1
|
Sandholm N, Dahlström EH, Groop PH. Genetic and epigenetic background of diabetic kidney disease. Front Endocrinol (Lausanne) 2023; 14:1163001. [PMID: 37324271 PMCID: PMC10262849 DOI: 10.3389/fendo.2023.1163001] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/10/2023] [Accepted: 05/10/2023] [Indexed: 06/17/2023] Open
Abstract
Diabetic kidney disease (DKD) is a severe diabetic complication that affects up to half of the individuals with diabetes. Elevated blood glucose levels are a key underlying cause of DKD, but DKD is a complex multifactorial disease, which takes years to develop. Family studies have shown that inherited factors also contribute to the risk of the disease. During the last decade, genome-wide association studies (GWASs) have emerged as a powerful tool to identify genetic risk factors for DKD. In recent years, the GWASs have acquired larger number of participants, leading to increased statistical power to detect more genetic risk factors. In addition, whole-exome and whole-genome sequencing studies are emerging, aiming to identify rare genetic risk factors for DKD, as well as epigenome-wide association studies, investigating DNA methylation in relation to DKD. This article aims to review the identified genetic and epigenetic risk factors for DKD.
Collapse
Affiliation(s)
- Niina Sandholm
- Folkhälsan Institute of Genetics, Folkhälsan Research Center, Helsinki, Finland
- Department of Nephrology, University of Helsinki and Helsinki University Hospital, Helsinki, Finland
- Research Program for Clinical and Molecular Metabolism, Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | - Emma H. Dahlström
- Folkhälsan Institute of Genetics, Folkhälsan Research Center, Helsinki, Finland
- Department of Nephrology, University of Helsinki and Helsinki University Hospital, Helsinki, Finland
- Research Program for Clinical and Molecular Metabolism, Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | - Per-Henrik Groop
- Folkhälsan Institute of Genetics, Folkhälsan Research Center, Helsinki, Finland
- Department of Nephrology, University of Helsinki and Helsinki University Hospital, Helsinki, Finland
- Research Program for Clinical and Molecular Metabolism, Faculty of Medicine, University of Helsinki, Helsinki, Finland
- Department of Diabetes, Central Clinical School, Monash University, Melbourne, VIC, Australia
| |
Collapse
|
2
|
Tziastoudi M, Cholevas C, Theoharides TC, Stefanidis I. Meta-Analysis and Bioinformatics Detection of Susceptibility Genes in Diabetic Nephropathy. Int J Mol Sci 2021; 23:ijms23010020. [PMID: 35008447 PMCID: PMC8744540 DOI: 10.3390/ijms23010020] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2021] [Revised: 12/15/2021] [Accepted: 12/18/2021] [Indexed: 11/16/2022] Open
Abstract
The latest meta-analysis of genome-wide linkage studies (GWLS) identified nine cytogenetic locations suggestive of a linkage with diabetic nephropathy (DN) due to type 1 diabetes mellitus (T1DM) and seven locations due to type 2 diabetes mellitus (T2DM). In order to gain biological insight about the functional role of the genes located in these regions and to prioritize the most significant genetic loci for further research, we conducted a gene ontology analysis with an over representation test for the functional annotation of the protein coding genes. Protein analysis through evolutionary relationships (PANTHER) version 16.0 software and Cytoscape with the relevant plugins were used for the gene ontology analysis, and the overrepresentation test and STRING database were used for the construction of the protein network. The findings of the over-representation test highlight the contribution of immune related molecules like immunoglobulins, cytokines, and chemokines with regard to the most overrepresented protein classes, whereas the most enriched signaling pathways include the VEGF signaling pathway, the Cadherin pathway, the Wnt pathway, the angiogenesis pathway, the p38 MAPK pathway, and the EGF receptor signaling pathway. The common section of T1DM and T2DM results include the significant over representation of immune related molecules, and the Cadherin and Wnt signaling pathways that could constitute potential therapeutic targets for the treatment of DN, irrespective of the type of diabetes.
