malley BW, He JC, Hyink DP, Klotman PE. Proteomics analysis of the non-muscle myosin heavy chain IIa-enriched actin-myosin complex reveals multiple functions within the podocyte. PLoS One 2014; 9:e100660. [PMID: 24949636 PMCID: PMC4065073 DOI: 10.1371/journal.pone.0100660] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2013] [Accepted: 05/29/2014] [Indexed: 12/12/2022] Open
Abstract
MYH9 encodes non-muscle myosin heavy chain IIA (NMMHCIIA), the predominant force-generating ATPase in non-muscle cells. Several lines of evidence implicate a role for MYH9 in podocytopathies. However, NMMHCIIA‘s function in podocytes remains unknown. To better understand this function, we performed immuno-precipitation followed by mass-spectrometry proteomics to identify proteins interacting with the NMMHCIIA-enriched actin-myosin complexes. Computational analyses revealed that these proteins belong to functional networks including regulators of cytoskeletal organization, metabolism and networks regulated by the HIV-1 gene nef. We further characterized the subcellular localization of NMMHCIIA within podocytes in vivo, and found it to be present within the podocyte major foot processes. Finally, we tested the effect of loss of MYH9 expression in podocytes in vitro, and found that it was necessary for cytoskeletal organization. Our results provide the first survey of NMMHCIIA-enriched actin-myosin-interacting proteins within the podocyte, demonstrating the important role of NMMHCIIA in organizing the elaborate cytoskeleton structure of podocytes. Our characterization of NMMHCIIA’s functions goes beyond the podocyte, providing important insights into its general molecular role.
Collapse
Affiliation(s)
- Thomas Hays
- Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, New York, United States of Americ
- * E-mail:
| | - Avi Ma’ayan
- Department of Pharmacology and Systems Therapeutics, Icahn School of Medicine at Mount Sinai, New York, New York, United States of America
| | - Neil R. Clark
- Department of Pharmacology and Systems Therapeutics, Icahn School of Medicine at Mount Sinai, New York, New York, United States of America
| | - Christopher M. Tan
- Department of Pharmacology and Systems Therapeutics, Icahn School of Medicine at Mount Sinai, New York, New York, United States of America
| | - Avelino Teixeira
- Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, New York, United States of Americ
| | - Angela Teixeira
- Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, New York, United States of Americ
| | - Jae W. Choi
- Department of Medicine, Baylor College of Medicine, Houston, Texas, United States of America
| | - Nora Burdis
- Department of Medicine, Baylor College of Medicine, Houston, Texas, United States of America
| | - Sung Yun Jung
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, Texas, United States of America
| | - Amol O. Bajaj
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, Texas, United States of America
| | - Bert W. O’Malley
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, Texas, United States of America
| | - John C. He
- Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, New York, United States of Americ
| | - Deborah P. Hyink
- Department of Medicine, Baylor College of Medicine, Houston, Texas, United States of America
| | - Paul E. Klotman
- Department of Medicine, Baylor College of Medicine, Houston, Texas, United States of America
| |
Collapse
|
195
|
Yorgov D, Edwards KL, Santorico SA. Use of admixture and association for detection of quantitative trait loci in the Type 2 Diabetes Genetic Exploration by Next-Generation Sequencing in Ethnic Samples (T2D-GENES) study. BMC Proc 2014; 8:S6. [PMID: 25519335 PMCID: PMC4143673 DOI: 10.1186/1753-6561-8-s1-s6] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Admixture mapping and association testing have been successfully applied to the detection of genes for complex diseases. Methods have also been developed to combine these approaches. As an initial step to determine the feasibility of combining admixture and association mapping in the context of whole genome sequencing, we have applied several methods to data from the Genetic Analysis Workshop 18. Here, we describe the steps necessary to carry out such a study from selection of reference populations and preprocessing of data through to the testing itself. We detected one significant result with a Bonferroni corrected p-value of 0.032 at single nucleotide polymorphism rs12639065. Computing local ancestry for Hispanic populations was challenging because there are relatively few methods by which to handle 3-way admixture, and publicly available Native American reference panels are scarce. However, combining admixture and association is a promising approach for detection of quantitative trait loci because it might be able to elevate the power of detection by combining 2 different sources of genetic signal.
