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Haukka JK, Antikainen AA, Valo E, Syreeni A, Dahlström EH, Lin BM, Franceschini N, Krolewski AS, Harjutsalo V, Groop PH, Sandholm N. Whole-exome and whole-genome sequencing of 1064 individuals with type 1 diabetes reveals novel genes for diabetic kidney disease. Diabetologia 2024:10.1007/s00125-024-06241-1. [PMID: 39103720 DOI: 10.1007/s00125-024-06241-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/20/2023] [Accepted: 06/10/2024] [Indexed: 08/07/2024]
Abstract
AIMS/HYPOTHESIS Diabetic kidney disease (DKD) is a severe diabetic complication that affects one third of individuals with type 1 diabetes. Although several genes and common variants have been shown to be associated with DKD, much of the predicted inheritance remains unexplained. Here, we performed next-generation sequencing to assess whether low-frequency variants, extending to a minor allele frequency (MAF) ≤10% (single or aggregated) contribute to the missing heritability in DKD. METHODS We performed whole-exome sequencing (WES) of 498 individuals and whole-genome sequencing (WGS) of 599 individuals with type 1 diabetes. After quality control, next-generation sequencing data were available for a total of 1064 individuals, of whom 541 had developed either severe albuminuria or end-stage kidney disease, and 523 had retained normal albumin excretion despite a long duration of type 1 diabetes. Single-variant and gene-aggregate tests for protein-altering variants (PAV) and protein-truncating variants (PTV) were performed separately for WES and WGS data and combined in a meta-analysis. We also performed genome-wide aggregate analyses on genomic windows (sliding window), promoters and enhancers using the WGS dataset. RESULTS In the single-variant meta-analysis, no variant reached genome-wide significance, but a suggestively associated common THAP7 rs369250 variant (p=1.50 × 10-5, MAF=49%) was replicated in the FinnGen general population genome-wide association study (GWAS) data for chronic kidney disease and DKD phenotypes. The gene-aggregate meta-analysis provided suggestive evidence (p<4.0 × 10-4) at four genes for DKD, of which NAT16 (MAFPAV≤10%) and LTA (also known as TNFβ, MAFPAV≤5%) are replicated in the FinnGen general population GWAS data. The LTA rs2229092 C allele was associated with significantly lower TNFR1, TNFR2 and TNFR3 serum levels in a subset of FinnDiane participants. Of the intergenic regions suggestively associated with DKD, the enhancer on chromosome 18q12.3 (p=3.94 × 10-5, MAFvariants≤5%) showed interaction with the METTL4 gene; the lead variant was replicated, and predicted to alter binding of the MafB transcription factor. CONCLUSIONS/INTERPRETATION Our sequencing-based meta-analysis revealed multiple genes, variants and regulatory regions that were suggestively associated with DKD. However, as no variant or gene reached genome-wide significance, further studies are needed to validate the findings.
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Affiliation(s)
- Jani K Haukka
- 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
| | - Anni A Antikainen
- 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
| | - Erkka Valo
- 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
| | - Anna Syreeni
- 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
| | - Bridget M Lin
- Department of Epidemiology, University of North Carolina, Chapel Hill, NC, USA
| | - Nora Franceschini
- Department of Epidemiology, University of North Carolina, Chapel Hill, NC, USA
| | - Andrzej S Krolewski
- Section on Genetics and Epidemiology, Research Division, Joslin Diabetes Center, Boston, MA, USA
- Department of Medicine, Harvard Medical School, Boston, MA, USA
| | - Valma Harjutsalo
- 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, Victoria, Australia.
| | - 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.
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Liang M, Gao Y, Shen Y, Zhang X, Gu J, Ji G. Serum metabolism distribution in individuals exposed to dioxins: A case study of residents near the municipal solid waste incinerators in China. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 947:174431. [PMID: 38960151 DOI: 10.1016/j.scitotenv.2024.174431] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/29/2024] [Revised: 05/27/2024] [Accepted: 06/30/2024] [Indexed: 07/05/2024]
Abstract
Polychlorinated dibenzo-p-dioxins (PCDDs) and polychlorinated dibenzofurans (PCDFs) have attracted considerable attention owing to their environmental persistence, bioaccumulation, and high toxicity. This study aimed to investigate changes in serum metabolites following exposure to PCDD/Fs and to reveal a novel pathogenesis of PCDD/Fs. Serum samples were collected from 75 residents living near a municipal solid waste incinerator in China to analyse the relationship between PCDD/Fs and serum metabolic components. The serum level in the low-exposure group [19.07 (13.44-23.89) pg-TEQ/L] was significantly lower than that in the high-exposure group [115.60 (52.28-592.65) pg-TEQ/L]. Non-targeted metabolomic studies based on liquid chromatography-high resolution mass spectrometry have been applied to the metabolomic analysis of serum. Thirty-seven metabolites with significant differences among the different groups were identified as biomarkers. Pathway analysis revealed that high dioxin exposure perturbed various biological processes, including glycerol phospholipid metabolism and the interconversion of pentose and glucuronate. The results of a population health survey showed that the serum dioxin concentration in patients with diabetes was significantly higher than that in the control population. These findings suggest that dioxin exposure is associated with several potential adverse health risks, including inflammation, diabetes, and cardiovascular disease, through metabolic changes.
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Affiliation(s)
- Mengyuan Liang
- Nanjing Institute of Environmental Sciences, Ministry of Ecology and Environment, Nanjing 210042, China
| | - Yuanyun Gao
- Nanjing Institute of Environmental Sciences, Ministry of Ecology and Environment, Nanjing 210042, China
| | - Yuehong Shen
- Nanjing Institute of Environmental Sciences, Ministry of Ecology and Environment, Nanjing 210042, China
| | - Xinyu Zhang
- School of Environmental Science and Engineering, Changzhou University, Changzhou 213164, China
| | - Jie Gu
- Nanjing Institute of Environmental Sciences, Ministry of Ecology and Environment, Nanjing 210042, China
| | - Guixiang Ji
- Nanjing Institute of Environmental Sciences, Ministry of Ecology and Environment, Nanjing 210042, China.
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Li D, Hsu FC, Palmer ND, Liu L, Choi YA, Murea M, Parks JS, Bowden DW, Freedman BI, Ma L. Multiomics Analyses Identify AKR1A1 as a Biomarker for Diabetic Kidney Disease. Diabetes 2024; 73:1188-1195. [PMID: 38394643 PMCID: PMC11189831 DOI: 10.2337/db23-0540] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/10/2023] [Accepted: 02/07/2024] [Indexed: 02/25/2024]
Abstract
Diabetic kidney disease (DKD) is the leading cause of end-stage kidney disease. Because many genes associate with DKD, multiomics approaches were used to narrow the list of functional genes, gene products, and related pathways providing insights into the pathophysiological mechanisms of DKD. The Kidney Precision Medicine Project human kidney single-cell RNA-sequencing (scRNA-seq) data set and Mendeley Data on human kidney cortex biopsy proteomics were used. The R package Seurat was used to analyze scRNA-seq data and data from a subset of proximal tubule cells. PathfindR was applied for pathway analysis in cell type-specific differentially expressed genes and the R limma package was used to analyze differential protein expression in kidney cortex. A total of 790 differentially expressed genes were identified in proximal tubule cells, including 530 upregulated and 260 downregulated transcripts. Compared with differentially expressed proteins, 24 genes or proteins were in common. An integrated analysis combining protein quantitative trait loci, genome-wide association study hits (namely, estimated glomerular filtration rate), and a plasma metabolomics analysis was performed using baseline metabolites predictive of DKD progression in our longitudinal Diabetes Heart Study samples. The aldo-keto reductase family 1 member A1 gene (AKR1A1) was revealed as a potential molecular hub for DKD cellular dysfunction in several cross-linked pathways featured by deficiency of this enzyme. ARTICLE HIGHLIGHTS
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Affiliation(s)
- DengFeng Li
- Department of Biostatistics and Data Science, Wake Forest University School of Medicine, Winston-Salem, NC
| | - Fang-Chi Hsu
- Department of Biostatistics and Data Science, Wake Forest University School of Medicine, Winston-Salem, NC
| | - Nicholette D. Palmer
- Department of Biochemistry, Wake Forest University School of Medicine, Winston-Salem, NC
| | - Liang Liu
- Bioinformatics Shared Resource, Department of Cancer Biology, Wake Forest University School of Medicine, Winston-Salem, NC
| | - Young A. Choi
- Section of Nephrology, Department of Internal Medicine, Wake Forest University School of Medicine, Winston-Salem, NC
| | - Mariana Murea
- Section of Nephrology, Department of Internal Medicine, Wake Forest University School of Medicine, Winston-Salem, NC
| | - John S. Parks
- Department of Molecular Medicine, Wake Forest University School of Medicine, Winston-Salem, NC
| | - Donald W. Bowden
- Department of Biochemistry, Wake Forest University School of Medicine, Winston-Salem, NC
| | - Barry I. Freedman
- Section of Nephrology, Department of Internal Medicine, Wake Forest University School of Medicine, Winston-Salem, NC
| | - Lijun Ma
- Section of Nephrology, Department of Internal Medicine, Wake Forest University School of Medicine, Winston-Salem, NC
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Antikainen AA, Haukka JK, Kumar A, Syreeni A, Hägg-Holmberg S, Ylinen A, Kilpeläinen E, Kytölä A, Palotie A, Putaala J, Thorn LM, Harjutsalo V, Groop PH, Sandholm N. Whole-genome sequencing identifies variants in ANK1, LRRN1, HAS1, and other genes and regulatory regions for stroke in type 1 diabetes. Sci Rep 2024; 14:13453. [PMID: 38862513 PMCID: PMC11166668 DOI: 10.1038/s41598-024-61840-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2023] [Accepted: 05/10/2024] [Indexed: 06/13/2024] Open
Abstract
Individuals with type 1 diabetes (T1D) carry a markedly increased risk of stroke, with distinct clinical and neuroimaging characteristics as compared to those without diabetes. Using whole-exome or whole-genome sequencing of 1,051 individuals with T1D, we aimed to find rare and low-frequency genomic variants associated with stroke in T1D. We analysed the genome comprehensively with single-variant analyses, gene aggregate analyses, and aggregate analyses on genomic windows, enhancers and promoters. In addition, we attempted replication in T1D using a genome-wide association study (N = 3,945) and direct genotyping (N = 3,263), and in the general population from the large-scale population-wide FinnGen project and UK Biobank summary statistics. We identified a rare missense variant on SREBF1 exome-wide significantly associated with stroke (rs114001633, p.Pro227Leu, p-value = 7.30 × 10-8), which replicated for hemorrhagic stroke in T1D. Using gene aggregate analysis, we identified exome-wide significant genes: ANK1 and LRRN1 displayed replication evidence in T1D, and LRRN1, HAS1 and UACA in the general population (UK Biobank). Furthermore, we performed sliding-window analyses and identified 14 genome-wide significant windows for stroke on 4q33-34.1, of which two replicated in T1D, and a suggestive genomic window on LINC01500, which replicated in T1D. Finally, we identified a suggestively stroke-associated TRPM2-AS promoter (p-value = 5.78 × 10-6) with borderline significant replication in T1D, which we validated with an in vitro cell-based assay. Due to the rarity of the identified genetic variants, future replication of the genomic regions represented here is required with sequencing of individuals with T1D. Nevertheless, we here report the first genome-wide analysis on stroke in individuals with diabetes.
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Affiliation(s)
- Anni A Antikainen
- 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
| | - Jani K Haukka
- 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
| | - Anmol Kumar
- 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
| | - Anna Syreeni
- 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
| | - Stefanie Hägg-Holmberg
- 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
| | - Anni Ylinen
- 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
| | - Elina Kilpeläinen
- Institute for Molecular Medicine Finland (FIMM), HiLIFE, University of Helsinki, Helsinki, Finland
| | - Anastasia Kytölä
- Institute for Molecular Medicine Finland (FIMM), HiLIFE, University of Helsinki, Helsinki, Finland
| | - Aarno Palotie
- Institute for Molecular Medicine Finland (FIMM), HiLIFE, University of Helsinki, Helsinki, Finland
- Analytic and Translational Genetics Unit, Department of Medicine, Department of Neurology and Department of Psychiatry, Massachusetts General Hospital, Boston, MA, USA
- The Stanley Center for Psychiatric Research and Program in Medical and Population Genetics, The Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Jukka Putaala
- Neurology, Helsinki University Hospital and University of Helsinki, Helsinki, Finland
| | - Lena M Thorn
- 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 General Practice and Primary Health Care, University of Helsinki and Helsinki University Hospital, Helsinki, Finland
| | - Valma Harjutsalo
- 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.
| | - 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.
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Yan Y, Liu H, Abedini A, Sheng X, Palmer M, Li H, Susztak K. Unraveling the epigenetic code: human kidney DNA methylation and chromatin dynamics in renal disease development. Nat Commun 2024; 15:873. [PMID: 38287030 PMCID: PMC10824731 DOI: 10.1038/s41467-024-45295-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2023] [Accepted: 01/19/2024] [Indexed: 01/31/2024] Open
Abstract
Epigenetic changes may fill a critical gap in our understanding of kidney disease development, as they not only reflect metabolic changes but are also preserved and transmitted during cell division. We conducted a genome-wide cytosine methylation analysis of 399 human kidney samples, along with single-nuclear open chromatin analysis on over 60,000 cells from 14 subjects, including controls, and diabetes and hypertension attributed chronic kidney disease (CKD) patients. We identified and validated differentially methylated positions associated with disease states, and discovered that nearly 30% of these alterations were influenced by underlying genetic variations, including variants known to be associated with kidney disease in genome-wide association studies. We also identified regions showing both methylation and open chromatin changes. These changes in methylation and open chromatin significantly associated gene expression changes, most notably those playing role in metabolism and expressed in proximal tubules. Our study further demonstrated that methylation risk scores (MRS) can improve disease state annotation and prediction of kidney disease development. Collectively, our results suggest a causal relationship between epigenetic changes and kidney disease pathogenesis, thereby providing potential pathways for the development of novel risk stratification methods.
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Affiliation(s)
- Yu Yan
- Renal, Electrolyte, and Hypertension Division, Department of Medicine, University of Pennsylvania, Perelman School of Medicine, Philadelphia, PA, 19014, USA
- Institute for Diabetes, Obesity, and Metabolism, University of Pennsylvania, Perelman School of Medicine, Philadelphia, PA, 19014, USA
- Department of Genetics, University of Pennsylvania, Perelman School of Medicine, Philadelphia, PA, 19014, USA
- Kidney Innovation Center, University of Pennsylvania, Perelman School of Medicine, Philadelphia, PA, 19014, USA
| | - Hongbo Liu
- Renal, Electrolyte, and Hypertension Division, Department of Medicine, University of Pennsylvania, Perelman School of Medicine, Philadelphia, PA, 19014, USA
- Institute for Diabetes, Obesity, and Metabolism, University of Pennsylvania, Perelman School of Medicine, Philadelphia, PA, 19014, USA
- Department of Genetics, University of Pennsylvania, Perelman School of Medicine, Philadelphia, PA, 19014, USA
- Kidney Innovation Center, University of Pennsylvania, Perelman School of Medicine, Philadelphia, PA, 19014, USA
| | - Amin Abedini
- Renal, Electrolyte, and Hypertension Division, Department of Medicine, University of Pennsylvania, Perelman School of Medicine, Philadelphia, PA, 19014, USA
- Institute for Diabetes, Obesity, and Metabolism, University of Pennsylvania, Perelman School of Medicine, Philadelphia, PA, 19014, USA
- Department of Genetics, University of Pennsylvania, Perelman School of Medicine, Philadelphia, PA, 19014, USA
- Kidney Innovation Center, University of Pennsylvania, Perelman School of Medicine, Philadelphia, PA, 19014, USA
| | - Xin Sheng
- Renal, Electrolyte, and Hypertension Division, Department of Medicine, University of Pennsylvania, Perelman School of Medicine, Philadelphia, PA, 19014, USA
- Institute for Diabetes, Obesity, and Metabolism, University of Pennsylvania, Perelman School of Medicine, Philadelphia, PA, 19014, USA
- Department of Genetics, University of Pennsylvania, Perelman School of Medicine, Philadelphia, PA, 19014, USA
- Kidney Innovation Center, University of Pennsylvania, Perelman School of Medicine, Philadelphia, PA, 19014, USA
| | - Matthew Palmer
- Kidney Innovation Center, University of Pennsylvania, Perelman School of Medicine, Philadelphia, PA, 19014, USA
- Department of Epidemiology and Biostatistics, Perelman School of Medicine, Philadelphia, PA, 19014, USA
| | - Hongzhe Li
- Kidney Innovation Center, University of Pennsylvania, Perelman School of Medicine, Philadelphia, PA, 19014, USA
- Department of Pathology, Perelman School of Medicine, Philadelphia, PA, 19014, USA
| | - Katalin Susztak
- Renal, Electrolyte, and Hypertension Division, Department of Medicine, University of Pennsylvania, Perelman School of Medicine, Philadelphia, PA, 19014, USA.
- Institute for Diabetes, Obesity, and Metabolism, University of Pennsylvania, Perelman School of Medicine, Philadelphia, PA, 19014, USA.
- Department of Genetics, University of Pennsylvania, Perelman School of Medicine, Philadelphia, PA, 19014, USA.
- Kidney Innovation Center, University of Pennsylvania, Perelman School of Medicine, Philadelphia, PA, 19014, USA.
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Eun M, Kim D, Shin SI, Yang HO, Kim KD, Choi SY, Park S, Kim DK, Jeong CW, Moon KC, Lee H, Park J. Chromatin accessibility analysis and architectural profiling of human kidneys reveal key cell types and a regulator of diabetic kidney disease. Kidney Int 2024; 105:150-164. [PMID: 37925023 DOI: 10.1016/j.kint.2023.09.030] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2023] [Revised: 08/22/2023] [Accepted: 09/25/2023] [Indexed: 11/06/2023]
Abstract
Diabetes is the leading cause of kidney disease that progresses to kidney failure. However, the key molecular and cellular pathways involved in diabetic kidney disease (DKD) pathogenesis are largely unknown. Here, we performed a comparative analysis of adult human kidneys by examining cell type-specific chromatin accessibility by single-nucleus ATAC-seq (snATAC-seq) and analyzing three-dimensional chromatin architecture via high-throughput chromosome conformation capture (Hi-C method) of paired samples. We mapped the cell type-specific and DKD-specific open chromatin landscape and found that genetic variants associated with kidney diseases were significantly enriched in the proximal tubule- (PT) and injured PT-specific open chromatin regions in samples from patients with DKD. BACH1 was identified as a core transcription factor of injured PT cells; its binding target genes were highly associated with fibrosis and inflammation, which were also key features of injured PT cells. Additionally, Hi-C analysis revealed global chromatin architectural changes in DKD, accompanied by changes in local open chromatin patterns. Combining the snATAC-seq and Hi-C data identified direct target genes of BACH1, and indicated that BACH1 binding regions showed increased chromatin contact frequency with promoters of their target genes in DKD. Thus, our multi-omics analysis revealed BACH1 target genes in injured PTs and highlighted the role of BACH1 as a novel regulator of tubular inflammation and fibrosis.
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Affiliation(s)
- Minho Eun
- School of Life Sciences, Gwangju Institute of Science and Technology (GIST), Gwangju, Republic of Korea
| | - Donggun Kim
- School of Life Sciences, Gwangju Institute of Science and Technology (GIST), Gwangju, Republic of Korea
| | - So-I Shin
- School of Life Sciences, Gwangju Institute of Science and Technology (GIST), Gwangju, Republic of Korea
| | - Hyun Oh Yang
- Department of Systems Biotechnology, Chung-Ang University, Anseong, Republic of Korea
| | - Kyoung-Dong Kim
- Department of Systems Biotechnology, Chung-Ang University, Anseong, Republic of Korea
| | - Sin Young Choi
- School of Life Sciences, Gwangju Institute of Science and Technology (GIST), Gwangju, Republic of Korea
| | - Sehoon Park
- Department of Internal Medicine, Seoul National University Hospital, Seoul, Republic of Korea
| | - Dong Ki Kim
- Department of Internal Medicine, Seoul National University Hospital, Seoul, Republic of Korea; Department of Internal Medicine, Seoul National University College of Medicine, Seoul, Republic of Korea
| | - Chang Wook Jeong
- Department of Urology, Seoul National University Hospital, Seoul, Republic of Korea
| | - Kyung Chul Moon
- Department of Pathology, Seoul National University College of Medicine, Seoul, Republic of Korea
| | - Hajeong Lee
- Department of Internal Medicine, Seoul National University Hospital, Seoul, Republic of Korea; Department of Internal Medicine, Seoul National University College of Medicine, Seoul, Republic of Korea.
| | - Jihwan Park
- School of Life Sciences, Gwangju Institute of Science and Technology (GIST), Gwangju, Republic of Korea.
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Chen J, Liu J, Cao D. Urine metabolomics for assessing fertility-sparing treatment efficacy in endometrial cancer: a non-invasive approach using ultra-performance liquid chromatography mass spectrometry. BMC Womens Health 2023; 23:583. [PMID: 37940929 PMCID: PMC10634093 DOI: 10.1186/s12905-023-02730-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2023] [Accepted: 10/25/2023] [Indexed: 11/10/2023] Open
Abstract
OBJECTIVE This study aimed to reveal the urine metabolic change of endometrial cancer (EC) patients during fertility-sparing treatment and establish non-invasive predictive models to identify patients with complete remission (CR). METHOD This study enrolled 20 EC patients prior to treatment (PT) and 22 patients with CR, aged 25-40 years. Eligibility criteria consisted of stage IA high-grade EC, lesions confined to endometrium, normal hepatic and renal function, normal urine test, no contraindication for fertility-sparing treatment and no prior therapy. Urine samples were analyzed using ultraperformance liquid chromatography mass spectrometry (UPLC-MS), a technique chosen for its high sensitivity and resolution, allows for rapid, accurate identification and quantification of metabolites, providing a comprehensive metabolic profile and facilitating the discovery of potential biomarkers. Analytical techniques were employed to determine distinct metabolites and altered metabolic pathways. The statistical analyses were performed using univariate and multivariate analyses, logistic regression and receiver operating characteristic (ROC) curves to discover and validate the potential biomarker models. RESULTS A total of 108 different urine metabolomes were identified between CR and PT groups. These metabolites were enriched in ascorbate and aldarate metabolism, one carbon pool by folate, and some amino acid metabolisms pathways. A panel consisting of Baicalin, 5beta-1,3,7 (11)-Eudesmatrien-8-one, Indolylacryloylglycine, Edulitine, and Physapubenolide were selected as biomarkers, which demonstrated the best predictive ability with the AUC values of 0.982/0.851 in training/10-fold-cross-validation group, achieving a sensitivity of 0.975 and specificity of 0.967, respectively. CONCLUSION The urine metabolic analysis revealed the metabolic changes in EC patients during the fertility-sparing treatment. The predictive biomarkers present great potential diagnostic value in fertility-sparing treatments for EC patients, offering a less invasive means of monitoring treatment efficacy. Further research should explore the mechanistic underpinnings of these metabolic changes and validate the biomarker panel in larger, diverse populations due to the small sample size and single-institution nature of our study.
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Affiliation(s)
- Junyu Chen
- Department of Obstetrics and Gynecology, Qilu Hospital of Shandong University, Jinan, 250012, China
- Department of Obstetrics and Gynecology, Peking Union Medical College Hospital, National Clinical Research Center for Obstetric & Gynecologic Diseases, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, 100730, China
| | - Jiale Liu
- Department of Obstetrics and Gynecology, Qilu Hospital of Shandong University, Jinan, 250012, China
| | - Dongyan Cao
- Department of Obstetrics and Gynecology, Peking Union Medical College Hospital, National Clinical Research Center for Obstetric & Gynecologic Diseases, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, 100730, China.