Collapse
Affiliation(s)
- Maria Tziastoudi
- Department of Nephrology, Faculty of Medicine, School of Health Sciences, University of Thessaly, 41500 Larisa, Greece;
- Correspondence: ; Tel.: +30-2413501667; Fax: +30-2413501015
| | - Christos Cholevas
- First Department of Ophthalmology, Faculty of Health Sciences, Aristotle University of Thessaloniki School of Medicine, AHEPA Hospital, 54636 Thessaloniki, Greece;
| | | | - Ioannis Stefanidis
- Department of Nephrology, Faculty of Medicine, School of Health Sciences, University of Thessaly, 41500 Larisa, Greece;
| |
Collapse
|
3
|
Tziastoudi M, Dardiotis E, Pissas G, Filippidis G, Golfinopoulos S, Siokas V, Tachmitzi SV, Eleftheriadis T, Hadjigeorgiou GM, Tsironi E, Stefanidis I. Serpin Family E Member 1 Tag Single-Nucleotide Polymorphisms in Patients with Diabetic Nephropathy: An Association Study and Meta-Analysis Using a Genetic Model-Free Approach. Genes (Basel) 2021; 12:1887. [PMID: 34946835 PMCID: PMC8701119 DOI: 10.3390/genes12121887] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2021] [Revised: 11/18/2021] [Accepted: 11/23/2021] [Indexed: 11/29/2022] Open
Abstract
BACKGROUND Many lines of evidence highlight the genetic contribution on the development of diabetic nephropathy (DN). One of the studied genes is SERPINE1 whose the role in the risk of developing DN remains questionable. In order to elucidate the contribution of SERPINE1 in DN progression in the context of type 2 diabetes mellitus (T2DM), we conducted an association study and meta-analysis of SERPINE1 genetic variants. MATERIALS AND METHODS A total of 190 patients with DN, 150 T2DM (type 2 diabetes mellitus) patients without DN and 238 healthy controls were recruited. We selected five tag single-nucleotide polymorphisms (SNPs) from the HapMap. The generalized odds ratio (ORG) was calculated to estimate the risk on DN development. Subgroup analyses based on ethnicity and type of diabetes were also performed. RESULTS Both the present association study regarding SERPINE1 SNPs (rs2227667, rs2070682, rs1050813, rs2227690, rs2227692) did not found any significant association between SERPINE1 variants and DN and the meta-analysis of variant 4G>5G (rs1799889) did not also reveal a significant association between 4G>5G variant and DN in main and subgroup analyses. DISCUSSION In conclusion, the present association study and meta-analysis provides strong evidence that SERPINE1 genetic variant 4G>5G is not implicated in the risk or development of DN in Caucasians. Further studies in other populations remain to further investigate the role of this variant in the course of DN.
Collapse
Affiliation(s)
- Maria Tziastoudi
- Department of Nephrology, Faculty of Medicine, School of Health Sciences, University of Thessaly, 41110 Larissa, Greece; (G.P.); (G.F.); (S.G.); (T.E.); (I.S.)
| | - Efthimios Dardiotis
- Laboratory of Neurogenetics, Department of Neurology, University Hospital of Larissa, University of Thessaly, 41110 Larissa, Greece; (E.D.); (V.S.); (G.M.H.)
| | - Georgios Pissas
- Department of Nephrology, Faculty of Medicine, School of Health Sciences, University of Thessaly, 41110 Larissa, Greece; (G.P.); (G.F.); (S.G.); (T.E.); (I.S.)
| | - Georgios Filippidis
- Department of Nephrology, Faculty of Medicine, School of Health Sciences, University of Thessaly, 41110 Larissa, Greece; (G.P.); (G.F.); (S.G.); (T.E.); (I.S.)
| | - Spyridon Golfinopoulos
- Department of Nephrology, Faculty of Medicine, School of Health Sciences, University of Thessaly, 41110 Larissa, Greece; (G.P.); (G.F.); (S.G.); (T.E.); (I.S.)