Collapse
Affiliation(s)
- Daniel Yorgov
- Department of Mathematical and Statistical Sciences, University of Colorado Denver, Denver, CO 80217-3364, USA
| | - Karen L Edwards
- Department of Epidemiology, School of Medicine, University of California Irvine, Irvine, CA 92697-7550, USA ; Department of Epidemiology, Institute for Public Health Genetics, University of Washington, Seattle, WA 98115, USA
| | - Stephanie A Santorico
- Department of Mathematical and Statistical Sciences, University of Colorado Denver, Denver, CO 80217-3364, USA
| |
Collapse
|
196
|
Freedman BI, Skorecki K. Gene-gene and gene-environment interactions in apolipoprotein L1 gene-associated nephropathy. Clin J Am Soc Nephrol 2014; 9:2006-13. [PMID: 24903390 DOI: 10.2215/cjn.01330214] [Citation(s) in RCA: 75] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Molecular genetics have revolutionized the understanding of susceptibility to the broad spectrum of kidney diseases with light microscopic appearance of FSGS, particularly in populations with recent African ancestry. These disorders include idiopathic FSGS, HIV-associated nephropathy, severe lupus nephritis, sickle cell nephropathy, and the primary kidney disorder focal global glomerulosclerosis, which had historically been ascribed to systemic hypertension. FSGS was once thought to include a multitude of unrelated disorders with similar histologic appearance. However, variation in the apolipoprotein L1 gene locus is now known to account for the vast majority of such cases in African Americans as well as nearly all the excess risk for FSGS and related forms of progressive nondiabetic nephropathy in populations with recent African ancestry, relative to European ancestry. Inheriting two coding apolipoprotein L1 gene nephropathy risk variants is necessary for susceptibility to CKD; however, these variants alone are insufficient to produce disease. This work reviews the evidence supporting second hits or modifying factors that affect risk for apolipoprotein L1 gene-associated nephropathy and produce the protean manifestations of this common and complex syndrome. Targeting modifiable second factors will lead to preventive therapies for slowing progression of nondiabetic nephropathy in many patients possessing two apolipoprotein L1 gene risk variants. This model of genetic risk coupled with modifiable second hits will serve as a paradigm applicable to patients with CKD of various etiologies as well as a host of other complex disorders.
Collapse
Affiliation(s)
- Barry I Freedman
- Department of Internal Medicine, Section on Nephrology, Wake Forest School of Medicine, Winston-Salem, North Carolina; and
| | - Karl Skorecki
- Molecular Medicine Laboratory, Rambam Healthcare Campus, Haifa, Israel
| |
Collapse
|
197
|
African ancestry influences CCR5 -2459G>A genotype-associated virologic success of highly active antiretroviral therapy. J Acquir Immune Defic Syndr 2014; 66:102-7. [PMID: 24714069 DOI: 10.1097/qai.0000000000000129] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
INTRODUCTION In a North American, HIV-positive, highly active antiretroviral therapy (HAART)-treated, adherent cohort of self-identified white and black patients, we previously observed that chemokine (C-C motif) receptor 5 (CCR5) -2459G>A genotype had a strong association with time to achieve virologic success (TVLS) in black but not in white patients. METHODS Using 128 genome-wide ancestry informative markers, we performed a quantitative assessment of ancestry in these patients (n = 310) to determine (1) whether CCR5 -2459G>A genotype is still associated with TVLS of HAART when ancestry, not self-identified race, is considered and (2) whether this association is influenced by varying African ancestry. RESULTS We found that the interaction between CCR5 -2459G>A genotype and African ancestry (≤ 0.125 vs. ≥ 0.425 and <0.71 vs. ≥ 0.71) was significantly associated with TVLS (GG compared with AA, P = 0.044 and 0.018, respectively). Furthermore, the association between CCR5 -2459G>A genotype and TVLS was stronger in patients with African ancestry ≥ 0.71 than in patients with African ancestry ≥ 0.452, in both Kaplan-Meier (log-rank P = 0.039 and 0.057, respectively, for AA, GA, and GG) and Cox proportional hazards regression (relative hazard for GG compared with AA 2.59 [95% confidence interval: 1.27 to 5.22; P = 0.01] and 2.26 [95% confidence interval: 1.18 to 4.32; P = 0.01], respectively) analyses. CONCLUSIONS We observed that the association between CCR5 -2459G>A genotype and TVLS of HAART increased with stronger African ancestry. Understanding the genomic mechanisms by which African ancestry influences this association is critical and requires further studies.