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Yu X, Luo Y, Yang L, Duan X. Plasma metabonomic study on the effect of Para‑hydroxybenzaldehyde intervention in a rat model of transient focal cerebral ischemia. Mol Med Rep 2023; 28:224. [PMID: 37800608 PMCID: PMC10577806 DOI: 10.3892/mmr.2023.13111] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2023] [Accepted: 06/28/2023] [Indexed: 10/07/2023] Open
Abstract
Gastrodia elata Blume has been widely used to treat various central and peripheral nerve diseases, and Para‑hydroxybenzaldehyde (PHBA) is one of the indicated components suggested to provide a neuroprotective effect. In our previous, it was shown that PHBA protected mitochondria against cerebral ischemia‑reperfusion (I/R) injury in rats. In the present study, how PHBA regulated the metabolic mechanism in blood following cerebral I/R was assessed to identify an effective therapeutic target for the prevention and treatment of ischemic stroke (IS). First, a rat model of cerebral ischemia‑reperfusion injury was established via middle cerebral artery occlusion/reperfusion (MCAO/R). The therapeutic effect of PHBA on brain I/R was evaluated by assessing the neurological function score, triphenyl tetrazolium chloride, hematoxylin and eosin, and Nissl staining. Next, a non‑targeted metabolomic based on high‑performance liquid chromatography quadrupole time‑of‑flight mass spectrometry was established to identify differential metabolites. Finally, a targeted metabolic spectrum was analyzed and the potential therapeutic targets were verified by Western blotting. The results showed that the neurological function score, cerebral infarction area, hippocampal morphology, and the number of neurons in the PHBA group were significantly improved compared with the model group. Metabonomic analysis showed that 13 different metabolites were identified between the model and PHBA group, which may be involved in the 'tricarboxylic acid cycle', 'glutathione metabolism', and 'mutual transformation of pentose and glucuronates', amongst others. Among these, the levels of the most significant differential metabolite, dGMP, decreased significantly following PHBA treatment. Western blotting was used to verify the expression of membrane‑associated guanosine kinase PSD‑95 and the subunit of glutamate AMPA receptor GluA1, which significantly increased after PHBA treatment. In addition, it was also found that PHBA increased the expression of the light chain‑3 protein and autophagy effector protein 1, whilst the expression of sequestosome‑1 decreased, indicating that PHBA promoted autophagy. Similarly, in TUNEL staining and detection of apoptosis‑related proteins, it was found that MCAO/R upregulated the expression of Bax and cleaved‑caspase‑3 whilst downregulating the expression of Bcl‑2 and increasing the apoptosis of hippocampal neurons; PHBA reversed this situation. These results suggest that cerebral I/R causes postsynaptic dysfunction by disrupting the interaction between PSD‑95 and AMPARs, and the inhibition of the autophagy system eventually leads to the apoptosis of hippocampal neurons.
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Affiliation(s)
- Xinglin Yu
- Yunnan Key Laboratory of Dai and Yi Medicines, Yunnan University of Chinese Medicine, Kunming, Yunnan 650500, P.R. China
| | - Yuan Luo
- Yunnan Key Laboratory of Dai and Yi Medicines, Yunnan University of Chinese Medicine, Kunming, Yunnan 650500, P.R. China
| | - Liping Yang
- Yunnan Key Laboratory of Dai and Yi Medicines, Yunnan University of Chinese Medicine, Kunming, Yunnan 650500, P.R. China
| | - Xiaohua Duan
- Yunnan Key Laboratory of Dai and Yi Medicines, Yunnan University of Chinese Medicine, Kunming, Yunnan 650500, P.R. China
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9
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Paranjpe I, Wang X, Anandakrishnan N, Haydak JC, Van Vleck T, DeFronzo S, Li Z, Mendoza A, Liu R, Fu J, Forrest I, Zhou W, Lee K, O'Hagan R, Dellepiane S, Menon KM, Gulamali F, Kamat S, Gusella GL, Charney AW, Hofer I, Cho JH, Do R, Glicksberg BS, He JC, Nadkarni GN, Azeloglu EU. Deep learning on electronic medical records identifies distinct subphenotypes of diabetic kidney disease driven by genetic variations in the Rho pathway. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2023:2023.09.06.23295120. [PMID: 37732187 PMCID: PMC10508814 DOI: 10.1101/2023.09.06.23295120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/22/2023]
Abstract
Kidney disease affects 50% of all diabetic patients; however, prediction of disease progression has been challenging due to inherent disease heterogeneity. We use deep learning to identify novel genetic signatures prognostically associated with outcomes. Using autoencoders and unsupervised clustering of electronic health record data on 1,372 diabetic kidney disease patients, we establish two clusters with differential prevalence of end-stage kidney disease. Exome-wide associations identify a novel variant in ARHGEF18, a Rho guanine exchange factor specifically expressed in glomeruli. Overexpression of ARHGEF18 in human podocytes leads to impairments in focal adhesion architecture, cytoskeletal dynamics, cellular motility, and RhoA/Rac1 activation. Mutant GEF18 is resistant to ubiquitin mediated degradation leading to pathologically increased protein levels. Our findings uncover the first known disease-causing genetic variant that affects protein stability of a cytoskeletal regulator through impaired degradation, a potentially novel class of expression quantitative trait loci that can be therapeutically targeted.
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10
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Kleibert M, Zygmunciak P, Łakomska K, Mila K, Zgliczyński W, Mrozikiewicz-Rakowska B. Insight into the Molecular Mechanism of Diabetic Kidney Disease and the Role of Metformin in Its Pathogenesis. Int J Mol Sci 2023; 24:13038. [PMID: 37685845 PMCID: PMC10487922 DOI: 10.3390/ijms241713038] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2023] [Revised: 08/10/2023] [Accepted: 08/13/2023] [Indexed: 09/10/2023] Open
Abstract
Diabetic kidney disease (DKD) is one of the leading causes of death among patients diagnosed with diabetes mellitus. Despite the growing knowledge about the pathogenesis of DKD, we still do not have effective direct pharmacotherapy. Accurate blood sugar control is essential in slowing down DKD. It seems that metformin has a positive impact on kidneys and this effect is not only mediated by its hypoglycemic action, but also by direct molecular regulation of pathways involved in DKD. The molecular mechanism of DKD is complex and we can distinguish polyol, hexosamine, PKC, and AGE pathways which play key roles in the development and progression of this disease. Each of these pathways is overactivated in a hyperglycemic environment and it seems that most of them may be regulated by metformin. In this article, we summarize the knowledge about DKD pathogenesis and the potential mechanism of the nephroprotective effect of metformin. Additionally, we describe the impact of metformin on glomerular endothelial cells and podocytes, which are harmed in DKD.
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Affiliation(s)
- Marcin Kleibert
- Chair and Department of Experimental and Clinical Physiology, Laboratory of Centre for Preclinical Research, Medical University of Warsaw, 02-097 Warsaw, Poland;
| | - Przemysław Zygmunciak
- Faculty of Medicine, Medical University of Warsaw, 02-091 Warsaw, Poland; (P.Z.); (K.M.)
| | - Klaudia Łakomska
- Faculty of Medicine, Wroclaw Medical University, 50-367 Wroclaw, Poland;
| | - Klaudia Mila
- Faculty of Medicine, Medical University of Warsaw, 02-091 Warsaw, Poland; (P.Z.); (K.M.)
| | - Wojciech Zgliczyński
- Department of Endocrinology, Centre of Postgraduate Medical Education, Bielanski Hospital, 01-809 Warsaw, Poland;
| | - Beata Mrozikiewicz-Rakowska
- Department of Endocrinology, Centre of Postgraduate Medical Education, Bielanski Hospital, 01-809 Warsaw, Poland;
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11
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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.
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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
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12
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Osman W, Mousa M, Albreiki M, Baalfaqih Z, Daggag H, Hill C, McKnight AJ, Maxwell AP, Al Safar H. A genome-wide association study identifies a possible role for cannabinoid signalling in the pathogenesis of diabetic kidney disease. Sci Rep 2023; 13:4661. [PMID: 36949158 PMCID: PMC10033677 DOI: 10.1038/s41598-023-31701-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2023] [Accepted: 03/16/2023] [Indexed: 03/24/2023] Open
Abstract
Diabetic kidney disease (DKD), also known as diabetic nephropathy, is the leading cause of renal impairment and end-stage renal disease. Patients with diabetes are at risk for DKD because of poor control of their blood glucose, as well as nonmodifiable risk factors including age, ethnicity, and genetics. This genome-wide association study (GWAS) was conducted for the first time in the Emirati population to investigate possible genetic factors associated with the development and progression of DKD. We included data on 7,921,925 single nucleotide polymorphism (SNPs) in 258 cases of type 2 diabetes mellitus (T2DM) who developed DKD and 938 control subjects with T2DM who did not develop DKD. GWAS suggestive results (P < 1 × 10-5) were further replicated using summary statistics from three cohorts with T2DM-induced DKD (Bio Bank Japan data, UK Biobank, and FinnGen Project data) and T1DM-induced DKD (UK-ROI cohort data from Belfast, UK). When conducting a multiple linear regression model for gene-set analyses, the CNR2 gene demonstrated genome-wide significance at 1.46 × 10-6. SNPs in CNR2 gene, encodes cannabinoid receptor 2 or CB2, were replicated in Japanese samples with the leading SNP rs2501391 showing a Pcombined = 9.3 × 10-7, and odds ratio = 0.67 in association with DKD associated with T2DM, but not with T1DM, without any significant association with T2DM itself. The allele frequencies of our cohort and those of the replication cohorts were in most cases markedly different. In addition, we replicated the association between rs1564939 in the GLRA3 gene and DKD in T2DM (P = 0.016, odds ratio = 0.54 per allele C). Our findings suggest evidence that cannabinoid signalling may be involved in the development of DKD through CB2, which is expressed in different kidney regions and known to be involved in insulin resistance, inflammation, and the development of kidney fibrosis.
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Affiliation(s)
- Wael Osman
- Center for Biotechnology, Khalifa University, PO Box 127788, Abu Dhabi, United Arab Emirates
- Department of Biology, College of Arts and Sciences, Khalifa University, Abu Dhabi, United Arab Emirates
| | - Mira Mousa
- Center for Biotechnology, Khalifa University, PO Box 127788, Abu Dhabi, United Arab Emirates
| | - Mohammed Albreiki
- Center for Biotechnology, Khalifa University, PO Box 127788, Abu Dhabi, United Arab Emirates
| | - Zahrah Baalfaqih
- Center for Biotechnology, Khalifa University, PO Box 127788, Abu Dhabi, United Arab Emirates
| | - Hinda Daggag
- Imperial College of London Diabetes Centre, Abu Dhabi, United Arab Emirates
| | - Claire Hill
- Centre for Public Health, Queen's University of Belfast, Belfast, UK
| | | | | | - Habiba Al Safar
- Center for Biotechnology, Khalifa University, PO Box 127788, Abu Dhabi, United Arab Emirates.
- Department of Biomedical Engineering, College of Engineering, Khalifa University, Abu Dhabi, United Arab Emirates.
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13
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Hill C, Duffy S, Coulter T, Maxwell AP, McKnight AJ. Harnessing Genomic Analysis to Explore the Role of Telomeres in the Pathogenesis and Progression of Diabetic Kidney Disease. Genes (Basel) 2023; 14:609. [PMID: 36980881 PMCID: PMC10048490 DOI: 10.3390/genes14030609] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2023] [Revised: 02/20/2023] [Accepted: 02/21/2023] [Indexed: 03/06/2023] Open
Abstract
The prevalence of diabetes is increasing globally, and this trend is predicted to continue for future decades. Research is needed to uncover new ways to manage diabetes and its co-morbidities. A significant secondary complication of diabetes is kidney disease, which can ultimately result in the need for renal replacement therapy, via dialysis or transplantation. Diabetic kidney disease presents a substantial burden to patients, their families and global healthcare services. This review highlights studies that have harnessed genomic, epigenomic and functional prediction tools to uncover novel genes and pathways associated with DKD that are useful for the identification of therapeutic targets or novel biomarkers for risk stratification. Telomere length regulation is a specific pathway gaining attention recently because of its association with DKD. Researchers are employing both observational and genetics-based studies to identify telomere-related genes associated with kidney function decline in diabetes. Studies have also uncovered novel functions for telomere-related genes beyond the immediate regulation of telomere length, such as transcriptional regulation and inflammation. This review summarises studies that have revealed the potential to harness therapeutics that modulate telomere length, or the associated epigenetic modifications, for the treatment of DKD, to potentially slow renal function decline and reduce the global burden of this disease.
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Affiliation(s)
- Claire Hill
- Centre for Public Health, Queen’s University of Belfast, Belfast BT12 6BA, UK
| | - Seamus Duffy
- Centre for Public Health, Queen’s University of Belfast, Belfast BT12 6BA, UK
| | - Tiernan Coulter
- Centre for Public Health, Queen’s University of Belfast, Belfast BT12 6BA, UK
| | - Alexander Peter Maxwell
- Centre for Public Health, Queen’s University of Belfast, Belfast BT12 6BA, UK
- Regional Nephrology Unit, Belfast City Hospital, Belfast BT9 7AB, UK
| | - Amy Jayne McKnight
- Centre for Public Health, Queen’s University of Belfast, Belfast BT12 6BA, UK
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14
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Mohandes S, Doke T, Hu H, Mukhi D, Dhillon P, Susztak K. Molecular pathways that drive diabetic kidney disease. J Clin Invest 2023; 133:165654. [PMID: 36787250 PMCID: PMC9927939 DOI: 10.1172/jci165654] [Citation(s) in RCA: 91] [Impact Index Per Article: 91.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/15/2023] Open
Abstract
Kidney disease is a major driver of mortality among patients with diabetes and diabetic kidney disease (DKD) is responsible for close to half of all chronic kidney disease cases. DKD usually develops in a genetically susceptible individual as a result of poor metabolic (glycemic) control. Molecular and genetic studies indicate the key role of podocytes and endothelial cells in driving albuminuria and early kidney disease in diabetes. Proximal tubule changes show a strong association with the glomerular filtration rate. Hyperglycemia represents a key cellular stress in the kidney by altering cellular metabolism in endothelial cells and podocytes and by imposing an excess workload requiring energy and oxygen for proximal tubule cells. Changes in metabolism induce early adaptive cellular hypertrophy and reorganization of the actin cytoskeleton. Later, mitochondrial defects contribute to increased oxidative stress and activation of inflammatory pathways, causing progressive kidney function decline and fibrosis. Blockade of the renin-angiotensin system or the sodium-glucose cotransporter is associated with cellular protection and slowing kidney function decline. Newly identified molecular pathways could provide the basis for the development of much-needed novel therapeutics.
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Affiliation(s)
- Samer Mohandes
- Renal, Electrolyte, and Hypertension Division, Department of Medicine;,Institute for Diabetes, Obesity, and Metabolism;,Department of Genetics; and,Kidney Innovation Center; Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Tomohito Doke
- Renal, Electrolyte, and Hypertension Division, Department of Medicine;,Institute for Diabetes, Obesity, and Metabolism;,Department of Genetics; and,Kidney Innovation Center; Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Hailong Hu
- Renal, Electrolyte, and Hypertension Division, Department of Medicine;,Institute for Diabetes, Obesity, and Metabolism;,Department of Genetics; and,Kidney Innovation Center; Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Dhanunjay Mukhi
- Renal, Electrolyte, and Hypertension Division, Department of Medicine;,Institute for Diabetes, Obesity, and Metabolism;,Department of Genetics; and,Kidney Innovation Center; Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Poonam Dhillon
- Renal, Electrolyte, and Hypertension Division, Department of Medicine;,Institute for Diabetes, Obesity, and Metabolism;,Department of Genetics; and,Kidney Innovation Center; Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Katalin Susztak
- Renal, Electrolyte, and Hypertension Division, Department of Medicine;,Institute for Diabetes, Obesity, and Metabolism;,Department of Genetics; and,Kidney Innovation Center; Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
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15
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Khurana I, Kaipananickal H, Maxwell S, Birkelund S, Syreeni A, Forsblom C, Okabe J, Ziemann M, Kaspi A, Rafehi H, Jørgensen A, Al-Hasani K, Thomas MC, Jiang G, Luk AO, Lee HM, Huang Y, Thewjitcharoen Y, Nakasatien S, Himathongkam T, Fogarty C, Njeim R, Eid A, Hansen TW, Tofte N, Ottesen EC, Ma RC, Chan JC, Cooper ME, Rossing P, Groop PH, El-Osta A. Reduced methylation correlates with diabetic nephropathy risk in type 1 diabetes. J Clin Invest 2023; 133:160959. [PMID: 36633903 PMCID: PMC9927943 DOI: 10.1172/jci160959] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2022] [Accepted: 12/29/2022] [Indexed: 01/13/2023] Open
Abstract
Diabetic nephropathy (DN) is a polygenic disorder with few risk variants showing robust replication in large-scale genome-wide association studies. To understand the role of DNA methylation, it is important to have the prevailing genomic view to distinguish key sequence elements that influence gene expression. This is particularly challenging for DN because genome-wide methylation patterns are poorly defined. While methylation is known to alter gene expression, the importance of this causal relationship is obscured by array-based technologies since coverage outside promoter regions is low. To overcome these challenges, we performed methylation sequencing using leukocytes derived from participants of the Finnish Diabetic Nephropathy (FinnDiane) type 1 diabetes (T1D) study (n = 39) that was subsequently replicated in a larger validation cohort (n = 296). Gene body-related regions made up more than 60% of the methylation differences and emphasized the importance of methylation sequencing. We observed differentially methylated genes associated with DN in 3 independent T1D registries originating from Denmark (n = 445), Hong Kong (n = 107), and Thailand (n = 130). Reduced DNA methylation at CTCF and Pol2B sites was tightly connected with DN pathways that include insulin signaling, lipid metabolism, and fibrosis. To define the pathophysiological significance of these population findings, methylation indices were assessed in human renal cells such as podocytes and proximal convoluted tubule cells. The expression of core genes was associated with reduced methylation, elevated CTCF and Pol2B binding, and the activation of insulin-signaling phosphoproteins in hyperglycemic cells. These experimental observations also closely parallel methylation-mediated regulation in human macrophages and vascular endothelial cells.
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Affiliation(s)
- Ishant Khurana
- Epigenetics in Human Health and Disease Laboratory and,Department of Diabetes, Central Clinical School, Monash University, Melbourne, Victoria, Australia
| | - Harikrishnan Kaipananickal
- Epigenetics in Human Health and Disease Laboratory and,Department of Diabetes, Central Clinical School, Monash University, Melbourne, Victoria, Australia.,Department of Clinical Pathology, The University of Melbourne, Parkville, Victoria, Australia
| | - Scott Maxwell
- Epigenetics in Human Health and Disease Laboratory and,Department of Diabetes, Central Clinical School, Monash University, Melbourne, Victoria, Australia
| | - Sørine Birkelund
- Epigenetics in Human Health and Disease Laboratory and,Department of Diabetes, Central Clinical School, Monash University, Melbourne, Victoria, Australia.,University College Copenhagen, Faculty of Health, Department of Technology, Biomedical Laboratory Science, Copenhagen, Denmark
| | - Anna Syreeni
- 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
| | - Carol Forsblom
- 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
| | - Jun Okabe
- Epigenetics in Human Health and Disease Laboratory and,Department of Diabetes, Central Clinical School, Monash University, Melbourne, Victoria, Australia
| | - Mark Ziemann
- Epigenetics in Human Health and Disease Laboratory and,Department of Diabetes, Central Clinical School, Monash University, Melbourne, Victoria, Australia
| | - Antony Kaspi
- Epigenetics in Human Health and Disease Laboratory and,Department of Diabetes, Central Clinical School, Monash University, Melbourne, Victoria, Australia
| | - Haloom Rafehi
- Epigenetics in Human Health and Disease Laboratory and,Department of Diabetes, Central Clinical School, Monash University, Melbourne, Victoria, Australia
| | - Anne Jørgensen
- Epigenetics in Human Health and Disease Laboratory and,Department of Diabetes, Central Clinical School, Monash University, Melbourne, Victoria, Australia.,Steno Diabetes Center Copenhagen, Herlev, Denmark
| | - Keith Al-Hasani
- Epigenetics in Human Health and Disease Laboratory and,Department of Diabetes, Central Clinical School, Monash University, Melbourne, Victoria, Australia
| | - Merlin C. Thomas
- Department of Diabetes, Central Clinical School, Monash University, Melbourne, Victoria, Australia
| | | | - Andrea O.Y. Luk
- Department of Medicine and Therapeutics,,Hong Kong Institute of Diabetes and Obesity,,Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Hong Kong, China
| | - Heung Man Lee
- Department of Medicine and Therapeutics,,Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Hong Kong, China
| | - Yu Huang
- Department of Biomedical Sciences, City University of Hong Kong, Hong Kong, China
| | | | | | | | - Christopher Fogarty
- 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
| | - Rachel Njeim
- Department of Anatomy, Cell Biology and Physiology, Faculty of Medicine, American University of Beirut, Beirut, Lebanon
| | - Assaad Eid
- Department of Anatomy, Cell Biology and Physiology, Faculty of Medicine, American University of Beirut, Beirut, Lebanon
| | | | - Nete Tofte
- Steno Diabetes Center Copenhagen, Herlev, Denmark
| | | | - Ronald C.W. Ma
- Department of Medicine and Therapeutics,,Hong Kong Institute of Diabetes and Obesity,,Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Hong Kong, China
| | - Juliana C.N. Chan
- Department of Medicine and Therapeutics,,Hong Kong Institute of Diabetes and Obesity,,Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Hong Kong, China
| | - Mark E. Cooper
- Department of Diabetes, Central Clinical School, Monash University, Melbourne, Victoria, Australia
| | - Peter Rossing
- Steno Diabetes Center Copenhagen, Herlev, Denmark.,Department of Clinical Medicine, University of Copenhagen, Copenhagen, Denmark
| | - Per-Henrik Groop
- Department of Diabetes, Central Clinical School, Monash University, Melbourne, Victoria, Australia.,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
| | - Assam El-Osta
- Epigenetics in Human Health and Disease Laboratory and,Department of Diabetes, Central Clinical School, Monash University, Melbourne, Victoria, Australia.,Department of Clinical Pathology, The University of Melbourne, Parkville, Victoria, Australia.,University College Copenhagen, Faculty of Health, Department of Technology, Biomedical Laboratory Science, Copenhagen, Denmark.,Hong Kong Institute of Diabetes and Obesity,,Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Hong Kong, China
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16
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Mohammedi K, Marre M, Hadjadj S, Potier L, Velho G. Redox Genetic Risk Score and the Incidence of End-Stage Kidney Disease in People with Type 1 Diabetes. Cells 2022; 11:cells11244131. [PMID: 36552894 PMCID: PMC9777489 DOI: 10.3390/cells11244131] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2022] [Revised: 11/23/2022] [Accepted: 12/16/2022] [Indexed: 12/24/2022] Open
Abstract
End-stage kidney disease (ESKD) is a multifactorial condition influenced by genetic background, but the extent to which a genetic risk score (GRS) improves ESKD prediction is unknown. We built a redox GRS on the base of previous association studies (six polymorphisms from six redox genes) and tested its relationship with ESKD in three cohorts of people with type 1 diabetes. Among 1012 participants, ESKD (hemodialysis requirement, kidney transplantation, eGFR < 15 mL/min/1.73 m2) occurred in 105 (10.4%) during a 14-year follow-up. High redox GRS was associated with increased ESKD risk (adjusted HR for the upper versus the lowest GRS tertile: 2.60 (95% CI, 1.51-4.48), p = 0.001). Each additional risk-allele was associated with a 20% increased risk of ESKD (95% CI, 8-33, p < 0.0001). High GRS yielded a relevant population attributable fraction (30%), but only a marginal enhancement in c-statistics index (0.928 [0.903-0.954]) over clinical factors 0.921 (0.892-0.950), p = 0.04). This is the first report of an independent association between redox GRS and increased risk of ESKD in type 1 diabetes. Our results do not support the use of this GRS in clinical practice but provide new insights into the involvement of oxidative stress genetic factors in ESKD risk in type 1 diabetes.