| | - Vasileios Siokas
- Laboratory of Neurogenetics, Department of Neurology, University Hospital of Larissa, University of Thessaly, 41110 Larissa, Greece; (E.D.); (V.S.); (G.M.H.)
| | - Sophia V. Tachmitzi
- Department of Ophthalmology, Faculty of Medicine, School of Health Sciences, University of Thessaly, 41110 Larissa, Greece; (S.V.T.); (E.T.)
| | - Theodoros Eleftheriadis
- Department of Nephrology, Faculty of Medicine, School of Health Sciences, University of Thessaly, 41110 Larissa, Greece; (G.P.); (G.F.); (S.G.); (T.E.); (I.S.)
| | - Georgios M. Hadjigeorgiou
- Laboratory of Neurogenetics, Department of Neurology, University Hospital of Larissa, University of Thessaly, 41110 Larissa, Greece; (E.D.); (V.S.); (G.M.H.)
- Department of Neurology, Medical School, University of Cyprus, Nicosia 22006, Cyprus
| | - Evangelia Tsironi
- Department of Ophthalmology, Faculty of Medicine, School of Health Sciences, University of Thessaly, 41110 Larissa, Greece; (S.V.T.); (E.T.)
| | - Ioannis Stefanidis
- Department of Nephrology, Faculty of Medicine, School of Health Sciences, University of Thessaly, 41110 Larissa, Greece; (G.P.); (G.F.); (S.G.); (T.E.); (I.S.)
| |
Collapse
|
4
|
Tziastoudi M, Tsezou A, Stefanidis I. Cadherin and Wnt signaling pathways as key regulators in diabetic nephropathy. PLoS One 2021; 16:e0255728. [PMID: 34411124 PMCID: PMC8375992 DOI: 10.1371/journal.pone.0255728] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2020] [Accepted: 07/22/2021] [Indexed: 12/14/2022] Open
Abstract
AIM A recent meta-analysis of genome-wide linkage studies (GWLS) has identified multiple genetic regions suggestive of linkage with DN harboring hundreds of genes. Moving this number of genetic loci forward into biological insight is truly the next step. Here, we approach this challenge with a gene ontology (GO) analysis in order to yield biological and functional role to the genes, an over-representation test to find which GO terms are enriched in the gene list, pathway analysis, as well as protein network analysis. METHOD GO analysis was performed using protein analysis through evolutionary relationships (PANTHER) version 14.0 software and P-values less than 0.05 were considered statistically significant. GO analysis was followed by over-representation test for the identification of enriched terms. Statistical significance was calculated by Fisher's exact test and adjusted using the false discovery rate (FDR) for correction of multiple tests. Cytoscape with the relevant plugins was used for the construction of the protein network and clustering analysis. RESULTS The GO analysis assign multiple GO terms to the genes regarding the molecular function, the biological process and the cellular component, protein class and pathway analysis. The findings of the over-representation test highlight the contribution of cell adhesion regarding the biological process, integral components of plasma membrane regarding the cellular component, chemokines and cytokines with regard to protein class, while the pathway analysis emphasizes the contribution of Wnt and cadherin signaling pathways. CONCLUSIONS Our results suggest that a core feature of the pathogenesis of DN may be a disturbance in Wnt and cadherin signaling pathways, whereas the contribution of chemokines and cytokines need to be studied in additional studies.
