1
|
Tan W, Chen J, Wang Y, Xiang K, Lu X, Han Q, Hou M, Yang J. Single-cell RNA sequencing in diabetic kidney disease: a literature review. Ren Fail 2024; 46:2387428. [PMID: 39099183 DOI: 10.1080/0886022x.2024.2387428] [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: 11/13/2023] [Revised: 07/06/2024] [Accepted: 07/29/2024] [Indexed: 08/06/2024] Open
Abstract
Diabetic kidney disease (DKD) is the leading cause of end-stage renal disease (ESRD), and its pathogenesis has not been clarified. Current research suggests that DKD involves multiple cell types and extra-renal factors, and it is particularly important to clarify the pathogenesis and identify new therapeutic targets. Single-cell RNA sequencing (scRNA-seq) technology is high-throughput sequencing of the transcriptomes of individual cells at the single-cell level, which is an effective technology for exploring the development of diseases by comparing genetic information, reflecting the differences in genetic information between cells, and identifying different cell subpopulations. Accumulating evidence supports the role of scRNA-seq in revealing the pathogenesis of diabetes and strengthening our understanding of the molecular mechanisms of DKD. We reviewed the scRNA-seq data this time. Then, we analyzed and discussed the applications of scRNA-seq technology in DKD research, including annotation of cell types, identification of novel cell types (or subtypes), identification of intercellular communication, analysis of cell differentiation trajectories, gene expression detection, and analysis of gene regulatory networks, and lastly, we explored the future perspectives of scRNA-seq technology in DKD research.
Collapse
Affiliation(s)
- Wei Tan
- Department of Nephrology, The Third Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Jiaoyan Chen
- Department of Nephrology, The Third Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Yunyan Wang
- Department of Nephrology, The Third Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Kui Xiang
- Department of Nephrology, The Third Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Xianqiong Lu
- Department of Nephrology, The Third Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Qiuyu Han
- Department of Nephrology, The Third Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Mingyue Hou
- Department of Nephrology, The Third Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Jurong Yang
- Department of Nephrology, The Third Affiliated Hospital of Chongqing Medical University, Chongqing, China
| |
Collapse
|
2
|
Xu X, Khunsriraksakul C, Eales JM, Rubin S, Scannali D, Saluja S, Talavera D, Markus H, Wang L, Drzal M, Maan A, Lay AC, Prestes PR, Regan J, Diwadkar AR, Denniff M, Rempega G, Ryszawy J, Król R, Dormer JP, Szulinska M, Walczak M, Antczak A, Matías-García PR, Waldenberger M, Woolf AS, Keavney B, Zukowska-Szczechowska E, Wystrychowski W, Zywiec J, Bogdanski P, Danser AHJ, Samani NJ, Guzik TJ, Morris AP, Liu DJ, Charchar FJ, Tomaszewski M. Genetic imputation of kidney transcriptome, proteome and multi-omics illuminates new blood pressure and hypertension targets. Nat Commun 2024; 15:2359. [PMID: 38504097 PMCID: PMC10950894 DOI: 10.1038/s41467-024-46132-y] [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: 07/26/2023] [Accepted: 02/14/2024] [Indexed: 03/21/2024] Open
Abstract
Genetic mechanisms of blood pressure (BP) regulation remain poorly defined. Using kidney-specific epigenomic annotations and 3D genome information we generated and validated gene expression prediction models for the purpose of transcriptome-wide association studies in 700 human kidneys. We identified 889 kidney genes associated with BP of which 399 were prioritised as contributors to BP regulation. Imputation of kidney proteome and microRNAome uncovered 97 renal proteins and 11 miRNAs associated with BP. Integration with plasma proteomics and metabolomics illuminated circulating levels of myo-inositol, 4-guanidinobutanoate and angiotensinogen as downstream effectors of several kidney BP genes (SLC5A11, AGMAT, AGT, respectively). We showed that genetically determined reduction in renal expression may mimic the effects of rare loss-of-function variants on kidney mRNA/protein and lead to an increase in BP (e.g., ENPEP). We demonstrated a strong correlation (r = 0.81) in expression of protein-coding genes between cells harvested from urine and the kidney highlighting a diagnostic potential of urinary cell transcriptomics. We uncovered adenylyl cyclase activators as a repurposing opportunity for hypertension and illustrated examples of BP-elevating effects of anticancer drugs (e.g. tubulin polymerisation inhibitors). Collectively, our studies provide new biological insights into genetic regulation of BP with potential to drive clinical translation in hypertension.
Collapse
Affiliation(s)
- Xiaoguang Xu
- Division of Cardiovascular Sciences, Faculty of Medicine, Biology and Health, University of Manchester, Manchester, UK
| | | | - James M Eales
- Division of Cardiovascular Sciences, Faculty of Medicine, Biology and Health, University of Manchester, Manchester, UK
| | - Sebastien Rubin
- Division of Cardiovascular Sciences, Faculty of Medicine, Biology and Health, University of Manchester, Manchester, UK
| | - David Scannali
- Division of Cardiovascular Sciences, Faculty of Medicine, Biology and Health, University of Manchester, Manchester, UK
| | - Sushant Saluja
- Division of Cardiovascular Sciences, Faculty of Medicine, Biology and Health, University of Manchester, Manchester, UK
| | - David Talavera
- Division of Cardiovascular Sciences, Faculty of Medicine, Biology and Health, University of Manchester, Manchester, UK
| | - Havell Markus
- Department of Public Health Sciences, Penn State College of Medicine, Hershey, PA, USA
| | - Lida Wang
- Department of Public Health Sciences, Penn State College of Medicine, Hershey, PA, USA
| | - Maciej Drzal
- Division of Cardiovascular Sciences, Faculty of Medicine, Biology and Health, University of Manchester, Manchester, UK
| | - Akhlaq Maan
- Division of Cardiovascular Sciences, Faculty of Medicine, Biology and Health, University of Manchester, Manchester, UK
| | - Abigail C Lay
- Division of Cardiovascular Sciences, Faculty of Medicine, Biology and Health, University of Manchester, Manchester, UK
| | - Priscilla R Prestes
- Health Innovation and Transformation Centre, Federation University Australia, Ballarat, Australia
| | - Jeniece Regan
- Department of Public Health Sciences, Penn State College of Medicine, Hershey, PA, USA
| | - Avantika R Diwadkar
- Department of Public Health Sciences, Penn State College of Medicine, Hershey, PA, USA
| | - Matthew Denniff
- Department of Cardiovascular Sciences, University of Leicester, Leicester, UK
| | - Grzegorz Rempega
- Department of Urology, Medical University of Silesia, Katowice, Poland
| | - Jakub Ryszawy
- Department of Urology, Medical University of Silesia, Katowice, Poland
| | - Robert Król
- Department of General, Vascular and Transplant Surgery, Faculty of Medical Sciences in Katowice, Medical University of Silesia, Katowice, Poland
| | - John P Dormer
- Department of Cellular Pathology, University Hospitals of Leicester, Leicester, UK
| | - Monika Szulinska
- Department of Obesity, Metabolic Disorders Treatment and Clinical Dietetics, Karol Marcinkowski University of Medical Sciences, Poznan, Poland
| | - Marta Walczak
- Department of Internal Diseases, Metabolic Disorders and Arterial Hypertension, Poznan University of Medical Sciences, Poznan, Poland
| | - Andrzej Antczak
- Department of Urology and Uro-oncology, Karol Marcinkowski University of Medical Sciences, Poznan, Poland
| | - Pamela R Matías-García
- Institute of Epidemiology, Helmholtz Center Munich, Neuherberg, Germany
- Research Unit Molecular Epidemiology, Helmholtz Center Munich, Neuherberg, Germany
- German Research Center for Cardiovascular Disease (DZHK), partner site Munich Heart Alliance, Munich, Germany
| | - Melanie Waldenberger
- Institute of Epidemiology, Helmholtz Center Munich, Neuherberg, Germany
- Research Unit Molecular Epidemiology, Helmholtz Center Munich, Neuherberg, Germany
- German Research Center for Cardiovascular Disease (DZHK), partner site Munich Heart Alliance, Munich, Germany
| | - Adrian S Woolf
- Division of Cell Matrix Biology and Regenerative Medicine, Faculty of Biology, Medicine and Health, University of Manchester, Manchester, UK
- Royal Manchester Children's Hospital and Manchester Academic Health Science Centre, Manchester University NHS Foundation Trust, Manchester, UK
| | - Bernard Keavney
- Division of Cardiovascular Sciences, Faculty of Medicine, Biology and Health, University of Manchester, Manchester, UK
- Manchester Academic Health Science Centre, Manchester University NHS Foundation Trust Manchester, Manchester Royal Infirmary, Manchester, UK
| | | | - Wojciech Wystrychowski
- Department of General, Vascular and Transplant Surgery, Faculty of Medical Sciences in Katowice, Medical University of Silesia, Katowice, Poland
| | - Joanna Zywiec
- Department of Internal Medicine, Diabetology and Nephrology, Zabrze, Medical University of Silesia, Katowice, Poland
| | - Pawel Bogdanski
- Department of Obesity, Metabolic Disorders Treatment and Clinical Dietetics, Karol Marcinkowski University of Medical Sciences, Poznan, Poland
| | - A H Jan Danser
- Department of Internal Medicine, Division of Pharmacology and Vascular Medicine, Erasmus Medical Centre, Rotterdam, The Netherlands
| | - Nilesh J Samani
- Department of Cardiovascular Sciences, University of Leicester, Leicester, UK
- NIHR Leicester Biomedical Research Centre, Glenfield Hospital, Leicester, UK
| | - Tomasz J Guzik
- Department of Internal Medicine, Jagiellonian University Medical College, Kraków, Poland
- Centre for Cardiovascular Sciences, Queen's Medical Research Institute, University of Edinburgh, Edinburgh, UK
- Center for Medical Genomics OMICRON, Jagiellonian University Medical College, Kraków, Poland
| | - Andrew P Morris
- Centre for Genetics and Genomics Versus Arthritis, Centre for Musculoskeletal Research, Division of Musculoskeletal & Dermatological Sciences, Faculty of Medicine, Biology and Health, University of Manchester, Manchester, UK
| | - Dajiang J Liu
- Department of Public Health Sciences, Penn State College of Medicine, Hershey, PA, USA
| | - Fadi J Charchar
- Health Innovation and Transformation Centre, Federation University Australia, Ballarat, Australia
- Department of Cardiovascular Sciences, University of Leicester, Leicester, UK
- Department of Physiology, University of Melbourne, Melbourne, Australia
| | - Maciej Tomaszewski
- Division of Cardiovascular Sciences, Faculty of Medicine, Biology and Health, University of Manchester, Manchester, UK.
- Manchester Academic Health Science Centre, Manchester University NHS Foundation Trust Manchester, Manchester Royal Infirmary, Manchester, UK.
| |
Collapse
|
3
|
Jia PP, Li Y, Zhang LC, Wu MF, Li TY, Pei DS. Metabolome evidence of CKDu risks after chronic exposure to simulated Sri Lanka drinking water in zebrafish. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2024; 273:116149. [PMID: 38412632 DOI: 10.1016/j.ecoenv.2024.116149] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/28/2023] [Revised: 02/10/2024] [Accepted: 02/22/2024] [Indexed: 02/29/2024]
Abstract
It is still a serious public health issue that chronic kidney disease of uncertain etiology (CKDu) in Sri Lanka poses challenges in identification, prevention, and treatment. What environmental factors in drinking water cause kidney damage remains unclear. This study aimed to investigate the risks of various environmental factors that may induce CKDu, including water hardness, fluoride (HF), heavy metals (HM), microcystin-LR (MC-LR), and their combined exposure (HFMM). The research focused on comprehensive metabolome analysis, and correlation with transcriptomic and gut microbiota changes. Results revealed that chronic exposure led to kidney damage and pancreatic toxicity in adult zebrafish. Metabolomics profiling showed significant alterations in biochemical processes, with enriched metabolic pathways of oxidative phosphorylation, folate biosynthesis, arachidonic acid metabolism, FoxO signaling pathway, lysosome, pyruvate metabolism, and purine metabolism. The network analysis revealed significant changes in metabolites associated with renal function and diseases, including 20-Hydroxy-LTE4, PS(18:0/22:2(13Z,16Z)), Neuromedin N, 20-Oxo-Leukotriene E4, and phenol sulfate, which are involved in the fatty acyls and glycerophospholipids class. These metabolites were closely associated with the disrupted gut bacteria of g_ZOR0006, g_Pseudomonas, g_Tsukamurella, g_Cetobacterium, g_Flavobacterium, which belonged to dominant phyla of Firmicutes and Proteobacteria, etc., and differentially expressed genes (DEGs) such as egln3, ca2, jun, slc2a1b, and gls2b in zebrafish. Exploratory omics analyses revealed the shared significantly changed pathways in transcriptome and metabolome like calcium signaling and necroptosis, suggesting potential biomarkers for assessing kidney disease.
Collapse
Affiliation(s)
- Pan-Pan Jia
- School of Public Health, Chongqing Medical University, Chongqing 400016, China
| | - Yan Li
- School of Public Health, Chongqing Medical University, Chongqing 400016, China
| | - Lan-Chen Zhang
- School of Public Health, Chongqing Medical University, Chongqing 400016, China
| | - Ming-Fei Wu
- School of Public Health, Chongqing Medical University, Chongqing 400016, China
| | - Tian-Yun Li
- Chongqing Institute of Green and Intelligent Technology, Chinese Academy of Sciences, Chongqing 400714, China
| | - De-Sheng Pei
- School of Public Health, Chongqing Medical University, Chongqing 400016, China.
| |
Collapse
|
4
|
Hughes O, Bentley AR, Breeze CE, Aguet F, Xu X, Nadkarni G, Sun Q, Lin BM, Gilliland T, Meyer MC, Du J, Raffield LM, Kramer H, Morton RW, Gouveia MH, Atkinson EG, Valladares-Salgado A, Wacher-Rodarte N, Dueker ND, Guo X, Hai Y, Adeyemo A, Best LG, Cai J, Chen G, Chong M, Doumatey A, Eales J, Goodarzi MO, Ipp E, Irvin MR, Jiang M, Jones AC, Kooperberg C, Krieger JE, Lange EM, Lanktree MB, Lash JP, Lotufo PA, Loos RJF, Ha My VT, Peralta-Romero J, Qi L, Raffel LJ, Rich SS, Rodriquez EJ, Tarazona-Santos E, Taylor KD, Umans JG, Wen J, Young BA, Yu Z, Zhang Y, Ida Chen YD, Rundek T, Rotter JI, Cruz M, Fornage M, Lima-Costa MF, Pereira AC, Paré G, Natarajan P, Cole SA, Carson AP, Lange LA, Li Y, Perez-Stable EJ, Do R, Charchar FJ, Tomaszewski M, Mychaleckyj JC, Rotimi C, Morris AP, Franceschini N. Genome-wide study investigating effector genes and polygenic prediction for kidney function in persons with ancestry from Africa and the Americas. CELL GENOMICS 2024; 4:100468. [PMID: 38190104 PMCID: PMC10794846 DOI: 10.1016/j.xgen.2023.100468] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/06/2023] [Revised: 08/31/2023] [Accepted: 11/28/2023] [Indexed: 01/09/2024]
Abstract
Chronic kidney disease is a leading cause of death and disability globally and impacts individuals of African ancestry (AFR) or with ancestry in the Americas (AMS) who are under-represented in genome-wide association studies (GWASs) of kidney function. To address this bias, we conducted a large meta-analysis of GWASs of estimated glomerular filtration rate (eGFR) in 145,732 AFR and AMS individuals. We identified 41 loci at genome-wide significance (p < 5 × 10-8), of which two have not been previously reported in any ancestry group. We integrated fine-mapped loci with epigenomic and transcriptomic resources to highlight potential effector genes relevant to kidney physiology and disease, and reveal key regulatory elements and pathways involved in renal function and development. We demonstrate the varying but increased predictive power offered by a multi-ancestry polygenic score for eGFR and highlight the importance of population diversity in GWASs and multi-omics resources to enhance opportunities for clinical translation for all.