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Affiliation(s)
- Kamel Mohammedi
- Centre Hospitalier de Bordeaux, Department of Endocrinology, Diabetes and Nutrition, University Hospital of Bordeaux, 33604 Pessac, France
- Population Health Research Institute, McMaster University and Hamilton Health Sciences, Hamilton, ON L8S 4L8, Canada
- Correspondence:
| | - Michel Marre
- Institut Necker-Enfants Malades, INSERM, Université de Paris, 75013 Paris, France
- Clinique Ambroise Paré, 92200 Neuilly-sur-Seine, France
| | - Samy Hadjadj
- Institut du Thorax, INSERM, CNRS, UNIV Nantes, CHU Nantes, 44109 Nantes, France
| | - Louis Potier
- Institut Necker-Enfants Malades, INSERM, Université de Paris, 75013 Paris, France
- Clinique Ambroise Paré, 92200 Neuilly-sur-Seine, France
- Service d’Endocrinologie Diabétologie Nutrition, Hôpital Bichat, AP-HP, 75013 Paris, France
| | - Gilberto Velho
- Institut Necker-Enfants Malades, INSERM, Université de Paris, 75013 Paris, France
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17
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Sandholm N, Hotakainen R, Haukka JK, Jansson Sigfrids F, Dahlström EH, Antikainen AA, Valo E, Syreeni A, Kilpeläinen E, Kytölä A, Palotie A, Harjutsalo V, Forsblom C, Groop PH. Whole-exome sequencing identifies novel protein-altering variants associated with serum apolipoprotein and lipid concentrations. Genome Med 2022; 14:132. [PMID: 36419110 PMCID: PMC9685920 DOI: 10.1186/s13073-022-01135-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2022] [Accepted: 11/04/2022] [Indexed: 11/25/2022] Open
Abstract
BACKGROUND Dyslipidemia is a major risk factor for cardiovascular disease, and diabetes impacts the lipid metabolism through multiple pathways. In addition to the standard lipid measurements, apolipoprotein concentrations provide added awareness of the burden of circulating lipoproteins. While common genetic variants modestly affect the serum lipid concentrations, rare genetic mutations can cause monogenic forms of hypercholesterolemia and other genetic disorders of lipid metabolism. We aimed to identify low-frequency protein-altering variants (PAVs) affecting lipoprotein and lipid traits. METHODS We analyzed whole-exome (WES) and whole-genome sequencing (WGS) data of 481 and 474 individuals with type 1 diabetes, respectively. The phenotypic data consisted of 79 serum lipid and apolipoprotein phenotypes obtained with clinical laboratory measurements and nuclear magnetic resonance spectroscopy. RESULTS The single-variant analysis identified an association between the LIPC p.Thr405Met (rs113298164) and serum apolipoprotein A1 concentrations (p=7.8×10-8). The burden of PAVs was significantly associated with lipid phenotypes in LIPC, RBM47, TRMT5, GTF3C5, MARCHF10, and RYR3 (p<2.9×10-6). The RBM47 gene is required for apolipoprotein B post-translational modifications, and in our data, the association between RBM47 and apolipoprotein C-III concentrations was due to a rare 21 base pair p.Ala496-Ala502 deletion; in replication, the burden of rare deleterious variants in RBM47 was associated with lower triglyceride concentrations in WES of >170,000 individuals from multiple ancestries (p=0.0013). Two PAVs in GTF3C5 were highly enriched in the Finnish population and associated with cardiovascular phenotypes in the general population. In the previously known APOB gene, we identified novel associations at two protein-truncating variants resulting in lower serum non-HDL cholesterol (p=4.8×10-4), apolipoprotein B (p=5.6×10-4), and LDL cholesterol (p=9.5×10-4) concentrations. CONCLUSIONS We identified lipid and apolipoprotein-associated variants in the previously known LIPC and APOB genes, as well as PAVs in GTF3C5 associated with LDLC, and in RBM47 associated with apolipoprotein C-III concentrations, implicated as an independent CVD risk factor. Identification of rare loss-of-function variants has previously revealed genes that can be targeted to prevent CVD, such as the LDL cholesterol-lowering loss-of-function variants in the PCSK9 gene. Thus, this study suggests novel putative therapeutic targets for the prevention of CVD.
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Affiliation(s)
- Niina Sandholm
- grid.428673.c0000 0004 0409 6302Folkhälsan Research Center, Biomedicum Helsinki, Haartmaninkatu 8, Helsinki, 00290 Finland ,grid.7737.40000 0004 0410 2071Department of Nephrology, University of Helsinki and Helsinki University Hospital, Helsinki, Finland ,grid.7737.40000 0004 0410 2071Research Program for Clinical and Molecular Metabolism, Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | - Ronja Hotakainen
- grid.428673.c0000 0004 0409 6302Folkhälsan Research Center, Biomedicum Helsinki, Haartmaninkatu 8, Helsinki, 00290 Finland ,grid.7737.40000 0004 0410 2071Department of Nephrology, University of Helsinki and Helsinki University Hospital, Helsinki, Finland ,grid.7737.40000 0004 0410 2071Research Program for Clinical and Molecular Metabolism, Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | - Jani K. Haukka
- grid.428673.c0000 0004 0409 6302Folkhälsan Research Center, Biomedicum Helsinki, Haartmaninkatu 8, Helsinki, 00290 Finland ,grid.7737.40000 0004 0410 2071Department of Nephrology, University of Helsinki and Helsinki University Hospital, Helsinki, Finland ,grid.7737.40000 0004 0410 2071Research Program for Clinical and Molecular Metabolism, Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | - Fanny Jansson Sigfrids
- grid.428673.c0000 0004 0409 6302Folkhälsan Research Center, Biomedicum Helsinki, Haartmaninkatu 8, Helsinki, 00290 Finland ,grid.7737.40000 0004 0410 2071Department of Nephrology, University of Helsinki and Helsinki University Hospital, Helsinki, Finland ,grid.7737.40000 0004 0410 2071Research Program for Clinical and Molecular Metabolism, Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | - Emma H. Dahlström
- grid.428673.c0000 0004 0409 6302Folkhälsan Research Center, Biomedicum Helsinki, Haartmaninkatu 8, Helsinki, 00290 Finland ,grid.7737.40000 0004 0410 2071Department of Nephrology, University of Helsinki and Helsinki University Hospital, Helsinki, Finland ,grid.7737.40000 0004 0410 2071Research Program for Clinical and Molecular Metabolism, Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | - Anni A. Antikainen
- grid.428673.c0000 0004 0409 6302Folkhälsan Research Center, Biomedicum Helsinki, Haartmaninkatu 8, Helsinki, 00290 Finland ,grid.7737.40000 0004 0410 2071Department of Nephrology, University of Helsinki and Helsinki University Hospital, Helsinki, Finland ,grid.7737.40000 0004 0410 2071Research Program for Clinical and Molecular Metabolism, Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | - Erkka Valo
- grid.428673.c0000 0004 0409 6302Folkhälsan Research Center, Biomedicum Helsinki, Haartmaninkatu 8, Helsinki, 00290 Finland ,grid.7737.40000 0004 0410 2071Department of Nephrology, University of Helsinki and Helsinki University Hospital, Helsinki, Finland ,grid.7737.40000 0004 0410 2071Research Program for Clinical and Molecular Metabolism, Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | - Anna Syreeni
- grid.428673.c0000 0004 0409 6302Folkhälsan Research Center, Biomedicum Helsinki, Haartmaninkatu 8, Helsinki, 00290 Finland ,grid.7737.40000 0004 0410 2071Department of Nephrology, University of Helsinki and Helsinki University Hospital, Helsinki, Finland ,grid.7737.40000 0004 0410 2071Research Program for Clinical and Molecular Metabolism, Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | - Elina Kilpeläinen
- grid.7737.40000 0004 0410 2071Institute for Molecular Medicine Finland (FIMM), HiLIFE, University of Helsinki, Helsinki, Finland
| | - Anastasia Kytölä
- grid.7737.40000 0004 0410 2071Institute for Molecular Medicine Finland (FIMM), HiLIFE, University of Helsinki, Helsinki, Finland
| | - Aarno Palotie
- grid.7737.40000 0004 0410 2071Institute for Molecular Medicine Finland (FIMM), HiLIFE, University of Helsinki, Helsinki, Finland ,grid.32224.350000 0004 0386 9924Analytic and Translational Genetics Unit, Department of Medicine, Department of Neurology and Department of Psychiatry, Massachusetts General Hospital, Boston, MA USA ,grid.66859.340000 0004 0546 1623The Stanley Center for Psychiatric Research and Program in Medical and Population Genetics, The Broad Institute of MIT and Harvard, Cambridge, MA USA
| | - Valma Harjutsalo
- grid.428673.c0000 0004 0409 6302Folkhälsan Research Center, Biomedicum Helsinki, Haartmaninkatu 8, Helsinki, 00290 Finland ,grid.7737.40000 0004 0410 2071Department of Nephrology, University of Helsinki and Helsinki University Hospital, Helsinki, Finland ,grid.7737.40000 0004 0410 2071Research Program for Clinical and Molecular Metabolism, Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | - Carol Forsblom
- grid.428673.c0000 0004 0409 6302Folkhälsan Research Center, Biomedicum Helsinki, Haartmaninkatu 8, Helsinki, 00290 Finland ,grid.7737.40000 0004 0410 2071Department of Nephrology, University of Helsinki and Helsinki University Hospital, Helsinki, Finland ,grid.7737.40000 0004 0410 2071Research Program for Clinical and Molecular Metabolism, Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | - Per-Henrik Groop
- grid.428673.c0000 0004 0409 6302Folkhälsan Research Center, Biomedicum Helsinki, Haartmaninkatu 8, Helsinki, 00290 Finland ,grid.7737.40000 0004 0410 2071Department of Nephrology, University of Helsinki and Helsinki University Hospital, Helsinki, Finland ,grid.7737.40000 0004 0410 2071Research Program for Clinical and Molecular Metabolism, Faculty of Medicine, University of Helsinki, Helsinki, Finland ,grid.1002.30000 0004 1936 7857Department of Diabetes, Central Clinical School, Monash University, Melbourne, Victoria Australia
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Khattab A, Torkamani A. Nidogen-1 could play a role in diabetic kidney disease development in type 2 diabetes: a genome-wide association meta-analysis. Hum Genomics 2022; 16:47. [PMID: 36271454 PMCID: PMC9587571 DOI: 10.1186/s40246-022-00422-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2022] [Accepted: 10/12/2022] [Indexed: 11/23/2022] Open
Abstract
BACKGROUND Diabetic kidney disease (DKD) affects about 40% of patients with diabetes. It is incurable and usually leads to end-stage renal disease (ESRD). The pathogenesis of DKD is still not fully understood, and the genetics of DKD have not yet been extensively studied. In this study, we investigate the genetic basis of DKD in type 2 diabetes (T2D) to provide more insights into the pathogenesis of the disease. RESULTS Using the data provided by the UK Biobank (UKBB), we performed a DKD genome-wide association study (GWAS) in 13,123 individuals with T2D as well as two creatinine estimated glomerular filtration rate (eGFR) GWA studies: one in 26,786 individuals with T2D and the other in 339,080 non-diabetic individuals. We also conducted a DKD GWAS meta-analysis combining our results with those published by the surrogate markers for micro- and macro-vascular hard endpoints for Innovative diabetes Tools (SUMMIT) consortium. We confirm two loci previously reported to be associated with chronic kidney disease (CKD) and eGFR in T2D. The UMOD-PDILT locus is associated with DKD (P = 1.17E-09) as well as creatinine eGFR in both people with T2D (P = 1.31E-15) and people without diabetes (P = 3.95E-73). The PRKAG2 locus is associated with creatinine eGFR in people with (P = 2.78E-10) and without (P = 5.65E-72) T2D. Our meta-analysis reveals a novel association between DKD and variant rs72763500 (chr1:236116561) which is a splicing quantitative trait locus (sQTL) for nidogen-1 (NID1) gene. CONCLUSION Our data confirm two loci previously reported in association with CKD and creatinine eGFR in T2D. It also suggests that NID1, a major component of the renal tubular basement membrane, could play a role in DKD development in T2D. While our NID1 finding remains to be replicated, it is a step toward a more comprehensive understanding of DKD pathogenesis.
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Affiliation(s)
- Ahmed Khattab
- Integrative Structural and Computational Biology, Scripps Research, 3344 North Torrey Pines Court, Suite 300, La Jolla, CA, 92037, USA.,Scripps Research Translational Institute, La Jolla, CA, 92037, USA
| | - Ali Torkamani
- Integrative Structural and Computational Biology, Scripps Research, 3344 North Torrey Pines Court, Suite 300, La Jolla, CA, 92037, USA. .,Scripps Research Translational Institute, La Jolla, CA, 92037, USA.
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19
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Nomogram-Based Chronic Kidney Disease Prediction Model for Type 1 Diabetes Mellitus Patients Using Routine Pathological Data. J Pers Med 2022; 12:jpm12091507. [PMID: 36143293 PMCID: PMC9501949 DOI: 10.3390/jpm12091507] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2022] [Revised: 09/12/2022] [Accepted: 09/13/2022] [Indexed: 11/16/2022] Open
Abstract
Type 1 diabetes mellitus (T1DM) patients are a significant threat to chronic kidney disease (CKD) development during their life. However, there is always a high chance of delay in CKD detection because CKD can be asymptomatic, and T1DM patients bypass traditional CKD tests during their routine checkups. This study aims to develop and validate a prediction model and nomogram of CKD in T1DM patients using readily available routine checkup data for early CKD detection. This research utilized 1375 T1DM patients’ sixteen years of longitudinal data from multi-center Epidemiology of Diabetes Interventions and Complications (EDIC) clinical trials conducted at 28 sites in the USA and Canada and considered 17 routinely available features. Three feature ranking algorithms, extreme gradient boosting (XGB), random forest (RF), and extremely randomized trees classifier (ERT), were applied to create three feature ranking lists, and logistic regression analyses were performed to develop CKD prediction models using these ranked feature lists to identify the best performing top-ranked features combination. Finally, the most significant features were selected to develop a multivariate logistic regression-based CKD prediction model for T1DM patients. This model was evaluated using sensitivity, specificity, accuracy, precision, and F1 score on train and test data. A nomogram of the final model was further generated for easy application in clinical practices. Hypertension, duration of diabetes, drinking habit, triglycerides, ACE inhibitors, low-density lipoprotein (LDL) cholesterol, age, and smoking habit were the top-8 features ranked by the XGB model and identified as the most important features for predicting CKD in T1DM patients. These eight features were selected to develop the final prediction model using multivariate logistic regression, which showed 90.04% and 88.59% accuracy in internal and test data validation. The proposed model showed excellent performance and can be used for CKD identification in T1DM patients during routine checkups.
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20
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Sandholm N, Cole JB, Nair V, Sheng X, Liu H, Ahlqvist E, van Zuydam N, Dahlström EH, Fermin D, Smyth LJ, Salem RM, Forsblom C, Valo E, Harjutsalo V, Brennan EP, McKay GJ, Andrews D, Doyle R, Looker HC, Nelson RG, Palmer C, McKnight AJ, Godson C, Maxwell AP, Groop L, McCarthy MI, Kretzler M, Susztak K, Hirschhorn JN, Florez JC, Groop PH. Genome-wide meta-analysis and omics integration identifies novel genes associated with diabetic kidney disease. Diabetologia 2022; 65:1495-1509. [PMID: 35763030 PMCID: PMC9345823 DOI: 10.1007/s00125-022-05735-0] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/13/2021] [Accepted: 03/30/2022] [Indexed: 11/29/2022]
Abstract
AIMS/HYPOTHESIS Diabetic kidney disease (DKD) is the leading cause of kidney failure and has a substantial genetic component. Our aim was to identify novel genetic factors and genes contributing to DKD by performing meta-analysis of previous genome-wide association studies (GWAS) on DKD and by integrating the results with renal transcriptomics datasets. METHODS We performed GWAS meta-analyses using ten phenotypic definitions of DKD, including nearly 27,000 individuals with diabetes. Meta-analysis results were integrated with estimated quantitative trait locus data from human glomerular (N=119) and tubular (N=121) samples to perform transcriptome-wide association study. We also performed gene aggregate tests to jointly test all available common genetic markers within a gene, and combined the results with various kidney omics datasets. RESULTS The meta-analysis identified a novel intronic variant (rs72831309) in the TENM2 gene associated with a lower risk of the combined chronic kidney disease (eGFR<60 ml/min per 1.73 m2) and DKD (microalbuminuria or worse) phenotype (p=9.8×10-9; although not withstanding correction for multiple testing, p>9.3×10-9). Gene-level analysis identified ten genes associated with DKD (COL20A1, DCLK1, EIF4E, PTPRN-RESP18, GPR158, INIP-SNX30, LSM14A and MFF; p<2.7×10-6). Integration of GWAS with human glomerular and tubular expression data demonstrated higher tubular AKIRIN2 gene expression in individuals with vs without DKD (p=1.1×10-6). The lead SNPs within six loci significantly altered DNA methylation of a nearby CpG site in kidneys (p<1.5×10-11). Expression of lead genes in kidney tubules or glomeruli correlated with relevant pathological phenotypes (e.g. TENM2 expression correlated positively with eGFR [p=1.6×10-8] and negatively with tubulointerstitial fibrosis [p=2.0×10-9], tubular DCLK1 expression correlated positively with fibrosis [p=7.4×10-16], and SNX30 expression correlated positively with eGFR [p=5.8×10-14] and negatively with fibrosis [p<2.0×10-16]). CONCLUSIONS/INTERPRETATION Altogether, the results point to novel genes contributing to the pathogenesis of DKD. DATA AVAILABILITY The GWAS meta-analysis results can be accessed via the type 1 and type 2 diabetes (T1D and T2D, respectively) and Common Metabolic Diseases (CMD) Knowledge Portals, and downloaded on their respective download pages ( https://t1d.hugeamp.org/downloads.html ; https://t2d.hugeamp.org/downloads.html ; https://hugeamp.org/downloads.html ).
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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
| | - Joanne B Cole
- Programs in Metabolism and Medical & Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Division of Endocrinology, Boston Children's Hospital, Boston, MA, USA
- Diabetes Unit and Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA
| | - Viji Nair
- Michigan Medicine, Ann Arbor, MI, USA
| | - Xin Sheng
- Renal, Electrolyte, and Hypertension Division, Department of Medicine, University of Pennsylvania, Perelman School of Medicine, Philadelphia, PA, USA
- Institute for Diabetes, Obesity, and Metabolism, University of Pennsylvania, Perelman School of Medicine, Philadelphia, PA, USA
- Department of Genetics, University of Pennsylvania, Perelman School of Medicine, Philadelphia, PA, USA
| | - Hongbo Liu
- Renal, Electrolyte, and Hypertension Division, Department of Medicine, University of Pennsylvania, Perelman School of Medicine, Philadelphia, PA, USA
- Institute for Diabetes, Obesity, and Metabolism, University of Pennsylvania, Perelman School of Medicine, Philadelphia, PA, USA
- Department of Genetics, University of Pennsylvania, Perelman School of Medicine, Philadelphia, PA, USA
| | - Emma Ahlqvist
- Department of Clinical Sciences, Lund University Diabetes Centre, Lund University and Skåne University Hospital, Malmö, Sweden
| | - Natalie van Zuydam
- Pat Macpherson Centre for Pharmacogenetics & Pharmacogenomics, Cardiovascular & Diabetes Medicine, School of Medicine, University of Dundee, Dundee, UK
- Oxford Centre for Diabetes, Endocrinology & Metabolism, Radcliffe Department of Medicine, University of Oxford, Oxford, UK
- Wellcome Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - 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
| | | | - Laura J Smyth
- Molecular Epidemiology Research Group, Centre for Public Health, Queen's University Belfast, Belfast, UK
| | - Rany M Salem
- Herbert Wertheim School of Public Health and Human Longevity Science, University of California San Diego, La Jolla, CA, USA
| | - Carol Forsblom
- 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
| | - Erkka Valo
- 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
| | - Valma Harjutsalo
- 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
- Finnish Institute for Health and Welfare, Helsinki, Finland
| | - Eoin P Brennan
- Diabetes Complications Research Centre, Conway Institute, School of Medicine, University College Dublin, Dublin, Ireland
| | - Gareth J McKay
- Molecular Epidemiology Research Group, Centre for Public Health, Queen's University Belfast, Belfast, UK
| | - Darrell Andrews
- Diabetes Complications Research Centre, Conway Institute, School of Medicine, University College Dublin, Dublin, Ireland
| | - Ross Doyle
- Diabetes Complications Research Centre, Conway Institute, School of Medicine, University College Dublin, Dublin, Ireland
| | - Helen C Looker
- Chronic Kidney Disease Section, National Institute of Diabetes and Digestive and Kidney Diseases, Phoenix, AZ, USA
| | - Robert G Nelson
- Chronic Kidney Disease Section, National Institute of Diabetes and Digestive and Kidney Diseases, Phoenix, AZ, USA
| | - Colin Palmer
- Pat Macpherson Centre for Pharmacogenetics & Pharmacogenomics, Cardiovascular & Diabetes Medicine, School of Medicine, University of Dundee, Dundee, UK
| | - Amy Jayne McKnight
- Molecular Epidemiology Research Group, Centre for Public Health, Queen's University Belfast, Belfast, UK
| | - Catherine Godson
- Diabetes Complications Research Centre, Conway Institute, School of Medicine, University College Dublin, Dublin, Ireland
| | - Alexander P Maxwell
- Molecular Epidemiology Research Group, Centre for Public Health, Queen's University Belfast, Belfast, UK
- Regional Nephrology Unit, Belfast City Hospital, Belfast, Northern Ireland, UK
| | - Leif Groop
- Department of Clinical Sciences, Lund University Diabetes Centre, Lund University and Skåne University Hospital, Malmö, Sweden
- Institute for Molecular Medicine Finland FIMM, University of Helsinki, Helsinki, Finland
| | - Mark I McCarthy
- Oxford Centre for Diabetes, Endocrinology & Metabolism, Radcliffe Department of Medicine, University of Oxford, Oxford, UK
- Wellcome Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | | | - Katalin Susztak
- Renal, Electrolyte, and Hypertension Division, Department of Medicine, University of Pennsylvania, Perelman School of Medicine, Philadelphia, PA, USA
- Institute for Diabetes, Obesity, and Metabolism, University of Pennsylvania, Perelman School of Medicine, Philadelphia, PA, USA
- Department of Genetics, University of Pennsylvania, Perelman School of Medicine, Philadelphia, PA, USA
| | - Joel N Hirschhorn
- Programs in Metabolism and Medical & Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA.
- Division of Endocrinology, Boston Children's Hospital, Boston, MA, USA.
- Departments of Pediatrics and Genetics, Harvard Medical School, Boston, MA, USA.
| | - Jose C Florez
- Programs in Metabolism and Medical & Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Diabetes Unit and Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA
- Department of Medicine, Harvard Medical School, Boston, MA, USA
| | - 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, Victoria, Australia.
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21
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Genetics in chronic kidney disease: conclusions from a Kidney Disease: Improving Global Outcomes (KDIGO) Controversies Conference. Kidney Int 2022; 101:1126-1141. [PMID: 35460632 PMCID: PMC9922534 DOI: 10.1016/j.kint.2022.03.019] [Citation(s) in RCA: 42] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2022] [Revised: 03/16/2022] [Accepted: 03/29/2022] [Indexed: 01/19/2023]
Abstract
Numerous genes for monogenic kidney diseases with classical patterns of inheritance, as well as genes for complex kidney diseases that manifest in combination with environmental factors, have been discovered. Genetic findings are increasingly used to inform clinical management of nephropathies, and have led to improved diagnostics, disease surveillance, choice of therapy, and family counseling. All of these steps rely on accurate interpretation of genetic data, which can be outpaced by current rates of data collection. In March of 2021, Kidney Diseases: Improving Global Outcomes (KDIGO) held a Controversies Conference on "Genetics in Chronic Kidney Disease (CKD)" to review the current state of understanding of monogenic and complex (polygenic) kidney diseases, processes for applying genetic findings in clinical medicine, and use of genomics for defining and stratifying CKD. Given the important contribution of genetic variants to CKD, practitioners with CKD patients are advised to "think genetic," which specifically involves obtaining a family history, collecting detailed information on age of CKD onset, performing clinical examination for extrarenal symptoms, and considering genetic testing. To improve the use of genetics in nephrology, meeting participants advised developing an advanced training or subspecialty track for nephrologists, crafting guidelines for testing and treatment, and educating patients, students, and practitioners. Key areas of future research, including clinical interpretation of genome variation, electronic phenotyping, global representation, kidney-specific molecular data, polygenic scores, translational epidemiology, and open data resources, were also identified.
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22
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Kim J, Jensen A, Ko S, Raghavan S, Phillips LS, Hung A, Sun Y, Zhou H, Reaven P, Zhou JJ. Systematic Heritability and Heritability Enrichment Analysis for Diabetes Complications in UK Biobank and ACCORD Studies. Diabetes 2022; 71:1137-1148. [PMID: 35133398 PMCID: PMC9044130 DOI: 10.2337/db21-0839] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/16/2021] [Accepted: 02/02/2022] [Indexed: 11/13/2022]
Abstract
Diabetes-related complications reflect longstanding damage to small and large vessels throughout the body. In addition to the duration of diabetes and poor glycemic control, genetic factors are important contributors to the variability in the development of vascular complications. Early heritability studies found strong familial clustering of both macrovascular and microvascular complications. However, they were limited by small sample sizes and large phenotypic heterogeneity, leading to less accurate estimates. We take advantage of two independent studies-UK Biobank and the Action to Control Cardiovascular Risk in Diabetes trial-to survey the single nucleotide polymorphism heritability for diabetes microvascular (diabetic kidney disease and diabetic retinopathy) and macrovascular (cardiovascular events) complications. Heritability for diabetic kidney disease was estimated at 29%. The heritability estimate for microalbuminuria ranged from 24 to 60% and was 41% for macroalbuminuria. Heritability estimates of diabetic retinopathy ranged from 6 to 33%, depending on the phenotype definition. More severe diabetes retinopathy possessed higher genetic contributions. We show, for the first time, that rare variants account for much of the heritability of diabetic retinopathy. This study suggests that a large portion of the genetic risk of diabetes complications is yet to be discovered and emphasizes the need for additional genetic studies of diabetes complications.
