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Guo J, Rackham OJL, Sandholm N, He B, Österholm AM, Valo E, Harjutsalo V, Forsblom C, Toppila I, Parkkonen M, Li Q, Zhu W, Harmston N, Chothani S, Öhman MK, Eng E, Sun Y, Petretto E, Groop PH, Tryggvason K. Whole-Genome Sequencing of Finnish Type 1 Diabetic Siblings Discordant for Kidney Disease Reveals DNA Variants associated with Diabetic Nephropathy. J Am Soc Nephrol 2020; 31:309-323. [PMID: 31919106 DOI: 10.1681/asn.2019030289] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2019] [Accepted: 10/19/2019] [Indexed: 12/19/2022] Open
Abstract
BACKGROUND Several genetic susceptibility loci associated with diabetic nephropathy have been documented, but no causative variants implying novel pathogenetic mechanisms have been elucidated. METHODS We carried out whole-genome sequencing of a discovery cohort of Finnish siblings with type 1 diabetes who were discordant for the presence (case) or absence (control) of diabetic nephropathy. Controls had diabetes without complications for 15-37 years. We analyzed and annotated variants at genome, gene, and single-nucleotide variant levels. We then replicated the associated variants, genes, and regions in a replication cohort from the Finnish Diabetic Nephropathy study that included 3531 unrelated Finns with type 1 diabetes. RESULTS We observed protein-altering variants and an enrichment of variants in regions associated with the presence or absence of diabetic nephropathy. The replication cohort confirmed variants in both regulatory and protein-coding regions. We also observed that diabetic nephropathy-associated variants, when clustered at the gene level, are enriched in a core protein-interaction network representing proteins essential for podocyte function. These genes include protein kinases (protein kinase C isoforms ε and ι) and protein tyrosine kinase 2. CONCLUSIONS Our comprehensive analysis of a diabetic nephropathy cohort of siblings with type 1 diabetes who were discordant for kidney disease points to variants and genes that are potentially causative or protective for diabetic nephropathy. This includes variants in two isoforms of the protein kinase C family not previously linked to diabetic nephropathy, adding support to previous hypotheses that the protein kinase C family members play a role in diabetic nephropathy and might be attractive therapeutic targets.
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Affiliation(s)
- Jing Guo
- Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden.,Cardiovascular and Metabolic Disorders Programme, Duke-National University of Singapore Medical School, Singapore
| | - Owen J L Rackham
- Cardiovascular and Metabolic Disorders Programme, Duke-National University of Singapore Medical School, Singapore
| | - Niina Sandholm
- Folkhälsan Institute of Genetics, Folkhälsan Research Centre, Helsinki, Finland.,Abdominal Center 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
| | - Bing He
- Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
| | - Anne-May Österholm
- Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden.,Cardiovascular and Metabolic Disorders Programme, Duke-National University of Singapore Medical School, Singapore
| | - Erkka Valo
- Folkhälsan Institute of Genetics, Folkhälsan Research Centre, Helsinki, Finland.,Abdominal Center 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
| | - Valma Harjutsalo
- Folkhälsan Institute of Genetics, Folkhälsan Research Centre, Helsinki, Finland.,Abdominal Center 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.,Chronic Disease Prevention Unit, National Institute for Health and Welfare, Helsinki, Finland
| | - Carol Forsblom
- Folkhälsan Institute of Genetics, Folkhälsan Research Centre, Helsinki, Finland.,Abdominal Center 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
| | - Iiro Toppila
- Folkhälsan Institute of Genetics, Folkhälsan Research Centre, Helsinki, Finland.,Abdominal Center 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
| | - Maija Parkkonen