Collapse
Affiliation(s)
- Odessica Hughes
- Centre for Genetics and Genomics Versus Arthritis, Centre for Musculoskeletal Research, The University of Manchester, Manchester, UK
| | - Amy R Bentley
- Center for Research on Genomics and Global Health, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
| | - Charles E Breeze
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Department Health and Human Services, Bethesda, MD, USA; UCL Cancer Institute, University College London, London, UK
| | - Francois Aguet
- The Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Xiaoguang Xu
- Division of Cardiovascular Sciences, Faculty of Biology, Medicine, and Health, The University of Manchester, Manchester, UK
| | - Girish Nadkarni
- The Charles Bronfman Institute of Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Quan Sun
- Department of Biostatistics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Bridget M Lin
- Department of Biostatistics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Thomas Gilliland
- Cardiovascular Research Center and Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA; Program in Medical and Population Genetics and the Cardiovascular Disease Initiative, Broad Institute, Cambridge, MA, USA; Department of Medicine, Harvard Medical School, Boston, MA, USA
| | - Mariah C Meyer
- Department of Biomedical Informatics, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - Jiawen Du
- Department of Biostatistics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Laura M Raffield
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Holly Kramer
- Division of Nephrology and Hypertension, Loyola University Chicago, Maywood, IL, USA
| | - Robert W Morton
- Population Health Research Institute, Hamilton, ON, Canada; Department of Pathology and Molecular Medicine, McMaster University, Hamilton, ON, Canada
| | - Mateus H Gouveia
- Center for Research on Genomics and Global Health, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
| | - Elizabeth G Atkinson
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Adan Valladares-Salgado
- Unidad de Investigación Médica en Bioquímica, Hospital de Especialidades, Centro Médico Nacional Siglo XXI, Instituto Mexicano del Seguro Social, Mexico City, Mexico
| | - Niels Wacher-Rodarte
- Unidad de Investigación Médica en Epidemiologia Clinica, Hospital de Especialidades, Centro Médico Nacional Siglo XXI, Instituto Mexicano del Seguro Social, Mexico City, Mexico
| | - Nicole D Dueker
- John P Hussman Institute for Human Genomics, University of Miami Miller School of Medicine, Miami, FL, USA
| | - Xiuqing Guo
- The Institute for Translational Genomics and Population Sciences, Department of Pediatrics, The Lundquist Institute for Biomedical Innovation at Harbor-UCLA Medical Center, Torrance, CA USA
| | - Yang Hai
- The Institute for Translational Genomics and Population Sciences, Department of Pediatrics, The Lundquist Institute for Biomedical Innovation at Harbor-UCLA Medical Center, Torrance, CA USA
| | - Adebowale Adeyemo
- Center for Research on Genomics and Global Health, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
| | - Lyle G Best
- Missouri Breaks Industries Research Inc., Eagle Butte, SD, USA
| | - Jianwen Cai
- Department of Biostatistics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Guanjie Chen
- Center for Research on Genomics and Global Health, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
| | - Michael Chong
- Population Health Research Institute, Hamilton, ON, Canada; Department of Pathology and Molecular Medicine, McMaster University, Hamilton, ON, Canada
| | - Ayo Doumatey
- Center for Research on Genomics and Global Health, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
| | - James Eales
- Division of Cardiovascular Sciences, Faculty of Biology, Medicine, and Health, The University of Manchester, Manchester, UK
| | - Mark O Goodarzi
- Division of Endocrinology, Diabetes, and Metabolism, Department of Medicine, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Eli Ipp
- Division of Endocrinology and Metabolism, Department of Medicine, The Lundquist Institute for Biomedical Innovation at Harbor-UCLA Medical Center, Torrance, CA, USA
| | - Marguerite Ryan Irvin
- Department of Epidemiology, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Minzhi Jiang
- Department of Applied Physical Sciences, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Alana C Jones
- Department of Epidemiology, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Charles Kooperberg
- Division of Public Health Sciences, Fred Hutchinson Cancer Center, Seattle, WA, USA
| | - Jose E Krieger
- Laboratório de Genética e Cardiologia Molecular do Instituto do Coração do Hospital das Clínicas da Faculdade de Medicina da Universidade de São Paulo, São Paulo, Brazil
| | - Ethan M Lange
- Department of Biomedical Informatics, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - Matthew B Lanktree
- Division of Nephrology, Department of Medicine, McMaster University, Hamilton, ON, Canada
| | - James P Lash
- Division of Nephrology, Department of Medicine, University of Illinois, Chicago, IL, USA
| | - Paulo A Lotufo
- Center for Clinical and Epidemiological Research, Hospital Universitário, Universidade de São Paulo (USP), São Paulo, Brazil
| | - Ruth J F Loos
- The Charles Bronfman Institute of Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA; Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Vy Thi Ha My
- The Charles Bronfman Institute of Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Jesús Peralta-Romero
- Unidad de Investigación Médica en Bioquímica, Hospital de Especialidades, Centro Médico Nacional Siglo XXI, Instituto Mexicano del Seguro Social, Mexico City, Mexico
| | - Lihong Qi
- Department of Public Health Sciences, School of Medicine, University of California Davis, Davis, CA, USA
| | - Leslie J Raffel
- Department of Pediatrics, Genetic and Genomic Medicine, University of California, Irvine, Irvine, CA, USA
| | - Stephen S Rich
- Center for Public Health Genomics, University of Virginia, Charlottesville, VA, USA
| | - Erik J Rodriquez
- Division of Intramural Research, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD, USA
| | - Eduardo Tarazona-Santos
- Departamento de Genética, Ecologia e Evolução, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | - 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, CA USA
| | - Jason G Umans
- MedStar Health Research Institute, Hyattsville MD and Georgetown-Howard Universities Center for Clinical and Translational Science, Washington, DC, USA
| | - Jia Wen
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Bessie A Young
- University of Washington School of Medicine, Seattle, WA, USA; Office of Healthcare Equity, UW Justice, Equity, Diversity, and Inclusion Center for Transformational Research (UW JEDI-CTR), University of Washington, Seattle, WA, USA; Division of Nephrology, Department of Medicine, University of Washington, Seattle, WA, USA; Kidney Research Institute, Department of Medicine, University of Washington, Seattle, WA, USA
| | - Zhi Yu
- Cardiovascular Research Center and Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA; Program in Medical and Population Genetics and the Cardiovascular Disease Initiative, Broad Institute, Cambridge, MA, USA
| | - Ying Zhang
- Center for American Indian Health Research, Department of Biostatistics and Epidemiology, Hudson College of Public Health, The University of Oklahoma Health Sciences Center, Oklahoma, OK, USA
| | - Yii-Der Ida Chen
- The Institute for Translational Genomics and Population Sciences, Department of Pediatrics, The Lundquist Institute for Biomedical Innovation at Harbor-UCLA Medical Center, Torrance, CA USA
| | - Tanja Rundek
- Department of Neurology, Epidemiology and Public Health, Miller School of Medicine, University of Miami, Miami, FL, USA
| | - 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, CA USA
| | - Miguel Cruz
- Unidad de Investigación Médica en Bioquímica, Hospital de Especialidades, Centro Médico Nacional Siglo XXI, Instituto Mexicano del Seguro Social, Mexico City, Mexico
| | - Myriam Fornage
- Brown Foundation Institute of Molecular Medicine, Houston, TX, USA
| | | | - Alexandre C Pereira
- Laboratório de Genética e Cardiologia Molecular do Instituto do Coração do Hospital das Clínicas da Faculdade de Medicina da Universidade de São Paulo, São Paulo, Brazil; Aging Division, Brigham Women's Hospital, Department of Medicine, Harvard Medical School, Boston, MA, USA
| | - Guillaume Paré
- Population Health Research Institute, Hamilton, ON, Canada; Department of Pathology and Molecular Medicine, McMaster University, Hamilton, ON, Canada
| | - Pradeep Natarajan
- Cardiovascular Research Center and Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA; Program in Medical and Population Genetics and the Cardiovascular Disease Initiative, Broad Institute, Cambridge, MA, USA; Department of Medicine, Harvard Medical School, Boston, MA, USA
| | - Shelley A Cole
- Texas Biomedical Research Institute, San Antonio, TX, USA
| | - April P Carson
- Department of Medicine, University of Mississippi Medical Center, Jackson, MS, USA
| | - Leslie A Lange
- Department of Biomedical Informatics, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - Yun Li
- Department of Biostatistics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Eliseo J Perez-Stable
- National Institute on Minority Health and Health Disparities, National Institutes of Health, Bethesda, MD, USA
| | - Ron Do
- The Charles Bronfman Institute of Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Fadi J Charchar
- School of Science, Psychology and Sport, Federation University, Ballarat, VIC, Australia; Department of Cardiovascular Sciences, University of Leicester, Leicester, UK; Department of Physiology, University of Melbourne, Melbourne, VIC, Australia
| | - Maciej Tomaszewski
- Division of Cardiovascular Sciences, Faculty of Biology, Medicine, and Health, The University of Manchester, Manchester, UK; Manchester Royal Infirmary, Manchester University NHS Foundation Trust, Manchester Academic Health Science Centre, Manchester, UK
| | - Josyf C Mychaleckyj
- Department of Public Health Sciences, School of Medicine, University of California Davis, Davis, CA, USA
| | - Charles Rotimi
- Center for Research on Genomics and Global Health, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
| | - Andrew P Morris
- Centre for Genetics and Genomics Versus Arthritis, Centre for Musculoskeletal Research, The University of Manchester, Manchester, UK.
| | - Nora Franceschini
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.
| |
Collapse
|
5
|
Naas S, Schiffer M, Schödel J. Hypoxia and renal fibrosis. Am J Physiol Cell Physiol 2023; 325:C999-C1016. [PMID: 37661918 DOI: 10.1152/ajpcell.00201.2023] [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: 05/23/2023] [Revised: 08/25/2023] [Accepted: 08/25/2023] [Indexed: 09/05/2023]
Abstract
Renal fibrosis is the final stage of most progressive kidney diseases. Chronic kidney disease (CKD) is associated with high comorbidity and mortality. Thus, preventing fibrosis and thereby preserving kidney function increases the quality of life and prolongs the survival of patients with CKD. Many processes such as inflammation or metabolic stress modulate the progression of kidney fibrosis. Hypoxia has also been implicated in the pathogenesis of renal fibrosis, and oxygen sensing in the kidney is of outstanding importance for the body. The dysregulation of oxygen sensing in the diseased kidney is best exemplified by the loss of stimulation of erythropoietin production from interstitial cells in the fibrotic kidney despite anemia. Furthermore, hypoxia is present in acute or chronic kidney diseases and may affect all cell types present in the kidney including tubular and glomerular cells as well as resident immune cells. Pro- and antifibrotic effects of the transcription factors hypoxia-inducible factors 1 and 2 have been described in a plethora of animal models of acute and chronic kidney diseases, but recent advances in sequencing technologies now allow for novel and deeper insights into the role of hypoxia and its cell type-specific effects on the progression of renal fibrosis, especially in humans. Here, we review existing literature on how hypoxia impacts the development and progression of renal fibrosis.
Collapse
Affiliation(s)
- Stephanie Naas
- Department of Nephrology and Hypertension, Uniklinikum Erlangen und Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, Germany
| | - Mario Schiffer
- Department of Nephrology and Hypertension, Uniklinikum Erlangen und Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, Germany
| | - Johannes Schödel
- Department of Nephrology and Hypertension, Uniklinikum Erlangen und Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, Germany
| |
Collapse
|
6
|
Naas S, Krüger R, Knaup KX, Naas J, Grampp S, Schiffer M, Wiesener M, Schödel J. Hypoxia controls expression of kidney-pathogenic MUC1 variants. Life Sci Alliance 2023; 6:e202302078. [PMID: 37316299 PMCID: PMC10267510 DOI: 10.26508/lsa.202302078] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2023] [Revised: 05/31/2023] [Accepted: 06/01/2023] [Indexed: 06/16/2023] Open
Abstract
The interplay between genetic and environmental factors influences the course of chronic kidney disease (CKD). In this context, genetic alterations in the kidney disease gene MUC1 (Mucin1) predispose to the development of CKD. These variations comprise the polymorphism rs4072037, which alters splicing of MUC1 mRNA, the length of a region with variable number of tandem repeats (VNTR), and rare autosomal-dominant inherited dominant-negative mutations in or 5' to the VNTR that causes autosomal dominant tubulointerstitial kidney disease (ADTKD-MUC1). As hypoxia plays a pivotal role in states of acute and chronic kidney injury, we explored the effects of hypoxia-inducible transcription factors (HIF) on the expression of MUC1 and its pathogenic variants in isolated primary human renal tubular cells. We defined a HIF-binding DNA regulatory element in the promoter-proximal region of MUC1 from which hypoxia or treatment with HIF stabilizers, which were recently approved for an anti-anemic therapy in CKD patients, increased levels of wild-type MUC1 and the disease-associated variants. Thus, application of these compounds might exert unfavorable effects in patients carrying MUC1 risk variants.