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Affiliation(s)
- Juhyun Kim
- Department of Biostatistics, University of California, Los Angeles, Los Angeles, CA
- Department of Biostatistics, University of Michigan, Ann Arbor, MI
| | - Aubrey Jensen
- Department of Biostatistics, University of California, Los Angeles, Los Angeles, CA
| | - Seyoon Ko
- Department of Biostatistics, University of California, Los Angeles, Los Angeles, CA
| | - Sridharan Raghavan
- University of Colorado School of Medicine, Aurora, CO
- Rocky Mountain Regional Veterans Affairs Medical Center, Aurora, CO
| | - Lawrence S. Phillips
- Division of Endocrinology, Emory University School of Medicine, Atlanta, GA
- Atlanta Veterans Affairs Medical Center, Decatur, GA
| | - Adriana Hung
- Tennessee Valley Healthcare System and Vanderbilt University, Nashville, TN
| | - Yan Sun
- Department of Epidemiology, Emory University, Atlanta, GA
| | - Hua Zhou
- Department of Biostatistics, University of California, Los Angeles, Los Angeles, CA
| | - Peter Reaven
- Phoenix Veterans Affairs Health Care System, Phoenix, AZ
| | - Jin J. Zhou
- Department of Biostatistics, University of California, Los Angeles, Los Angeles, CA
- Phoenix Veterans Affairs Health Care System, Phoenix, AZ
- Department of Epidemiology and Biostatistics, University of Arizona, Tucson, AZ
- Department of Medicine, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA
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23
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Khan K, Ahram DF, Liu YP, Westland R, Sampogna RV, Katsanis N, Davis EE, Sanna-Cherchi S. Multidisciplinary approaches for elucidating genetics and molecular pathogenesis of urinary tract malformations. Kidney Int 2022; 101:473-484. [PMID: 34780871 PMCID: PMC8934530 DOI: 10.1016/j.kint.2021.09.034] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2021] [Revised: 09/15/2021] [Accepted: 09/30/2021] [Indexed: 12/28/2022]
Abstract
Advances in clinical diagnostics and molecular tools have improved our understanding of the genetically heterogeneous causes underlying congenital anomalies of kidney and urinary tract (CAKUT). However, despite a sharp incline of CAKUT reports in the literature within the past 2 decades, there remains a plateau in the genetic diagnostic yield that is disproportionate to the accelerated ability to generate robust genome-wide data. Explanations for this observation include (i) diverse inheritance patterns with incomplete penetrance and variable expressivity, (ii) rarity of single-gene drivers such that large sample sizes are required to meet the burden of proof, and (iii) multigene interactions that might produce either intra- (e.g., copy number variants) or inter- (e.g., effects in trans) locus effects. These challenges present an opportunity for the community to implement innovative genetic and molecular avenues to explain the missing heritability and to better elucidate the mechanisms that underscore CAKUT. Here, we review recent multidisciplinary approaches at the intersection of genetics, genomics, in vivo modeling, and in vitro systems toward refining a blueprint for overcoming the diagnostic hurdles that are pervasive in urinary tract malformation cohorts. These approaches will not only benefit clinical management by reducing age at molecular diagnosis and prompting early evaluation for comorbid features but will also serve as a springboard for therapeutic development.
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Affiliation(s)
- Kamal Khan
- Center for Human Disease Modeling, Duke University, Durham, North Carolina, USA.,Stanley Manne Children’s Research Institute, Ann & Robert H. Lurie Children’s Hospital of Chicago, Chicago, Illinois, USA (current address)
| | - Dina F. Ahram
- Division of Nephrology, Columbia University, New York, USA
| | - Yangfan P. Liu
- Center for Human Disease Modeling, Duke University, Durham, North Carolina, USA
| | - Rik Westland
- Division of Nephrology, Columbia University, New York, USA.,Department of Pediatric Nephrology, Amsterdam UMC- Emma Children’s Hospital, Amsterdam, NL
| | | | - Nicholas Katsanis
- Center for Human Disease Modeling, Duke University, Durham, North Carolina, USA; Stanley Manne Children's Research Institute, Ann & Robert H. Lurie Children's Hospital of Chicago, Chicago, Illinois, USA (current address); Department of Pediatrics, Feinberg School of Medicine, Northwestern University, Chicago, Illinois, USA; Department of Cell and Developmental Biology, Feinberg School of Medicine, Northwestern University, Chicago, Illinois, USA.
| | - Erica E. Davis
- Center for Human Disease Modeling, Duke University, Durham, North Carolina, USA.,Stanley Manne Children’s Research Institute, Ann & Robert H. Lurie Children’s Hospital of Chicago, Chicago, Illinois, USA (current address).,Department of Pediatrics and Department of Cell and Molecular Biology, Feinberg School of Medicine, Northwestern University, Chicago, Illinois, USA.,To whom correspondence should be addressed: ADDRESS CORRESPONDENCE TO: Simone Sanna-Cherchi, MD, Division of Nephrology, Columbia University, College of Physicians and Surgeons, New York, NY 10032, USA; Phone: 212-851-4925; Fax: 212-851-5461; . Erica E. Davis, PhD, Stanley Manne Children’s Research Institute, Ann & Robert H. Lurie Children’s Hospital of Chicago, Chicago, IL 60611, USA; Phone: 312-503-7662; Fax: 312-503-7343; , Nicholas Katsanis, PhD, Stanley Manne Children’s Research Institute, Ann & Robert H. Lurie Children’s Hospital of Chicago, Chicago, IL 60611, USA; Phone: 312-503-7339; Fax: 312-503-7343;
| | - Simone Sanna-Cherchi
- Department of Medicine, Division of Nephrology, Columbia University Irving Medical Center, New York, New York, USA.
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24
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Fauchier L, Boriani G, de Groot JR, Kreutz R, Rossing P, Camm AJ. Medical therapies for prevention of cardiovascular and renal events in patients with atrial fibrillation and diabetes mellitus. Europace 2021; 23:1873-1891. [PMID: 34411235 DOI: 10.1093/europace/euab184] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2021] [Accepted: 07/05/2021] [Indexed: 02/06/2023] Open
Abstract
Atrial fibrillation (AF), type 2 diabetes mellitus (DM), and chronic kidney disease (CKD) are three global epidemics with significant effects on morbidity and mortality. Diabetes is a risk factor for AF, and a risk factor for thromboembolism, comorbidity, and mortality when AF is present. The pathophysiology of diabetes-related AF and interrelationships with cardiovascular events and renal events is not fully understood but is in part related to structural, electrical, electromechanical, and autonomic remodelling. The current practice guidelines offer limited recommendations on the management of patients with AF (or risk of AF) and diabetes with its own heterogeneity for the prevention of cardiovascular and renal events. This document discusses possible clinical approaches for these patients. In the last decade, there have been major improvements for the prevention of stroke in AF patients with direct oral anticoagulants, which are preferable to vitamin K antagonists for stroke prevention in DM. Because of the increased risk rate for several cardiovascular adverse events in diabetic patients, a similar relative risk reduction generally translates into greater absolute risk reduction in the diabetic population. Recent trials with non-insulin diabetes drugs using glucagon-like peptide-1 agonists and sodium-glucose cotransporter-2 inhibitors showed a significant reduction for the risk of major adverse cardiovascular events in patients with type 2 DM. Sodium-glucose cotransporter-2 inhibitors also showed a large reduction in hospitalization for heart failure and renal events, which need to be more completely evaluated in patients with AF. Mechanisms, risks, and optimal management of AF patients with DM who have or are under risk of developing heart failure or CKD are also discussed in this document. The benefits of medical therapies for these patients still need to be put into perspective, and gaps in evidence on some of these issues are likely to be addressed in future years.
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Affiliation(s)
- Laurent Fauchier
- Department of Cardiology, Centre Hospitalier Universitaire Trousseau et Université de Tours, Tours 37044, France
| | - Giuseppe Boriani
- Cardiology Division, Department of Biomedical, Metabolic and Neural Sciences, University of Modena and Reggio Emilia, Policlinico di Modena, Modena, Italy
| | - Joris R de Groot
- Department of Cardiology, Amsterdam University Medical Centres/University of Amsterdam, Amsterdam, The Netherlands
| | - Reinhold Kreutz
- Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Berlin, Germany
- Department of Clinical Pharmacology and Toxicology, Charité University Medicine, Berlin, Germany
| | - Peter Rossing
- Steno Diabetes Center Copenhagen, Gentofte, Denmark
- Department of Clinical Medicine, University of Copenhagen, Copenhagen, Denmark
| | - A John Camm
- Cardiology Clinical Academic Group Molecular and Clinical Sciences Institute, St George's University of London, London, UK
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25
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Ma C, He J, Lai L, Chen Y, Xue W, Chen J, Dai W, Tang D, Yan Q, Dai Y. Intestinal microbiome and metabolome analyses reveal metabolic disorders in the early stage of renal transplantation. Mol Omics 2021; 17:985-996. [PMID: 34676841 DOI: 10.1039/d1mo00279a] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Renal transplantation is the most effective treatment for end-stage renal disease, but the long-term prognosis of organs after transplantation is not ideal. In recent years, the importance of gut microbes and metabolites in the study of disease mechanisms has gradually received attention. However, the coordination between gut microbes and the metabolism of renal transplant patients needs further study. We integrated 16s sequencing and metabolomics data to describe the changes in the serum and fecal metabolites of renal transplant patients. Our data revealed that the gut microbial diversity decreased and the relative abundance of many bacteria, such as Enterococcus and Streptococcus, significantly changed after transplantation. In addition, a large number of amino acids and peptides in serum and feces significantly changed, suggesting an abnormal amino acid metabolism after transplantation. Spearman's correlation analysis revealed the changes in the co-metabolism pattern between gut microbes and the host metabolism after transplantation. Furthermore, Enterococcus was found to be correlated with renal functions and metabolites reflecting renal damage. This study provides potential gut microbes and metabolites impacting renal health, which helps in understanding the renal damage in patients with kidney transplantation.
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Affiliation(s)
- Chiyu Ma
- Guangxi Key Laboratory of Metabolic Disease Research, Nephrology Department, Central Laboratory of Guilin, NO. 924 Hospital, Guilin, 541002, China. .,Clinical Medical Research Center, The Second Clinical Medical College of Jinan University, The First Affiliated Hospital of Southern University of Science and Technology, Shenzhen People's Hospital, Shenzhen 518020, China
| | - Jingquan He
- Clinical Medical Research Center, The Second Clinical Medical College of Jinan University, The First Affiliated Hospital of Southern University of Science and Technology, Shenzhen People's Hospital, Shenzhen 518020, China
| | - Liusheng Lai
- Guangxi Key Laboratory of Metabolic Disease Research, Nephrology Department, Central Laboratory of Guilin, NO. 924 Hospital, Guilin, 541002, China.
| | - Yumei Chen
- Clinical Medical Research Center, The Second Clinical Medical College of Jinan University, The First Affiliated Hospital of Southern University of Science and Technology, Shenzhen People's Hospital, Shenzhen 518020, China
| | - Wen Xue
- Guangxi Key Laboratory of Metabolic Disease Research, Nephrology Department, Central Laboratory of Guilin, NO. 924 Hospital, Guilin, 541002, China.
| | - Jieping Chen
- Clinical Medical Research Center, The Second Clinical Medical College of Jinan University, The First Affiliated Hospital of Southern University of Science and Technology, Shenzhen People's Hospital, Shenzhen 518020, China
| | - Weier Dai
- College of Natural Science, University of Texas at Austin, Austin, Texas, 78712, USA
| | - Donge Tang
- Guangxi Key Laboratory of Metabolic Disease Research, Nephrology Department, Central Laboratory of Guilin, NO. 924 Hospital, Guilin, 541002, China. .,Clinical Medical Research Center, The Second Clinical Medical College of Jinan University, The First Affiliated Hospital of Southern University of Science and Technology, Shenzhen People's Hospital, Shenzhen 518020, China
| | - Qiang Yan
- Guangxi Key Laboratory of Metabolic Disease Research, Nephrology Department, Central Laboratory of Guilin, NO. 924 Hospital, Guilin, 541002, China.
| | - Yong Dai
- Guangxi Key Laboratory of Metabolic Disease Research, Nephrology Department, Central Laboratory of Guilin, NO. 924 Hospital, Guilin, 541002, China. .,Clinical Medical Research Center, The Second Clinical Medical College of Jinan University, The First Affiliated Hospital of Southern University of Science and Technology, Shenzhen People's Hospital, Shenzhen 518020, China
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26
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van Zuydam NR, Stiby A, Abdalla M, Austin E, Dahlström EH, McLachlan S, Vlachopoulou E, Ahlqvist E, Di Liao C, Sandholm N, Forsblom C, Mahajan A, Robertson NR, Rayner NW, Lindholm E, Sinisalo J, Perola M, Kallio M, Weiss E, Price J, Paterson A, Klein B, Salomaa V, Palmer CN, Groop PH, Groop L, McCarthy MI, de Andrade M, Morris AP, Hopewell JC, Colhoun HM, Kullo IJ. Genome-Wide Association Study of Peripheral Artery Disease. CIRCULATION. GENOMIC AND PRECISION MEDICINE 2021; 14:e002862. [PMID: 34601942 PMCID: PMC8542067 DOI: 10.1161/circgen.119.002862] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/25/2019] [Accepted: 08/31/2021] [Indexed: 12/24/2022]
Abstract
BACKGROUND Peripheral artery disease (PAD) affects >200 million people worldwide and is associated with high mortality and morbidity. We sought to identify genomic variants associated with PAD overall and in the contexts of diabetes and smoking status. METHODS We identified genetic variants associated with PAD and then meta-analyzed with published summary statistics from the Million Veterans Program and UK Biobank to replicate their findings. Next, we ran stratified genome-wide association analysis in ever smokers, never smokers, individuals with diabetes, and individuals with no history of diabetes and corresponding interaction analyses, to identify variants that modify the risk of PAD by diabetic or smoking status. RESULTS We identified 5 genome-wide significant (Passociation ≤5×10-8) associations with PAD in 449 548 (Ncases=12 086) individuals of European ancestry near LPA (lipoprotein [a]), CDKN2BAS1 (CDKN2B antisense RNA 1), SH2B3 (SH2B adaptor protein 3) - PTPN11 (protein tyrosine phosphatase non-receptor type 11), HDAC9 (histone deacetylase 9), and CHRNA3 (cholinergic receptor nicotinic alpha 3 subunit) loci (which overlapped previously reported associations). Meta-analysis with variants previously associated with PAD showed that 18 of 19 published variants remained genome-wide significant. In individuals with diabetes, rs116405693 at the CCSER1 (coiled-coil serine rich protein 1) locus was associated with PAD (odds ratio [95% CI], 1.51 [1.32-1.74], Pdiabetes=2.5×10-9, Pinteractionwithdiabetes=5.3×10-7). Furthermore, in smokers, rs12910984 at the CHRNA3 locus was associated with PAD (odds ratio [95% CI], 1.15 [1.11-1.19], Psmokers=9.3×10-10, Pinteractionwithsmoking=3.9×10-5). CONCLUSIONS Our analyses confirm the published genetic associations with PAD and identify novel variants that may influence susceptibility to PAD in the context of diabetes or smoking status.
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Affiliation(s)
- Natalie R. van Zuydam
- Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University, Sweden (N.R.v.Z.)
- Wellcome Centre for Human Genetics, Nuffield Department of Medicine (N.R.v.Z., M.A., A.M., N.R.R., N.W.R., M.I.M., A.P.M.), University of Oxford, United Kingdom
- Oxford Centre for Diabetes, Endocrinology and Metabolism, Radcliffe Department of Medicine (N.R.v.Z., A.M., N.R.R., N.W.R., M.I.M.), University of Oxford, United Kingdom
| | - Alexander Stiby
- Clinical Trial Service Unit and Epidemiological Studies Unit, Nuffield Department of Population Health (A.S., J.C.H.), University of Oxford, United Kingdom
| | - Moustafa Abdalla
- Wellcome Centre for Human Genetics, Nuffield Department of Medicine (N.R.v.Z., M.A., A.M., N.R.R., N.W.R., M.I.M., A.P.M.), University of Oxford, United Kingdom
| | - Erin Austin
- Department of Cardiovascular Medicine and the Gonda Vascular Center, Mayo Clinic, Rochester, MN (E. Austin, M.d.A., I.J.K.)
| | - Emma H. Dahlström
- Folkhälsan Institute of Genetics, Folkhälsan Research Center, Helsinki, Finland (E.H.D., N.S., C.F., P.-H.G.)
- Abdominal Center, Nephrology (E.H.D., N.S., C.F., P.-H.G.), University of Helsinki, Finland
- Helsinki University Hospital, Research Program for Clinical and Molecular Metabolism, Faculty of Medicine (E.H.D., N.S., C.F., P.-H.G.), University of Helsinki, Finland
| | - Stela McLachlan
- Usher Institute of Population Health Sciences and Informatics, The University of Edinburgh, United Kingdom (S.M., E.W., J.P.)
| | - Efthymia Vlachopoulou
- Department of Medicine, Helsinki University Central Hospital (E.V.), University of Helsinki, Finland
| | - Emma Ahlqvist
- Genomics, Diabetes and Endocrinology, Lund University Diabetes Centre, Malmö, Sweden (E. Ahlqvist, E.L., L.G.)
| | - Chen Di Liao
- Dalla Lana School of Public Health, University of Toronto, ON, Canada (C.D.L., A.P.)
- Genetics & Genome Biology, SickKids, Toronto, ON, Canada (C.D.L., A.P.)
| | - Niina Sandholm
- Folkhälsan Institute of Genetics, Folkhälsan Research Center, Helsinki, Finland (E.H.D., N.S., C.F., P.-H.G.)
- Abdominal Center, Nephrology (E.H.D., N.S., C.F., P.-H.G.), University of Helsinki, Finland
- Helsinki University Hospital, Research Program for Clinical and Molecular Metabolism, Faculty of Medicine (E.H.D., N.S., C.F., P.-H.G.), University of Helsinki, Finland
| | - Carol Forsblom
- Folkhälsan Institute of Genetics, Folkhälsan Research Center, Helsinki, Finland (E.H.D., N.S., C.F., P.-H.G.)
- Abdominal Center, Nephrology (E.H.D., N.S., C.F., P.-H.G.), University of Helsinki, Finland
- Helsinki University Hospital, Research Program for Clinical and Molecular Metabolism, Faculty of Medicine (E.H.D., N.S., C.F., P.-H.G.), University of Helsinki, Finland
| | - Anubha Mahajan
- Wellcome Centre for Human Genetics, Nuffield Department of Medicine (N.R.v.Z., M.A., A.M., N.R.R., N.W.R., M.I.M., A.P.M.), University of Oxford, United Kingdom
- Oxford Centre for Diabetes, Endocrinology and Metabolism, Radcliffe Department of Medicine (N.R.v.Z., A.M., N.R.R., N.W.R., M.I.M.), University of Oxford, United Kingdom
- Now with Genentech, South San Francisco, CA (A.M., M.I.M.)
| | - Neil R. Robertson
- Wellcome Centre for Human Genetics, Nuffield Department of Medicine (N.R.v.Z., M.A., A.M., N.R.R., N.W.R., M.I.M., A.P.M.), University of Oxford, United Kingdom
- Oxford Centre for Diabetes, Endocrinology and Metabolism, Radcliffe Department of Medicine (N.R.v.Z., A.M., N.R.R., N.W.R., M.I.M.), University of Oxford, United Kingdom
| | - N. William Rayner
- Wellcome Centre for Human Genetics, Nuffield Department of Medicine (N.R.v.Z., M.A., A.M., N.R.R., N.W.R., M.I.M., A.P.M.), University of Oxford, United Kingdom
- Oxford Centre for Diabetes, Endocrinology and Metabolism, Radcliffe Department of Medicine (N.R.v.Z., A.M., N.R.R., N.W.R., M.I.M.), University of Oxford, United Kingdom
- Department of Human Genetics, Wellcome Trust Sanger Institute, Hinxton, Cambridgeshire, United Kingdom (N.W.R.)
| | - Eero Lindholm
- Genomics, Diabetes and Endocrinology, Lund University Diabetes Centre, Malmö, Sweden (E. Ahlqvist, E.L., L.G.)
| | - Juha Sinisalo
- Heart and Lung Center (J.S.), University of Helsinki, Finland
| | - Markus Perola
- Institute for Molecular Medicine Finland (FIMM) (M.P., L.G.), University of Helsinki, Finland
- Finnish Institute for Health and Welfare, Helsinki, Finland (M.P., V.S.)
| | - Milla Kallio
- Vascular Surgery, Abdominal Center (M.K.), University of Helsinki, Finland
| | - Emily Weiss
- Usher Institute of Population Health Sciences and Informatics, The University of Edinburgh, United Kingdom (S.M., E.W., J.P.)
| | - Jackie Price
- Usher Institute of Population Health Sciences and Informatics, The University of Edinburgh, United Kingdom (S.M., E.W., J.P.)
| | - Andrew Paterson
- Dalla Lana School of Public Health, University of Toronto, ON, Canada (C.D.L., A.P.)
- Genetics & Genome Biology, SickKids, Toronto, ON, Canada (C.D.L., A.P.)
| | - Barbara Klein
- Ocular Epidemiology Research Group, University of Wisconsin-Madison (B.K.)
| | - Veikko Salomaa
- Finnish Institute for Health and Welfare, Helsinki, Finland (M.P., V.S.)
| | - Colin N.A. Palmer
- Pat Macpherson Centre for Pharmacogenetics and Pharmacogenomics, Ninewells Hospital and Medical School, University of Dundee, United Kingdom (C.N.A.P.)
| | - Per-Henrik Groop
- Folkhälsan Institute of Genetics, Folkhälsan Research Center, Helsinki, Finland (E.H.D., N.S., C.F., P.-H.G.)
- Abdominal Center, Nephrology (E.H.D., N.S., C.F., P.-H.G.), University of Helsinki, Finland
- Helsinki University Hospital, Research Program for Clinical and Molecular Metabolism, Faculty of Medicine (E.H.D., N.S., C.F., P.-H.G.), University of Helsinki, Finland
- Department of Medicine, Central Clinical School, Monash University, Melbourne, Victoria, Australia (P.-H.G.)
| | - Leif Groop
- Institute for Molecular Medicine Finland (FIMM) (M.P., L.G.), University of Helsinki, Finland
- Genomics, Diabetes and Endocrinology, Lund University Diabetes Centre, Malmö, Sweden (E. Ahlqvist, E.L., L.G.)
| | - Mark I. McCarthy
- Wellcome Centre for Human Genetics, Nuffield Department of Medicine (N.R.v.Z., M.A., A.M., N.R.R., N.W.R., M.I.M., A.P.M.), University of Oxford, United Kingdom
- Oxford Centre for Diabetes, Endocrinology and Metabolism, Radcliffe Department of Medicine (N.R.v.Z., A.M., N.R.R., N.W.R., M.I.M.), University of Oxford, United Kingdom
- Oxford NIHR Biomedical Research Centre, Oxford University Hospitals Trust, United Kingdom (M.I.M.)
- Now with Genentech, South San Francisco, CA (A.M., M.I.M.)
| | - Mariza de Andrade
- Department of Cardiovascular Medicine and the Gonda Vascular Center, Mayo Clinic, Rochester, MN (E. Austin, M.d.A., I.J.K.)
| | - Andrew P. Morris
- Wellcome Centre for Human Genetics, Nuffield Department of Medicine (N.R.v.Z., M.A., A.M., N.R.R., N.W.R., M.I.M., A.P.M.), University of Oxford, United Kingdom
- Department of Biostatistics, University of Liverpool, United Kingdom (A.P.M.)