Collapse
Affiliation(s)
- Maria Tziastoudi
- Department of Nephrology, School of Medicine, University of Thessaly, Larissa, Greece
| | - Aspasia Tsezou
- Laboratory of Biology, Faculty of Medicine, School of Health Sciences, University of Thessaly, Larissa, Greece
- Laboratory of Cytogenetics and Molecular Genetics, Faculty of Medicine, School of Health Sciences, University of Thessaly, Larissa, Greece
| | - Ioannis Stefanidis
- Department of Nephrology, School of Medicine, University of Thessaly, Larissa, Greece
| |
Collapse
|
5
|
Haukka J, Sandholm N, Valo E, Forsblom C, Harjutsalo V, Cole JB, McGurnaghan SJ, Colhoun HM, Groop PH. Novel Linkage Peaks Discovered for Diabetic Nephropathy in Individuals With Type 1 Diabetes. Diabetes 2021; 70:986-995. [PMID: 33414249 PMCID: PMC8928864 DOI: 10.2337/db20-0158] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/13/2020] [Accepted: 01/01/2021] [Indexed: 11/13/2022]
Abstract
Genome-wide association studies (GWAS) and linkage studies have had limited success in identifying genome-wide significantly linked regions or risk loci for diabetic nephropathy (DN) in individuals with type 1 diabetes (T1D). As GWAS cohorts have grown, they have also included more documented and undocumented familial relationships. Here we computationally inferred and manually curated pedigrees in a study cohort of >6,000 individuals with T1D and their relatives without diabetes. We performed a linkage study for 177 pedigrees consisting of 452 individuals with T1D and their relatives using a genome-wide genotyping array with >300,000 single nucleotide polymorphisms and PSEUDOMARKER software. Analysis resulted in genome-wide significant linkage peaks on eight chromosomal regions from five chromosomes (logarithm of odds score >3.3). The highest peak was localized at the HLA region on chromosome 6p, but whether the peak originated from T1D or DN remained ambiguous. Of other significant peaks, the chromosome 4p22 region was localized on top of ARHGAP24, a gene associated with focal segmental glomerulosclerosis, suggesting this gene may play a role in DN as well. Furthermore, rare variants have been associated with DN and chronic kidney disease near the 4q25 peak, localized on top of CCSER1.
Collapse
Affiliation(s)
- Jani Haukka
- Folkhälsan Institute of Genetics, Folkhälsan Research Center, Helsinki, Finland
- Nephrology, Abdominal Center, University of Helsinki and Helsinki University Hospital, Helsinki, Finland
- Research Program for Clinical and Molecular Metabolism, Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | - Niina Sandholm
- Folkhälsan Institute of Genetics, Folkhälsan Research Center, Helsinki, Finland
- Nephrology, Abdominal Center, University of Helsinki and Helsinki University Hospital, Helsinki, Finland
- Research Program for Clinical and Molecular Metabolism, Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | - Erkka Valo
- Folkhälsan Institute of Genetics, Folkhälsan Research Center, Helsinki, Finland
- Nephrology, Abdominal Center, University of Helsinki and Helsinki University Hospital, Helsinki, Finland
- Research Program for Clinical and Molecular Metabolism, Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | - Carol Forsblom
- Folkhälsan Institute of Genetics, Folkhälsan Research Center, Helsinki, Finland
- Nephrology, Abdominal Center, University of Helsinki and Helsinki University Hospital, Helsinki, Finland
- Research Program for Clinical and Molecular Metabolism, Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | - Valma Harjutsalo
- Folkhälsan Institute of Genetics, Folkhälsan Research Center, Helsinki, Finland
- Nephrology, Abdominal Center, University of Helsinki and Helsinki University Hospital, Helsinki, Finland
- Research Program for Clinical and Molecular Metabolism, Faculty of Medicine, University of Helsinki, Helsinki, Finland
- Chronic Disease Prevention Unit, National Institute for Health and Welfare, Helsinki, Finland
| | - Joanne B. Cole
- Division of Endocrinology, Department of Pediatrics, Boston Children’s Hospital, Boston, MA
- Programs in Metabolism, Broad Institute, Cambridge, MA
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA
- Programs in Medical and Population Genetics, Broad Institute, Cambridge, MA