Collapse
Affiliation(s)
- Stephanie Naas
- Department of Nephrology and Hypertension, Uniklinikum Erlangen und Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, Germany
| | - René Krüger
- Department of Nephrology and Hypertension, Uniklinikum Erlangen und Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, Germany
| | - Karl Xaver Knaup
- Department of Nephrology and Hypertension, Uniklinikum Erlangen und Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, Germany
| | - Julia Naas
- Center for Integrative Bioinformatics Vienna (CIBIV), Max Perutz Labs, University of Vienna and Medical University of Vienna, Wien, Austria
| | - Steffen Grampp
- Department of Nephrology and Hypertension, Uniklinikum Erlangen und Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, Germany
| | - Mario Schiffer
- Department of Nephrology and Hypertension, Uniklinikum Erlangen und Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, Germany
| | - Michael Wiesener
- Department of Nephrology and Hypertension, Uniklinikum Erlangen und Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, Germany
| | - Johannes Schödel
- Department of Nephrology and Hypertension, Uniklinikum Erlangen und Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, Germany
| |
Collapse
|
7
|
Leggatt GP, Seaby EG, Veighey K, Gast C, Gilbert RD, Ennis S. A Role for Genetic Modifiers in Tubulointerstitial Kidney Diseases. Genes (Basel) 2023; 14:1582. [PMID: 37628633 PMCID: PMC10454709 DOI: 10.3390/genes14081582] [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: 07/17/2023] [Revised: 07/31/2023] [Accepted: 08/01/2023] [Indexed: 08/27/2023] Open
Abstract
With the increased availability of genomic sequencing technologies, the molecular bases for kidney diseases such as nephronophthisis and mitochondrially inherited and autosomal-dominant tubulointerstitial kidney diseases (ADTKD) has become increasingly apparent. These tubulointerstitial kidney diseases (TKD) are monogenic diseases of the tubulointerstitium and result in interstitial fibrosis and tubular atrophy (IF/TA). However, monogenic inheritance alone does not adequately explain the highly variable onset of kidney failure and extra-renal manifestations. Phenotypes vary considerably between individuals harbouring the same pathogenic variant in the same putative monogenic gene, even within families sharing common environmental factors. While the extreme end of the disease spectrum may have dramatic syndromic manifestations typically diagnosed in childhood, many patients present a more subtle phenotype with little to differentiate them from many other common forms of non-proteinuric chronic kidney disease (CKD). This review summarises the expanding repertoire of genes underpinning TKD and their known phenotypic manifestations. Furthermore, we collate the growing evidence for a role of modifier genes and discuss the extent to which these data bridge the historical gap between apparently rare monogenic TKD and polygenic non-proteinuric CKD (excluding polycystic kidney disease).
Collapse
Affiliation(s)
- Gary P. Leggatt
- Human Genetics & Genomic Medicine, University of Southampton, Southampton SO16 6YD, UK; (E.G.S.); (K.V.); (C.G.); (R.D.G.); (S.E.)
- Wessex Kidney Centre, Queen Alexandra Hospital, Portsmouth Hospitals NHS Trust, Portsmouth PO6 3LY, UK
- Renal Department, University Hospital Southampton, Southampton SO16 6YD, UK
| | - Eleanor G. Seaby
- Human Genetics & Genomic Medicine, University of Southampton, Southampton SO16 6YD, UK; (E.G.S.); (K.V.); (C.G.); (R.D.G.); (S.E.)
| | - Kristin Veighey
- Human Genetics & Genomic Medicine, University of Southampton, Southampton SO16 6YD, UK; (E.G.S.); (K.V.); (C.G.); (R.D.G.); (S.E.)
- Renal Department, University Hospital Southampton, Southampton SO16 6YD, UK
| | - Christine Gast
- Human Genetics & Genomic Medicine, University of Southampton, Southampton SO16 6YD, UK; (E.G.S.); (K.V.); (C.G.); (R.D.G.); (S.E.)
- Wessex Kidney Centre, Queen Alexandra Hospital, Portsmouth Hospitals NHS Trust, Portsmouth PO6 3LY, UK
| | - Rodney D. Gilbert
- Human Genetics & Genomic Medicine, University of Southampton, Southampton SO16 6YD, UK; (E.G.S.); (K.V.); (C.G.); (R.D.G.); (S.E.)
- Department of Paediatric Nephrology, Southampton Children’s Hospital, University Hospital Southampton NHS Foundation Trust, Southampton SO16 6YD, UK
| | - Sarah Ennis
- Human Genetics & Genomic Medicine, University of Southampton, Southampton SO16 6YD, UK; (E.G.S.); (K.V.); (C.G.); (R.D.G.); (S.E.)
| |
Collapse
|
8
|
Jia PP, Chandrajith R, Junaid M, Li TY, Li YZ, Wei XY, Liu L, Pei DS. Elucidating environmental factors and their combined effects on CKDu in Sri Lanka using zebrafish. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2023:121967. [PMID: 37290634 DOI: 10.1016/j.envpol.2023.121967] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/18/2023] [Revised: 05/23/2023] [Accepted: 06/05/2023] [Indexed: 06/10/2023]
Abstract
Chronic kidney disease with uncertain etiology (CKDu) in Sri Lanka has attracted much attention as a global health issue. However, how environmental factors in local drinking water induce kidney damage in organisms is still elusive. We investigated multiple environmental factors including water hardness and fluoride (HF), heavy metals (HM), microcystin-LR (MC-LR), and their combined exposure (HFMM) to elucidate their toxic effects on CKDu risk in zebrafish. Acute exposure affected renal development and inhibited the fluorescence of Na, K-ATPase alpha1A4:GFP zebrafish kidney. Chronic exposure influenced the body weight of both genders of adult fish and induced kidney damage by histopathological analyses. Furthermore, the exposure significantly disturbed differential expression genes (DEGs), diversity and richness of gut microbiota, and critical metabolites related to renal functions. The transcriptomic analysis revealed that kidney-related DEGs were linked with renal cell carcinoma, proximal tubule bicarbonate reclamation, calcium signaling pathway, and HIF-1 signaling pathway. The significantly disrupted intestinal microbiota was closely related to the environmental factors and H&E score, which demonstrated the mechanisms of kidney risks. Notably, the Spearman correlation analysis indicated that the changed bacteria such as Pseudomonas, Paracoccus, and ZOR0006, etc were significantly connected to the DEGs and metabolites. Therefore, the assessment of multiple environmental factors provided new insights on "bio-markers" as potential therapies of the target signaling pathways, metabolites, and gut bacteria to monitor or protect residents from CKDu.
Collapse
Affiliation(s)
- Pan-Pan Jia
- School of Public Health, Chongqing Medical University, Chongqing, 400016, China
| | - Rohana Chandrajith
- Chongqing Institute of Green and Intelligent Technology, Chinese Academy of Sciences, Chongqing, 400714, China; Department of Geology, Faculty of Science, University of Peradeniya, Peradeniya, Sri Lanka
| | - Muhammad Junaid
- Chongqing Institute of Green and Intelligent Technology, Chinese Academy of Sciences, Chongqing, 400714, China
| | - Tian-Yun Li
- Chongqing Institute of Green and Intelligent Technology, Chinese Academy of Sciences, Chongqing, 400714, China
| | - Yong-Zhi Li
- Chongqing Institute of Green and Intelligent Technology, Chinese Academy of Sciences, Chongqing, 400714, China
| | - Xing-Yi Wei
- Chongqing Institute of Green and Intelligent Technology, Chinese Academy of Sciences, Chongqing, 400714, China
| | - Li Liu
- Chongqing Institute of Green and Intelligent Technology, Chinese Academy of Sciences, Chongqing, 400714, China
| | - De-Sheng Pei
- School of Public Health, Chongqing Medical University, Chongqing, 400016, China.
| |
Collapse
|
9
|
Schlosser P, Scherer N, Grundner-Culemann F, Monteiro-Martins S, Haug S, Steinbrenner I, Uluvar B, Wuttke M, Cheng Y, Ekici AB, Gyimesi G, Karoly ED, Kotsis F, Mielke J, Gomez MF, Yu B, Grams ME, Coresh J, Boerwinkle E, Köttgen M, Kronenberg F, Meiselbach H, Mohney RP, Akilesh S, Schmidts M, Hediger MA, Schultheiss UT, Eckardt KU, Oefner PJ, Sekula P, Li Y, Köttgen A. Genetic studies of paired metabolomes reveal enzymatic and transport processes at the interface of plasma and urine. Nat Genet 2023:10.1038/s41588-023-01409-8. [PMID: 37277652 DOI: 10.1038/s41588-023-01409-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2022] [Accepted: 04/26/2023] [Indexed: 06/07/2023]
Abstract
The kidneys operate at the interface of plasma and urine by clearing molecular waste products while retaining valuable solutes. Genetic studies of paired plasma and urine metabolomes may identify underlying processes. We conducted genome-wide studies of 1,916 plasma and urine metabolites and detected 1,299 significant associations. Associations with 40% of implicated metabolites would have been missed by studying plasma alone. We detected urine-specific findings that provide information about metabolite reabsorption in the kidney, such as aquaporin (AQP)-7-mediated glycerol transport, and different metabolomic footprints of kidney-expressed proteins in plasma and urine that are consistent with their localization and function, including the transporters NaDC3 (SLC13A3) and ASBT (SLC10A2). Shared genetic determinants of 7,073 metabolite-disease combinations represent a resource to better understand metabolic diseases and revealed connections of dipeptidase 1 with circulating digestive enzymes and with hypertension. Extending genetic studies of the metabolome beyond plasma yields unique insights into processes at the interface of body compartments.
Collapse
Affiliation(s)
- Pascal Schlosser
- Institute of Genetic Epidemiology, Faculty of Medicine and Medical Center - University of Freiburg, Freiburg, Germany.
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA.
| | - Nora Scherer
- Institute of Genetic Epidemiology, Faculty of Medicine and Medical Center - University of Freiburg, Freiburg, Germany
- Spemann Graduate School of Biology and Medicine, University of Freiburg, Freiburg, Germany
| | - Franziska Grundner-Culemann
- Institute of Genetic Epidemiology, Faculty of Medicine and Medical Center - University of Freiburg, Freiburg, Germany
| | - Sara Monteiro-Martins
- Institute of Genetic Epidemiology, Faculty of Medicine and Medical Center - University of Freiburg, Freiburg, Germany
| | - Stefan Haug
- Institute of Genetic Epidemiology, Faculty of Medicine and Medical Center - University of Freiburg, Freiburg, Germany
| | - Inga Steinbrenner
- Institute of Genetic Epidemiology, Faculty of Medicine and Medical Center - University of Freiburg, Freiburg, Germany
| | - Burulça Uluvar
- Institute of Genetic Epidemiology, Faculty of Medicine and Medical Center - University of Freiburg, Freiburg, Germany
| | - Matthias Wuttke
- Institute of Genetic Epidemiology, Faculty of Medicine and Medical Center - University of Freiburg, Freiburg, Germany
| | - Yurong Cheng
- Institute of Genetic Epidemiology, Faculty of Medicine and Medical Center - University of Freiburg, Freiburg, Germany
| | - Arif B Ekici
- Institute of Human Genetics, University Hospital Erlangen, Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, Germany
| | - Gergely Gyimesi
- Membrane Transport Discovery Lab, Department of Nephrology and Hypertension and Department of Biomedical Research, University of Bern, Bern, Switzerland
| | | | - Fruzsina Kotsis
- Institute of Genetic Epidemiology, Faculty of Medicine and Medical Center - University of Freiburg, Freiburg, Germany
- Department of Medicine IV-Nephrology and Primary Care, Faculty of Medicine and Medical Center, University of Freiburg, Freiburg, Germany
| | - Johanna Mielke
- Research and Early Development, Pharmaceuticals Division, Bayer AG, Wuppertal, Germany
| | - Maria F Gomez
- Department of Clinical Sciences in Malmö, Lund University Diabetes Centre, Lund University, Lund, Sweden
| | - Bing Yu
- Epidemiology, Human Genetics and Environmental Sciences, School of Public Health, University of Texas Health Science Center at Houston, Houston, TX, USA
| | - Morgan E Grams
- New York University Grossman School of Medicine, New York, NY, USA
| | - Josef Coresh
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA
| | - Eric Boerwinkle
- Epidemiology, Human Genetics and Environmental Sciences, School of Public Health, University of Texas Health Science Center at Houston, Houston, TX, USA
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA
| | - Michael Köttgen
- Department of Medicine IV-Nephrology and Primary Care, Faculty of Medicine and Medical Center, University of Freiburg, Freiburg, Germany
- Centre for Integrative Biological Signalling Studies (CIBSS), Albert-Ludwigs-University Freiburg, Freiburg, Germany
| | - Florian Kronenberg
- Institute of Genetic Epidemiology, Department of Genetics, Medical University of Innsbruck, Innsbruck, Austria
| | - Heike Meiselbach
- Department of Nephrology and Hypertension, University Hospital Erlangen, Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, Germany
| | | | - Shreeram Akilesh
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA, USA
| | - Miriam Schmidts
- Centre for Integrative Biological Signalling Studies (CIBSS), Albert-Ludwigs-University Freiburg, Freiburg, Germany
- Freiburg University Faculty of Medicine, Center for Pediatrics and Adolescent Medicine, University Hospital Freiburg, Freiburg, Germany
| | - Matthias A Hediger
- Membrane Transport Discovery Lab, Department of Nephrology and Hypertension and Department of Biomedical Research, University of Bern, Bern, Switzerland
| | - Ulla T Schultheiss
- Institute of Genetic Epidemiology, Faculty of Medicine and Medical Center - University of Freiburg, Freiburg, Germany
- Department of Medicine IV-Nephrology and Primary Care, Faculty of Medicine and Medical Center, University of Freiburg, Freiburg, Germany
| | - Kai-Uwe Eckardt
- Department of Nephrology and Hypertension, University Hospital Erlangen, Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, Germany
- Department of Nephrology and Medical Intensive Care, Charité-Universitätsmedizin Berlin, Berlin, Germany
| | - Peter J Oefner
- Institute of Functional Genomics, University of Regensburg, Regensburg, Germany
| | - Peggy Sekula
- Institute of Genetic Epidemiology, Faculty of Medicine and Medical Center - University of Freiburg, Freiburg, Germany
| | - Yong Li
- Institute of Genetic Epidemiology, Faculty of Medicine and Medical Center - University of Freiburg, Freiburg, Germany
| | - Anna Köttgen
- Institute of Genetic Epidemiology, Faculty of Medicine and Medical Center - University of Freiburg, Freiburg, Germany.
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA.