- Centre for Genetics and Genomics Versus Arthritis, Centre for Musculoskeletal Research, The University of Manchester, United Kingdom (A.P.M.)
| | - Jemma C. Hopewell
- Clinical Trial Service Unit and Epidemiological Studies Unit, Nuffield Department of Population Health (A.S., J.C.H.), University of Oxford, United Kingdom
| | - Helen M. Colhoun
- Institute of Genetics and Molecular Medicine, University of Edinburgh, Western General Hospital Campus, United Kingdom (H.M.C.)
| | - Iftikhar J. Kullo
- Department of Cardiovascular Medicine and the Gonda Vascular Center, Mayo Clinic, Rochester, MN (E. Austin, M.d.A., I.J.K.)
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27
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Mychaleckyj JC, Valo E, Ichimura T, Ahluwalia TS, Dina C, Miller RG, Shabalin IG, Gyorgy B, Cao J, Onengut-Gumuscu S, Satake E, Smiles AM, Haukka JK, Tregouet DA, Costacou T, O’Neil K, Paterson AD, Forsblom C, Keenan HA, Pezzolesi MG, Pragnell M, Galecki A, Rich SS, Sandholm N, Klein R, Klein BE, Susztak K, Orchard TJ, Korstanje R, King GL, Hadjadj S, Rossing P, Bonventre JV, Groop PH, Warram JH, Krolewski AS. Association of Coding Variants in Hydroxysteroid 17-beta Dehydrogenase 14 ( HSD17B14) with Reduced Progression to End Stage Kidney Disease in Type 1 Diabetes. J Am Soc Nephrol 2021; 32:2634-2651. [PMID: 34261756 PMCID: PMC8722802 DOI: 10.1681/asn.2020101457] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2020] [Accepted: 05/27/2021] [Indexed: 02/04/2023] Open
Abstract
BACKGROUND Rare variants in gene coding regions likely have a greater impact on disease-related phenotypes than common variants through disruption of their encoded protein. We searched for rare variants associated with onset of ESKD in individuals with type 1 diabetes at advanced kidney disease stage. METHODS Gene-based exome array analyses of 15,449 genes in five large incidence cohorts of individuals with type 1 diabetes and proteinuria were analyzed for survival time to ESKD, testing the top gene in a sixth cohort (n=2372/1115 events all cohorts) and replicating in two retrospective case-control studies (n=1072 cases, 752 controls). Deep resequencing of the top associated gene in five cohorts confirmed the findings. We performed immunohistochemistry and gene expression experiments in human control and diseased cells, and in mouse ischemia reperfusion and aristolochic acid nephropathy models. RESULTS Protein coding variants in the hydroxysteroid 17-β dehydrogenase 14 gene (HSD17B14), predicted to affect protein structure, had a net protective effect against development of ESKD at exome-wide significance (n=4196; P value=3.3 × 10-7). The HSD17B14 gene and encoded enzyme were robustly expressed in healthy human kidney, maximally in proximal tubular cells. Paradoxically, gene and protein expression were attenuated in human diabetic proximal tubules and in mouse kidney injury models. Expressed HSD17B14 gene and protein levels remained low without recovery after 21 days in a murine ischemic reperfusion injury model. Decreased gene expression was found in other CKD-associated renal pathologies. CONCLUSIONS HSD17B14 gene is mechanistically involved in diabetic kidney disease. The encoded sex steroid enzyme is a druggable target, potentially opening a new avenue for therapeutic development.
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Affiliation(s)
- Josyf C. Mychaleckyj
- Center for Public Health Genomics, University of Virginia, Charlottesville, Virginia
| | - Erkka Valo
- 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, Finland
| | - Takaharu Ichimura
- Renal Division, Brigham and Women’s Hospital, Department of Medicine, Harvard Medical School, Boston, Massachusetts
| | | | - Christian Dina
- Université de Nantes, CNRS INSERM, L’institut du thorax, Nantes, France
| | - Rachel G. Miller
- Department of Epidemiology, University of Pittsburgh, Pittsburgh, Pennsylvania
| | - Ivan G. Shabalin
- Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, Virginia
| | - Beata Gyorgy
- INSERM UMRS1166, Institute of CardioMetabolism and Nutrition, Sorbonne Université, Paris, France
| | - JingJing Cao
- Genetics & Genome Biology Research Institute, SickKids Hospital, Toronto, Ontario, Canada
| | - Suna Onengut-Gumuscu
- Center for Public Health Genomics, University of Virginia, Charlottesville, Virginia
| | - Eiichiro Satake
- Research Division, Joslin Diabetes Center, Boston, Massachusetts
- Department of Medicine, Harvard Medical School, Boston, Massachusetts
| | - Adam M. Smiles
- Research Division, Joslin Diabetes Center, Boston, Massachusetts
| | - Jani K. Haukka
- 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, Finland
| | - David-Alexandre Tregouet
- INSERM UMRS1166, Institute of CardioMetabolism and Nutrition, Sorbonne Université, Paris, France
- Université de Bordeaux, INSERM, Bordeaux Population Health, Bordeaux U1219, France
| | - Tina Costacou
- Department of Epidemiology, University of Pittsburgh, Pittsburgh, Pennsylvania
| | - Kristina O’Neil
- Research Division, Joslin Diabetes Center, Boston, Massachusetts
| | - Andrew D. Paterson
- Genetics & Genome Biology Research Institute, SickKids Hospital, Toronto, Ontario, Canada
| | - Carol Forsblom
- 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, Finland
| | - Hillary A. Keenan
- Research Division, Joslin Diabetes Center, Boston, Massachusetts
- Department of Medicine, Harvard Medical School, Boston, Massachusetts
| | - Marcus G. Pezzolesi
- Research Division, Joslin Diabetes Center, Boston, Massachusetts
- Department of Medicine, Harvard Medical School, Boston, Massachusetts
- Division of Nephrology and Hypertension, University of Utah, Salt Lake City, Utah
| | | | - Andrzej Galecki
- Department of Internal Medicine, University of Michigan Medical School, Ann Arbor, Michigan
| | - Stephen S. Rich
- Center for Public Health Genomics, University of Virginia, Charlottesville, Virginia
| | - 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, Finland
| | - Ronald Klein
- Department of Ophthalmology and Visual Sciences, University of Wisconsin School of Medicine and Public Health, Madison, Wisconsin
| | - Barbara E. Klein
- Department of Ophthalmology and Visual Sciences, University of Wisconsin School of Medicine and Public Health, Madison, Wisconsin
| | - Katalin Susztak
- Department of Medicine and Genetics, University of Pennsylvania, Philadelphia, Pennsylvania
| | - Trevor J. Orchard
- Department of Epidemiology, University of Pittsburgh, Pittsburgh, Pennsylvania
| | | | - George L. King
- Research Division, Joslin Diabetes Center, Boston, Massachusetts
- Department of Medicine, Harvard Medical School, Boston, Massachusetts
| | - Samy Hadjadj
- INSERM CIC 1402 and U 1082, Poitiers, France
- Department of Endocrinology, L’institut du thorax, INSERM, CNRS, Centre Hospitalier Universitaire de Nantes, Nantes, France
| | - Peter Rossing
- Steno Diabetes Center Copenhagen, Copenhagen, Denmark
- University of Copenhagen, Copenhagen, Denmark
| | - Joseph V. Bonventre
- Renal Division, Brigham and Women’s Hospital, Department of Medicine, Harvard Medical School, Boston, Massachusetts
| | - 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, Finland
- Department of Diabetes, Central Clinical School, Monash University, Melbourne, Victoria, Australia
| | - James H. Warram
- Research Division, Joslin Diabetes Center, Boston, Massachusetts
| | - Andrzej S. Krolewski
- Research Division, Joslin Diabetes Center, Boston, Massachusetts
- Department of Medicine, Harvard Medical School, Boston, Massachusetts
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Amatruda M, Gembillo G, Giuffrida AE, Santoro D, Conti G. The Aggressive Diabetic Kidney Disease in Youth-Onset Type 2 Diabetes: Pathogenetic Mechanisms and Potential Therapies. ACTA ACUST UNITED AC 2021; 57:medicina57090868. [PMID: 34577791 PMCID: PMC8467670 DOI: 10.3390/medicina57090868] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2021] [Revised: 08/21/2021] [Accepted: 08/22/2021] [Indexed: 02/07/2023]
Abstract
Youth-onset Type 2 Diabetes Mellitus (T2DM) represents a major burden worldwide. In the last decades, the prevalence of T2DM became higher than that of Type 1 Diabetes Mellitus (T1DM), helped by the increasing rate of childhood obesity. The highest prevalence rates of youth-onset T2DM are recorded in China (520 cases/100,000) and in the United States (212 cases/100,000), and the numbers are still increasing. T2DM young people present a strong hereditary component, often unmasked by social and environmental risk factors. These patients are affected by multiple coexisting risk factors, including obesity, hyperglycemia, dyslipidemia, insulin resistance, hypertension, and inflammation. Juvenile T2DM nephropathy occurs earlier in life compared to T1DM-related nephropathy in children or T2DM-related nephropathy in adult. Diabetic kidney disease (DKD) is T2DM major long term microvascular complication. This review summarizes the main mechanisms involved in the pathogenesis of the DKD in young population and the recent evolution of treatment, in order to reduce the risk of DKD progression.
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Affiliation(s)
- Michela Amatruda
- Unit of Pediatric Nephrology with Dialysis, AOU Policlinic G Martino, University of Messina, 98125 Messina, Italy;
| | - Guido Gembillo
- Unit of Nephrology and Dialysis, Department of Clinical and Experimental Medicine, University of Messina, 98125 Messina, Italy; (G.G.); (A.E.G.); (D.S.)
- Department of Biomedical and Dental Sciences and Morpho-functional Imaging, University of Messina, 98125 Messina, Italy
| | - Alfio Edoardo Giuffrida
- Unit of Nephrology and Dialysis, Department of Clinical and Experimental Medicine, University of Messina, 98125 Messina, Italy; (G.G.); (A.E.G.); (D.S.)
| | - Domenico Santoro
- Unit of Nephrology and Dialysis, Department of Clinical and Experimental Medicine, University of Messina, 98125 Messina, Italy; (G.G.); (A.E.G.); (D.S.)
| | - Giovanni Conti
- Unit of Pediatric Nephrology with Dialysis, AOU Policlinic G Martino, University of Messina, 98125 Messina, Italy;
- Correspondence:
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29
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Gao J, Zhou N, Wu Y, Lu M, Wang Q, Xia C, Zhou M, Xu Y. Urinary metabolomic changes and microbiotic alterations in presenilin1/2 conditional double knockout mice. J Transl Med 2021; 19:351. [PMID: 34399766 PMCID: PMC8365912 DOI: 10.1186/s12967-021-03032-9] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2021] [Accepted: 08/07/2021] [Indexed: 12/13/2022] Open
Abstract
Background Given the clinical low efficient treatment based on mono-brain-target design in Alzheimer’s disease (AD) and an increasing emphasis on microbiome-gut-brain axis which was considered as a crucial pathway to affect the progress of AD along with metabolic changes, integrative metabolomic signatures and microbiotic community profilings were applied on the early age (2-month) and mature age (6-month) of presenilin1/2 conditional double knockout (PS cDKO) mice which exhibit a series of AD-like phenotypes, comparing with gender and age-matched C57BL/6 wild-type (WT) mice to clarify the relationship between microbiota and metabolomic changes during the disease progression of AD. Materials and methods Urinary and fecal samples from PS cDKO mice and gender-matched C57BL/6 wild-type (WT) mice both at age of 2 and 6 months were collected. Urinary metabolomic signatures were measured by the gas chromatography-time-of-flight mass spectrometer, as well as 16S rRNA sequence analysis was performed to analyse the microbiota composition at both ages. Furthermore, combining microbiotic functional prediction and Spearman’s correlation coefficient analysis to explore the relationship between differential urinary metabolites and gut microbiota. Results In addition to memory impairment, PS cDKO mice displayed metabolic and microbiotic changes at both of early and mature ages. By longitudinal study, xylitol and glycine were reduced at both ages. The disturbed metabolic pathways were involved in glycine, serine and threonine metabolism, glyoxylate and dicarboxylate metabolism, pentose and glucuronate interconversions, starch and sucrose metabolism, and citrate cycle, which were consistent with functional metabolic pathway predicted by the gut microbiome, including energy metabolism, lipid metabolism, glycan biosynthesis and metabolism. Besides reduced richness and evenness in gut microbiome, PS cDKO mice displayed increases in Lactobacillus, while decreases in norank_f_Muribaculaceae, Lachnospiraceae_NK4A136_group, Mucispirillum, and Odoribacter. Those altered microbiota were exceedingly associated with the levels of differential metabolites. Conclusions The urinary metabolomics of AD may be partially mediated by the gut microbiota. The integrated analysis between gut microbes and host metabolism may provide a reference for the pathogenesis of AD. Supplementary Information The online version contains supplementary material available at 10.1186/s12967-021-03032-9.
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Affiliation(s)
- Jie Gao
- Department of Physiology, School of Basic Medicine, Shanghai University of Traditional Chinese Medicine, 1200 Cailun Road, Shanghai, 201203, China.,Department of Rehabilitation Medicine, Affiliated Hospital of Nantong University, 20 Xisi Road, Nantong, 226001, Jiangsu, China
| | - Nian Zhou
- Center for Chinese Medicine Therapy and Systems Biology, Institute of Interdisciplinary Integrative Medicine Research, Shanghai University of Traditional Chinese Medicine, 1200 Cailun Road, Pudong District, Shanghai, 201203, China
| | - Yongkang Wu
- Department of Physiology, School of Basic Medicine, Shanghai University of Traditional Chinese Medicine, 1200 Cailun Road, Shanghai, 201203, China
| | - Mengna Lu
- Center for Chinese Medicine Therapy and Systems Biology, Institute of Interdisciplinary Integrative Medicine Research, Shanghai University of Traditional Chinese Medicine, 1200 Cailun Road, Pudong District, Shanghai, 201203, China.,School of Pharmacy, Shanghai University of Traditional Chinese Medicine, 1200 Cailun Road, Shanghai, 201203, China
| | - Qixue Wang
- Center for Chinese Medicine Therapy and Systems Biology, Institute of Interdisciplinary Integrative Medicine Research, Shanghai University of Traditional Chinese Medicine, 1200 Cailun Road, Pudong District, Shanghai, 201203, China
| | - Chenyi Xia
- Department of Physiology, School of Basic Medicine, Shanghai University of Traditional Chinese Medicine, 1200 Cailun Road, Shanghai, 201203, China
| | - Mingmei Zhou
- Center for Chinese Medicine Therapy and Systems Biology, Institute of Interdisciplinary Integrative Medicine Research, Shanghai University of Traditional Chinese Medicine, 1200 Cailun Road, Pudong District, Shanghai, 201203, China.
| | - Ying Xu
- Department of Physiology, School of Basic Medicine, Shanghai University of Traditional Chinese Medicine, 1200 Cailun Road, Shanghai, 201203, China.
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30
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Abouleka Y, Mohammedi K, Carpentier C, Dubois S, Gourdy P, Gautier JF, Roussel R, Scheen A, Alhenc-Gelas F, Hadjadj S, Velho G, Marre M. ACE I/D Polymorphism, Plasma ACE Levels, and Long-term Kidney Outcomes or All-Cause Death in Patients With Type 1 Diabetes. Diabetes Care 2021; 44:1377-1384. [PMID: 33827803 PMCID: PMC8247517 DOI: 10.2337/dc20-3036] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/15/2020] [Accepted: 02/22/2021] [Indexed: 02/03/2023]
Abstract
OBJECTIVE The deletion (D) allele of the ACE insertion/deletion (I/D) polymorphism is a risk factor for diabetic kidney disease. We assessed its contribution to long-term kidney outcomes and all-cause death in patients with long-standing type 1 diabetes. RESEARCH DESIGN AND METHODS A total of 1,155 participants from three French and Belgian cohorts were monitored for a median duration of 14 (interquartile range 13) years. The primary outcome was the occurrence of end-stage kidney disease (ESKD) or a 40% drop in the estimated glomerular filtration rate (eGFR). Secondary outcomes were the individual components of the primary outcome, rapid decline in eGFR (steeper than -3 mL/min/1.73 m2 per year), incident albuminuria, all-cause death, and a composite ESKD or all-cause death. Hazard ratios (HRs) for XD versus II genotype and for baseline plasma ACE levels were computed by Cox analysis. Genotype performance in stratifying the primary outcome was tested. RESULTS Genotype distribution was 954 XD and 201 II. The primary outcome occurred in 20% of XD and 13% of II carriers: adjusted HR 2.07 (95% CI 1.32-3.40; P = 0.001). Significant associations were also observed for rapid decline in eGFR, incident albuminuria, ESKD, all-cause death, and ESKD or all-cause death. Baseline plasma ACE levels were higher in XD carriers and significantly associated with an increased risk of the primary outcome. The ACE genotype enhanced net reclassification improvement (0.154, 95% CI 0.007-0.279; P = 0.04) and integrated discrimination improvement (0.012, 95%CI 0.001-0.021; P = 0.02) for primary outcome stratification. CONCLUSIONS The D-allele of the ACE I/D polymorphism was associated with an increased risk of major kidney events and all-cause death in patients with long-standing type 1 diabetes.
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Affiliation(s)
- Yawa Abouleka
- Centre de Recherche des Cordeliers, INSERM, Université de Paris, Sorbonne Université, Paris, France.,Service d'Endocrinologie Diabétologie Nutrition, Hôpital Bichat, Assistance Publique-Hôpitaux de Paris, Paris, France
| | - Kamel Mohammedi
- Bordeaux University and Hospital, INSERM U1219, Bordeaux, France
| | - Charlyne Carpentier
- Service d'Endocrinologie Diabétologie Nutrition, CHU d'Angers, Angers, France
| | - Severine Dubois
- Service d'Endocrinologie Diabétologie Nutrition, CHU d'Angers, Angers, France
| | - Pierre Gourdy
- Service d'Endocrinologie Diabétologie Nutrition, CHU de Toulouse, Toulouse, France.,Institut des Maladies Métaboliques et Cardiovasculaires, UMR1048 INSERM/UPS, Université Toulouse III - Paul Sabatier, Toulouse, France
| | - Jean-François Gautier
- Centre de Recherche des Cordeliers, INSERM, Université de Paris, Sorbonne Université, Paris, France.,Service de Diabétologie et d'Endocrinologie, Hôpital Lariboisière, Assistance Publique-Hôpitaux de Paris, Université de Paris, Paris, France
| | - Ronan Roussel
- Centre de Recherche des Cordeliers, INSERM, Université de Paris, Sorbonne Université, Paris, France.,Service d'Endocrinologie Diabétologie Nutrition, Hôpital Bichat, Assistance Publique-Hôpitaux de Paris, Paris, France
| | | | - François Alhenc-Gelas
- Centre de Recherche des Cordeliers, INSERM, Université de Paris, Sorbonne Université, Paris, France
| | - Samy Hadjadj
- Institut du Thorax, INSERM, CNRS, Université de Nantes, CHU Nantes, Nantes, France
| | - Gilberto Velho
- Centre de Recherche des Cordeliers, INSERM, Université de Paris, Sorbonne Université, Paris, France
| | - Michel Marre
- Centre de Recherche des Cordeliers, INSERM, Université de Paris, Sorbonne Université, Paris, France .,Clinique Ambroise Paré, Neuilly-sur-Seine, France
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31
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Giandalia A, Giuffrida AE, Gembillo G, Cucinotta D, Squadrito G, Santoro D, Russo GT. Gender Differences in Diabetic Kidney Disease: Focus on Hormonal, Genetic and Clinical Factors. Int J Mol Sci 2021; 22:5808. [PMID: 34071671 PMCID: PMC8198374 DOI: 10.3390/ijms22115808] [Citation(s) in RCA: 37] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2021] [Revised: 05/21/2021] [Accepted: 05/25/2021] [Indexed: 02/07/2023] Open
Abstract
Diabetic kidney disease (DKD) is one of the most serious complications of both type 1 (T1DM) and type 2 diabetes mellitus (T2DM). Current guidelines recommend a personalized approach in order to reduce the burden of DM and its complications. Recognizing sex and gender- differences in medicine is considered one of the first steps toward personalized medicine, but the gender issue in DM has been scarcely explored so far. Gender differences have been reported in the incidence and the prevalence of DKD, in its phenotypes and clinical manifestations, as well as in several risk factors, with a different impact in the two genders. Hormonal factors, especially estrogen loss, play a significant role in explaining these differences. Additionally, the impact of sex chromosomes as well as the influence of gene-sex interactions with several susceptibility genes for DKD have been investigated. In spite of the increasing evidence that sex and gender should be included in the evaluation of DKD, several open issues remain uncovered, including the potentially different effects of newly recommended drugs, such as SGLT2i and GLP1Ras. This narrative review explored current evidence on sex/gender differences in DKD, taking into account hormonal, genetic and clinical factors.
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Affiliation(s)
- Annalisa Giandalia
- Department of Clinical and Experimental Medicine, University of Messina, 98125 Messina, Italy
| | - Alfio Edoardo Giuffrida
- Unit of Nephrology and Dialysis, Department of Clinical and Experimental Medicine, University of Messina, 98125 Messina, Italy
| | - Guido Gembillo
- Unit of Nephrology and Dialysis, Department of Clinical and Experimental Medicine, University of Messina, 98125 Messina, Italy
- Department of Biomedical, Dental, Morphological and Functional Imaging Sciences, University of Messina, 98125 Messina, Italy
| | - Domenico Cucinotta
- Department of Clinical and Experimental Medicine, University of Messina, 98125 Messina, Italy
| | - Giovanni Squadrito
- Department of Clinical and Experimental Medicine, University of Messina, 98125 Messina, Italy
| | - Domenico Santoro
- Unit of Nephrology and Dialysis, Department of Clinical and Experimental Medicine, University of Messina, 98125 Messina, Italy
| | - Giuseppina T Russo
- Department of Clinical and Experimental Medicine, University of Messina, 98125 Messina, Italy
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32
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Smyth LJ, Kilner J, Nair V, Liu H, Brennan E, Kerr K, Sandholm N, Cole J, Dahlström E, Syreeni A, Salem RM, Nelson RG, Looker HC, Wooster C, Anderson K, McKay GJ, Kee F, Young I, Andrews D, Forsblom C, Hirschhorn JN, Godson C, Groop PH, Maxwell AP, Susztak K, Kretzler M, Florez JC, McKnight AJ. Assessment of differentially methylated loci in individuals with end-stage kidney disease attributed to diabetic kidney disease: an exploratory study. Clin Epigenetics 2021; 13:99. [PMID: 33933144 PMCID: PMC8088646 DOI: 10.1186/s13148-021-01081-x] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2020] [Accepted: 04/15/2021] [Indexed: 12/16/2022] Open
Abstract
BACKGROUND A subset of individuals with type 1 diabetes mellitus (T1DM) are predisposed to developing diabetic kidney disease (DKD), the most common cause globally of end-stage kidney disease (ESKD). Emerging evidence suggests epigenetic changes in DNA methylation may have a causal role in both T1DM and DKD. The aim of this exploratory investigation was to assess differences in blood-derived DNA methylation patterns between individuals with T1DM-ESKD and individuals with long-duration T1DM but no evidence of kidney disease upon repeated testing to identify potential blood-based biomarkers. Blood-derived DNA from individuals (107 cases, 253 controls and 14 experimental controls) were bisulphite treated before DNA methylation patterns from both groups were generated and analysed using Illumina's Infinium MethylationEPIC BeadChip arrays (n = 862,927 sites). Differentially methylated CpG sites (dmCpGs) were identified (false discovery rate adjusted p ≤ × 10-8 and fold change ± 2) by comparing methylation levels between ESKD cases and T1DM controls at single site resolution. Gene annotation and functionality was investigated to enrich and rank methylated regions associated with ESKD in T1DM. RESULTS Top-ranked genes within which several dmCpGs were located and supported by functional data with methylation look-ups in other cohorts include: AFF3, ARID5B, CUX1, ELMO1, FKBP5, HDAC4, ITGAL, LY9, PIM1, RUNX3, SEPTIN9 and UPF3A. Top-ranked enrichment pathways included pathways in cancer, TGF-β signalling and Th17 cell differentiation. CONCLUSIONS Epigenetic alterations provide a dynamic link between an individual's genetic background and their environmental exposures. This robust evaluation of DNA methylation in carefully phenotyped individuals has identified biomarkers associated with ESKD, revealing several genes and implicated key pathways associated with ESKD in individuals with T1DM.