Collapse
|
198
|
Bailey JNC, Palmer ND, Ng MC, Bonomo JA, Hicks PJ, Hester JM, Langefeld CD, Freedman BI, Bowden DW. Analysis of coding variants identified from exome sequencing resources for association with diabetic and non-diabetic nephropathy in African Americans. Hum Genet 2014; 133:769-779. [PMID: 24385048 PMCID: PMC4024071 DOI: 10.1007/s00439-013-1415-z] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2013] [Accepted: 12/24/2013] [Indexed: 01/22/2023]
Abstract
Prior studies have identified common genetic variants influencing diabetic and non-diabetic nephropathy, diseases which disproportionately affect African Americans. Recently, exome sequencing techniques have facilitated identification of coding variants on a genome-wide basis in large samples. Exonic variants in known or suspected end-stage kidney disease (ESKD) or nephropathy genes can be tested for their ability to identify association either singly or in combination with known associated common variants. Coding variants in genes with prior evidence for association with ESKD or nephropathy were identified in the NHLBI-ESP GO database and genotyped in 5,045 African Americans (3,324 cases with type 2 diabetes associated nephropathy [T2D-ESKD] or non-T2D ESKD, and 1,721 controls) and 1,465 European Americans (568 T2D-ESKD cases and 897 controls). Logistic regression analyses were performed to assess association, with admixture and APOL1 risk status incorporated as covariates. Ten of 31 SNPs were associated in African Americans; four replicated in European Americans. In African Americans, SNPs in OR2L8, OR2AK2, C6orf167 (MMS22L), LIMK2, APOL3, APOL2, and APOL1 were nominally associated (P = 1.8 × 10(-4)-0.044). Haplotype analysis of common and coding variants increased evidence of association at the OR2L13 and APOL1 loci (P = 6.2 × 10(-5) and 4.6 × 10(-5), respectively). SNPs replicating in European Americans were in OR2AK2, LIMK2, and APOL2 (P = 0.0010-0.037). Meta-analyses highlighted four SNPs associated in T2D-ESKD and all-cause ESKD. Results from this study suggest a role for coding variants in the development of diabetic, non-diabetic, and/or all-cause ESKD in African Americans and/or European Americans.