- Centre for Integrative Biological Signalling Studies (CIBSS), Albert-Ludwigs-University Freiburg, Freiburg, Germany.
| |
Collapse
|
10
|
Barry A, McNulty MT, Jia X, Gupta Y, Debiec H, Luo Y, Nagano C, Horinouchi T, Jung S, Colucci M, Ahram DF, Mitrotti A, Sinha A, Teeninga N, Jin G, Shril S, Caridi G, Bodria M, Lim TY, Westland R, Zanoni F, Marasa M, Turudic D, Giordano M, Gesualdo L, Magistroni R, Pisani I, Fiaccadori E, Reiterova J, Maringhini S, Morello W, Montini G, Weng PL, Scolari F, Saraga M, Tasic V, Santoro D, van Wijk JAE, Milošević D, Kawai Y, Kiryluk K, Pollak MR, Gharavi A, Lin F, Simœs E Silva AC, Loos RJF, Kenny EE, Schreuder MF, Zurowska A, Dossier C, Ariceta G, Drozynska-Duklas M, Hogan J, Jankauskiene A, Hildebrandt F, Prikhodina L, Song K, Bagga A, Cheong H, Ghiggeri GM, Vachvanichsanong P, Nozu K, Lee D, Vivarelli M, Raychaudhuri S, Tokunaga K, Sanna-Cherchi S, Ronco P, Iijima K, Sampson MG. Multi-population genome-wide association study implicates immune and non-immune factors in pediatric steroid-sensitive nephrotic syndrome. Nat Commun 2023; 14:2481. [PMID: 37120605 PMCID: PMC10148875 DOI: 10.1038/s41467-023-37985-w] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2022] [Accepted: 04/10/2023] [Indexed: 05/01/2023] Open
Abstract
Pediatric steroid-sensitive nephrotic syndrome (pSSNS) is the most common childhood glomerular disease. Previous genome-wide association studies (GWAS) identified a risk locus in the HLA Class II region and three additional independent risk loci. But the genetic architecture of pSSNS, and its genetically driven pathobiology, is largely unknown. Here, we conduct a multi-population GWAS meta-analysis in 38,463 participants (2440 cases). We then conduct conditional analyses and population specific GWAS. We discover twelve significant associations-eight from the multi-population meta-analysis (four novel), two from the multi-population conditional analysis (one novel), and two additional novel loci from the European meta-analysis. Fine-mapping implicates specific amino acid haplotypes in HLA-DQA1 and HLA-DQB1 driving the HLA Class II risk locus. Non-HLA loci colocalize with eQTLs of monocytes and numerous T-cell subsets in independent datasets. Colocalization with kidney eQTLs is lacking but overlap with kidney cell open chromatin suggests an uncharacterized disease mechanism in kidney cells. A polygenic risk score (PRS) associates with earlier disease onset. Altogether, these discoveries expand our knowledge of pSSNS genetic architecture across populations and provide cell-specific insights into its molecular drivers. Evaluating these associations in additional cohorts will refine our understanding of population specificity, heterogeneity, and clinical and molecular associations.
Collapse
Affiliation(s)
- Alexandra Barry
- Division of Nephrology, Boston Children's Hospital, Boston, MA, USA
- Kidney Disease Initiative & Medical and Population Genetics Program, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Michelle T McNulty
- Division of Nephrology, Boston Children's Hospital, Boston, MA, USA
- Kidney Disease Initiative & Medical and Population Genetics Program, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Xiaoyuan Jia
- Genome Medical Science Project (Toyama), National Center for Global Health and Medicine (NCGM), Tokyo, Japan
- Department of Human Genetics, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Yask Gupta
- Division of Nephrology, Department of Medicine, Columbia University College of Physicians and Surgeons, New York, NY, USA
| | - Hanna Debiec
- Sorbonne Université, UPMC Paris 06, Institut National de la Santé et de la Recherde Médicale, Unité Mixte de Rechereche, S 1155, Paris, France
| | - Yang Luo
- Kennedy Institute of Rheumatology, University of Oxford, Roosevelt Drive, Headington, Oxford, OX3 7FY, United Kingdom
- Center for Data Sciences, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
- Divisions of Genetics and Rheumatology, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - China Nagano
- Division of Nephrology, Boston Children's Hospital, Boston, MA, USA
- Kidney Disease Initiative & Medical and Population Genetics Program, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Pediatrics, Kobe University Graduate School of Medicine, Kobe, Japan
| | - Tomoko Horinouchi
- Department of Pediatrics, Kobe University Graduate School of Medicine, Kobe, Japan
| | - Seulgi Jung
- Department of Biochemistry and Molecular Biology, University of Ulsan College of Medicine, Songpa-gu, Seoul, Korea
| | - Manuela Colucci
- Renal Diseases Research Unit, Genetics and Rare Diseases Research Division, Istituto di Ricovero e Cura a Carattere Scientifico Ospedale Pediatrico Bambino Gesù, Rome, Italy
| | - Dina F Ahram
- Division of Nephrology, Department of Medicine, Columbia University College of Physicians and Surgeons, New York, NY, USA
| | - Adele Mitrotti
- Division of Nephrology, Department of Medicine, Columbia University College of Physicians and Surgeons, New York, NY, USA
- Nephrology, Dialysis and Transplantation Unit, Department of Emergency and Organ Transplantation, University of Bari Aldo Moro, Bari, Italy
| | - Aditi Sinha
- Department of Pediatrics, AIIMS, New Delhi, India
| | - Nynke Teeninga
- Department of Pediatric Nephrology, Amalia Children's Hospital, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Gina Jin
- Division of Nephrology, Department of Medicine, Columbia University College of Physicians and Surgeons, New York, NY, USA
| | - Shirlee Shril
- Department of Medicine, Boston Children's Hospital, Boston, MA, USA
- Department of Pediatrics, Harvard Medical School, Boston, MA, USA
| | - Gianluca Caridi
- Laboratory on Molecular Nephrology, IRCCS Instituto Giannina Gaslini, Genoa, Italy
| | - Monica Bodria
- Department of Nephrology and Renal Transplantation, IRCCS Instituto Giannina Gaslini, Genoa, Italy
| | - Tze Y Lim
- Division of Nephrology, Department of Medicine, Columbia University College of Physicians and Surgeons, New York, NY, USA
| | - Rik Westland
- Department of Pediatric Nephrology, VU University Medical Center, Amsterdam, The Netherlands
| | - Francesca Zanoni
- Division of Nephrology, Department of Medicine, Columbia University College of Physicians and Surgeons, New York, NY, USA
- Division of Transplantation, Department of Surgery, University of Pennsylvania, Philadelphia, PA, USA
| | - Maddalena Marasa
- Division of Nephrology, Department of Medicine, Columbia University College of Physicians and Surgeons, New York, NY, USA
| | - Daniel Turudic
- Department of Pediatric Nephrology, Dialysis and Transplantation, Clinical Hospital Hospital Center Zagreb, University of Zagreb Medical School, Zagreb, Croatia
| | - Mario Giordano
- Division of Nephrology and Pediatric Dialysis, Bari Polyclinic Giovanni XXIII Children's Hospital, Bari, Italy
| | - Loreto Gesualdo
- Nephrology, Dialysis and Transplantation Unit, Department of Emergency and Organ Transplantation, University of Bari Aldo Moro, Bari, Italy
| | - Riccardo Magistroni
- Department of Nephrology, Dialysis and Transplant Unit, University Hospital of Modena, Modena, Italy
- Surgical, Medical and Dental Department of Morphological Sciences, Section of Nephrology, University of Modena and Reggio Emilia, Modena, Italy
| | - Isabella Pisani
- Unità Operativa Nefrologia, Azienda Ospedaliero-Universitaria di Parma, Dipartimento di Medicina e Chirurgia, Università di Parma, Parma, Italy
| | - Enrico Fiaccadori
- Unità Operativa Nefrologia, Azienda Ospedaliero-Universitaria di Parma, Dipartimento di Medicina e Chirurgia, Università di Parma, Parma, Italy
| | - Jana Reiterova
- Department of Nephrology, Medicine and General University Hospital, Charles University, Prague, Czech Republic
| | | | - William Morello
- Pediatric Nephrology, Dialysis and Transplant Unit, Fondazione IRCCS Ca' Granda-Ospedale Maggiore Policlinico, Milano, Italy
| | - Giovanni Montini
- Pediatric Nephrology, Dialysis and Transplant Unit, Fondazione IRCCS Ca' Granda-Ospedale Maggiore Policlinico, Milano, Italy
- Department of Clinical Sciences and Community Health, University of Milan, Milan, Italy
| | - Patricia L Weng
- Department of Pediatric Nephrology, UCLA Medical Center and UCLA Medical Center-Santa Monica, Los Angeles, CA, USA
| | - Francesco Scolari
- Department of Medical and Surgical Specialties, Radiological Sciences, and Public Health, Division of Nephrology and Dialysis, University of Brescia and ASST Spedali Civili of Brescia, Brescia, Italy
| | - Marijan Saraga
- Department of Pediatrics, University of Split, Split, Croatia
| | - Velibor Tasic
- Department of Pediatric Nephrology, University Children's Hospital, Skopje, Macedonia
| | - Domenica Santoro
- Division of Nephrology and Dialysis Unit, University of Messina, Sicily, Italy
| | - Joanna A E van Wijk
- Department of Pediatric Nephrology, VU University Medical Center, Amsterdam, The Netherlands
| | - Danko Milošević
- Department of Pediatric Nephrology, Dialysis and Transplantation, Clinical Hospital Hospital Center Zagreb, University of Zagreb Medical School, Zagreb, Croatia
- Croatian Academy of Medical Sciences, Praska 2/III p.p. 27, 10000, Zagreb, Croatia
| | - Yosuke Kawai
- Genome Medical Science Project (Toyama), National Center for Global Health and Medicine (NCGM), Tokyo, Japan
- Department of Human Genetics, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Krzysztof Kiryluk
- Division of Nephrology, Department of Medicine, Columbia University College of Physicians and Surgeons, New York, NY, USA
| | - Martin R Pollak
- Division of Nephrology, Beth Israel Deaconess Medical Center, Boston, MA, USA
- Department of Pediatric, Division of Pediatric Nephrology, Columbia University Irving Medical Center New York-Presbyterian Morgan Stanley Children's Hospital in New York, New York, NY, USA
| | - Ali Gharavi
- Division of Nephrology, Department of Medicine, Columbia University College of Physicians and Surgeons, New York, NY, USA
| | - Fangmin Lin
- Department of Pediatric, Division of Pediatric Nephrology, Columbia University Irving Medical Center New York-Presbyterian Morgan Stanley Children's Hospital in New York, New York, NY, USA
| | - Ana Cristina Simœs E Silva
- Department of Pediatrics, Interdisciplinary Laboratory of Medical Investigation, Faculty of Medicine, Federal University of Minas Gerais, Belo Horizonte, Brazil
| | - Ruth J F Loos
- The Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Eimear E Kenny
- Institute for Genomic Health, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Division of Genomic Medicine, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Division of General Internal Medicine, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Michiel F Schreuder
- Department of Pediatric Nephrology, Amalia Children's Hospital, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Aleksandra Zurowska
- Department of Pediatrics, Nephrology and Hypertension, Medical University Gdansk, Gdansk, Poland
| | - Claire Dossier
- AP-HP, Pediatric Nephrology Department, Hôpital Robert-Debré, Paris, France
| | - Gema Ariceta
- Pediatric Nephrology, Hospital Universitari Vall d'Hebron, Universitat Autónoma de Barcelona, Barcelona, Spain
| | | | - Julien Hogan
- AP-HP, Pediatric Nephrology Department, Hôpital Robert-Debré, Paris, France
| | - Augustina Jankauskiene
- Institute of Clinical Medicine, Faculty of Medicine, Vilnius University, Vilnius, Lithuania
| | - Friedhelm Hildebrandt
- Division of Nephrology, Boston Children's Hospital, Boston, MA, USA
- Department of Pediatrics, Harvard Medical School, Boston, MA, USA
| | - Larisa Prikhodina
- Research and Clinical Institute for Pediatrics, Pirogov Russian National Research Medical University, Taldomskava St, 2, Moscow, Russia
| | - Kyuyoung Song
- Department of Biochemistry and Molecular Biology, University of Ulsan College of Medicine, Songpa-gu, Seoul, Korea
| | - Arvind Bagga
- Department of Pediatrics, AIIMS, New Delhi, India
| | - Hae Cheong
- Department of Pediatrics, Hallym University Sacred Heart Hospital, 22, Gwanpyeong-ro 170 beon-gil, Dongan-gu, Anyang-si, Gyeonggi-do, 14068, Korea
| | - Gian Marco Ghiggeri
- Department of Nephrology and Renal Transplantation, IRCCS Instituto Giannina Gaslini, Genoa, Italy
| | - Prayong Vachvanichsanong
- Department of Pediatrics, Faculty of Medicine, Prince of Songkla University, Hat-Yai, Songkhla, 90110, Thailand
| | - Kandai Nozu
- Department of Pediatrics, Kobe University Graduate School of Medicine, Kobe, Japan
| | - Dongwon Lee
- Division of Nephrology, Boston Children's Hospital, Boston, MA, USA
- Kidney Disease Initiative & Medical and Population Genetics Program, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Pediatrics, Harvard Medical School, Boston, MA, USA
| | - Marina Vivarelli
- Division of Nephrology, and Dialysis, Department of Pediatric Subspecialities, Istituto di Ricovero e Cura a Carattere Scientifico Ospedale Pediatrico Bambino Gesù, Rome, Italy
| | - Soumya Raychaudhuri
- Center for Data Sciences, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
- Divisions of Genetics and Rheumatology, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA
- Centre for Genetics and Genomics Versus Arthritis, University of Manchester, Manchester, UK
| | - Katsushi Tokunaga
- Genome Medical Science Project (Toyama), National Center for Global Health and Medicine (NCGM), Tokyo, Japan
- Department of Human Genetics, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Simone Sanna-Cherchi
- Division of Nephrology, Department of Medicine, Columbia University College of Physicians and Surgeons, New York, NY, USA
| | - Pierre Ronco
- Sorbonne Université, UPMC Paris 06, Institut National de la Santé et de la Recherde Médicale, Unité Mixte de Rechereche, S 1155, Paris, France
- Department of Nephrology, Centre Hospitalier du Mans, Le Mans, France
| | - Kazumoto Iijima
- Hyogo Prefectural Kobe Children's Hospital, Kobe, Japan
- Department of Advanced Pediatric Medicine, Kobe University Graduate School of Medicine, Kobe, Japan
| | - Matthew G Sampson
- Division of Nephrology, Boston Children's Hospital, Boston, MA, USA.