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Affiliation(s)
- L J Smyth
- Molecular Epidemiology Research Group, Centre for Public Health, Queen's University Belfast, Belfast, UK.
| | - J Kilner
- Molecular Epidemiology Research Group, Centre for Public Health, Queen's University Belfast, Belfast, UK
| | - V Nair
- Internal Medicine, Department of Nephrology, University of Michigan, Ann Arbor, MI, USA
| | - H Liu
- Department of Department of Medicine/ Nephrology, Department of Genetics, Institute of Diabetes, Obesity and Metabolism, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | - E Brennan
- Diabetes Complications Research Centre, Conway Institute of Biomolecular and Biomedical Research, School of Medicine, University College Dublin, Dublin 4, Ireland
| | - K Kerr
- Molecular Epidemiology Research Group, Centre for Public Health, Queen's University Belfast, Belfast, UK
| | - N Sandholm
- Folkhälsan Institute of Genetics, Folkhälsan Research Center, 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
| | - J Cole
- Programs in Metabolism and Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA.,Division of Endocrinology and Center for Basic and Translational Obesity Research, Boston Children's Hospital, Boston, MA, USA.,Diabetes Unit and Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA
| | - E Dahlström
- Folkhälsan Institute of Genetics, Folkhälsan Research Center, 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
| | - A Syreeni
- Folkhälsan Institute of Genetics, Folkhälsan Research Center, 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
| | - R M Salem
- Department of Family Medicine and Public Health, UC San Diego, San Diego, CA, USA
| | - R G Nelson
- Chronic Kidney Disease Section, National Institute of Diabetes and Digestive and Kidney Diseases, Phoenix, AZ, USA
| | - H C Looker
- Chronic Kidney Disease Section, National Institute of Diabetes and Digestive and Kidney Diseases, Phoenix, AZ, USA
| | - C Wooster
- Molecular Epidemiology Research Group, Centre for Public Health, Queen's University Belfast, Belfast, UK
| | - K Anderson
- Molecular Epidemiology Research Group, Centre for Public Health, Queen's University Belfast, Belfast, UK
| | - G J McKay
- Molecular Epidemiology Research Group, Centre for Public Health, Queen's University Belfast, Belfast, UK
| | - F Kee
- Molecular Epidemiology Research Group, Centre for Public Health, Queen's University Belfast, Belfast, UK
| | - I Young
- Molecular Epidemiology Research Group, Centre for Public Health, Queen's University Belfast, Belfast, UK
| | - D Andrews
- Diabetes Complications Research Centre, Conway Institute of Biomolecular and Biomedical Research, School of Medicine, University College Dublin, Dublin 4, Ireland
| | - C Forsblom
- Folkhälsan Institute of Genetics, Folkhälsan Research Center, 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
| | - J N Hirschhorn
- Programs in Metabolism and Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA.,Division of Endocrinology and Center for Basic and Translational Obesity Research, Boston Children's Hospital, Boston, MA, USA.,Department of Genetics, Harvard Medical School, Boston, MA, USA
| | - C Godson
- Diabetes Complications Research Centre, Conway Institute of Biomolecular and Biomedical Research, School of Medicine, University College Dublin, Dublin 4, Ireland
| | - P H Groop
- Folkhälsan Institute of Genetics, Folkhälsan Research Center, 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, VIC, Australia
| | - A P Maxwell
- Molecular Epidemiology Research Group, Centre for Public Health, Queen's University Belfast, Belfast, UK.,Regional Nephrology Unit, Belfast City Hospital, Belfast, Northern Ireland, UK
| | - K Susztak
- Department of Department of Medicine/ Nephrology, Department of Genetics, Institute of Diabetes, Obesity and Metabolism, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | - M Kretzler
- Internal Medicine, Department of Nephrology, University of Michigan, Ann Arbor, MI, USA
| | - J C Florez
- Programs in Metabolism and Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA.,Division of Endocrinology and Center for Basic and Translational Obesity Research, Boston Children's Hospital, Boston, MA, USA.,Department of Medicine, Harvard Medical School, Boston, MA, USA
| | - A J McKnight
- Molecular Epidemiology Research Group, Centre for Public Health, Queen's University Belfast, Belfast, UK
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33
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Abstract
As part of the centennial celebration of insulin's discovery, this review summarizes the current understanding of the genetics, pathogenesis, treatment, and outcomes in type 1 diabetes (T1D). T1D results from an autoimmune response that leads to destruction of the β cells in the pancreatic islet and requires lifelong insulin therapy. While much has been learned about T1D, it is now clear that there is considerable heterogeneity in T1D with regard to genetics, pathology, response to immune-based therapies, clinical course, and susceptibility to diabetes-related complications. This Review highlights knowledge gaps and opportunities to improve the understanding of T1D pathogenesis and outlines emerging therapies to treat or prevent T1D and reduce the burden of T1D.
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34
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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.
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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,
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Gorski M, Jung B, Li Y, Matias-Garcia PR, Wuttke M, Coassin S, Thio CHL, Kleber ME, Winkler TW, Wanner V, Chai JF, Chu AY, Cocca M, Feitosa MF, Ghasemi S, Hoppmann A, Horn K, Li M, Nutile T, Scholz M, Sieber KB, Teumer A, Tin A, Wang J, Tayo BO, Ahluwalia TS, Almgren P, Bakker SJL, Banas B, Bansal N, Biggs ML, Boerwinkle E, Bottinger EP, Brenner H, Carroll RJ, Chalmers J, Chee ML, Chee ML, Cheng CY, Coresh J, de Borst MH, Degenhardt F, Eckardt KU, Endlich K, Franke A, Freitag-Wolf S, Gampawar P, Gansevoort RT, Ghanbari M, Gieger C, Hamet P, Ho K, Hofer E, Holleczek B, Xian Foo VH, Hutri-Kähönen N, Hwang SJ, Ikram MA, Josyula NS, Kähönen M, Khor CC, Koenig W, Kramer H, Krämer BK, Kühnel B, Lange LA, Lehtimäki T, Lieb W, Loos RJF, Lukas MA, Lyytikäinen LP, Meisinger C, Meitinger T, Melander O, Milaneschi Y, Mishra PP, Mononen N, Mychaleckyj JC, Nadkarni GN, Nauck M, Nikus K, Ning B, Nolte IM, O'Donoghue ML, Orho-Melander M, Pendergrass SA, Penninx BWJH, Preuss MH, Psaty BM, Raffield LM, Raitakari OT, Rettig R, Rheinberger M, Rice KM, Rosenkranz AR, Rossing P, Rotter JI, Sabanayagam C, Schmidt H, Schmidt R, Schöttker B, Schulz CA, Sedaghat S, Shaffer CM, Strauch K, Szymczak S, Taylor KD, Tremblay J, Chaker L, van der Harst P, van der Most PJ, Verweij N, Völker U, Waldenberger M, Wallentin L, Waterworth DM, White HD, Wilson JG, Wong TY, Woodward M, Yang Q, Yasuda M, Yerges-Armstrong LM, Zhang Y, Snieder H, Wanner C, Böger CA, Köttgen A, Kronenberg F, Pattaro C, Heid IM. Meta-analysis uncovers genome-wide significant variants for rapid kidney function decline. Kidney Int 2021; 99:926-939. [PMID: 33137338 PMCID: PMC8010357 DOI: 10.1016/j.kint.2020.09.030] [Citation(s) in RCA: 38] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2020] [Revised: 08/21/2020] [Accepted: 09/17/2020] [Indexed: 12/19/2022]
Abstract
Rapid decline of glomerular filtration rate estimated from creatinine (eGFRcrea) is associated with severe clinical endpoints. In contrast to cross-sectionally assessed eGFRcrea, the genetic basis for rapid eGFRcrea decline is largely unknown. To help define this, we meta-analyzed 42 genome-wide association studies from the Chronic Kidney Diseases Genetics Consortium and United Kingdom Biobank to identify genetic loci for rapid eGFRcrea decline. Two definitions of eGFRcrea decline were used: 3 mL/min/1.73m2/year or more ("Rapid3"; encompassing 34,874 cases, 107,090 controls) and eGFRcrea decline 25% or more and eGFRcrea under 60 mL/min/1.73m2 at follow-up among those with eGFRcrea 60 mL/min/1.73m2 or more at baseline ("CKDi25"; encompassing 19,901 cases, 175,244 controls). Seven independent variants were identified across six loci for Rapid3 and/or CKDi25: consisting of five variants at four loci with genome-wide significance (near UMOD-PDILT (2), PRKAG2, WDR72, OR2S2) and two variants among 265 known eGFRcrea variants (near GATM, LARP4B). All these loci were novel for Rapid3 and/or CKDi25 and our bioinformatic follow-up prioritized variants and genes underneath these loci. The OR2S2 locus is novel for any eGFRcrea trait including interesting candidates. For the five genome-wide significant lead variants, we found supporting effects for annual change in blood urea nitrogen or cystatin-based eGFR, but not for GATM or LARP4B. Individuals at high compared to those at low genetic risk (8-14 vs. 0-5 adverse alleles) had a 1.20-fold increased risk of acute kidney injury (95% confidence interval 1.08-1.33). Thus, our identified loci for rapid kidney function decline may help prioritize therapeutic targets and identify mechanisms and individuals at risk for sustained deterioration of kidney function.
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Affiliation(s)
- Mathias Gorski
- Department of Genetic Epidemiology, University of Regensburg, Regensburg, Germany; Department of Nephrology, University Hospital Regensburg, Regensburg, Germany.
| | - Bettina Jung
- Department of Nephrology, University Hospital Regensburg, Regensburg, Germany
| | - Yong Li
- Institute of Genetic Epidemiology, Department of Biometry, Epidemiology and Medical Bioinformatics, Faculty of Medicine and Medical Center-University of Freiburg, Freiburg, Germany
| | - Pamela R Matias-Garcia
- Research Unit of Molecular Epidemiology, Helmholtz Zentrum München-German Research Center for Environmental Health, Neuherberg, Germany; Institute of Epidemiology, Helmholtz Zentrum München-German Research Center for Environmental Health, Neuherberg, Germany; TUM School of Medicine, Technical University of Munich, Munich, Germany
| | - Matthias Wuttke
- Institute of Genetic Epidemiology, Department of Biometry, Epidemiology and Medical Bioinformatics, Faculty of Medicine and Medical Center-University of Freiburg, Freiburg, Germany; Renal Division, Department of Medicine IV, Faculty of Medicine and Medical Center-University of Freiburg, Freiburg, Germany
| | - Stefan Coassin
- Department of Genetics and Pharmacology, Institute of Genetic Epidemiology, Medical University of Innsbruck, Innsbruck, Austria
| | - Chris H L Thio
- Department of Epidemiology, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Marcus E Kleber
- Vth Department of Medicine (Nephrology, Hypertensiology, Rheumatology, Endocrinology, Diabetology), Medical Faculty Mannheim, University of Heidelberg, Mannheim, Germany
| | - Thomas W Winkler
- Department of Genetic Epidemiology, University of Regensburg, Regensburg, Germany
| | - Veronika Wanner
- Department of Genetic Epidemiology, University of Regensburg, Regensburg, Germany
| | - Jin-Fang Chai
- Saw Swee Hock School of Public Health, National University of Singapore and National University Health System, Singapore, Singapore
| | - Audrey Y Chu
- Genetics, Merck & Co., Inc., Kenilworth, New Jersey, USA
| | - Massimiliano Cocca
- Institute for Maternal and Child Health, IRCCS "Burlo Garofolo," Trieste, Italy
| | - Mary F Feitosa
- Division of Statistical Genomics, Department of Genetics, Washington University School of Medicine, St. Louis, Missouri, USA
| | - Sahar Ghasemi
- Institute for Community Medicine, University Medicine Greifswald, Greifswald, Germany; DZHK (German Center for Cardiovascular Research), Partner Site Greifswald, Greifswald, Germany
| | - Anselm Hoppmann
- Institute of Genetic Epidemiology, Department of Biometry, Epidemiology and Medical Bioinformatics, Faculty of Medicine and Medical Center-University of Freiburg, Freiburg, Germany
| | - Katrin Horn
- Institute for Medical Informatics, Statistics and Epidemiology, University of Leipzig, Leipzig, Germany; LIFE Research Center for Civilization Diseases, University of Leipzig, Leipzig, Germany
| | - Man Li
- Division of Nephrology and Hypertension, Department of Medicine, University of Utah, Salt Lake City, Utah, USA
| | - Teresa Nutile
- Institute of Genetics and Biophysics "Adriano Buzzati-Traverso"-CNR, Naples, Italy
| | - Markus Scholz
- Institute for Medical Informatics, Statistics and Epidemiology, University of Leipzig, Leipzig, Germany; LIFE Research Center for Civilization Diseases, University of Leipzig, Leipzig, Germany
| | - Karsten B Sieber
- Human Genetics, GlaxoSmithKline, Collegeville, Pennsylvania, USA
| | - Alexander Teumer
- Institute for Community Medicine, University Medicine Greifswald, Greifswald, Germany; DZHK (German Center for Cardiovascular Research), Partner Site Greifswald, Greifswald, Germany
| | - Adrienne Tin
- Memory Impairment and Neurodegenerative Dementia (MIND) Center, University of Mississippi Medical Center, Jackson, Mississippi, USA; Division of Nephrology, Department of Medicine, University of Mississippi Medical Center, Jackson, Mississippi, USA
| | - Judy Wang
- Division of Statistical Genomics, Department of Genetics, Washington University School of Medicine, St. Louis, Missouri, USA
| | - Bamidele O Tayo
- Department of Public Health Sciences, Loyola University Chicago, Maywood, Illinois, USA
| | | | - Peter Almgren
- Diabetes and Cardiovascular Disease-Genetic Epidemiology, Department of Clinical Sciences in Malmö, Lund University, Malmö, Sweden
| | - Stephan J L Bakker
- Division of Nephrology, Department of Internal Medicine, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Bernhard Banas
- Department of Nephrology, University Hospital Regensburg, Regensburg, Germany
| | - Nisha Bansal
- Division of Nephrology, University of Washington, Seattle, Washington, USA; Kidney Research Institute, University of Washington, Seattle, Washington, USA
| | - Mary L Biggs
- Cardiovascular Health Research Unit, Department of Medicine, University of Washington, Seattle, Washington, USA; Department of Biostatistics, University of Washington, Seattle, Washington, USA
| | - Eric Boerwinkle
- Human Genetics Center, University of Texas Health Science Center, Houston, Texas, USA
| | - Erwin P Bottinger
- Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, New York, USA; Digital Health Center, Hasso Plattner Institute and University of Potsdam, Potsdam, Germany
| | - Hermann Brenner
- Division of Clinical Epidemiology and Aging Research, German Cancer Research Center (DKFZ), Heidelberg, Germany; Network Aging Research, University of Heidelberg, Heidelberg, Germany
| | - Robert J Carroll
- Department of Biomedical Informatics, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - John Chalmers
- The George Institute for Global Health, University of New South Wales, Sydney, Australia; The George Institute for Global Health, University of Oxford, Oxford, UK; Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland, USA
| | - Miao-Li Chee
- Singapore Eye Research Institute, Singapore National Eye Center, Singapore, Singapore
| | - Miao-Ling Chee
- Singapore Eye Research Institute, Singapore National Eye Center, Singapore, Singapore
| | - Ching-Yu Cheng
- Singapore Eye Research Institute, Singapore National Eye Center, Singapore, Singapore; Ophthalmology and Visual Sciences Academic Clinical Program (Eye ACP), Duke-NUS Medical School, Singapore, Singapore; Department of Ophthalmology, Yong Loo Lin School of Medicine, National University of Singapore and National University Health System, Singapore, Singapore
| | - Josef Coresh
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland, USA
| | - Martin H de Borst
- Division of Nephrology, Department of Internal Medicine, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Frauke Degenhardt
- Institute of Clinical Molecular Biology, Christian-AlbrechtsUniversity of Kiel, Kiel, Germany
| | - Kai-Uwe Eckardt
- Department of Nephrology and Medical Intensive Care, Charité-Universitätsmedizin Berlin, Berlin, Germany; Department of Nephrology and Hypertension, Friedrich Alexander University Erlangen-Nürnberg (FAU), Erlangen, Germany
| | - Karlhans Endlich
- DZHK (German Center for Cardiovascular Research), Partner Site Greifswald, Greifswald, Germany; Department of Anatomy and Cell Biology, University Medicine Greifswald, Greifswald, Germany
| | - Andre Franke
- Institute of Clinical Molecular Biology, Christian-AlbrechtsUniversity of Kiel, Kiel, Germany
| | - Sandra Freitag-Wolf
- Institute of Medical Informatics and Statistics, Kiel University, University Hospital Schleswig-Holstein, Kiel, Germany
| | - Piyush Gampawar
- Institute of Molecular Biology and Biochemistry, Center for Molecular Medicine, Medical University of Graz, Graz, Austria
| | - Ron T Gansevoort
- Division of Nephrology, Department of Internal Medicine, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Mohsen Ghanbari
- Department of Epidemiology, Erasmus MC, University Medical Center Rotterdam, Rotterdam, the Netherlands; Department of Genetics, School of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Christian Gieger
- Research Unit of Molecular Epidemiology, Helmholtz Zentrum München-German Research Center for Environmental Health, Neuherberg, Germany; Institute of Epidemiology, Helmholtz Zentrum München-German Research Center for Environmental Health, Neuherberg, Germany; German Center for Diabetes Research (DZD), Neuherberg, Germany
| | - Pavel Hamet
- Montreal University Hospital Research Center, CHUM, Montreal, Quebec, Canada; Medpharmgene, Montreal, Quebec, Canada; CRCHUM, Montreal, Canada
| | - Kevin Ho
- Kidney Health Research Institute (KHRI), Geisinger, Danville, Pennsylvania, USA; Department of Nephrology, Geisinger, Danville, Pennsylvania, USA
| | - Edith Hofer
- Clinical Division of Neurogeriatrics, Department of Neurology, Medical University of Graz, Graz, Austria; Institute for Medical Informatics, Statistics and Documentation, Medical University of Graz, Graz, Austria
| | - Bernd Holleczek
- Division of Clinical Epidemiology and Aging Research, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Valencia Hui Xian Foo
- Singapore Eye Research Institute, Singapore National Eye Center, Singapore, Singapore
| | - Nina Hutri-Kähönen
- Department of Pediatrics, Tampere University Hospital, Tampere, Finland; Department of Pediatrics, Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland
| | - Shih-Jen Hwang
- NHLBI's Framingham Heart Study, Framingham, Massachusetts, USA; The Center for Population Studies, NHLBI, Framingham, Massachusetts, USA
| | - M Arfan Ikram
- Department of Epidemiology, Erasmus MC, University Medical Center Rotterdam, Rotterdam, the Netherlands
| | - Navya Shilpa Josyula
- Geisinger Research, Biomedical and Translational Informatics Institute, Rockville, Maryland, USA
| | - Mika Kähönen
- Department of Clinical Physiology, Tampere University Hospital, Tampere, Finland; Department of Clinical Physiology, Finnish Cardiovascular Research Center-Tampere, Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland
| | - Chiea-Chuen Khor
- Singapore Eye Research Institute, Singapore National Eye Center, Singapore, Singapore; Genome Institute of Singapore, Agency for Science Technology and Research, Singapore, Singapore
| | - Wolfgang Koenig
- Deutsches Herzzentrum München, Technische Universität München, Munich, Germany; DZHK (German Center for Cardiovascular Research), Partner Site Munich Heart Alliance, Munich, Germany; Institute of Epidemiology and Medical Biometry, University of Ulm, Ulm, Germany
| | - Holly Kramer
- Department of Public Health Sciences, Loyola University Chicago, Maywood, Illinois, USA; Division of Nephrology and Hypertension, Loyola University Chicago, Chicago, Illinois, USA
| | - Bernhard K Krämer
- Department of Medicine (Nephrology, Hypertensiology, Rheumatology, Endocrinology, Diabetology), Medical Faculty Mannheim, University of Heidelberg, Mannheim, Germany
| | - Brigitte Kühnel
- Research Unit of Molecular Epidemiology, Helmholtz Zentrum München-German Research Center for Environmental Health, Neuherberg, Germany
| | - Leslie A Lange
- Division of Biomedical Informatics and Personalized Medicine, School of Medicine, University of Colorado Denver-Anschutz Medical Campus, Aurora, Colorado, USA
| | - Terho Lehtimäki
- Department of Clinical Chemistry, Fimlab Laboratories, Tampere, Finland; Department of Clinical Chemistry, Finnish Cardiovascular Research Center-Tampere, Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland
| | - Wolfgang Lieb
- Institute of Epidemiology and Biobank Popgen, Kiel University, Kiel, Germany
| | - Ruth J F Loos
- Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, New York, USA; The Mindich Child Health and Development Institute, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Mary Ann Lukas
- Target Sciences-Genetics, GlaxoSmithKline, Albuquerque, New Mexico, USA
| | - Leo-Pekka Lyytikäinen
- Department of Clinical Chemistry, Fimlab Laboratories, Tampere, Finland; Department of Clinical Chemistry, Finnish Cardiovascular Research Center-Tampere, Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland
| | - Christa Meisinger
- Independent Research Group Clinical Epidemiology, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany; Chair of Epidemiology, Ludwig-Maximilians-Universität München at UNIKA-T Augsburg, Augsburg, Germany
| | - Thomas Meitinger
- DZHK (German Center for Cardiovascular Research), Partner Site Munich Heart Alliance, Munich, Germany; Institute of Human Genetics, Helmholtz Zentrum München, Neuherberg, Germany; Institute of Human Genetics, Technische Universität München, Munich, Germany
| | - Olle Melander
- Hypertension and Cardiovascular Disease, Department of Clinical Sciences Malmö, Lund University, Malmö, Sweden
| | - Yuri Milaneschi
- Department of Psychiatry, Amsterdam Public Health and Amsterdam Neuroscience, Amsterdam UMC/Vrije Universiteit and GGZ inGeest, Amsterdam, the Netherlands
| | - Pashupati P Mishra
- Department of Clinical Chemistry, Fimlab Laboratories, Tampere, Finland; Department of Clinical Chemistry, Finnish Cardiovascular Research Center-Tampere, Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland
| | - Nina Mononen
- Department of Clinical Chemistry, Fimlab Laboratories, Tampere, Finland; Department of Clinical Chemistry, Finnish Cardiovascular Research Center-Tampere, Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland
| | - Josyf C Mychaleckyj
- Center for Public Health Genomics, University of Virginia, Charlottesville, Charlottesville, Virginia, USA
| | - Girish N Nadkarni
- Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, New York, USA; Division of Nephrology, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Matthias Nauck
- DZHK (German Center for Cardiovascular Research), Partner Site Greifswald, Greifswald, Germany; Institute of Clinical Chemistry and Laboratory Medicine, University Medicine Greifswald, Greifswald, Germany
| | - Kjell Nikus
- Department of Cardiology, Heart Center, Tampere University Hospital, Tampere, Finland; Department of Cardiology, Finnish Cardiovascular Research Center-Tampere, Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland
| | - Boting Ning
- Department of Biostatistics, Boston University School of Public Health, Boston, Massachusetts, USA
| | - Ilja M Nolte
- Department of Epidemiology, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Michelle L O'Donoghue
- Cardiovascular Division, Brigham and Women's Hospital, Boston, Massachusetts, USA; TIMI Study Group, Boston, Massachusetts, USA
| | - Marju Orho-Melander
- Diabetes and Cardiovascular Disease-Genetic Epidemiology, Department of Clinical Sciences in Malmö, Lund University, Malmö, Sweden
| | - Sarah A Pendergrass
- Geisinger Research, Biomedical and Translational Informatics Institute, Danville, Pennsylvania, USA
| | - Brenda W J H Penninx
- Department of Psychiatry, Amsterdam Public Health and Amsterdam Neuroscience, Amsterdam UMC/Vrije Universiteit and GGZ inGeest, Amsterdam, the Netherlands
| | - Michael H Preuss
- Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Bruce M Psaty
- Cardiovascular Health Research Unit, Department of Medicine, Department of Epidemiology, Department of Health Services, University of Washington, Seattle, Washington, USA; Kaiser Permanente Washington Health Research Institute, Seattle, Washington, USA
| | - Laura M Raffield
- Department of Genetics, University of North Carolina, Chapel Hill, North Carolina, USA
| | - Olli T Raitakari
- Department of Clinical Physiology and Nuclear Medicine, Turku University Hospital, Turku, Finland; Research Center of Applied and Preventive Cardiovascular Medicine, University of Turku, Turku, Finland; Centre for Population Health Research, University of Turku and Turku University Hospital, Turku, Finland
| | - Rainer Rettig
- Institute of Physiology, University Medicine Greifswald, Karlsburg, Germany
| | - Myriam Rheinberger
- Department of Nephrology, University Hospital Regensburg, Regensburg, Germany; Department of Nephrology and Rheumatology, Kliniken Südostbayern, Regensburg, Germany
| | - Kenneth M Rice
- Department of Biostatistics, University of Washington, Seattle, Washington, USA
| | - Alexander R Rosenkranz
- Department of Internal Medicine, Division of Nephrology, Medical University Graz, Graz, Austria
| | | | - Jerome I Rotter
- The Institute for Translational Genomics and Population Sciences, Department of Pediatrics, The Lundquist Institute for Biomedical Innovation at Harbor-UCLA Medical Center, Torrance, California, USA
| | - Charumathi Sabanayagam
- Singapore Eye Research Institute, Singapore National Eye Center, Singapore, Singapore; Ophthalmology and Visual Sciences Academic Clinical Program (Eye ACP), Duke-NUS Medical School, Singapore, Singapore
| | - Helena Schmidt
- Institute of Molecular Biology and Biochemistry, Center for Molecular Medicine, Medical University of Graz, Graz, Austria
| | - Reinhold Schmidt
- Clinical Division of Neurogeriatrics, Department of Neurology, Medical University of Graz, Graz, Austria
| | - Ben Schöttker
- Division of Clinical Epidemiology and Aging Research, German Cancer Research Center (DKFZ), Heidelberg, Germany; Network Aging Research, University of Heidelberg, Heidelberg, Germany
| | - Christina-Alexandra Schulz
- Diabetes and Cardiovascular Disease-Genetic Epidemiology, Department of Clinical Sciences in Malmö, Lund University, Malmö, Sweden
| | - Sanaz Sedaghat
- Department of Epidemiology, Erasmus MC, University Medical Center Rotterdam, Rotterdam, the Netherlands; Department of Preventive Medicine, Northwestern University, Feinberg School of Medicine, Chicago, Illinois, USA
| | - Christian M Shaffer
- Department of Biomedical Informatics, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - Konstantin Strauch
- Institute of Genetic Epidemiology, Helmholtz Zentrum München-German Research Center for Environmental Health, Neuherberg, Germany; Chair of Genetic Epidemiology, IBE, Faculty of Medicine, Ludwig-Maximilians-Universität München, München, Germany
| | - Silke Szymczak
- Institute of Medical Informatics and Statistics, Kiel University, University Hospital Schleswig-Holstein, Kiel, Germany
| | - Kent D Taylor
- The Institute for Translational Genomics and Population Sciences, Department of Pediatrics, The Lundquist Institute for Biomedical Innovation at Harbor-UCLA Medical Center, Torrance, California, USA
| | - Johanne Tremblay
- Montreal University Hospital Research Center, CHUM, Montreal, Quebec, Canada; CRCHUM, Montreal, Canada; Medpharmgene, Montreal, Quebec, Canada
| | - Layal Chaker
- Department of Epidemiology, Erasmus MC, University Medical Center Rotterdam, Rotterdam, the Netherlands; Department of Internal Medicine, Erasmus MC, University Medical Center Rotterdam, Rotterdam, the Netherlands
| | - Pim van der Harst
- Department of Cardiology, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands; Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands; Durrer Center for Cardiovascular Research, The Netherlands Heart Institute, Utrecht, the Netherlands
| | - Peter J van der Most
- Department of Epidemiology, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Niek Verweij
- Department of Cardiology, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Uwe Völker
- DZHK (German Center for Cardiovascular Research), Partner Site Greifswald, Greifswald, Germany; Interfaculty Institute for Genetics and Functional Genomics, University Medicine Greifswald, Greifswald, Germany
| | - Melanie Waldenberger
- Research Unit of Molecular Epidemiology, Helmholtz Zentrum München-German Research Center for Environmental Health, Neuherberg, Germany; Institute of Epidemiology, Helmholtz Zentrum München-German Research Center for Environmental Health, Neuherberg, Germany; DZHK (German Center for Cardiovascular Research), Partner Site Munich Heart Alliance, Munich, Germany
| | - Lars Wallentin
- Cardiology, Department of Medical Sciences, Uppsala University, Uppsala, Sweden; Uppsala Clinical Research Center, Uppsala University, Uppsala, Sweden
| | | | - Harvey D White
- Green Lane Cardiovascular Service, Auckland City Hospital and University of Auckland, Auckland, New Zealand
| | - James G Wilson
- Department of Physiology and Biophysics, University of Mississippi Medical Center, Jackson, Mississippi, USA
| | - Tien-Yin Wong
- Singapore Eye Research Institute, Singapore National Eye Center, Singapore, Singapore; Ophthalmology and Visual Sciences Academic Clinical Program (Eye ACP), Duke-NUS Medical School, Singapore, Singapore
| | - Mark Woodward
- The George Institute for Global Health, University of New South Wales, Sydney, Australia; The George Institute for Global Health, University of Oxford, Oxford, UK; Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland, USA
| | - Qiong Yang
- Department of Biostatistics, Boston University School of Public Health, Boston, Massachusetts, USA
| | - Masayuki Yasuda
- Singapore Eye Research Institute, Singapore National Eye Center, Singapore, Singapore; Department of Ophthalmology, Tohoku University Graduate School of Medicine, Miyagi, Japan
| | | | - Yan Zhang
- Division of Clinical Epidemiology and Aging Research, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Harold Snieder
- Department of Epidemiology, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Christoph Wanner
- Division of Nephrology, University Clinic, University of Würzburg, Würzburg, Germany
| | - Carsten A Böger
- Department of Nephrology, University Hospital Regensburg, Regensburg, Germany; Department of Nephrology and Rheumatology, Kliniken Südostbayern, Regensburg, Germany
| | - Anna Köttgen
- Institute of Genetic Epidemiology, Department of Biometry, Epidemiology and Medical Bioinformatics, Faculty of Medicine and Medical Center-University of Freiburg, Freiburg, Germany; Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland, USA
| | - Florian Kronenberg
- Department of Genetics and Pharmacology, Institute of Genetic Epidemiology, Medical University of Innsbruck, Innsbruck, Austria
| | - Cristian Pattaro
- Eurac Research, Institute for Biomedicine (affiliated with the University of Lübeck), Bolzano, Italy
| | - Iris M Heid
- Department of Genetic Epidemiology, University of Regensburg, Regensburg, Germany.