Collapse
MESH Headings
- Adult
- Black or African American
- Aged
- Apolipoprotein L1
- Apolipoproteins/genetics
- Databases, Genetic
- Diabetes Mellitus, Type 2/complications
- Diabetes Mellitus, Type 2/ethnology
- Diabetes Mellitus, Type 2/genetics
- Diabetes Mellitus, Type 2/pathology
- Diabetic Nephropathies/ethnology
- Diabetic Nephropathies/etiology
- Diabetic Nephropathies/genetics
- Diabetic Nephropathies/pathology
- Exome
- Female
- Genome-Wide Association Study
- Haplotypes
- Humans
- Kidney Failure, Chronic/ethnology
- Kidney Failure, Chronic/genetics
- Kidney Failure, Chronic/pathology
- Lipoproteins, HDL/genetics
- Male
- Middle Aged
- Open Reading Frames
- Polymorphism, Single Nucleotide
- Sequence Analysis, DNA
- United States
- White People
Collapse
Affiliation(s)
- Jessica N. Cooke Bailey
- Program in Molecular Medicine and Translational Science, Wake Forest School of Medicine, Medical Center Blvd., Winston-Salem, North Carolina 27157
- Center for Genomics and Personalized Medicine Research, Wake Forest School of Medicine, Medical Center Blvd., Winston-Salem, North Carolina 27157
- Center for Diabetes Research, Wake Forest School of Medicine, Medical Center Blvd., Winston-Salem, North Carolina 27157
| | - Nicholette D. Palmer
- Center for Genomics and Personalized Medicine Research, Wake Forest School of Medicine, Medical Center Blvd., Winston-Salem, North Carolina 27157
- Center for Diabetes Research, Wake Forest School of Medicine, Medical Center Blvd., Winston-Salem, North Carolina 27157
- Department of Biochemistry, Wake Forest School of Medicine, Medical Center Blvd., Winston-Salem, North Carolina 27157
| | - Maggie C.Y. Ng
- Center for Genomics and Personalized Medicine Research, Wake Forest School of Medicine, Medical Center Blvd., Winston-Salem, North Carolina 27157
- Center for Diabetes Research, Wake Forest School of Medicine, Medical Center Blvd., Winston-Salem, North Carolina 27157
| | - Jason A. Bonomo
- Program in Molecular Medicine and Translational Science, Wake Forest School of Medicine, Medical Center Blvd., Winston-Salem, North Carolina 27157
- Center for Genomics and Personalized Medicine Research, Wake Forest School of Medicine, Medical Center Blvd., Winston-Salem, North Carolina 27157
- Center for Diabetes Research, Wake Forest School of Medicine, Medical Center Blvd., Winston-Salem, North Carolina 27157
| | - Pamela J. Hicks
- Center for Genomics and Personalized Medicine Research, Wake Forest School of Medicine, Medical Center Blvd., Winston-Salem, North Carolina 27157
- Center for Diabetes Research, Wake Forest School of Medicine, Medical Center Blvd., Winston-Salem, North Carolina 27157
- Department of Biochemistry, Wake Forest School of Medicine, Medical Center Blvd., Winston-Salem, North Carolina 27157
| | - Jessica M. Hester
- Center for Genomics and Personalized Medicine Research, Wake Forest School of Medicine, Medical Center Blvd., Winston-Salem, North Carolina 27157
- Center for Diabetes Research, Wake Forest School of Medicine, Medical Center Blvd., Winston-Salem, North Carolina 27157
- Molecular Genetics and Genomics Program, Wake Forest School of Medicine, Medical Center Blvd., Winston-Salem, North Carolina 27157
| | - Carl D. Langefeld
- Department of Biostatistical Sciences - Division of Public Health Sciences, Wake Forest School of Medicine, Medical Center Blvd., Winston-Salem, North Carolina 27157
| | - Barry I. Freedman
- Department of Internal Medicine - Section on Nephrology, Wake Forest School of Medicine, Medical Center Blvd., Winston-Salem, North Carolina 27157
| | - Donald W. Bowden
- Center for Genomics and Personalized Medicine Research, Wake Forest School of Medicine, Medical Center Blvd., Winston-Salem, North Carolina 27157
- Center for Diabetes Research, Wake Forest School of Medicine, Medical Center Blvd., Winston-Salem, North Carolina 27157
- Department of Biochemistry, Wake Forest School of Medicine, Medical Center Blvd., Winston-Salem, North Carolina 27157
- Department of Internal Medicine - Section on Endocrinology; Wake Forest School of Medicine, Medical Center Blvd., Winston-Salem, North Carolina 27157
| |
Collapse
|
199
|
Fornoni A, Merscher S, Kopp JB. Lipid biology of the podocyte--new perspectives offer new opportunities. Nat Rev Nephrol 2014; 10:379-88. [PMID: 24861084 DOI: 10.1038/nrneph.2014.87] [Citation(s) in RCA: 83] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