- Kidney Disease Initiative & Medical and Population Genetics Program, Broad Institute of MIT and Harvard, Cambridge, MA, USA.
- Department of Pediatrics, Harvard Medical School, Boston, MA, USA.
- Division of Renal Medicine, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA.
| |
Collapse
|
11
|
Pan Y, Sun X, Mi X, Huang Z, Hsu Y, Hixson JE, Munzy D, Metcalf G, Franceschini N, Tin A, Köttgen A, Francis M, Brody JA, Kestenbaum B, Sitlani CM, Mychaleckyj JC, Kramer H, Lange LA, Guo X, Hwang SJ, Irvin MR, Smith JA, Yanek LR, Vaidya D, Chen YDI, Fornage M, Lloyd-Jones DM, Hou L, Mathias RA, Mitchell BD, Peyser PA, Kardia SLR, Arnett DK, Correa A, Raffield LM, Vasan RS, Cupple LA, Levy D, Kaplan RC, North KE, Rotter JI, Kooperberg C, Reiner AP, Psaty BM, Tracy RP, Gibbs RA, Morrison AC, Feldman H, Boerwinkle E, He J, Kelly TN. Whole-exome sequencing study identifies four novel gene loci associated with diabetic kidney disease. Hum Mol Genet 2023; 32:1048-1060. [PMID: 36444934 PMCID: PMC9990994 DOI: 10.1093/hmg/ddac290] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2022] [Revised: 11/21/2022] [Accepted: 11/23/2022] [Indexed: 12/03/2022] Open
Abstract
Diabetic kidney disease (DKD) is recognized as an important public health challenge. However, its genomic mechanisms are poorly understood. To identify rare variants for DKD, we conducted a whole-exome sequencing (WES) study leveraging large cohorts well-phenotyped for chronic kidney disease and diabetes. Our two-stage WES study included 4372 European and African ancestry participants from the Chronic Renal Insufficiency Cohort and Atherosclerosis Risk in Communities studies (stage 1) and 11 487 multi-ancestry Trans-Omics for Precision Medicine participants (stage 2). Generalized linear mixed models, which accounted for genetic relatedness and adjusted for age, sex and ancestry, were used to test associations between single variants and DKD. Gene-based aggregate rare variant analyses were conducted using an optimized sequence kernel association test implemented within our mixed model framework. We identified four novel exome-wide significant DKD-related loci through initiating diabetes. In single-variant analyses, participants carrying a rare, in-frame insertion in the DIS3L2 gene (rs141560952) exhibited a 193-fold increased odds [95% confidence interval (CI): 33.6, 1105] of DKD compared with noncarriers (P = 3.59 × 10-9). Likewise, each copy of a low-frequency KRT6B splice-site variant (rs425827) conferred a 5.31-fold higher odds (95% CI: 3.06, 9.21) of DKD (P = 2.72 × 10-9). Aggregate gene-based analyses further identified ERAP2 (P = 4.03 × 10-8) and NPEPPS (P = 1.51 × 10-7), which are both expressed in the kidney and implicated in renin-angiotensin-aldosterone system modulated immune response. In the largest WES study of DKD, we identified novel rare variant loci attaining exome-wide significance. These findings provide new insights into the molecular mechanisms underlying DKD.
Collapse
Affiliation(s)
- Yang Pan
- Division of Nephrology, Department of Medicine, College of Medicine, University of Illinois at Chicago, Chicago, IL 60612, USA
| | - Xiao Sun
- Department of Epidemiology, School of Public Health and Tropical Medicine, Tulane University, New Orleans, LA 70112, USA
| | - Xuenan Mi
- Department of Epidemiology, School of Public Health and Tropical Medicine, Tulane University, New Orleans, LA 70112, USA
| | - Zhijie Huang
- Department of Epidemiology, School of Public Health and Tropical Medicine, Tulane University, New Orleans, LA 70112, USA
| | - Yenchih Hsu
- Center for Clinical Epidemiology and Biostatistics, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA 19104, USA
| | - James E Hixson
- Human Genetics Center, Department of Epidemiology, Human Genetics, and Environmental Sciences, School of Public Health, The University of Texas Health Science Center at Houston, Houston, TX 77030, USA
| | - Donna Munzy
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030, USA
| | - Ginger Metcalf
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030, USA
| | - Nora Franceschini
- Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27516, USA
| | - Adrienne Tin
- University of Mississippi Medical Center, Jackson, MS 39216, USA
| | - Anna Köttgen
- Institute of Genetic Epidemiology, Faculty of Medicine and Medical Center – University of Freiburg, Freiburg 79106, Germany
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD 21205, USA
| | - Michael Francis
- Institute of Bioinformatics, University of Georgia, Athens, GA 30602, USA
| | | | - Jennifer A Brody
- Cardiovascular Health Research Unit, Departments of Medicine, University of Washington, Seattle, WA 98195, USA
| | - Bryan Kestenbaum
- University of Washington, Department of Medicine, Division of Nephrology, Kidney Research Institute, Seattle, WA 98195, USA
| | - Colleen M Sitlani
- Cardiovascular Health Research Unit, Departments of Medicine, University of Washington, Seattle, WA 98195, USA
| | - Josyf C Mychaleckyj
- Center for Public Health Genomics, University of Virginia, Charlottesville, Charlottesville, VA 22903, USA
| | - Holly Kramer
- Department of Public Health Sciences, Loyola University Chicago, Maywood, IL 60153, USA
| | - Leslie A Lange
- Division of Biomedical Informatics and Personalized Medicine, School of Medicine, University of Colorado Denver, Aurora, CO 80045, USA
| | - Xiuqing Guo
- The Institute for Translational Genomics and Population Sciences, Department of Pediatrics, The Lundquist Institute for Biomedical Innovation at Harbor-UCLA Medical Centre, Torrance, CA 90502, USA
| | - Shih-Jen Hwang
- Framingham Heart Study, Framingham, MA 01702, USA
- Department of Biostatistics, Boston University School of Public Health, Boston, MA 02118, USA
| | - Marguerite R Irvin
- Department of Epidemiology, University of Alabama at Birmingham School of Public Health, Birmingham, AL 35233, USA
| | - Jennifer A Smith
- Department of Epidemiology, School of Public Health, University of Michigan, Ann Arbor, MI 48109, USA
| | - Lisa R Yanek
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Dhananjay Vaidya
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Yii-Der Ida Chen
- The Institute for Translational Genomics and Population Sciences, Department of Pediatrics, The Lundquist Institute for Biomedical Innovation at Harbor-UCLA Medical Centre, Torrance, CA 90502, USA
| | - Myriam Fornage
- Human Genetics Center, Department of Epidemiology, Human Genetics, and Environmental Sciences, School of Public Health, The University of Texas Health Science Center at Houston, Houston, TX 77030, USA
- Brown Foundation Institute of Molecular Medicine, McGovern Medical School, University of Texas Health Science Center at Houston, Houston, TX 77030, USA
| | - Donald M Lloyd-Jones
- Department of Preventive Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
| | - Lifang Hou
- Department of Preventive Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
| | - Rasika A Mathias
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Braxton D Mitchell
- Department of Medicine, University of Maryland School of Medicine, Baltimore, MD 21201, USA
- Geriatrics Research and Education Clinical Center, Baltimore Veterans Administration Medical Center, Baltimore, MD 21201, USA
| | - Patricia A Peyser
- Department of Epidemiology, School of Public Health, University of Michigan, Ann Arbor, MI 48109, USA
| | - Sharon L R Kardia
- Department of Epidemiology, School of Public Health, University of Michigan, Ann Arbor, MI 48109, USA
| | - Donna K Arnett
- Department of Epidemiology, University of Kentucky, Lexington, KY 40506, USA
| | - Adolfo Correa
- University of Mississippi Medical Center, Jackson, MS 39216, USA
| | - Laura M Raffield
- Department of Genetics, University of North Carolina, Chapel Hill, NC 27516, USA
| | - Ramachandran S Vasan
- Framingham Heart Study, Framingham, MA 01702, USA
- Department of Medicine, Boston University School of Medicine, Boston, MA 02118, USA
| | - L Adrienne Cupple
- Framingham Heart Study, Framingham, MA 01702, USA
- Department of Biostatistics, Boston University School of Public Health, Boston, MA 02118, USA
| | - Daniel Levy
- Framingham Heart Study, Framingham, MA 01702, USA
- Department of Medicine, Boston University School of Medicine, Boston, MA 02118, USA
- Population Sciences Branch, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD 20814, USA
| | - Robert C Kaplan
- Department of Epidemiology & Population Health, Albert Einstein College of Medicine, Bronx, NY 10461, USA
| | - Kari E North
- Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27516, USA
| | - Jerome I Rotter
- The Institute for Translational Genomics and Population Sciences, Department of Pediatrics, The Lundquist Institute for Biomedical Innovation at Harbor-UCLA Medical Centre, Torrance, CA 90502, USA
| | - Charles Kooperberg
- Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
| | - Alexander P Reiner
- Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
- Department of Epidemiology, University of Washington, Seattle, WA 98195, USA
| | - Bruce M Psaty
- Cardiovascular Health Research Unit, Departments of Medicine, University of Washington, Seattle, WA 98195, USA
- Department of Epidemiology, University of Washington, Seattle, WA 98195, USA
- Department of Health Services, University of Washington, Seattle, WA 98195, USA
| | - Russell P Tracy
- Departments of Pathology & Laboratory Medicine and Biochemistry, Larner College of Medicine, University of Vermont, Burlington, VT 05405, USA
| | - Richard A Gibbs
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030, USA
| | - Alanna C Morrison
- Human Genetics Center, Department of Epidemiology, Human Genetics, and Environmental Sciences, School of Public Health, The University of Texas Health Science Center at Houston, Houston, TX 77030, USA
| | - Harold Feldman
- Center for Clinical Epidemiology and Biostatistics, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Eric Boerwinkle
- Human Genetics Center, Department of Epidemiology, Human Genetics, and Environmental Sciences, School of Public Health, The University of Texas Health Science Center at Houston, Houston, TX 77030, USA
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030, USA
| | - Jiang He
- Department of Epidemiology, School of Public Health and Tropical Medicine, Tulane University, New Orleans, LA 70112, USA
| | - Tanika N Kelly
- Division of Nephrology, Department of Medicine, College of Medicine, University of Illinois at Chicago, Chicago, IL 60612, USA
| | | |
Collapse
|
12
|
Guo X, Peng H, Liu P, Tang L, Fang J, Aoieong C, Tou T, Tsai T, Liu X. Metabolic profiling identifies the significance of caffeine metabolism in CKD. Front Bioeng Biotechnol 2023; 11:1006246. [PMID: 36873366 PMCID: PMC9981652 DOI: 10.3389/fbioe.2023.1006246] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2022] [Accepted: 02/06/2023] [Indexed: 02/19/2023] Open
Abstract
Background: With the development of chronic kidney disease (CKD), there are various changes in metabolites. However, the effect of these metabolites on the etiology, progression and prognosis of CKD remains unclear. Objective: We aimed to identify significant metabolic pathways in CKD progression by screening metabolites through metabolic profiling, thus identifying potential targets for CKD treatment. Methods: Clinical data were collected from 145 CKD participants. GFR (mGFR) was measured by the iohexol method and participants were divided into four groups according to their mGFR. Untargeted metabolomics analysis was performed via UPLC-MS/MSUPLC-MSMS/MS assays. Metabolomic data were analyzed by MetaboAnalyst 5.0, one-way ANOVA, principal component analysis (PCA), and partial least squares discriminant analysis (PLS-DA) to identify differential metabolites for further analysis. The open database sources of MBRole2.0, including KEGG and HMDB, were used to identify significant metabolic pathways in CKD progression. Results: Four metabolic pathways were classified as important in CKD progression, among which the most significant was caffeine metabolism. A total of 12 differential metabolites were enriched in caffeine metabolism, four of which decreased with the deterioration of the CKD stage, and two of which increased with the deterioration of the CKD stage. Of the four decreased metabolites, the most important was caffeine. Conclusion: Caffeine metabolism appears to be the most important pathway in the progression of CKD as identified by metabolic profiling. Caffeine is the most important metabolite that decreases with the deterioration of the CKD stage.
Collapse
Affiliation(s)
- Xinghua Guo
- Department of Rheumatology, The Third Affiliated Hospital of Sun Yat-Sen University, Guangzhou, Guangdong, China
| | - Hongquan Peng
- Department of Nephrology, Kiang Wu Hospital, Macau, Macao SAR, China
| | - Peijia Liu
- Department of Nephrology, GuangZhou Eighth People's Hospital, GuangZhou Medical University, Guangzhou, Guangdong, China
| | - Leile Tang
- Department of Cardiovasology, The Third Affiliated Hospital of Sun Yat-Sen University, Guangzhou, Guangdong, China
| | - Jia Fang
- Department of Rheumatology, The Third Affiliated Hospital of Sun Yat-Sen University, Guangzhou, Guangdong, China
| | - Chiwa Aoieong
- Department of Nephrology, Kiang Wu Hospital, Macau, Macao SAR, China
| | - Tou Tou
- Department of Nephrology, Kiang Wu Hospital, Macau, Macao SAR, China
| | - Tsungyang Tsai
- Department of Nephrology, Kiang Wu Hospital, Macau, Macao SAR, China
| | - Xun Liu
- Department of Nephrology, The Third Affiliated Hospital of Sun Yat-Sen University, Guangzhou, Guangdong, China
| |
Collapse
|
13
|
Tomaszewski M, Morris AP, Howson JMM, Franceschini N, Eales JM, Xu X, Dikalov S, Guzik TJ, Humphreys BD, Harrap S, Charchar FJ. Kidney omics in hypertension: from statistical associations to biological mechanisms and clinical applications. Kidney Int 2022; 102:492-505. [PMID: 35690124 PMCID: PMC9886011 DOI: 10.1016/j.kint.2022.04.045] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2021] [Revised: 03/10/2022] [Accepted: 04/22/2022] [Indexed: 02/06/2023]
Abstract
Hypertension is a major cardiovascular disease risk factor and contributor to premature death globally. Family-based investigations confirmed a significant heritable component of blood pressure (BP), whereas genome-wide association studies revealed >1000 common and rare genetic variants associated with BP and/or hypertension. The kidney is not only an organ of key relevance to BP regulation and the development of hypertension, but it also acts as the tissue mediator of genetic predisposition to hypertension. The identity of kidney genes, pathways, and related mechanisms underlying the genetic associations with BP has started to emerge through integration of genomics with kidney transcriptomics, epigenomics, and other omics as well as through applications of causal inference, such as Mendelian randomization. Single-cell methods further enabled mapping of BP-associated kidney genes to cell types, and in conjunction with other omics, started to illuminate the biological mechanisms underpinning associations of BP-associated genetic variants and kidney genes. Polygenic risk scores derived from genome-wide association studies and refined on kidney omics hold the promise of enhanced diagnostic prediction, whereas kidney omics-informed drug discovery is likely to contribute new therapeutic opportunities for hypertension and hypertension-mediated kidney damage.