- Folkhälsan Institute of Genetics, Folkhälsan Research Centre, Helsinki, Finland.,Abdominal Center 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
| | - Qibin Li
- Complex Disease Research Center, BGI Genomics, Shenzhen, China
| | - Wenjuan Zhu
- Complex Disease Research Center, BGI Genomics, Shenzhen, China
| | - Nathan Harmston
- Cardiovascular and Metabolic Disorders Programme, Duke-National University of Singapore Medical School, Singapore.,Science Division, Yale-National University of Singapore College, National University of Singapore, Singapore
| | - Sonia Chothani
- Cardiovascular and Metabolic Disorders Programme, Duke-National University of Singapore Medical School, Singapore
| | - Miina K Öhman
- Cardiovascular and Metabolic Disorders Programme, Duke-National University of Singapore Medical School, Singapore
| | - Eudora Eng
- Cardiovascular and Metabolic Disorders Programme, Duke-National University of Singapore Medical School, Singapore
| | - Yang Sun
- Cardiovascular and Metabolic Disorders Programme, Duke-National University of Singapore Medical School, Singapore
| | - Enrico Petretto
- Cardiovascular and Metabolic Disorders Programme, Duke-National University of Singapore Medical School, Singapore; .,MRC London Institute of Medical Sciences, Imperial College London, London, United Kingdom
| | - Per-Henrik Groop
- Folkhälsan Institute of Genetics, Folkhälsan Research Centre, Helsinki, Finland; .,Abdominal Center 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, Victoria, Australia; and
| | - Karl Tryggvason
- Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden; .,Cardiovascular and Metabolic Disorders Programme, Duke-National University of Singapore Medical School, Singapore.,Division of Nephrology, Department of Medicine, Duke University, Durham, North Carolina
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Williams WW, Salem RM, McKnight AJ, Sandholm N, Forsblom C, Taylor A, Guiducci C, McAteer JB, McKay GJ, Isakova T, Brennan EP, Sadlier DM, Palmer C, Söderlund J, Fagerholm E, Harjutsalo V, Lithovius R, Gordin D, Hietala K, Kytö J, Parkkonen M, Rosengård-Bärlund M, Thorn L, Syreeni A, Tolonen N, Saraheimo M, Wadén J, Pitkäniemi J, Sarti C, Tuomilehto J, Tryggvason K, Österholm AM, He B, Bain S, Martin F, Godson C, Hirschhorn JN, Maxwell AP, Groop PH, Florez JC. Association testing of previously reported variants in a large case-control meta-analysis of diabetic nephropathy. Diabetes 2012; 61:2187-94. [PMID: 22721967 PMCID: PMC3402313 DOI: 10.2337/db11-0751] [Citation(s) in RCA: 69] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
We formed the GEnetics of Nephropathy-an International Effort (GENIE) consortium to examine previously reported genetic associations with diabetic nephropathy (DN) in type 1 diabetes. GENIE consists of 6,366 similarly ascertained participants of European ancestry with type 1 diabetes, with and without DN, from the All Ireland-Warren 3-Genetics of Kidneys in Diabetes U.K. and Republic of Ireland (U.K.-R.O.I.) collection and the Finnish Diabetic Nephropathy Study (FinnDiane), combined with reanalyzed data from the Genetics of Kidneys in Diabetes U.S. Study (U.S. GoKinD). We found little evidence for the association of the EPO promoter polymorphism, rs161740, with the combined phenotype of proliferative retinopathy and end-stage renal disease in U.K.-R.O.I. (odds ratio [OR] 1.14, P = 0.19) or FinnDiane (OR 1.06, P = 0.60). However, a fixed-effects meta-analysis that included the previously reported cohorts retained a genome-wide significant association with that phenotype (OR 1.31, P = 2 × 10(-9)). An expanded investigation of the ELMO1 locus and genetic regions reported to be associated with DN in the U.S. GoKinD yielded only nominal statistical significance for these loci. Finally, top candidates identified in a recent meta-analysis failed to reach genome-wide significance. In conclusion, we were unable to replicate most of the previously reported genetic associations for DN, and significance for the EPO promoter association was attenuated.