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Pan WW, Gardner TW, Harder JL. Integrative Biology of Diabetic Retinal Disease: Lessons from Diabetic Kidney Disease. J Clin Med 2021; 10:1254. [PMID: 33803590 PMCID: PMC8003049 DOI: 10.3390/jcm10061254] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2021] [Revised: 03/09/2021] [Accepted: 03/12/2021] [Indexed: 01/13/2023] Open
Abstract
Diabetic retinal disease (DRD) remains the most common cause of vision loss in adults of working age. Progress on the development of new therapies for DRD has been limited by the complexity of the human eye, which constrains the utility of traditional research techniques, including animal and tissue culture models-a problem shared by those in the field of kidney disease research. By contrast, significant progress in the study of diabetic kidney disease (DKD) has resulted from the successful employment of systems biology approaches. Systems biology is widely used to comprehensively understand complex human diseases through the unbiased integration of genetic, environmental, and phenotypic aspects of the disease with the functional and structural manifestations of the disease. The application of a systems biology approach to DRD may help to clarify the molecular basis of the disease and its progression. Acquiring this type of information might enable the development of personalized treatment approaches, with the goal of discovering new therapies targeted to an individual's specific DRD pathophysiology and phenotype. Furthermore, recent efforts have revealed shared and distinct pathways and molecular targets of DRD and DKD, highlighting the complex pathophysiology of these diseases and raising the possibility of therapeutics beneficial to both organs. The objective of this review is to survey the current understanding of DRD pathophysiology and to demonstrate the investigative approaches currently applied to DKD that could promote a more thorough understanding of the structure, function, and progression of DRD.
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Affiliation(s)
- Warren W. Pan
- Department of Ophthalmology and Visual Sciences, University of Michigan Medical School, Ann Arbor, MI 48105, USA; (W.W.P.); (T.W.G.)
| | - Thomas W. Gardner
- Department of Ophthalmology and Visual Sciences, University of Michigan Medical School, Ann Arbor, MI 48105, USA; (W.W.P.); (T.W.G.)
- Department of Internal Medicine (Metabolism, Endocrinology and Diabetes), University of Michigan Medical School, Ann Arbor, MI 48109, USA
- Department of Molecular and Integrative Physiology, University of Michigan Medical School, Ann Arbor, MI 48109, USA
| | - Jennifer L. Harder
- Department of Internal Medicine (Nephrology), University of Michigan Medical School, Ann Arbor, MI 48109, USA
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Imamura M, Takahashi A, Matsunami M, Horikoshi M, Iwata M, Araki SI, Toyoda M, Susarla G, Ahn J, Park KH, Kong J, Moon S, Sobrin L, Yamauchi T, Tobe K, Maegawa H, Kadowaki T, Maeda S. Genome-wide association studies identify two novel loci conferring susceptibility to diabetic retinopathy in Japanese patients with type 2 diabetes. Hum Mol Genet 2021; 30:716-726. [PMID: 33607655 DOI: 10.1093/hmg/ddab044] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2020] [Revised: 01/14/2021] [Accepted: 02/03/2021] [Indexed: 12/21/2022] Open
Abstract
Several reports have suggested that genetic susceptibility contributes to the development and progression of diabetic retinopathy. We aimed to identify genetic loci that confer susceptibility to diabetic retinopathy in Japanese patients with type 2 diabetes. We analysed 5 790 508 single nucleotide polymorphisms (SNPs) in 8880 Japanese patients with type 2 diabetes, 4839 retinopathy cases and 4041 controls, as well as 2217 independent Japanese patients with type 2 diabetes, 693 retinopathy cases and 1524 controls. The results of these two genome-wide association studies (GWAS) were combined with an inverse variance meta-analysis (Stage-1), followed by de novo genotyping for the candidate SNP loci (P < 1.0 × 10-4) in an independent case-control study (Stage-2, 2260 cases and 723 controls). After combining the association data (Stages 1 and 2) using meta-analysis, the associations of two loci reached a genome-wide significance level: rs12630354 near STT3B on chromosome 3, P = 1.62 × 10-9, odds ratio (OR) = 1.17, 95% confidence interval (CI) 1.11-1.23, and rs140508424 within PALM2 on chromosome 9, P = 4.19 × 10-8, OR = 1.61, 95% CI 1.36-1.91. However, the association of these two loci was not replicated in Korean, European or African American populations. Gene-based analysis using Stage-1 GWAS data identified a gene-level association of EHD3 with susceptibility to diabetic retinopathy (P = 2.17 × 10-6). In conclusion, we identified two novel SNP loci, STT3B and PALM2, and a novel gene, EHD3, that confers susceptibility to diabetic retinopathy; however, further replication studies are required to validate these associations.
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Affiliation(s)
- Minako Imamura
- Department of Advanced Genomic and Laboratory Medicine, Graduate School of Medicine, University of the Ryukyus, Okinawa 903-0215, Japan.,Division of Clinical Laboratory and Blood Transfusion, University of the Ryukyus Hospital, Okinawa 903-0215, Japan.,Laboratory for Genomics of Diabetes and Metabolism, RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa 230-0045, Japan
| | - Atsushi Takahashi
- Department of Genomic Medicine, Research Institute, National Cerebral and Cardiovascular Center, Osaka 564-8565, Japan.,Laboratory for Statistical and Translational Genetics, RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa 230-0045, Japan
| | - Masatoshi Matsunami
- Department of Advanced Genomic and Laboratory Medicine, Graduate School of Medicine, University of the Ryukyus, Okinawa 903-0215, Japan.,Laboratory for Genomics of Diabetes and Metabolism, RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa 230-0045, Japan
| | - Momoko Horikoshi
- Laboratory for Genomics of Diabetes and Metabolism, RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa 230-0045, Japan
| | - Minoru Iwata
- First Department of Internal Medicine, University of Toyama, Toyama 930-0194, Japan.,Itoigawa Community Medical Unit, Toyama University Hospital, Toyama 930-0194, Japan
| | - Shin-Ichi Araki
- Department of Medicine, Shiga University of Medical Science, Shiga 520-2192, Japan
| | - Masao Toyoda
- Division of Nephrology, Endocrinology and Metabolism, Department of Internal Medicine, Tokai University School of Medicine, Kanagawa 259-1193, Japan
| | - Gayatri Susarla
- Massachusetts Eye and Ear Department of Ophthalmology, Harvard Medical School, Boston, MA 02114, USA
| | - Jeeyun Ahn
- Department of Ophthalmology, Seoul National University College of Medicine, Seoul Municipal Government Seoul National University Boramae Medical Center, Seoul 07061, Korea
| | - Kyu Hyung Park
- Department of Ophthalmology, Seoul National University College of Medicine, Seoul National University Bundang Hospital, Seongnam 13620, Korea
| | - Jinhwa Kong
- Division of Genome Research, Center for Genome Science, Korea National Institute of Health, Chungcheongbuk-do 28159, Korea
| | - Sanghoon Moon
- Division of Genome Research, Center for Genome Science, Korea National Institute of Health, Chungcheongbuk-do 28159, Korea
| | - Lucia Sobrin
- Massachusetts Eye and Ear Department of Ophthalmology, Harvard Medical School, Boston, MA 02114, USA
| | | | - Toshimasa Yamauchi
- Department of Diabetes and Metabolic Diseases, Graduate School of Medicine, The University of Tokyo, Tokyo 113-8655, Japan
| | - Kazuyuki Tobe
- First Department of Internal Medicine, University of Toyama, Toyama 930-0194, Japan
| | - Hiroshi Maegawa
- Department of Medicine, Shiga University of Medical Science, Shiga 520-2192, Japan
| | - Takashi Kadowaki
- Department of Diabetes and Metabolic Diseases, Graduate School of Medicine, The University of Tokyo, Tokyo 113-8655, Japan.,Toranomon Hospital, Tokyo 105-8470, Japan.,Okinaka Memorial Institute for Medical Research, Tokyo 105-8470, Japan
| | - Shiro Maeda
- Department of Advanced Genomic and Laboratory Medicine, Graduate School of Medicine, University of the Ryukyus, Okinawa 903-0215, Japan.,Division of Clinical Laboratory and Blood Transfusion, University of the Ryukyus Hospital, Okinawa 903-0215, Japan.,Laboratory for Genomics of Diabetes and Metabolism, RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa 230-0045, Japan
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38
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Whole-genome sequencing analysis of the cardiometabolic proteome. Nat Commun 2020; 11:6336. [PMID: 33303764 PMCID: PMC7729872 DOI: 10.1038/s41467-020-20079-2] [Citation(s) in RCA: 37] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2020] [Accepted: 10/26/2020] [Indexed: 12/14/2022] Open
Abstract
The human proteome is a crucial intermediate between complex diseases and their genetic and environmental components, and an important source of drug development targets and biomarkers. Here, we comprehensively assess the genetic architecture of 257 circulating protein biomarkers of cardiometabolic relevance through high-depth (22.5×) whole-genome sequencing (WGS) in 1328 individuals. We discover 131 independent sequence variant associations (P < 7.45 × 10−11) across the allele frequency spectrum, all of which replicate in an independent cohort (n = 1605, 18.4x WGS). We identify for the first time replicating evidence for rare-variant cis-acting protein quantitative trait loci for five genes, involving both coding and noncoding variation. We construct and validate polygenic scores that explain up to 45% of protein level variation. We find causal links between protein levels and disease risk, identifying high-value biomarkers and drug development targets. The human proteome represents a crucial link between complex disease and genetic/environmental factors. Here, the authors investigate 257 cardiometabolic-relevant protein biomarkers in whole genome sequencing data from 1328 individuals, revealing the genetic architecture underlying biomarker variation.
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39
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Smyth LJ, Patterson CC, Swan EJ, Maxwell AP, McKnight AJ. DNA Methylation Associated With Diabetic Kidney Disease in Blood-Derived DNA. Front Cell Dev Biol 2020; 8:561907. [PMID: 33178681 PMCID: PMC7593403 DOI: 10.3389/fcell.2020.561907] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2020] [Accepted: 09/15/2020] [Indexed: 12/23/2022] Open
Abstract
A subset of individuals with type 1 diabetes will develop diabetic kidney disease (DKD). DKD is heritable and large-scale genome-wide association studies have begun to identify genetic factors that influence DKD. Complementary to genetic factors, we know that a person’s epigenetic profile is also altered with DKD. This study reports analysis of DNA methylation, a major epigenetic feature, evaluating methylome-wide loci for association with DKD. Unique features (n = 485,577; 482,421 CpG probes) were evaluated in blood-derived DNA from carefully phenotyped White European individuals diagnosed with type 1 diabetes with (cases) or without (controls) DKD (n = 677 samples). Explicitly, 150 cases were compared to 100 controls using the 450K array, with subsequent analysis using data previously generated for a further 96 cases and 96 controls on the 27K array, and de novo methylation data generated for replication in 139 cases and 96 controls. Following stringent quality control, raw data were quantile normalized and beta values calculated to reflect the methylation status at each site. The difference in methylation status was evaluated between cases and controls; resultant P-values for array-based data were adjusted for multiple testing. Genes with significantly increased (hypermethylated) and/or decreased (hypomethylated) levels of DNA methylation were considered for biological relevance by functional enrichment analysis using KEGG pathways. Twenty-two loci demonstrated statistically significant fold changes associated with DKD and additional support for these associated loci was sought using independent samples derived from patients recruited with similar inclusion criteria. Markers associated with CCNL1 and ZNF187 genes are supported as differentially regulated loci (P < 10–8), with evidence also presented for AFF3, which has been identified from a meta-analysis and subsequent replication of genome-wide association studies. Further supporting evidence for differential gene expression in CCNL1 and ZNF187 is presented from kidney biopsy and blood-derived RNA in people with and without kidney disease from NephroSeq. Evidence confirming that methylation sites influence the development of DKD may aid risk prediction tools and stimulate research to identify epigenomic therapies which might be clinically useful for this disease.
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Affiliation(s)
- Laura J Smyth
- Centre for Public Health, Queen's University Belfast, Belfast, United Kingdom
| | | | - Elizabeth J Swan
- Centre for Public Health, Queen's University Belfast, Belfast, United Kingdom
| | - Alexander P Maxwell
- Centre for Public Health, Queen's University Belfast, Belfast, United Kingdom.,Regional Nephrology Unit, Belfast City Hospital, Belfast, United Kingdom
| | - Amy Jayne McKnight
- Centre for Public Health, Queen's University Belfast, Belfast, United Kingdom
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40
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Chen YC, Wu MY, Yu ZL, Chou WH, Lai YT, Kao CC, Faridah IN, Wu MS, Chang WC. Association of UBE3C Variants with Reduced Kidney Function in Patients with Diabetic Kidney Disease. J Pers Med 2020; 10:jpm10040210. [PMID: 33171965 PMCID: PMC7712123 DOI: 10.3390/jpm10040210] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2020] [Revised: 11/01/2020] [Accepted: 11/04/2020] [Indexed: 12/17/2022] Open
Abstract
Diabetic kidney disease (DKD) is the leading cause of morbidity and mortality in patients with diabetes mellitus (DM) and the most common variant of end-stage renal disease (ESRD) globally. The economic burden of ESRD treatment with dialysis is substantial. The incidence and prevalence of ESRD in Taiwan remain the highest worldwide. Therefore, identifying genetic factors affecting kidney function would have valuable clinical implications. We performed microarray experiments and identified that ubiquitin protein ligase E3C (UBE3C) is differentially expressed in two DKD patient groups with extreme (low and high) urine protein-to-creatinine ratios. A follow-up genotyping study was performed in a larger group to investigate any specific variants of UBE3C associated with DKD. A total of 263 patients were included in the study, comprising 172 patients with DKD and 91 control subjects (patients with DM without chronic kidney disease (CKD)). Two UBE3C variants (rs3802129(AA) and rs7807(CC)) were determined to be associated with reduced kidney function. The haplotype analysis revealed that rs3802129/rs3815217 (block 1) with A/G haplotype and rs8101/rs7807 (block 2) with T/C haplotype were associated with higher risks of CKD phenotypes. These findings suggest a clinical role of UBE3C variants in DKD risk.
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Affiliation(s)
- Ying-Chun Chen
- Master Program in Clinical Pharmacogenomics and Pharmacoproteomics, School of Pharmacy, Taipei Medical University, Taipei 11031, Taiwan; (Y.-C.C.); (M.-Y.W.)
- Department of Pharmacy, Shuang Ho Hospital, Taipei Medical University, New Taipei City 23561, Taiwan
| | - Mei-Yi Wu
- Master Program in Clinical Pharmacogenomics and Pharmacoproteomics, School of Pharmacy, Taipei Medical University, Taipei 11031, Taiwan; (Y.-C.C.); (M.-Y.W.)
- Division of Nephrology, Department of Internal Medicine, School of Medicine, College of Medicine, Taipei Medical University, Taipei 11031, Taiwan;
- Division of Nephrology, Department of Internal Medicine, Shuang Ho Hospital, Taipei Medical University, New Taipei City 23561, Taiwan
- TMU Research Center of Urology and Kidney, Taipei Medical University, Taipei 11031, Taiwan
| | - Zhi-Lei Yu
- Department of Clinical Pharmacy, School of Pharmacy, Taipei Medical University, Taipei 11031, Taiwan; (Z.-L.Y.); (W.-H.C.); (Y.-T.L.); (I.N.F.)
| | - Wan-Hsuan Chou
- Department of Clinical Pharmacy, School of Pharmacy, Taipei Medical University, Taipei 11031, Taiwan; (Z.-L.Y.); (W.-H.C.); (Y.-T.L.); (I.N.F.)
| | - Yi-Ting Lai
- Department of Clinical Pharmacy, School of Pharmacy, Taipei Medical University, Taipei 11031, Taiwan; (Z.-L.Y.); (W.-H.C.); (Y.-T.L.); (I.N.F.)
| | - Chih-Chin Kao
- Division of Nephrology, Department of Internal Medicine, School of Medicine, College of Medicine, Taipei Medical University, Taipei 11031, Taiwan;
| | - Imaniar Noor Faridah
- Department of Clinical Pharmacy, School of Pharmacy, Taipei Medical University, Taipei 11031, Taiwan; (Z.-L.Y.); (W.-H.C.); (Y.-T.L.); (I.N.F.)
- Faculty of Pharmacy, University of Ahmad Dahlan, Yogyakarta 55164, Indonesia
| | - Mai-Szu Wu
- Division of Nephrology, Department of Internal Medicine, School of Medicine, College of Medicine, Taipei Medical University, Taipei 11031, Taiwan;
- Division of Nephrology, Department of Internal Medicine, Shuang Ho Hospital, Taipei Medical University, New Taipei City 23561, Taiwan
- TMU Research Center of Urology and Kidney, Taipei Medical University, Taipei 11031, Taiwan
- Correspondence: (M.-S.W.); (W.-C.C.)
| | - Wei-Chiao Chang
- Master Program in Clinical Pharmacogenomics and Pharmacoproteomics, School of Pharmacy, Taipei Medical University, Taipei 11031, Taiwan; (Y.-C.C.); (M.-Y.W.)
- Department of Clinical Pharmacy, School of Pharmacy, Taipei Medical University, Taipei 11031, Taiwan; (Z.-L.Y.); (W.-H.C.); (Y.-T.L.); (I.N.F.)
- Integrative Research Center for Critical Care, Wan Fang Hospital, Taipei Medical University, Taipei 11696, Taiwan
- Department of Medical Research, Shuang Ho Hospital, Taipei Medical University, New Taipei City 23561, Taiwan
- Correspondence: (M.-S.W.); (W.-C.C.)
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41
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Systematic integrated analysis of genetic and epigenetic variation in diabetic kidney disease. Proc Natl Acad Sci U S A 2020; 117:29013-29024. [PMID: 33144501 DOI: 10.1073/pnas.2005905117] [Citation(s) in RCA: 46] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Poor metabolic control and host genetic predisposition are critical for diabetic kidney disease (DKD) development. The epigenome integrates information from sequence variations and metabolic alterations. Here, we performed a genome-wide methylome association analysis in 500 subjects with DKD from the Chronic Renal Insufficiency Cohort for DKD phenotypes, including glycemic control, albuminuria, kidney function, and kidney function decline. We show distinct methylation patterns associated with each phenotype. We define methylation variations that are associated with underlying nucleotide variations (methylation quantitative trait loci) and show that underlying genetic variations are important drivers of methylation changes. We implemented Bayesian multitrait colocalization analysis (moloc) and summary data-based Mendelian randomization to systematically annotate genomic regions that show association with kidney function, methylation, and gene expression. We prioritized 40 loci, where methylation and gene-expression changes likely mediate the genotype effect on kidney disease development. Functional annotation suggested the role of inflammation, specifically, apoptotic cell clearance and complement activation in kidney disease development. Our study defines methylation changes associated with DKD phenotypes, the key role of underlying genetic variations driving methylation variations, and prioritizes methylome and gene-expression changes that likely mediate the genotype effect on kidney disease pathogenesis.