Collapse
Affiliation(s)
- Maciej Tomaszewski
- Division of Cardiovascular Sciences, Faculty of Medicine, Biology and Health, University of Manchester, Manchester, UK; Manchester Heart Centre and Manchester Academic Health Science Centre, Manchester University NHS Foundation Trust, Manchester, UK.
| | - Andrew P Morris
- Centre for Genetics and Genomics Versus Arthritis, Centre for Musculoskeletal Research, Division of Musculoskeletal and Dermatological Sciences, University of Manchester, Manchester, UK
| | - Joanna M M Howson
- Department of Genetics, Novo Nordisk Research Centre Oxford, Novo Nordisk Ltd, Oxford, UK
| | - Nora Franceschini
- Department of Epidemiology, Gillings School of Global Public Health, University of North Carolina, Chapel Hill, North Carolina, USA
| | - James M Eales
- Division of Cardiovascular Sciences, Faculty of Medicine, Biology and Health, University of Manchester, Manchester, UK
| | - Xiaoguang Xu
- Division of Cardiovascular Sciences, Faculty of Medicine, Biology and Health, University of Manchester, Manchester, UK
| | - Sergey Dikalov
- Division of Clinical Pharmacology, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - Tomasz J Guzik
- Institute of Cardiovascular and Medical Sciences, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, UK; Department of Internal and Agricultural Medicine, Jagiellonian University College of Medicine, Kraków, Poland
| | - Benjamin D Humphreys
- Division of Nephrology, Department of Medicine, Washington University in St. Louis, St. Louis, Missouri, USA
| | - Stephen Harrap
- Department of Anatomy and Physiology, University of Melbourne, Melbourne, Victoria, Australia
| | - Fadi J Charchar
- Department of Anatomy and Physiology, University of Melbourne, Melbourne, Victoria, Australia; Health Innovation and Transformation Centre, School of Science, Psychology and Sport, Federation University Australia, Ballarat, Victoria, Australia; Department of Cardiovascular Sciences, University of Leicester, Leicester, UK
| |
Collapse
|
14
|
Lucio-Gutiérrez JR, Cordero-Pérez P, Farías-Navarro IC, Tijerina-Marquez R, Sánchez-Martínez C, Ávila-Velázquez JL, García-Hernández PA, Náñez-Terreros H, Coello-Bonilla J, Pérez-Trujillo M, Parella T, Torres-González L, Waksman-Minsky NH, Saucedo AL. Using nuclear magnetic resonance urine metabolomics to develop a prediction model of early stages of renal disease in subjects with type 2 diabetes. J Pharm Biomed Anal 2022; 219:114885. [DOI: 10.1016/j.jpba.2022.114885] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2022] [Revised: 06/01/2022] [Accepted: 06/08/2022] [Indexed: 12/01/2022]
|
15
|
Hill C, Avila-Palencia I, Maxwell AP, Hunter RF, McKnight AJ. Harnessing the Full Potential of Multi-Omic Analyses to Advance the Study and Treatment of Chronic Kidney Disease. FRONTIERS IN NEPHROLOGY 2022; 2:923068. [PMID: 37674991 PMCID: PMC10479694 DOI: 10.3389/fneph.2022.923068] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/18/2022] [Accepted: 05/30/2022] [Indexed: 09/08/2023]
Abstract
Chronic kidney disease (CKD) was the 12th leading cause of death globally in 2017 with the prevalence of CKD estimated at ~9%. Early detection and intervention for CKD may improve patient outcomes, but standard testing approaches even in developed countries do not facilitate identification of patients at high risk of developing CKD, nor those progressing to end-stage kidney disease (ESKD). Recent advances in CKD research are moving towards a more personalised approach for CKD. Heritability for CKD ranges from 30% to 75%, yet identified genetic risk factors account for only a small proportion of the inherited contribution to CKD. More in depth analysis of genomic sequencing data in large cohorts is revealing new genetic risk factors for common diagnoses of CKD and providing novel diagnoses for rare forms of CKD. Multi-omic approaches are now being harnessed to improve our understanding of CKD and explain some of the so-called 'missing heritability'. The most common omic analyses employed for CKD are genomics, epigenomics, transcriptomics, metabolomics, proteomics and phenomics. While each of these omics have been reviewed individually, considering integrated multi-omic analysis offers considerable scope to improve our understanding and treatment of CKD. This narrative review summarises current understanding of multi-omic research alongside recent experimental and analytical approaches, discusses current challenges and future perspectives, and offers new insights for CKD.
Collapse
Affiliation(s)
| | | | | | | | - Amy Jayne McKnight
- Centre for Public Health, Queen’s University Belfast, Belfast, United Kingdom
| |
Collapse
|
16
|
Zebrafish: A Model to Study and Understand the Diabetic Nephropathy and Other Microvascular Complications of Type 2 Diabetes Mellitus. Vet Sci 2022; 9:vetsci9070312. [PMID: 35878329 PMCID: PMC9323928 DOI: 10.3390/vetsci9070312] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2022] [Revised: 06/14/2022] [Accepted: 06/16/2022] [Indexed: 12/02/2022] Open
Abstract
Simple Summary Diabetes is a chronic metabolic disease characterized by high blood glucose levels (hyperglycemia). Type 2 diabetes mellitus (T2DM) and its complications are a worldwide public health problem, affecting people from all developed and developing countries. Hyperglycemia can cause damage to the vascular system and dysfunction of organs, such as the kidneys, heart, retina of the eyes, and nerves. Diabetic nephropathy (DN) is one of the most severe micro-vascular complications, which can lead to ESRD (end-stage renal disease). Zebrafish are ideal for wide-scale analysis or screening, due to their small size, quick growth, transparent embryos, vast number of offspring, and gene similarity with humans, which combine to make zebrafish an ideal model for diabetes. The readily available tools for gene editing using morpholinos or CRISPR/Cas9, as well as chemical/drug therapy by microinjection or skin absorption, enable zebrafish diabetes mellitus models to be established in a number of ways. In this review, we emphasize the physiological and pathological processes relating to micro-vascular problems in zebrafish, as well as the many experimental zebrafish models used to research DN, and the DN-related outcomes and mechanisms observed in zebrafish. This study specifies the benefits and drawbacks and future perspective of using zebrafish as a disease model. Abstract Diabetes mellitus (DM) is a complicated metabolic illness that has had a worldwide impact and placed an unsustainable load on both developed and developing countries’ health care systems. According to the International Diabetes Federation, roughly 537 million individuals had diabetes in 2021, with type 2 diabetes mellitus accounting for the majority of cases (T2DM). T2DM is a chronic illness defined by insufficient insulin production from pancreatic islet cells. T2DM generates various micro and macrovascular problems, with diabetic nephropathy (DN) being one of the most serious microvascular consequences, and which can lead to end-stage renal disease. The zebrafish (Danio rerio) has set the way for its future as a disease model organism. As numerous essential developmental processes, such as glucose metabolism and reactive metabolite production pathways, have been identified in zebrafish that are comparable to those seen in humans, it is a good model for studying diabetes and its consequences. It also has many benefits over other vertebrate models, including the permeability of its embryos to small compounds, disease-driven therapeutic target selection, in vivo validation, and deconstruction of biological networks. The organism can also be utilized to investigate and understand the genetic abnormalities linked to the onset of diabetes problems. Zebrafish may be used to examine and visualize the growth, morphology, and function of organs under normal physiological and diabetic settings. The zebrafish has become one of the most useful models for studying DN, especially when combined with genetic alterations and/or mutant or transgenic fish lines. The significant advancements of CRISPR and next-generation sequencing technology for disease modelling in zebrafish, as well as developments in molecular and nano technologies, have advanced the understanding of the molecular mechanisms of several human diseases, including DN. In this review, we emphasize the physiological and pathological processes relating to microvascular problems in zebrafish, as well as the many experimental zebrafish models used to research DN, and the DN-related outcomes and mechanisms observed in zebrafish.
Collapse
|
17
|
Lowe M, Jervis S, Payton A, Poulton K, Worthington J, Gemmell I, Verma A. Systematic review of associations between HLA and renal function. Int J Immunogenet 2021; 49:46-62. [PMID: 34919330 PMCID: PMC9300076 DOI: 10.1111/iji.12566] [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: 07/27/2021] [Revised: 11/01/2021] [Accepted: 11/17/2021] [Indexed: 11/30/2022]
Abstract
Introduction Kidney dysfunction is a highly significant disease, both in the United Kingdom and globally. Many previous studies have reported associations between human leukocyte antigens (HLA) and renal function; this systematic review attempts to identify, summarize and appraise all published studies of these associations. Methods A literature search was performed using Medline, Embase and Cochrane Central Register of Controlled Trials to identify papers whose keywords included each of the following concepts: HLA, renal failure and genetic association. A total of 245 papers were identified and assessed for eligibility; 35 of these were included in the final study. Results A total of 95 HLA types and 14 three‐locus haplotypes were reported to be associated with either increased or decreased renal function. A number of these findings were replicated by independent studies that reported 16 types were protective against renal dysfunction and 15 types were associated with reduced renal function. A total of 20 HLA types were associated with both increased risk of renal disease and decreased risk by independent studies. Discussion There is very little consensus on which HLA types have a protective or deleterious effect on renal function. Ethnicity may play a role, with HLA types possibly having different effects among different populations, and it is possible that the different primary diseases that lead to ESRD may have different HLA associations. Some of the studies may contain type I and type II errors caused by insufficient sample sizes, cohort selection and statistical methods. Although we have compiled a comprehensive list of published associations between renal function and HLA, in many cases, it is unclear which associations are reliable. Further studies are required to confirm or refute these findings.
Collapse
Affiliation(s)
- Marcus Lowe
- Transplantation Laboratory, Manchester Royal Infirmary, Manchester University NHS Foundation Trust, Manchester, UK.,Faculty of Biology, Medicine and Health, Division of Population Health, Health Services Research and Primary Care, School of Health Sciences, University of Manchester, Manchester, England
| | - Steven Jervis
- Transplantation Laboratory, Manchester Royal Infirmary, Manchester University NHS Foundation Trust, Manchester, UK.,Faculty of Biology, Medicine and Health, Division of Population Health, Health Services Research and Primary Care, School of Health Sciences, University of Manchester, Manchester, England
| | - Antony Payton
- Faculty of Biology, Medicine and Health, Division of Informatics, Imaging & Data Sciences, School of Health Sciences, University of Manchester, Manchester, England
| | - Kay Poulton
- Transplantation Laboratory, Manchester Royal Infirmary, Manchester University NHS Foundation Trust, Manchester, UK.,Faculty of Biology, Medicine and Health, Division of Population Health, Health Services Research and Primary Care, School of Health Sciences, University of Manchester, Manchester, England
| | - Judith Worthington
- Transplantation Laboratory, Manchester Royal Infirmary, Manchester University NHS Foundation Trust, Manchester, UK
| | - Isla Gemmell
- Faculty of Biology, Medicine and Health, Division of Population Health, Health Services Research and Primary Care, School of Health Sciences, University of Manchester, Manchester, England
| | - Arpana Verma
- Faculty of Biology, Medicine and Health, Division of Population Health, Health Services Research and Primary Care, School of Health Sciences, University of Manchester, Manchester, England
| |
Collapse
|
18
|
Xu X, Eales JM, Jiang X, Sanderson E, Drzal M, Saluja S, Scannali D, Williams B, Morris AP, Guzik TJ, Charchar FJ, Holmes MV, Tomaszewski M. Contributions of obesity to kidney health and disease: insights from Mendelian randomization and the human kidney transcriptomics. Cardiovasc Res 2021; 118:3151-3161. [PMID: 34893803 PMCID: PMC9732514 DOI: 10.1093/cvr/cvab357] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/23/2021] [Accepted: 12/06/2021] [Indexed: 12/16/2022] Open
Abstract
AIMS Obesity and kidney diseases are common complex disorders with an increasing clinical and economic impact on healthcare around the globe. Our objective was to examine if modifiable anthropometric obesity indices show putatively causal association with kidney health and disease and highlight biological mechanisms of potential relevance to the association between obesity and the kidney. METHODS AND RESULTS We performed observational, one-sample, two-sample Mendelian randomization (MR) and multivariable MR studies in ∼300 000 participants of white-British ancestry from UK Biobank and participants of predominantly European ancestry from genome-wide association studies. The MR analyses revealed that increasing values of genetically predicted body mass index and waist circumference were causally associated with biochemical indices of renal function, kidney health index (a composite renal outcome derived from blood biochemistry, urine analysis, and International Classification of Disease-based kidney disease diagnoses), and both acute and chronic kidney diseases of different aetiologies including hypertensive renal disease and diabetic nephropathy. Approximately 13-16% and 21-26% of the potentially causal effect of obesity indices on kidney health were mediated by blood pressure and type 2 diabetes, respectively. A total of 61 pathways mapping primarily onto transcriptional/translational regulation, innate and adaptive immunity, and extracellular matrix and metabolism were associated with obesity measures in gene set enrichment analysis in up to 467 kidney transcriptomes. CONCLUSIONS Our data show that a putatively causal association of obesity with renal health is largely independent of blood pressure and type 2 diabetes and uncover the signatures of obesity on the transcriptome of human kidney.