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Affiliation(s)
- Winfred W. Williams
- Center for Human Genetic Research, Massachusetts General Hospital, Boston, Massachusetts
- Program in Medical and Population Genetics, Broad Institute, Cambridge, Massachusetts
- Division of Nephrology, Department of Medicine, Massachusetts General Hospital, Boston, Massachusetts
- Department of Medicine, Harvard Medical School, Boston, Massachusetts
| | - Rany M. Salem
- Program in Medical and Population Genetics, Broad Institute, Cambridge, Massachusetts
- Endocrine Research Unit, Department of Endocrinology, Children’s Hospital, Boston, Massachusetts
| | - Amy Jayne McKnight
- Nephrology Research, Centre for Public Health, Queen’s University of Belfast, Belfast, U.K
| | - Niina Sandholm
- Folkhälsan Institute of Genetics, Folkhälsan Research Center, Biomedicum Helsinki, Helsinki, Finland
- Division of Nephrology, Department of Medicine, Helsinki University Central Hospital, Helsinki, Finland
- Department of Biomedical Engineering and Computational Science, Aalto University, Helsinki, Finland
| | - Carol Forsblom
- Folkhälsan Institute of Genetics, Folkhälsan Research Center, Biomedicum Helsinki, Helsinki, Finland
- Division of Nephrology, Department of Medicine, Helsinki University Central Hospital, Helsinki, Finland
| | - Andrew Taylor
- Center for Human Genetic Research, Massachusetts General Hospital, Boston, Massachusetts
- Program in Medical and Population Genetics, Broad Institute, Cambridge, Massachusetts
- Diabetes Research Center (Diabetes Unit), Department of Medicine, Massachusetts General Hospital, Boston, Massachusetts
| | - Candace Guiducci
- Program in Medical and Population Genetics, Broad Institute, Cambridge, Massachusetts
| | - Jarred B. McAteer
- Center for Human Genetic Research, Massachusetts General Hospital, Boston, Massachusetts
- Program in Medical and Population Genetics, Broad Institute, Cambridge, Massachusetts
- Diabetes Research Center (Diabetes Unit), Department of Medicine, Massachusetts General Hospital, Boston, Massachusetts
| | - Gareth J. McKay
- Nephrology Research, Centre for Public Health, Queen’s University of Belfast, Belfast, U.K
| | - Tamara Isakova
- Division of Nephrology, University of Miami, Miller School of Medicine, Miami, Florida
| | - Eoin P. Brennan
- UCD Diabetes Research Centre, Conway Institute, University College Dublin, Belfield, Dublin, Ireland
- School of Medicine, University College Dublin, Belfield, Dublin, Ireland
| | - Denise M. Sadlier
- UCD Diabetes Research Centre, Conway Institute, University College Dublin, Belfield, Dublin, Ireland
- School of Medicine, University College Dublin, Belfield, Dublin, Ireland
- Mater University Hospital, Dublin, Ireland
| | - Cameron Palmer
- Program in Medical and Population Genetics, Broad Institute, Cambridge, Massachusetts
- Endocrine Research Unit, Department of Endocrinology, Children’s Hospital, Boston, Massachusetts
| | - Jenny Söderlund
- Folkhälsan Institute of Genetics, Folkhälsan Research Center, Biomedicum Helsinki, Helsinki, Finland
- Division of Nephrology, Department of Medicine, Helsinki University Central Hospital, Helsinki, Finland
| | - Emma Fagerholm
- Folkhälsan Institute of Genetics, Folkhälsan Research Center, Biomedicum Helsinki, Helsinki, Finland
- Division of Nephrology, Department of Medicine, Helsinki University Central Hospital, Helsinki, Finland
| | - Valma Harjutsalo
- Folkhälsan Institute of Genetics, Folkhälsan Research Center, Biomedicum Helsinki, Helsinki, Finland
- Division of Nephrology, Department of Medicine, Helsinki University Central Hospital, Helsinki, Finland
- Department of Chronic Disease Prevention, Welfare and Health Promotion Division, National Institute for Health and Welfare, Helsinki, Finland
| | - Raija Lithovius
- Folkhälsan Institute of Genetics, Folkhälsan Research Center, Biomedicum Helsinki, Helsinki, Finland
- Division of Nephrology, Department of Medicine, Helsinki University Central Hospital, Helsinki, Finland
| | - Daniel Gordin
- Folkhälsan Institute of Genetics, Folkhälsan Research Center, Biomedicum Helsinki, Helsinki, Finland
- Division of Nephrology, Department of Medicine, Helsinki University Central Hospital, Helsinki, Finland
| | - Kustaa Hietala