| | - Stuart J. McGurnaghan
- Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, U.K
| | - Helen M. Colhoun
- Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, U.K
| | - Per-Henrik Groop
- Folkhälsan Institute of Genetics, Folkhälsan Research Center, Helsinki, Finland
- Nephrology, Abdominal Center, University of Helsinki and Helsinki University Hospital, Helsinki, Finland
- Research Program for Clinical and Molecular Metabolism, Faculty of Medicine, University of Helsinki, Helsinki, Finland
- Department of Diabetes, Central Clinical School, Monash University, Melbourne, Australia
- Corresponding author: Per-Henrik Groop,
| |
Collapse
|
6
|
Tziastoudi M, Stefanidis I, Stravodimos K, Zintzaras E. Identification of Chromosomal Regions Linked to Diabetic Nephropathy: A Meta-Analysis of Genome-Wide Linkage Scans. Genet Test Mol Biomarkers 2019; 23:105-117. [DOI: 10.1089/gtmb.2018.0209] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Affiliation(s)
- Maria Tziastoudi
- Department of Biomathematics, Faculty of Medicine, University of Thessaly, Larissa, Greece
| | - Ioannis Stefanidis
- Department of Nephrology, Faculty of Medicine, University of Thessaly, Larissa, Greece
| | - Konstantinos Stravodimos
- 1st University Department of Urology, Laiko General Hospital, National and Kapodistrian Athens University, Athens, Greece
| | - Elias Zintzaras
- Department of Biomathematics, Faculty of Medicine, University of Thessaly, Larissa, Greece
- The Institute for Clinical Research and Health Policy Studies, Tufts Medical Center, Tufts University School of Medicine, Boston, Massachusetts
| | | |
Collapse
|
7
|
Sandholm N, Van Zuydam N, Ahlqvist E, Juliusdottir T, Deshmukh HA, Rayner NW, Di Camillo B, Forsblom C, Fadista J, Ziemek D, Salem RM, Hiraki LT, Pezzolesi M, Trégouët D, Dahlström E, Valo E, Oskolkov N, Ladenvall C, Marcovecchio ML, Cooper J, Sambo F, Malovini A, Manfrini M, McKnight AJ, Lajer M, Harjutsalo V, Gordin D, Parkkonen M, Tuomilehto J, Lyssenko V, McKeigue PM, Rich SS, Brosnan MJ, Fauman E, Bellazzi R, Rossing P, Hadjadj S, Krolewski A, Paterson AD, Florez JC, Hirschhorn JN, Maxwell AP, Dunger D, Cobelli C, Colhoun HM, Groop L, McCarthy MI, Groop PH. The Genetic Landscape of Renal Complications in Type 1 Diabetes. J Am Soc Nephrol 2016; 28:557-574. [PMID: 27647854 DOI: 10.1681/asn.2016020231] [Citation(s) in RCA: 76] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2016] [Accepted: 07/17/2016] [Indexed: 12/14/2022] Open
Abstract
Diabetes is the leading cause of ESRD. Despite evidence for a substantial heritability of diabetic kidney disease, efforts to identify genetic susceptibility variants have had limited success. We extended previous efforts in three dimensions, examining a more comprehensive set of genetic variants in larger numbers of subjects with type 1 diabetes characterized for a wider range of cross-sectional diabetic kidney disease phenotypes. In 2843 subjects, we estimated that the heritability of diabetic kidney disease was 35% (P=6.4×10-3). Genome-wide association analysis and replication in 12,540 individuals identified no single variants reaching stringent levels of significance and, despite excellent power, provided little independent confirmation of previously published associated variants. Whole-exome sequencing in 997 subjects failed to identify any large-effect coding alleles of lower frequency influencing the risk of diabetic kidney disease. However, sets of alleles increasing body mass index (P=2.2×10-5) and the risk of type 2 diabetes (P=6.1×10-4) associated with the risk of diabetic kidney disease. We also found genome-wide genetic correlation between diabetic kidney disease and failure at smoking cessation (P=1.1×10-4). Pathway analysis implicated ascorbate and aldarate metabolism (P=9.0×10-6), and pentose and glucuronate interconversions (P=3.0×10-6) in pathogenesis of diabetic kidney disease. These data provide further evidence for the role of genetic factors influencing diabetic kidney disease in those with type 1 diabetes and highlight some key pathways that may be responsible. Altogether these results reveal important biology behind the major cause of kidney disease.