Collapse
Affiliation(s)
- Xiaoguang Xu
- Division of Cardiovascular Sciences, Faculty of Medicine, Biology and Health, University of Manchester, AV Hill Building, Manchester, M13 9PT, UK
| | - James M Eales
- Division of Cardiovascular Sciences, Faculty of Medicine, Biology and Health, University of Manchester, AV Hill Building, Manchester, M13 9PT, UK
| | - Xiao Jiang
- Division of Cardiovascular Sciences, Faculty of Medicine, Biology and Health, University of Manchester, AV Hill Building, Manchester, M13 9PT, UK
| | - Eleanor Sanderson
- MRC Integrative Epidemiology Unit, University of Bristol, Oakfield House, Bristol, BS8 2BN, UK
| | - Maciej Drzal
- Division of Cardiovascular Sciences, Faculty of Medicine, Biology and Health, University of Manchester, AV Hill Building, Manchester, M13 9PT, UK
| | - Sushant Saluja
- Division of Cardiovascular Sciences, Faculty of Medicine, Biology and Health, University of Manchester, AV Hill Building, Manchester, M13 9PT, UK
| | - David Scannali
- Division of Cardiovascular Sciences, Faculty of Medicine, Biology and Health, University of Manchester, AV Hill Building, Manchester, M13 9PT, UK
| | - Bryan Williams
- Institute of Cardiovascular Sciences, University College London, Roger Williams Building, London, WC1E 6HX, UK
| | - Andrew P Morris
- Centre for Genetics and Genomics Versus Arthritis, Centre for Musculoskeletal Research, Division of Musculoskeletal & Dermatological Sciences, Faculty of Medicine, Biology and Health, University of Manchester, AV Hill Building, Manchester, M13 9PT, UK
| | - Tomasz J Guzik
- BHF Glasgow Cardiovascular Research Centre, Institute of Cardiovascular and Medical Sciences, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, G12 8TA, UK,Department of Internal and Agricultural Medicine, Jagiellonian University College of Medicine, Skarbowa 1, 31-121 Kraków, Poland
| | - Fadi J Charchar
- School of Science, Psychology and Sport, Federation University, Ballarat, Victoria, 3353, Australia,Department of Cardiovascular Sciences, University of Leicester, University Road, Leicester, LE1 7RH, UK,Department of Physiology, University of Melbourne, Medical Building 181, Melbourne, Victoria, 3010, Australia
| | - Michael V Holmes
- NIHR Oxford Biomedical Research Centre, Oxford University Hospitals NHS Foundation Trust, John Radcliffe Hospital, Oxford, OX4 2PG, UK,Medical Research Council Population Health Research Unit at the University of Oxford, Nuffield Department of Population Health, University of Oxford, Oxford, OX3 7LF, UK,Clinical Trial Service Unit & Epidemiological Studies Unit (CTSU), Nuffield Department of Population Health, University of Oxford, Big Data Institute Building, Roosevelt Drive, Oxford, OX3 7LF, UK
| | | |
Collapse
|
19
|
Dhande IS, Braun MC, Doris PA. Emerging Insights Into Chronic Renal Disease Pathogenesis in Hypertension From Human and Animal Genomic Studies. Hypertension 2021; 78:1689-1700. [PMID: 34757770 PMCID: PMC8577298 DOI: 10.1161/hypertensionaha.121.18112] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Abstract
The pathogenic links between elevated blood pressure and chronic kidney disease remain obscure. This article examines progress in population genetics and in animal models of hypertension and chronic kidney disease. It also provides a critique of the application of genome-wide association studies to understanding the heritability of renal function. Emerging themes identified indicate that heritable risk of chronic kidney disease in hypertension can arise from genetic variation in (1) glomerular and tubular protein handling mechanisms; (2) autoregulatory capacity of the renal vasculature; and (3) innate and adaptive immune mechanisms. Increased prevalence of hypertension-associated chronic kidney disease that occurs with aging may reflect amplification of heritable risks by normal aging processes affecting immunity and autoregulation.
Collapse
Affiliation(s)
- Isha S. Dhande
- Center for Human Genetics, Brown Foundation Institute of Molecular Medicine, McGovern Medical School, University of Texas HSC, Houston (I.S.D., P.A.D.)
| | - Michael C. Braun
- Department of Pediatrics, Baylor College of Medicine, Texas Children's Hospital, Houston (M.C.B.)
| | - Peter A. Doris
- Center for Human Genetics, Brown Foundation Institute of Molecular Medicine, McGovern Medical School, University of Texas HSC, Houston (I.S.D., P.A.D.)
| |
Collapse
|
20
|
Zeng H, Yang X, Luo S, Zhou Y. The Advances of Single-Cell RNA-Seq in Kidney Immunology. Front Physiol 2021; 12:752679. [PMID: 34721077 PMCID: PMC8548579 DOI: 10.3389/fphys.2021.752679] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2021] [Accepted: 09/20/2021] [Indexed: 01/14/2023] Open
Abstract
Kidney diseases are highly prevalent and treatment is costly. Immune cells play important roles in kidney diseases; however, it has been challenging to investigate the contribution of each cell type in kidney pathophysiology. Recently, the development of single-cell sequencing technology has allowed the extensive study of immune cells in blood, secondary lymphoid tissues, kidney biopsy and urine samples, helping researchers generate a comprehensive immune cell atlas for various kidney diseases. Here, we discuss several recent studies using scRNA-seq technology to explore the immune-related kidney diseases, including lupus nephritis, diabetic kidney disease, IgA nephropathy, and anti-neutrophil cytoplasmic antibody-associated glomerulonephritis. Application of scRNA-seq successfully defined the transcriptome profiles of resident and infiltrating immune cells, as well as the intracellular communication networks between immune and adjacent cells. In addition, the discovery of similar immune cells in blood and urine suggests the possibility of examining kidney immunity without biopsy. In conclusion, these immune cell atlases will increase our understanding of kidney immunology and contribute to novel therapeutics for patients with kidney diseases.
Collapse
Affiliation(s)
- Honghui Zeng
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Guangdong-Hong Kong Joint Laboratory for RNA Medicine, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, China.,Medical Research Center, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, China
| | - Xiaoqiang Yang
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Guangdong-Hong Kong Joint Laboratory for RNA Medicine, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, China.,Medical Research Center, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, China
| | - Siweier Luo
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Guangdong-Hong Kong Joint Laboratory for RNA Medicine, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, China.,Medical Research Center, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, China
| | - Yiming Zhou
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Guangdong-Hong Kong Joint Laboratory for RNA Medicine, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, China.,Medical Research Center, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, China
| |
Collapse
|
21
|
Pleiotropic Effects of Functional MUC1 Variants on Cardiometabolic, Renal, and Hematological Traits in the Taiwanese Population. Int J Mol Sci 2021; 22:ijms221910641. [PMID: 34638981 PMCID: PMC8509060 DOI: 10.3390/ijms221910641] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2021] [Revised: 09/09/2021] [Accepted: 09/27/2021] [Indexed: 12/27/2022] Open
Abstract
MUC1 is a transmembrane mucin involved in carcinogenesis and cell signaling. Functional MUC1 variants are associated with multiple metabolic and biochemical traits. This study investigated the association of functional MUC1 variants with MUC1 DNA methylation and various metabolic, biochemical, and hematological parameters. In total, 80,728 participants from the Taiwan Biobank were enrolled for association analysis using functional MUC1 variants and a nearby gene regional plot association study. A subgroup of 1686 participants was recruited for MUC1 DNA methylation analysis. After Bonferroni correction, we found that two MUC1 variants, rs4072037 and rs12411216, were significantly associated with waist circumference, systolic blood pressure, hemoglobin A1C, renal functional parameters (blood urea nitrogen, serum creatinine levels, and estimated glomerular filtration rate), albuminuria, hematocrit, hemoglobin, red blood cell count, serum uric acid level, and gout risk, with both favorable and unfavorable effects. Causal inference analysis revealed that the association between the variants and gout was partially dependent on the serum uric acid level. Both gene variants showed genome-wide significant associations with MUC1 gene-body methylation. Regional plot association analysis further revealed lead single-nucleotide polymorphisms situated at the nearby TRIM46-MUC1-THBS3-MTX1 gene region for the studied phenotypes. In conclusion, our data demonstrated the pleiotropic effects of MUC1 variants with novel associations for gout, red blood cell parameters, and MUC1 DNA methylation. These results provide further evidence in understanding the critical role of TRIM46-MUC1-THBS3-MTX1 gene region variants in the pathogenesis of cardiometabolic, renal, and hematological disorders.
Collapse
|
22
|
Matías-García PR, Wilson R, Guo Q, Zaghlool SB, Eales JM, Xu X, Charchar FJ, Dormer J, Maalmi H, Schlosser P, Elhadad MA, Nano J, Sharma S, Peters A, Fornoni A, Mook-Kanamori DO, Winkelmann J, Danesh J, Di Angelantonio E, Ouwehand WH, Watkins NA, Roberts DJ, Petrera A, Graumann J, Koenig W, Hveem K, Jonasson C, Köttgen A, Butterworth A, Prunotto M, Hauck SM, Herder C, Suhre K, Gieger C, Tomaszewski M, Teumer A, Waldenberger M. Plasma Proteomics of Renal Function: A Transethnic Meta-Analysis and Mendelian Randomization Study. J Am Soc Nephrol 2021; 32:1747-1763. [PMID: 34135082 PMCID: PMC8425654 DOI: 10.1681/asn.2020071070] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2020] [Revised: 02/24/2021] [Accepted: 03/22/2021] [Indexed: 02/04/2023] Open
Abstract
BACKGROUND Studies on the relationship between renal function and the human plasma proteome have identified several potential biomarkers. However, investigations have been conducted largely in European populations, and causality of the associations between plasma proteins and kidney function has never been addressed. METHODS A cross-sectional study of 993 plasma proteins among 2882 participants in four studies of European and admixed ancestries (KORA, INTERVAL, HUNT, QMDiab) identified transethnic associations between eGFR/CKD and proteomic biomarkers. For the replicated associations, two-sample bidirectional Mendelian randomization (MR) was used to investigate potential causal relationships. Publicly available datasets and transcriptomic data from independent studies were used to examine the association between gene expression in kidney tissue and eGFR. RESULTS In total, 57 plasma proteins were associated with eGFR, including one novel protein. Of these, 23 were additionally associated with CKD. The strongest inferred causal effect was the positive effect of eGFR on testican-2, in line with the known biological role of this protein and the expression of its protein-coding gene (SPOCK2) in renal tissue. We also observed suggestive evidence of an effect of melanoma inhibitory activity (MIA), carbonic anhydrase III, and cystatin-M on eGFR. CONCLUSIONS In a discovery-replication setting, we identified 57 proteins transethnically associated with eGFR. The revealed causal relationships are an important stepping stone in establishing testican-2 as a clinically relevant physiological marker of kidney disease progression, and point to additional proteins warranting further investigation.
Collapse
Affiliation(s)
- Pamela R. Matías-García
- Research Unit Molecular Epidemiology, German Research Center for Environmental Health, Neuherberg, Germany
- Institute of Epidemiology, German Research Center for Environmental Health, Neuherberg, Germany
- TUM School of Medicine, Technical University of Munich, Munich, Germany
- German Center for Cardiovascular Research, Munich, Germany
| | - Rory Wilson
- Research Unit Molecular Epidemiology, German Research Center for Environmental Health, Neuherberg, Germany
- Institute of Epidemiology, German Research Center for Environmental Health, Neuherberg, Germany
| | - Qi Guo
- Department of Public Health and Primary Care, University of Cambridge, Cambridge, United Kingdom
| | - Shaza B. Zaghlool
- Department of Physiology and Biophysics, Weill Cornell Medicine-Qatar, Doha, Qatar
| | - James M. Eales
- Division of Cardiovascular Sciences, University of Manchester, Manchester, United Kingdom
| | - Xiaoguang Xu
- Division of Cardiovascular Sciences, University of Manchester, Manchester, United Kingdom
| | - Fadi J. Charchar
- School of Health and Life Sciences, Federation University Australia, Ballarat, Australia
- Department of Cardiovascular Sciences, University of Leicester, Leicester, United Kingdom
- Department of Physiology, University of Melbourne, Melbourne, Australia
| | - John Dormer
- Department of Cellular Pathology, University Hospitals of Leicester National Health Service Trust, Leicester, United Kingdom
| | - Haifa Maalmi
- Institute for Clinical Diabetology, Leibniz Center for Diabetes Research at Heinrich Heine University Düsseldorf, Düsseldorf, Germany
- German Center for Diabetes Research, München-Neuherberg, Germany
| | - Pascal Schlosser
- Department of Data-Driven Medicine, Institute of Genetic Epidemiology, Faculty of Medicine and Medical Center-University of Freiburg, Freiburg, Germany
| | - Mohamed A. Elhadad
- Research Unit Molecular Epidemiology, German Research Center for Environmental Health, Neuherberg, Germany
- Institute of Epidemiology, German Research Center for Environmental Health, Neuherberg, Germany
- German Center for Cardiovascular Research, Munich, Germany
| | - Jana Nano
- Institute of Epidemiology, German Research Center for Environmental Health, Neuherberg, Germany
- German Center for Diabetes Research, München-Neuherberg, Germany
| | - Sapna Sharma
- Research Unit Molecular Epidemiology, German Research Center for Environmental Health, Neuherberg, Germany
- Institute of Epidemiology, German Research Center for Environmental Health, Neuherberg, Germany
| | - Annette Peters
- Institute of Epidemiology, German Research Center for Environmental Health, Neuherberg, Germany
- German Center for Cardiovascular Research, Munich, Germany
- German Center for Diabetes Research, München-Neuherberg, Germany
| | - Alessia Fornoni
- Department of Medicine, Katz Family Division of Nephrology and Hypertension, University of Miami Miller School of Medicine, Miami, Florida
| | - Dennis O. Mook-Kanamori
- Department of Clinical Epidemiology, Leiden University Medical Centre, Leiden, The Netherlands
| | - Juliane Winkelmann
- Institute of Neurogenomics, German Research Center for Environmental Health, Neuherberg, Germany
- Department of Neurogenetics and Institute of Human Genetics, Technical University of Munich, Munich, Germany
| | - John Danesh
- Department of Public Health and Primary Care, University of Cambridge, Cambridge, United Kingdom