- Folkhälsan Institute of Genetics, Folkhälsan Research Center, Biomedicum Helsinki, Helsinki, Finland
- Department of Ophthalmology, Helsinki University Central Hospital, Helsinki, Finland
| | - Janne Kytö
- Folkhälsan Institute of Genetics, Folkhälsan Research Center, Biomedicum Helsinki, Helsinki, Finland
- Department of Ophthalmology, Helsinki University Central Hospital, Helsinki, Finland
| | - Maija Parkkonen
- Folkhälsan Institute of Genetics, Folkhälsan Research Center, Biomedicum Helsinki, Helsinki, Finland
- Division of Nephrology, Department of Medicine, Helsinki University Central Hospital, Helsinki, Finland
| | - Milla Rosengård-Bärlund
- Folkhälsan Institute of Genetics, Folkhälsan Research Center, Biomedicum Helsinki, Helsinki, Finland
- Division of Nephrology, Department of Medicine, Helsinki University Central Hospital, Helsinki, Finland
| | - Lena Thorn
- Folkhälsan Institute of Genetics, Folkhälsan Research Center, Biomedicum Helsinki, Helsinki, Finland
- Division of Nephrology, Department of Medicine, Helsinki University Central Hospital, Helsinki, Finland
| | - Anna Syreeni
- Folkhälsan Institute of Genetics, Folkhälsan Research Center, Biomedicum Helsinki, Helsinki, Finland
- Division of Nephrology, Department of Medicine, Helsinki University Central Hospital, Helsinki, Finland
| | - Nina Tolonen
- Folkhälsan Institute of Genetics, Folkhälsan Research Center, Biomedicum Helsinki, Helsinki, Finland
- Division of Nephrology, Department of Medicine, Helsinki University Central Hospital, Helsinki, Finland
| | - Markku Saraheimo
- Folkhälsan Institute of Genetics, Folkhälsan Research Center, Biomedicum Helsinki, Helsinki, Finland
- Division of Nephrology, Department of Medicine, Helsinki University Central Hospital, Helsinki, Finland
| | - Johan Wadén
- Folkhälsan Institute of Genetics, Folkhälsan Research Center, Biomedicum Helsinki, Helsinki, Finland
- Division of Nephrology, Department of Medicine, Helsinki University Central Hospital, Helsinki, Finland
| | - Janne Pitkäniemi
- Department of Public Health, University of Helsinki, Helsinki, Finland
| | - Cinzia Sarti
- Department of Public Health, University of Helsinki, Helsinki, Finland
| | - Jaakko Tuomilehto
- Department of Chronic Disease Prevention, Welfare and Health Promotion Division, National Institute for Health and Welfare, Helsinki, Finland
- Department of Public Health, University of Helsinki, Helsinki, Finland
- South Ostrobothnia Central Hospital, Seinäjoki, Finland
| | - Karl Tryggvason
- Division of Matrix Biology, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
| | - Anne-May Österholm
- Division of Matrix Biology, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
| | - Bing He
- Division of Matrix Biology, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
| | - Steve Bain
- Institute of Life Sciences, Swansea University, Swansea, U.K
| | - Finian Martin
- UCD Diabetes Research Centre, Conway Institute, University College Dublin, Belfield, Dublin, Ireland
- School of Biomolecular and Biomedical Sciences, University College Dublin, Belfield, Dublin, Ireland
| | - Catherine Godson
- UCD Diabetes Research Centre, Conway Institute, University College Dublin, Belfield, Dublin, Ireland
- School of Medicine, University College Dublin, Belfield, Dublin, Ireland
| | - Joel N. Hirschhorn
- Program in Medical and Population Genetics, Broad Institute, Cambridge, Massachusetts
- Endocrine Research Unit, Department of Endocrinology, Children’s Hospital, Boston, Massachusetts
| | - Alexander P. Maxwell
- Nephrology Research, Centre for Public Health, Queen’s University of Belfast, Belfast, U.K
| | - Per-Henrik Groop
- Folkhälsan Institute of Genetics, Folkhälsan Research Center, Biomedicum Helsinki, Helsinki, Finland
- Division of Nephrology, Department of Medicine, Helsinki University Central Hospital, Helsinki, Finland
| | - Jose C. Florez
- Center for Human Genetic Research, Massachusetts General Hospital, Boston, Massachusetts
- Program in Medical and Population Genetics, Broad Institute, Cambridge, Massachusetts
- Department of Medicine, Harvard Medical School, Boston, Massachusetts
- Diabetes Research Center (Diabetes Unit), Department of Medicine, Massachusetts General Hospital, Boston, Massachusetts