In the past 15 years, major advances have been made in understanding the role of lipids in podocyte biology. First, susceptibility to focal segmental glomerulosclerosis (FSGS) and glomerular disease is associated with an APOL1 sequence variant, is expressed in podocytes and encodes apolipoprotein L1, an important component of HDL. Second, acid sphingomyelinase-like phosphodiesterase 3b encoded by SMPDL3b has a role in the conversion of sphingomyelin to ceramide and its levels are reduced in renal biopsy samples from patients with recurrent FSGS. Furthermore, decreased SMPDL3b expression is associated with increased susceptibility of podocytes to injury after exposure to sera from these patients. Third, in many individuals with membranous nephropathy, autoantibodies against the phospholipase A2 (PLA2) receptor, which is expressed in podocytes, have been identified. Whether these autoantibodies affect the activity of PLA2, which liberates arachidonic acid from glycerophospholipids and modulates podocyte function, is unknown. Fourth, clinical and experimental evidence support a role for ATP-binding cassette sub-family A member 1-dependent cholesterol efflux, free fatty acids and glycerophospolipids in the pathogenesis of diabetic kidney disease. An improved understanding of lipid biology in podocytes might provide insights to develop therapeutic targets for primary and secondary glomerulopathies.
Collapse
Affiliation(s)
- Alessia Fornoni
- Peggy and Harold Katz Family Drug Discovery Center, Division of Nephrology and Hypertension, University of Miami Miller School of Medicine, 1580 North West 10th Avenue, Miami, FL 33136, USA
| | - Sandra Merscher
- Peggy and Harold Katz Family Drug Discovery Center, Division of Nephrology and Hypertension, University of Miami Miller School of Medicine, 1580 North West 10th Avenue, Miami, FL 33136, USA
| | - Jeffrey B Kopp
- Kidney Disease Section, Kidney Diseases Branch, National Institute of Diabetes and Digestive and Kidney Diseases, NIH, 10 Center Drive, 3N116 Bethesda, MD 20892-1268, USA
| |
Collapse
|
200
|
Abstract
Infectious pathogens are among the strongest selective forces that shape the human genome. Migrations and cultural changes in the past 100,000 years exposed populations to dangerous new pathogens. Host genetics influences susceptibility to infectious disease. Evolutionary adaptations for resistance and symbiosis may underlie common immune-mediated diseases. Signatures of selection and methods to detect them vary with the age, geographical spread and virulence of the pathogen. A history of selection on a trait adds power to association studies by driving the emergence of common alleles of strong effect. Combining selection and association metrics can further increase power. Genome-wide association studies (GWASs) of susceptibility to pathogens that are moderately old (1,000–50,000 years ago), geographically limited in history and exerted strong positive selective pressure will have the most power if GWASs can be done in the historically affected population. An understanding of host–pathogen interactions can inform the development of new therapies for both infectious diseases and common immune-mediated diseases.
The impact of various infectious agents on human survival and reproduction over thousands of years has exerted selective pressure on numerous regions of the human genome. This Review describes how such signatures of selection can be detected and integrated with data from complementary approaches, such as genome-wide association studies, to provide biological insights into host–pathogen interactions. The ancient biological 'arms race' between microbial pathogens and humans has shaped genetic variation in modern populations, and this has important implications for the growing field of medical genomics. As humans migrated throughout the world, populations encountered distinct pathogens, and natural selection increased the prevalence of alleles that are advantageous in the new ecosystems in both host and pathogens. This ancient history now influences human infectious disease susceptibility and microbiome homeostasis, and contributes to common diseases that show geographical disparities, such as autoimmune and metabolic disorders. Using new high-throughput technologies, analytical methods and expanding public data resources, the investigation of natural selection is leading to new insights into the function and dysfunction of human biology.
Collapse
|