Collapse
Affiliation(s)
- Niina Sandholm
- Folkhälsan Institute of Genetics, Folkhälsan Research Center, Helsinki, Finland.,Abdominal Center, Nephrology, University of Helsinki and Helsinki University Hospital, Helsinki, Finland.,Research Programs Unit, Diabetes and Obesity, University of Helsinki, Helsinki, Finland
| | - Natalie Van Zuydam
- Wellcome Trust Centre for Human Genetics,Oxford Centre for Diabetes, Endocrinology and Metabolism, University of Oxford, Oxford, United Kingdom.,Medical Research Institute
| | - Emma Ahlqvist
- Department of Clinical Sciences, Diabetes and Endocrinology, Skåne University Hospital, Lund University, Malmö, Sweden
| | | | - Harshal A Deshmukh
- Division of Population Health Sciences, University of Dundee, Dundee, United Kingdom
| | - N William Rayner
- Wellcome Trust Centre for Human Genetics,Oxford Centre for Diabetes, Endocrinology and Metabolism, University of Oxford, Oxford, United Kingdom.,Human Genetics, Wellcome Trust Sanger Institute, Hinxton, United Kingdom
| | - Barbara Di Camillo
- Department of Information Engineering, University of Padova, Padova, Italy
| | - Carol Forsblom
- Folkhälsan Institute of Genetics, Folkhälsan Research Center, Helsinki, Finland.,Abdominal Center, Nephrology, University of Helsinki and Helsinki University Hospital, Helsinki, Finland.,Research Programs Unit, Diabetes and Obesity, University of Helsinki, Helsinki, Finland
| | - Joao Fadista
- Department of Clinical Sciences, Diabetes and Endocrinology, Skåne University Hospital, Lund University, Malmö, Sweden
| | - Daniel Ziemek
- Computational Sciences, Pfizer Worldwide Research and Development, Berlin, Germany
| | - Rany M Salem
- Departments of Genetics,Programs in Metabolism and Medical and Population Genetics, Broad Institute of the Massachusetts Institute of Technology and Harvard University, Cambridge, Massachusetts.,Divisions of Endocrinology and Genetics, Boston Children's Hospital, Boston, Massachusetts
| | - Linda T Hiraki
- Genetics and Genome Biology Program, Hospital for Sick Children, Toronto, Ontario, Canada
| | - Marcus Pezzolesi
- Section on Genetics and Epidemiology, Joslin Diabetes Center, Boston, Massachusetts
| | - David Trégouët
- Sorbonne Universities, Pierre et Marie Curie University (UPMC) and National Institute for Health and Medical Research, Mixed Research Unit in Health (UMR_S) 1166, Paris, France.,Institute for Cardiometabolism and Nutrition, Genomics and pathophysiology of Cardiovascular diseases, Paris, France
| | - Emma Dahlström
- Folkhälsan Institute of Genetics, Folkhälsan Research Center, Helsinki, Finland.,Abdominal Center, Nephrology, University of Helsinki and Helsinki University Hospital, Helsinki, Finland.,Research Programs Unit, Diabetes and Obesity, University of Helsinki, Helsinki, Finland
| | - Erkka Valo
- Folkhälsan Institute of Genetics, Folkhälsan Research Center, Helsinki, Finland.,Abdominal Center, Nephrology, University of Helsinki and Helsinki University Hospital, Helsinki, Finland.,Research Programs Unit, Diabetes and Obesity, University of Helsinki, Helsinki, Finland
| | - Nikolay Oskolkov
- Department of Clinical Sciences, Diabetes and Endocrinology, Skåne University Hospital, Lund University, Malmö, Sweden
| | - Claes Ladenvall
- Department of Clinical Sciences, Diabetes and Endocrinology, Skåne University Hospital, Lund University, Malmö, Sweden
| | | | - Jason Cooper
- Department of Chemical Engineering and Biotechnology, University of Cambridge, Cambridge, United Kingdom
| | - Francesco Sambo
- Department of Information Engineering, University of Padova, Padova, Italy
| | - Alberto Malovini