- Corresponding author: Jose C. Florez,
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5
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He B, Österholm AM, Hoverfält A, Forsblom C, Hjörleifsdóttir EE, Nilsson AS, Parkkonen M, Pitkäniemi J, Hreidarsson Á, Sarti C, McKnight AJ, Maxwell AP, Tuomilehto J, Groop PH, Tryggvason K. Association of genetic variants at 3q22 with nephropathy in patients with type 1 diabetes mellitus. Am J Hum Genet 2009; 84:5-13. [PMID: 19084216 PMCID: PMC2668055 DOI: 10.1016/j.ajhg.2008.11.012] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2008] [Revised: 11/18/2008] [Accepted: 11/19/2008] [Indexed: 12/21/2022] Open
Abstract
Diabetic nephropathy (DN) is the primary cause of morbidity and mortality in patients with type 1 diabetes mellitus (T1DM) and affects about 30% of these patients. We have previously localized a DN locus on chromosome 3q with suggestive linkage in Finnish individuals. Linkage to this region has also been reported earlier by several other groups. To fine map this locus, we conducted a multistage case-control association study in T1DM patients, comprising 1822 cases with nephropathy and 1874 T1DM patients free of nephropathy, from Finland, Iceland, and the British Isles. At the screening stage, we genotyped 3072 tag SNPs, spanning a 28 Mb region, in 234 patients and 215 controls from Finland. SNPs that met the significance threshold of p < 0.01 at this stage were followed up by a series of sample sets. A genetic variant, rs1866813, in the noncoding region at 3q22 was associated with increased risk of DN (overall p = 7.07 x 10(-6), combined odds ratio [OR] of the allele = 1.33). The estimated genotypic ORs of this variant in all Finnish samples suggested a codominant effect, resulting in significant association, with a p value of 4.7 x 10(-5) (OR = 1.38; 95% confidence interval = 1.18-1.62). Additionally, an 11 kb segment flanked by rs62408925 and rs1866813, two strongly correlated variants (r(2) = 0.95), contains three elements highly conserved across multiple species. Independent replication will clarify the role of the associated variants at 3q22 in influencing the risk of DN.
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Affiliation(s)
- Bing He
- Division of Matrix Biology, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, 171 77 Stockholm, Sweden
| | - Anne-May Österholm
- Division of Matrix Biology, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, 171 77 Stockholm, Sweden
| | - Anna Hoverfält
- Folkhälsan Institute of Genetics, Biomedicum Helsinki, 00014 Helsinki, Finland and the Division of Nephrology, Department of Medicine, Helsinki University Central Hospital, 00029 HUS, Helsinki, Finland
| | - Carol Forsblom
- Folkhälsan Institute of Genetics, Biomedicum Helsinki, 00014 Helsinki, Finland and the Division of Nephrology, Department of Medicine, Helsinki University Central Hospital, 00029 HUS, Helsinki, Finland
| | - Eyrún Edda Hjörleifsdóttir
- Division of Matrix Biology, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, 171 77 Stockholm, Sweden
| | - Ann-Sofie Nilsson
- Division of Matrix Biology, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, 171 77 Stockholm, Sweden
| | - Maikki Parkkonen
- Folkhälsan Institute of Genetics, Biomedicum Helsinki, 00014 Helsinki, Finland and the Division of Nephrology, Department of Medicine, Helsinki University Central Hospital, 00029 HUS, Helsinki, Finland
| | - Janne Pitkäniemi
- Finnish National Public Health Institute, 00300 Helsinki, Finland
| | | | - Cinzia Sarti
- Finnish National Public Health Institute, 00300 Helsinki, Finland
| | - Amy Jayne McKnight
- Nephrology Research Group, Queen's University of Belfast, Belfast BT9 7AB, Northern Ireland
| | - A. Peter Maxwell
- Nephrology Research Group, Queen's University of Belfast, Belfast BT9 7AB, Northern Ireland
| | | | - Per-Henrik Groop
- Folkhälsan Institute of Genetics, Biomedicum Helsinki, 00014 Helsinki, Finland and the Division of Nephrology, Department of Medicine, Helsinki University Central Hospital, 00029 HUS, Helsinki, Finland
| | - Karl Tryggvason
- Division of Matrix Biology, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, 171 77 Stockholm, Sweden
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