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42
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Groopman EE, Povysil G, Goldstein DB, Gharavi AG. Rare genetic causes of complex kidney and urological diseases. Nat Rev Nephrol 2020; 16:641-656. [PMID: 32807983 PMCID: PMC7772719 DOI: 10.1038/s41581-020-0325-2] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/03/2020] [Indexed: 02/08/2023]
Abstract
Although often considered a single-entity, chronic kidney disease (CKD) comprises many pathophysiologically distinct disorders that result in persistently abnormal kidney structure and/or function, and encompass both monogenic and polygenic aetiologies. Rare inherited forms of CKD frequently span diverse phenotypes, reflecting genetic phenomena including pleiotropy, incomplete penetrance and variable expressivity. Use of chromosomal microarray and massively parallel sequencing technologies has revealed that genomic disorders and monogenic aetiologies contribute meaningfully to seemingly complex forms of CKD across different clinically defined subgroups and are characterized by high genetic and phenotypic heterogeneity. Investigations of prevalent genomic disorders in CKD have integrated genetic, bioinformatic and functional studies to pinpoint the genetic drivers underlying their renal and extra-renal manifestations, revealing both monogenic and polygenic mechanisms. Similarly, massively parallel sequencing-based analyses have identified gene- and allele-level variation that contribute to the clinically diverse phenotypes observed for many monogenic forms of nephropathy. Genome-wide sequencing studies suggest that dual genetic diagnoses are found in at least 5% of patients in whom a genetic cause of disease is identified, highlighting the fact that complex phenotypes can also arise from multilocus variation. A multifaceted approach that incorporates genetic and phenotypic data from large, diverse cohorts will help to elucidate the complex relationships between genotype and phenotype for different forms of CKD, supporting personalized medicine for individuals with kidney disease.
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Affiliation(s)
- Emily E Groopman
- Division of Nephrology, Columbia University College of Physicians and Surgeons, New York, NY, USA
| | - Gundula Povysil
- Institute for Genomic Medicine, Columbia University, New York, NY, USA
| | - David B Goldstein
- Institute for Genomic Medicine, Columbia University, New York, NY, USA
| | - Ali G Gharavi
- Division of Nephrology, Columbia University College of Physicians and Surgeons, New York, NY, USA.
- Institute for Genomic Medicine, Columbia University, New York, NY, USA.
- Center for Precision Medicine and Genomics, Vagelos College of Physicians and Surgeons, Columbia University Irving Medical Center, New York, NY, USA.
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43
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Yu ZL, Wong CS, Lai YT, Chou WH, Faridah IN, Kao CC, Lin YF, Chang WC. Gender Differences in Genetic Associations of RAB38 with Urinary Protein-to-Creatinine Ratio (UPCR) Levels in Diabetic Nephropathy Patients. J Pers Med 2020; 10:jpm10040184. [PMID: 33096837 PMCID: PMC7711808 DOI: 10.3390/jpm10040184] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2020] [Revised: 10/14/2020] [Accepted: 10/16/2020] [Indexed: 11/16/2022] Open
Abstract
Renal dysfunction is common in patients with diabetes mellitus (DM). Previous findings from a meta-analysis of GWAS indicated that the variation of RAB38/CTSC is highly associated with the urinary albumin-to-creatinine ratio (UACR) in European populations. In addition, RAB38 knockout rats showed an increase in urinary albumins. Although the prevalence of chronic kidney disease is high in Taiwan, the role of genetic variants in diabetic renal function is still unclear. In the current study, 275 diabetic nephropathy (DN) patients were recruited to perform a genetic association study. Our results indicated that rs1027027, rs302647, and rs302646 in RAB38 were significantly associated with urinary protein-to-creatinine ratio (UPCR) levels in DN patients. Importantly, after analysis stratified by gender, a significant genetic influence on UPCR levels was observed in the male population. The findings confirmed the roles of gender and variants of RAB38 in the risk of UPCR in Diabetic Nephropathy patients.
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Affiliation(s)
- Zhi-Lei Yu
- Department of Clinical Pharmacy, School of Pharmacy, Taipei Medical University, Taipei 110301, Taiwan; (Z.-L.Y.); (Y.T.L.); (W.-H.C.); (I.N.F.)
| | - Chung-Shun Wong
- Graduate Institute of Clinical Medicine, College of Medicine, Taipei Medical University, Taipei 110301, Taiwan;
- Department of Emergency Medicine, Taipei Medical University-Shuang Ho Hospital, New Taipei City 235041, Taiwan
- Department of Emergency Medicine, School of Medicine, College of Medicine, Taipei Medical University, Taipei 11031, Taiwan
| | - Yi Ting Lai
- Department of Clinical Pharmacy, School of Pharmacy, Taipei Medical University, Taipei 110301, Taiwan; (Z.-L.Y.); (Y.T.L.); (W.-H.C.); (I.N.F.)
| | - Wan-Hsuan Chou
- Department of Clinical Pharmacy, School of Pharmacy, Taipei Medical University, Taipei 110301, Taiwan; (Z.-L.Y.); (Y.T.L.); (W.-H.C.); (I.N.F.)
| | - Imaniar Noor Faridah
- Department of Clinical Pharmacy, School of Pharmacy, Taipei Medical University, Taipei 110301, Taiwan; (Z.-L.Y.); (Y.T.L.); (W.-H.C.); (I.N.F.)
- Faculty of Pharmacy, Ahmad Dahlan University, Yogyakarta 55164, Indonesia
| | - Chih-Chin Kao
- Division of Nephrology, Department of Internal Medicine, Taipei Medical University Hospital, Taipei 110301, Taiwan;
- Division of Nephrology, Department of Internal Medicine, School of Medicine, College of Medicine, Taipei Medical University, Taipei 110301, Taiwan
| | - Yuh-Feng Lin
- Graduate Institute of Clinical Medicine, College of Medicine, Taipei Medical University, Taipei 110301, Taiwan;
- Division of Nephrology, Department of Internal Medicine, School of Medicine, College of Medicine, Taipei Medical University, Taipei 110301, Taiwan
- Division of Nephrology, Department of Internal Medicine, Shuang Ho Hospital, Taipei Medical University, New Taipei City 235041, Taiwan
- Correspondence: (Y.-F.L.); (W.-C.C.)
| | - Wei-Chiao Chang
- Department of Clinical Pharmacy, School of Pharmacy, Taipei Medical University, Taipei 110301, Taiwan; (Z.-L.Y.); (Y.T.L.); (W.-H.C.); (I.N.F.)
- Master Program for Clinical Pharmacogenomics and Pharmacoproteomics, School of Pharmacy, Taipei Medical University, Taipei 110301, Taiwan
- Integrative Research Center for Critical Care, Wan Fang Hospital, Taipei Medical University, Taipei 110301, Taiwan
- Department of Medical Research, Shuang Ho Hospital, Taipei Medical University, New Taipei City 235041, Taiwan
- Correspondence: (Y.-F.L.); (W.-C.C.)
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44
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Chen Z, Miao F, Braffett BH, Lachin JM, Zhang L, Wu X, Roshandel D, Carless M, Li XA, Tompkins JD, Kaddis JS, Riggs AD, Paterson AD, Natarajan R. DNA methylation mediates development of HbA1c-associated complications in type 1 diabetes. Nat Metab 2020; 2:744-762. [PMID: 32694834 PMCID: PMC7590966 DOI: 10.1038/s42255-020-0231-8] [Citation(s) in RCA: 50] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/30/2019] [Accepted: 05/29/2020] [Indexed: 01/09/2023]
Abstract
Metabolic memory, the persistent benefits of early glycaemic control on preventing and/or delaying the development of diabetic complications, has been observed in the Diabetes Control and Complications Trial (DCCT) and in the Epidemiology of Diabetes Interventions and Complications (EDIC) follow-up study, but the underlying mechanisms remain unclear. Here, we show the involvement of epigenetic DNA methylation (DNAme) in metabolic memory by examining its associations with preceding glycaemic history, and with subsequent development of complications over an 18-yr period in the blood DNA of 499 randomly selected DCCT participants with type 1 diabetes who are also followed up in EDIC. We demonstrate the associations between DNAme near the closeout of DCCT and mean HbA1c during DCCT (mean-DCCT HbA1c) at 186 cytosine-guanine dinucleotides (CpGs) (FDR < 15%, including 43 at FDR < 5%), many of which were located in genes related to complications. Exploration studies into biological function reveal that these CpGs are enriched in binding sites for the C/EBP transcription factor, as well as enhancer/transcription regions in blood cells and haematopoietic stem cells, and open chromatin states in myeloid cells. Mediation analyses show that, remarkably, several CpGs in combination explain 68-97% of the association of mean-DCCT HbA1c with the risk of complications during EDIC. In summary, DNAme at key CpGs appears to mediate the association between hyperglycaemia and complications in metabolic memory, through modifying enhancer activity at myeloid and other cells.
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Affiliation(s)
- Zhuo Chen
- Department of Diabetes Complications and Metabolism, Diabetes Metabolism Research Institute, Beckman Research Institute of City of Hope, Duarte, CA, USA
| | - Feng Miao
- Department of Diabetes Complications and Metabolism, Diabetes Metabolism Research Institute, Beckman Research Institute of City of Hope, Duarte, CA, USA
| | - Barbara H Braffett
- The Biostatistics Center, The George Washington University, Rockville, MD, USA
| | - John M Lachin
- The Biostatistics Center, The George Washington University, Rockville, MD, USA
| | - Lingxiao Zhang
- Department of Diabetes Complications and Metabolism, Diabetes Metabolism Research Institute, Beckman Research Institute of City of Hope, Duarte, CA, USA
| | - Xiwei Wu
- Integrative Genomics Core, Beckman Research Institute of City of Hope, Duarte, CA, USA
| | - Delnaz Roshandel
- Genetics and Genome Biology Program, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Melanie Carless
- Department of Biology, University of Texas at San Antonio, San Antonio, TX, USA
| | - Xuejun Arthur Li
- Biostatistics Core, Department of Computational and Quantitative Medicine, Beckman Research Institute of City of Hope, Duarte, CA, USA
| | - Joshua D Tompkins
- Department of Diabetes Complications and Metabolism, Diabetes Metabolism Research Institute, Beckman Research Institute of City of Hope, Duarte, CA, USA
| | - John S Kaddis
- Department of Diabetes Immunology, Diabetes and Metabolism Research Institute, Beckman Research Institute of City of Hope, Duarte, CA, USA
- Department of Diabetes and Cancer Discovery Science, Diabetes and Metabolism Research Institute, Beckman Research Institute of City of Hope, Duarte, CA, USA
| | - Arthur D Riggs
- Department of Diabetes Complications and Metabolism, Diabetes Metabolism Research Institute, Beckman Research Institute of City of Hope, Duarte, CA, USA
| | - Andrew D Paterson
- Genetics and Genome Biology Program, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Rama Natarajan
- Department of Diabetes Complications and Metabolism, Diabetes Metabolism Research Institute, Beckman Research Institute of City of Hope, Duarte, CA, USA.
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45
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Zhang Y, Li W, Zhou Y. Identification of hub genes in diabetic kidney disease via multiple-microarray analysis. ANNALS OF TRANSLATIONAL MEDICINE 2020; 8:997. [PMID: 32953797 PMCID: PMC7475500 DOI: 10.21037/atm-20-5171] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Background Diabetic kidney disease (DKD) is a leading cause of end-stage renal disease; however, the underlying molecular mechanisms remain unclear. Recently, bioinformatics analysis has provided a comprehensive insight toward the molecular mechanisms of DKD. Here, we re-analyzed three mRNA microarray datasets including a single-cell RNA sequencing (scRNA-seq) dataset, with the aim of identifying crucial genes correlated with DKD and contribute to a better understanding of DKD pathogenesis. Methods Three datasets including GSE131882, GSE30122, and GSE30529 were utilized to find differentially expressed genes (DEGs). The potential functions of DEGs were analyzed by the Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analysis. A protein-protein interaction (PPI) network was constructed, and hub genes were selected with the top three molecular complex detection (MCODE) score. A correlation analysis between hub genes and clinical indicators was also performed. Results In total, 84 upregulated DEGs and 49 downregulated DEGs were identified. Enriched pathways of the upregulated DEGs included extracellular matrix (ECM) receptor interaction, focal adhesion, human papillomavirus infection, malaria, and cell adhesion molecules. The downregulated DEGs were mainly enriched in ascorbate and aldarate metabolism, arginine and proline metabolism, endocrine- and other factor-regulated calcium reabsorption, mineral absorption and longevity regulating pathway, and multiple species signaling pathway. Seventeen hub genes were identified, and correlation analysis between unexplored hub genes and clinical features of DKD suggested that EGF, KNG1, GADD45B, and CDH2 might have reno-protective roles in DKD. Meanwhile, ATF3, B2M, VCAM1, CLDN4, SPP1, SOX9, JAG1, C3, and CD24 might promote the progression of DKD. Finally, most hub genes were found present in the immune cells of diabetic kidneys, which suggest the important role of inflammation infiltration in DKD pathogenesis. Conclusions In this study, we found seventeen hub genes using a scRNA-seq contained multiple-microarray analysis, which enriched the present understanding of molecular mechanisms underlying the pathogenesis of DKD in cells' level and provided candidate targets for diagnosis and treatment of DKD.
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Affiliation(s)
- Yumin Zhang
- Department of Endocrinology, Zhongda Hospital, Southeast University, Nanjing, China.,Institute of Diabetes, Medical School, Southeast University, Nanjing, China
| | - Wei Li
- Department of Endocrinology, Zhongda Hospital, Southeast University, Nanjing, China.,Institute of Diabetes, Medical School, Southeast University, Nanjing, China.,Suzhou Hospital Affiliated To Anhui Medical University, Suzhou, China
| | - Yunting Zhou
- Department of Endocrinology, Zhongda Hospital, Southeast University, Nanjing, China.,Institute of Diabetes, Medical School, Southeast University, Nanjing, China.,Department of Endocrinology, Nanjing First Hospital, Nanjing Medical University, Nanjing, China
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46
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Wang D, Yang J, Fan J, Chen W, Nikolic‐Paterson DJ, Li J. Omics technologies for kidney disease research. Anat Rec (Hoboken) 2020; 303:2729-2742. [PMID: 32592293 DOI: 10.1002/ar.24413] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2019] [Revised: 12/31/2019] [Accepted: 02/17/2020] [Indexed: 12/24/2022]
Affiliation(s)
- Dan Wang
- Department of NephrologyThe First Affiliated Hospital, Sun Yat‐sen University Guangzhou China
- Key Laboratory of Nephrology, National Health Commission and Guangdong Province Guangzhou China
| | - Jiayi Yang
- Department of NephrologyThe First Affiliated Hospital, Sun Yat‐sen University Guangzhou China
- Key Laboratory of Nephrology, National Health Commission and Guangdong Province Guangzhou China
| | - Jinjin Fan
- Department of NephrologyThe First Affiliated Hospital, Sun Yat‐sen University Guangzhou China
- Key Laboratory of Nephrology, National Health Commission and Guangdong Province Guangzhou China
| | - Wei Chen
- Department of NephrologyThe First Affiliated Hospital, Sun Yat‐sen University Guangzhou China
- Key Laboratory of Nephrology, National Health Commission and Guangdong Province Guangzhou China
| | | | - Jinhua Li
- Department of NephrologyThe First Affiliated Hospital, Sun Yat‐sen University Guangzhou China
- Key Laboratory of Nephrology, National Health Commission and Guangdong Province Guangzhou China
- Shunde Women and Children Hospital, Guangdong Medical University Shunde Guangdong China
- The Second Clinical College, Guangdong Medical University Dongguan Guangdong China
- Department of Anatomy and Developmental BiologyMonash Biomedicine Discovery Institute, Monash University Clayton Victoria Australia
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47
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Cole JB, Florez JC. Genetics of diabetes mellitus and diabetes complications. Nat Rev Nephrol 2020; 16:377-390. [PMID: 32398868 DOI: 10.1038/s41581-020-0278-5] [Citation(s) in RCA: 628] [Impact Index Per Article: 157.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/29/2020] [Indexed: 12/12/2022]
Abstract
Diabetes is one of the fastest growing diseases worldwide, projected to affect 693 million adults by 2045. Devastating macrovascular complications (cardiovascular disease) and microvascular complications (such as diabetic kidney disease, diabetic retinopathy and neuropathy) lead to increased mortality, blindness, kidney failure and an overall decreased quality of life in individuals with diabetes. Clinical risk factors and glycaemic control alone cannot predict the development of vascular complications; numerous genetic studies have demonstrated a clear genetic component to both diabetes and its complications. Early research aimed at identifying genetic determinants of diabetes complications relied on familial linkage analysis suited to strong-effect loci, candidate gene studies prone to false positives, and underpowered genome-wide association studies limited by sample size. The explosion of new genomic datasets, both in terms of biobanks and aggregation of worldwide cohorts, has more than doubled the number of genetic discoveries for both diabetes and diabetes complications. We focus herein on genetic discoveries for diabetes and diabetes complications, empowered primarily through genome-wide association studies, and emphasize the gaps in research for taking genomic discovery to the next level.
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Affiliation(s)
- Joanne B Cole
- Programs in Metabolism and Medical & Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA.,Diabetes Unit and Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA.,Division of Endocrinology and Center for Basic and Translational Obesity Research, Boston Children's Hospital, Boston, MA, USA
| | - Jose C Florez
- Programs in Metabolism and Medical & Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA. .,Diabetes Unit and Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA. .,Department of Medicine, Harvard Medical School, Boston, MA, USA.
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48
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Matar O, Potier L, Abouleka Y, Hallot-Feron M, Fumeron F, Mohammedi K, Hadjadj S, Roussel R, Velho G, Marre M. Relationship between renal capacity to reabsorb glucose and renal status in patients with diabetes. DIABETES & METABOLISM 2020; 46:488-495. [PMID: 32259661 DOI: 10.1016/j.diabet.2020.03.002] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/09/2019] [Revised: 03/04/2020] [Accepted: 03/19/2020] [Indexed: 10/24/2022]
Abstract
AIMS Interindividual variability in capacity to reabsorb glucose at the proximal renal tubule could contribute to risk of diabetic kidney disease. Our present study investigated, in patients with diabetes, the association between fractional reabsorption of glucose (FRGLU) and degree of renal disease as assessed by urinary albumin excretion (UAE) and estimated glomerular filtration rate (eGFR). METHODS FRGLU [1-(glucose clearance/creatinine clearance)] was assessed in 637 diabetes patients attending our tertiary referral centre, looking for correlations between FRGLU and UAE (normo-, micro-, macro-albuminuria) and Kidney Disease: Improving Global Outcomes (KDIGO) eGFR categories: >90 (G1); 90-60 (G2); 59-30 (G3); and<30-16 (G4) mL/min/1.73 m2. Patients were stratified by admission fasting plasma glucose (FPG) into three groups: low (<6mmol/L); intermediate (6-11mmol/L); and high (>11mmol/L). RESULTS Median (interquartile range, IQR) FRGLU levels were blood glucose-dependent: 99.90% (0.05) for low (n=106); 99.90% (0.41) for intermediate (n=288); and 96.36% (12.57) for high (n=243) blood glucose categories (P<0.0001). Also, FRGLU increased with renal disease severity in patients in the high FPG group: normoalbuminuria, 93.50% (17.74) (n=135); microalbuminuria, 96.56% (5.94) (n=77); macroalbuminuria, 99.12% (5.44) (n=31; P<0.001); eGFR G1, 94.13% (16.24) (n=111); G2, 96.35% (11.94) (n=72); G3 98.88% (7.59) (n=46); and G4, 99.11% (2.20) (n=14; P<0.01). On multiple regression analyses, FRGLU remained significantly and independently associated with UAE and eGFR in patients in the high blood glucose group. CONCLUSION High glucose reabsorption capacity in renal proximal tubules is associated with high UAE and low eGFR in patients with diabetes and blood glucose levels>11mmol/L.
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Affiliation(s)
- O Matar
- Service de diabétologie, endocrinologie et nutrition, hôpital Bichat, Assistance publique-hôpitaux de Paris, Paris, France; UFR de médecine, université de Paris, Paris, France; Inserm, Centre de recherches des Cordeliers, Sorbonne université, université de Paris, Paris, France
| | - L Potier
- Service de diabétologie, endocrinologie et nutrition, hôpital Bichat, Assistance publique-hôpitaux de Paris, Paris, France; UFR de médecine, université de Paris, Paris, France; Inserm, Centre de recherches des Cordeliers, Sorbonne université, université de Paris, Paris, France
| | - Y Abouleka
- Service de diabétologie, endocrinologie et nutrition, hôpital Bichat, Assistance publique-hôpitaux de Paris, Paris, France; UFR de médecine, université de Paris, Paris, France; Inserm, Centre de recherches des Cordeliers, Sorbonne université, université de Paris, Paris, France
| | - M Hallot-Feron
- Service de diabétologie, endocrinologie et nutrition, hôpital Bichat, Assistance publique-hôpitaux de Paris, Paris, France; UFR de médecine, université de Paris, Paris, France
| | - F Fumeron
- UFR de médecine, université de Paris, Paris, France; Inserm, Centre de recherches des Cordeliers, Sorbonne université, université de Paris, Paris, France
| | - K Mohammedi
- Faculté de médecine Paul-Broca, université de Bordeaux, Bordeaux, France
| | - S Hadjadj
- Inserm, CNRS, Institut du thorax, université de Nantes, Nantes, France
| | - R Roussel
- Service de diabétologie, endocrinologie et nutrition, hôpital Bichat, Assistance publique-hôpitaux de Paris, Paris, France; UFR de médecine, université de Paris, Paris, France; Inserm, Centre de recherches des Cordeliers, Sorbonne université, université de Paris, Paris, France
| | - G Velho
- Inserm, Centre de recherches des Cordeliers, Sorbonne université, université de Paris, Paris, France
| | - M Marre
- Service de diabétologie, endocrinologie et nutrition, hôpital Bichat, Assistance publique-hôpitaux de Paris, Paris, France; UFR de médecine, université de Paris, Paris, France; Inserm, Centre de recherches des Cordeliers, Sorbonne université, université de Paris, Paris, France; CMC Ambroise-Paré, Neuilly-sur-Seine, France.
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49
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Kato M, Natarajan R. Epigenetics and epigenomics in diabetic kidney disease and metabolic memory. Nat Rev Nephrol 2020; 15:327-345. [PMID: 30894700 DOI: 10.1038/s41581-019-0135-6] [Citation(s) in RCA: 300] [Impact Index Per Article: 75.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
The development and progression of diabetic kidney disease (DKD), a highly prevalent complication of diabetes mellitus, are influenced by both genetic and environmental factors. DKD is an important contributor to the morbidity of patients with diabetes mellitus, indicating a clear need for an improved understanding of disease aetiology to inform the development of more efficacious treatments. DKD is characterized by an accumulation of extracellular matrix, hypertrophy and fibrosis in kidney glomerular and tubular cells. Increasing evidence shows that genes associated with these features of DKD are regulated not only by classical signalling pathways but also by epigenetic mechanisms involving chromatin histone modifications, DNA methylation and non-coding RNAs. These mechanisms can respond to changes in the environment and, importantly, might mediate the persistent long-term expression of DKD-related genes and phenotypes induced by prior glycaemic exposure despite subsequent glycaemic control, a phenomenon called metabolic memory. Detection of epigenetic events during the early stages of DKD could be valuable for timely diagnosis and prompt treatment to prevent progression to end-stage renal disease. Identification of epigenetic signatures of DKD via epigenome-wide association studies might also inform precision medicine approaches. Here, we highlight the emerging role of epigenetics and epigenomics in DKD and the translational potential of candidate epigenetic factors and non-coding RNAs as biomarkers and drug targets for DKD.
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Affiliation(s)
- Mitsuo Kato
- Department of Diabetes Complications and Metabolism, Diabetes Metabolism Research Institute, Beckman Research Institute of City of Hope, Duarte, CA, USA.
| | - Rama Natarajan
- Department of Diabetes Complications and Metabolism, Diabetes Metabolism Research Institute, Beckman Research Institute of City of Hope, Duarte, CA, USA.
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50
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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] [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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