- Department of Electrical, Computer and Biomedical Engineering, University of Pavia, Pavia, Italy.,Laboratory of Informatics and Systems Engineering for Clinical Research, Scientific Institute for Research, Hospitalization and Health Care, IRCCS (Instituto di Ricovero e Cura a Carattere Scientifico); Salvatore Maugeri Foundation, Pavia, Italy
| | - Marco Manfrini
- Department of Information Engineering, University of Padova, Padova, Italy
| | - Amy Jayne McKnight
- Nephrology Research, Centre for Public Health, Queen's University of Belfast, Belfast, United Kingdom
| | - Maria Lajer
- Diabetic Complications, Steno Diabetes Center, Gentofte, Denmark
| | - Valma Harjutsalo
- Folkhälsan Institute of Genetics, Folkhälsan Research Center, Helsinki, Finland.,Abdominal Center, Nephrology, University of Helsinki and Helsinki University Hospital, Helsinki, Finland.,Research Programs Unit, Diabetes and Obesity, University of Helsinki, Helsinki, Finland.,The Chronic Disease Prevention Unit, National Institute for Health and Welfare, Helsinki, Finland
| | - Daniel Gordin
- Folkhälsan Institute of Genetics, Folkhälsan Research Center, Helsinki, Finland.,Abdominal Center, Nephrology, University of Helsinki and Helsinki University Hospital, Helsinki, Finland.,Research Programs Unit, Diabetes and Obesity, University of Helsinki, Helsinki, Finland
| | - Maija Parkkonen
- Folkhälsan Institute of Genetics, Folkhälsan Research Center, Helsinki, Finland.,Abdominal Center, Nephrology, University of Helsinki and Helsinki University Hospital, Helsinki, Finland.,Research Programs Unit, Diabetes and Obesity, University of Helsinki, Helsinki, Finland
| | | | - Jaakko Tuomilehto
- The Chronic Disease Prevention Unit, National Institute for Health and Welfare, Helsinki, Finland.,Centre for Vascular Prevention, Danube University Krems, Krems, Austria
| | - Valeriya Lyssenko
- Department of Clinical Sciences, Diabetes and Endocrinology, Skåne University Hospital, Lund University, Malmö, Sweden.,Diabetic Complications, Steno Diabetes Center, Gentofte, Denmark
| | - Paul M McKeigue
- Centre for Population Health Sciences, University of Edinburgh, Edinburgh, United Kingdom
| | - Stephen S Rich
- Center for Public Health Genomics, University of Virginia, Charlottesville, Virginia
| | | | - Eric Fauman
- Computational Sciences, Pfizer Worldwide Research and Development, Cambridge, Massachusetts
| | - Riccardo Bellazzi
- Department of Electrical, Computer and Biomedical Engineering, University of Pavia, Pavia, Italy
| | - Peter Rossing
- Diabetic Complications, Steno Diabetes Center, Gentofte, Denmark.,Department of Health, Aarhus University, Aarhus, Denmark.,Novo Nordisk Foundation Center for Basic Metabolic Research, University of Copenhagen, Copenhagen, Denmark
| | - Samy Hadjadj
- Functional Research Unit of Medicine and Pharmacy, University of Poitiers, Poitiers, France.,Department of Endocrinology-Diabetology and Center of Clinical Investigation, Poitiers University Hospital, Poitiers, France.,Institute National pour la Santé et la Recherche Médicale, National Institute for Health and Medical Research, Center of Clinical Investigation 1402 and Unit 1082, Poitiers, France
| | - Andrzej Krolewski
- Section on Genetics and Epidemiology, Joslin Diabetes Center, Boston, Massachusetts
| | - Andrew D Paterson
- Genetics and Genome Biology Program, Hospital for Sick Children, Toronto, Ontario, Canada
| | | | - Jose C Florez
- Programs in Metabolism and Medical and Population Genetics, Broad Institute of the Massachusetts Institute of Technology and Harvard University, Cambridge, Massachusetts.,Diabetes Unit and Center for Human Genetic Research, Massachusetts General Hospital, Boston, Massachusetts
| | - Joel N Hirschhorn
- Departments of Genetics,Programs in Metabolism and Medical and Population Genetics, Broad Institute of the Massachusetts Institute of Technology and Harvard University, Cambridge, Massachusetts.,Divisions of Endocrinology and Genetics, Boston Children's Hospital, Boston, Massachusetts
| | - Alexander P Maxwell
- Nephrology Research, Centre for Public Health, Queen's University of Belfast, Belfast, United Kingdom.,Regional Nephrology Unit, Belfast City Hospital, Belfast, United Kingdom; and
| | | | - David Dunger
- Department of Paediatrics, Institute of Metabolic Science, and
| | - Claudio Cobelli
- Department of Information Engineering, University of Padova, Padova, Italy
| | - Helen M Colhoun
- Division of Population Health Sciences, University of Dundee, Dundee, United Kingdom
| | - Leif Groop
- Department of Clinical Sciences, Diabetes and Endocrinology, Skåne University Hospital, Lund University, Malmö, Sweden
| | - Mark I McCarthy
- Wellcome Trust Centre for Human Genetics,Oxford Centre for Diabetes, Endocrinology and Metabolism, University of Oxford, Oxford, United Kingdom.,Oxford NIHR Biomedical Research Centre, Oxford University Hospitals Trust, Oxford, United Kingdom
| | - Per-Henrik Groop
- Folkhälsan Institute of Genetics, Folkhälsan Research Center, Helsinki, Finland,Abdominal Center, Nephrology, University of Helsinki and Helsinki University Hospital, Helsinki, Finland.,Research Programs Unit, Diabetes and Obesity, University of Helsinki, Helsinki, Finland.,Baker IDI (International Diabetes Institute) Heart and Diabetes Institute, Melbourne, Victoria, Australia
| | | |
Collapse
|
8
|
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: 13] [Impact Index Per Article: 1.3] [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
|
9
|
Li JY, Tan YZ, Feng GY, He L, Zhou LG, Lu H. [Advances of genetics in diabetic nephropathy]. YI CHUAN = HEREDITAS 2012; 34:1537-44. [PMID: 23262100 DOI: 10.3724/sp.j.1005.2012.01537] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
Diabetic nephropathy (DN) is one of the most serious chronic complications of diabetes mellitus. The observed incidence patterns in different ethnics and familial clustering have suggested that the genetic factor plays an important role in the development and progression of DN. This paper reviews the recent advances on genetics of DN, including candidate genes association studies, linkage studies and genome-wide association studies (GWASs). Candidate genes association studies and meta-analysis showed that a few candidate genes have been reproducibly associated with DN, such as ACE, AGT and PPARG genes. Linkage studies and genome-wide linkage studies have also identified susceptibility chromosomal loci. With the development of high-throughput sequencing and chip techniques, GWAS has become an important strategy to identify variants responsible for DN. The genetic factor has been the significant contribution to the pathobiology of DN. However, it is not the only cause of the pathobiology of DN, because the environment factor also influences the pathobiology of DN. Nonetheless, genetic studies may provide valuable information for the pathobiology of nephropathy and potential targets of its treatment.
Collapse
Affiliation(s)
- Jun-Yan Li
- Diabetes Research Institute, Department of Endocrinology, Shanghai Key Laboratory of Traditional Chinese Clinical Medice, Shuguang Hospital Affiliated to Shanghai University of Traditional Chinese Medicine, Shanghai 201203, China.
| | | | | | | | | | | |
Collapse
|