- British Heart Foundation Centre of Research Excellence, University of Cambridge, Cambridge, United Kingdom
- National Institute for Health Research Blood and Transplant Research Unit in Donor Health and Genomics, University of Cambridge, Cambridge, United Kingdom
- National Institute for Health Research Cambridge Biomedical Research Centre, University of Cambridge and Cambridge University Hospitals, Cambridge, United Kingdom
- Health Data Research UK Cambridge, Wellcome Genome Campus and University of Cambridge, Cambridge, United Kingdom
- Department of Human Genetics, Wellcome Sanger Institute, Hinxton, United Kingdom
| | - Emanuele Di Angelantonio
- Department of Public Health and Primary Care, University of Cambridge, Cambridge, United Kingdom
- British Heart Foundation Centre of Research Excellence, University of Cambridge, Cambridge, United Kingdom
- National Institute for Health Research Blood and Transplant Research Unit in Donor Health and Genomics, University of Cambridge, Cambridge, United Kingdom
- National Institute for Health Research Cambridge Biomedical Research Centre, University of Cambridge and Cambridge University Hospitals, Cambridge, United Kingdom
- Health Data Research UK Cambridge, Wellcome Genome Campus and University of Cambridge, Cambridge, United Kingdom
| | - Willem H. Ouwehand
- British Heart Foundation Centre of Research Excellence, University of Cambridge, Cambridge, United Kingdom
- Department of Haematology, University of Cambridge, Cambridge, United Kingdom
- National Health Service Blood and Transplant, Cambridge Biomedical Campus, Long Road, Cambridge, United Kingdom
- Wellcome Sanger Institute, Hinxton, United Kingdom
| | - Nicholas A. Watkins
- National Health Service Blood and Transplant, Cambridge Biomedical Campus, Long Road, Cambridge, United Kingdom
| | - David J. Roberts
- National Institute for Health Research Blood and Transplant Research Unit in Donor Health and Genomics, University of Cambridge, Cambridge, United Kingdom
- National Health Service Blood and Transplant Oxford Centre, Oxford, United Kingdom
- Radcliffe Department of Medicine, University of Oxford, Oxford, United Kingdom
| | - Agnese Petrera
- Research Unit Protein Science and Metabolomics and Proteomics Core Facility, Helmholtz Zentrum Munich - German Research Center for Environmental Health, Neuherberg, Germany
| | - Johannes Graumann
- Scientific Service Group Biomolecular Mass Spectrometry, Max Planck Institute for Heart and Lung Research, Bad Nauheim, Germany
- German Centre for Cardiovascular Research (DZHK), Partner Site Rhine-Main, Max Planck Institute of Heart and Lung Research, Bad Nauheim, Germany
| | - Wolfgang Koenig
- German Center for Cardiovascular Research, Munich, Germany
- Klinik für Herz-Kreislauferkrankungen, Deutsches Herzzentrum München, Technical University of Munich, Munich, Germany
- Institute of Epidemiology and Medical Biometry, University of Ulm, Ulm, Germany
| | - Kristian Hveem
- Department of Public Health and Nursing, Norwegian University of Science and Technology, Trondheim, Norway
- Nord-Trøndelag Health Study HUNT Research Centre, Faculty of Medicine, Norwegian University of Science and Technology, Levanger, Norway
| | - Christian Jonasson
- Department of Public Health and Nursing, Norwegian University of Science and Technology, Trondheim, Norway
- Nord-Trøndelag Health Study HUNT Research Centre, Faculty of Medicine, Norwegian University of Science and Technology, Levanger, Norway
| | - Anna Köttgen
- Department of Data-Driven Medicine, Institute of Genetic Epidemiology, Faculty of Medicine and Medical Center-University of Freiburg, Freiburg, Germany
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland
| | - Adam Butterworth
- Department of Public Health and Primary Care, University of Cambridge, Cambridge, United Kingdom
| | - Marco Prunotto
- School of Pharmaceutical Sciences, University of Geneva, Geneva, Switzerland
| | - Stefanie M. Hauck
- Research Unit Protein Science and Metabolomics and Proteomics Core Facility, Helmholtz Zentrum Munich - German Research Center for Environmental Health, Neuherberg, Germany
| | - Christian Herder
- Institute for Clinical Diabetology, Leibniz Center for Diabetes Research at Heinrich Heine University Düsseldorf, Düsseldorf, Germany
- German Center for Diabetes Research, München-Neuherberg, Germany
- Department of Endocrinology and Diabetology, Medical Faculty and University Hospital Düsseldorf, Heinrich-Heine-University Düsseldorf, Düsseldorf, Germany
| | - Karsten Suhre
- Department of Physiology and Biophysics, Weill Cornell Medicine-Qatar, Doha, Qatar
| | - Christian Gieger
- Research Unit Molecular Epidemiology, German Research Center for Environmental Health, Neuherberg, Germany
- Institute of Epidemiology, German Research Center for Environmental Health, Neuherberg, Germany
- German Center for Cardiovascular Research, Munich, Germany
| | - Maciej Tomaszewski
- Division of Cardiovascular Sciences, University of Manchester, Manchester, United Kingdom
- Manchester Heart Centre and Manchester Academic Health Science Centre, Manchester University NHS Foundation Trust, Manchester, United Kingdom
| | - Alexander Teumer
- Department SHIP/Clinical-Epidemiological Research, Institute for Community Medicine, University Medicine Greifswald, Greifswald, Germany
- German Center for Cardiovascular Research, partner site Greifswald, Greifswald, Germany
| | - Melanie Waldenberger
- Research Unit Molecular Epidemiology, German Research Center for Environmental Health, Neuherberg, Germany
- Institute of Epidemiology, German Research Center for Environmental Health, Neuherberg, Germany
- German Center for Cardiovascular Research, Munich, Germany
| | | |
Collapse
|
23
|
Šalamon Š, Bevc S, Ekart R, Hojs R, Potočnik U. Polymorphism in the GATM Locus Associated with Dialysis-Independent Chronic Kidney Disease but Not Dialysis-Dependent Kidney Failure. Genes (Basel) 2021; 12:834. [PMID: 34071541 PMCID: PMC8228672 DOI: 10.3390/genes12060834] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2021] [Revised: 05/22/2021] [Accepted: 05/25/2021] [Indexed: 12/19/2022] Open
Abstract
The ten most statistically significant estimated glomerular filtration rate (eGFRcrea)-associated loci from genome-wide association studies (GWAs) are tested for associations with chronic kidney disease (CKD) in 208 patients, including dialysis-independent CKD and dialysis-dependent end-stage renal disease (kidney failure). The allele A of intergenic SNP rs2453533 (near GATM) is more frequent in dialysis-independent CKD patients (n = 135, adjusted p = 0.020) but not dialysis-dependent kidney failure patients (n = 73) compared to healthy controls (n = 309). The allele C of intronic SNP rs4293393 (UMOD) is more frequent in healthy controls (adjusted p = 0.042) than in CKD patients. The Allele T of intronic SNP rs9895661 (BCAS3) is associated with decreased eGFRcys (adjusted p = 0.001) and eGFRcrea (adjusted p = 0.017). Our results provide further evidence of a genetic difference between dialysis-dialysis-independent CKD and dialysis-dependent kidney failure, and add the GATM gene locus to the list of loci associated only with dialysis-independent CKD. GATM risk allele carriers in the dialysis-independent group may have a genetic susceptibility to higher creatinine production rather than increased serum creatinine due to kidney malfunction, and therefore, do not progress to dialysis-dependent kidney failure. When using eGFRcrea for CKD diagnosis, physicians might benefit from information about creatinine-increasing loci.
Collapse
Affiliation(s)
- Špela Šalamon
- Center for Human Molecular Genetics and Pharmacogenomics, Faculty of Medicine, University of Maribor, Taborska ul. 8, 2000 Maribor, Slovenia;
| | - Sebastjan Bevc
- Department of Nephrology, Clinic for Internal Medicine, University Medical Centre Maribor, Ljubljanska Ulica 5, 2000 Maribor, Slovenia; (S.B.); (R.H.)
- Department of Internal Medicine and Department of Pharmacology, Faculty of Medicine, University of Maribor, Taborska Ulica 8, 2000 Maribor, Slovenia;
| | - Robert Ekart
- Department of Internal Medicine and Department of Pharmacology, Faculty of Medicine, University of Maribor, Taborska Ulica 8, 2000 Maribor, Slovenia;
- Department of Dialysis, Clinic for Internal Medicine, University Medical Centre Maribor, Ljubljanska Ulica 5, 2000 Maribor, Slovenia
| | - Radovan Hojs
- Department of Nephrology, Clinic for Internal Medicine, University Medical Centre Maribor, Ljubljanska Ulica 5, 2000 Maribor, Slovenia; (S.B.); (R.H.)
- Department of Internal Medicine and Department of Pharmacology, Faculty of Medicine, University of Maribor, Taborska Ulica 8, 2000 Maribor, Slovenia;
| | - Uroš Potočnik
- Center for Human Molecular Genetics and Pharmacogenomics, Faculty of Medicine, University of Maribor, Taborska ul. 8, 2000 Maribor, Slovenia;
- Laboratory for Biochemistry, Molecular Biology and Genomics, Faculty for Chemistry and Chemical Engineering, University of Maribor, Smetanova ul. 17, 2000 Maribor, Slovenia
| |
Collapse
|
24
|
Eales JM, Jiang X, Xu X, Saluja S, Akbarov A, Cano-Gamez E, McNulty MT, Finan C, Guo H, Wystrychowski W, Szulinska M, Thomas HB, Pramanik S, Chopade S, Prestes PR, Wise I, Evangelou E, Salehi M, Shakanti Y, Ekholm M, Denniff M, Nazgiewicz A, Eichinger F, Godfrey B, Antczak A, Glyda M, Król R, Eyre S, Brown J, Berzuini C, Bowes J, Caulfield M, Zukowska-Szczechowska E, Zywiec J, Bogdanski P, Kretzler M, Woolf AS, Talavera D, Keavney B, Maffia P, Guzik TJ, O'Keefe RT, Trynka G, Samani NJ, Hingorani A, Sampson MG, Morris AP, Charchar FJ, Tomaszewski M. Uncovering genetic mechanisms of hypertension through multi-omic analysis of the kidney. Nat Genet 2021; 53:630-637. [PMID: 33958779 DOI: 10.1038/s41588-021-00835-w] [Citation(s) in RCA: 31] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2020] [Accepted: 03/04/2021] [Indexed: 02/02/2023]
Abstract
The kidney is an organ of key relevance to blood pressure (BP) regulation, hypertension and antihypertensive treatment. However, genetically mediated renal mechanisms underlying susceptibility to hypertension remain poorly understood. We integrated genotype, gene expression, alternative splicing and DNA methylation profiles of up to 430 human kidneys to characterize the effects of BP index variants from genome-wide association studies (GWASs) on renal transcriptome and epigenome. We uncovered kidney targets for 479 (58.3%) BP-GWAS variants and paired 49 BP-GWAS kidney genes with 210 licensed drugs. Our colocalization and Mendelian randomization analyses identified 179 unique kidney genes with evidence of putatively causal effects on BP. Through Mendelian randomization, we also uncovered effects of BP on renal outcomes commonly affecting patients with hypertension. Collectively, our studies identified genetic variants, kidney genes, molecular mechanisms and biological pathways of key relevance to the genetic regulation of BP and inherited susceptibility to hypertension.
Collapse
Affiliation(s)
- James M Eales
- Division of Cardiovascular Sciences, Faculty of Medicine, Biology and Health, University of Manchester, Manchester, UK
| | - Xiao Jiang
- Division of Cardiovascular Sciences, Faculty of Medicine, Biology and Health, University of Manchester, Manchester, UK
| | - Xiaoguang Xu
- Division of Cardiovascular Sciences, Faculty of Medicine, Biology and Health, University of Manchester, Manchester, UK
| | - Sushant Saluja
- Division of Cardiovascular Sciences, Faculty of Medicine, Biology and Health, University of Manchester, Manchester, UK
| | - Artur Akbarov
- Division of Cardiovascular Sciences, Faculty of Medicine, Biology and Health, University of Manchester, Manchester, UK
| | - Eddie Cano-Gamez
- Department of Human Genetics, Wellcome Sanger Institute, Cambridge, UK
| | - Michelle T McNulty
- Division of Nephrology, Boston Children's Hospital, Boston, MA, USA.,The Broad Institute, Cambridge, MA, USA
| | - Christopher Finan
- Institute of Cardiovascular Science, University College London, London, UK
| | - Hui Guo
- Centre for Biostatistics, School of Health Sciences, Faculty of Medicine, Biology and Health, University of Manchester, Manchester, UK
| | - Wojciech Wystrychowski
- Department of General, Vascular and Transplant Surgery, Medical University of Silesia, Katowice, Poland
| | - Monika Szulinska
- Department of Obesity, Metabolic Disorders Treatment and Clinical Dietetics, Karol Marcinkowski University of Medical Sciences, Poznan, Poland
| | - Huw B Thomas
- Division of Evolution and Genomic Sciences, Faculty of Medicine, Biology and Health, University of Manchester, Manchester, UK
| | - Sanjeev Pramanik
- Division of Cardiovascular Sciences, Faculty of Medicine, Biology and Health, University of Manchester, Manchester, UK.,East Lancashire Hospitals NHS Trust, Blackburn, UK
| | - Sandesh Chopade
- Institute of Cardiovascular Science, University College London, London, UK
| | - Priscilla R Prestes
- Health Innovation and Transformation Centre, School of Science, Psychology and Sport, Federation University Australia, Ballarat, Victoria, Australia
| | - Ingrid Wise
- Australian Institute of Tropical Health & Medicine, James Cook University, Cairns, Queensland, Australia
| | - Evangelos Evangelou
- Department of Epidemiology and Biostatistics, School of Public Health, Imperial College London, London, UK.,Department of Hygiene and Epidemiology, University of Ioannina Medical School, Ioannina, Greece
| | - Mahan Salehi
- Division of Cardiovascular Sciences, Faculty of Medicine, Biology and Health, University of Manchester, Manchester, UK
| | - Yusif Shakanti
- Division of Cardiovascular Sciences, Faculty of Medicine, Biology and Health, University of Manchester, Manchester, UK
| | - Mikael Ekholm
- Division of Cardiovascular Sciences, Faculty of Medicine, Biology and Health, University of Manchester, Manchester, UK.,Department of Clinical Sciences, Danderyd Hospital, Karolinska Institutet, Stockholm, Sweden
| | - Matthew Denniff
- Department of Cardiovascular Sciences, University of Leicester, Leicester, UK
| | - Alicja Nazgiewicz
- Division of Cardiovascular Sciences, Faculty of Medicine, Biology and Health, University of Manchester, Manchester, UK
| | - Felix Eichinger
- Department of Medicine, University of Michigan, Ann Arbor, MI, USA
| | - Bradley Godfrey
- Department of Urology and Uro-oncology, Karol Marcinkowski University of Medical Sciences, Poznan, Poland
| | - Andrzej Antczak
- Department of Urology and Uro-oncology, Karol Marcinkowski University of Medical Sciences, Poznan, Poland
| | - Maciej Glyda
- Department of Transplantology and General Surgery Poznan, Collegium Medicum, Nicolaus Copernicus University, Bydgoszcz, Poland
| | - Robert Król
- Department of General, Vascular and Transplant Surgery, Medical University of Silesia, Katowice, Poland
| | - Stephen Eyre
- Division of Musculoskeletal and Dermatological Sciences, Faculty of Medicine, Biology and Health, University of Manchester, Manchester, UK
| | - Jason Brown
- Division of Research and Innovation, Manchester University NHS Foundation Trust, Manchester, UK
| | - Carlo Berzuini
- Centre for Biostatistics, School of Health Sciences, Faculty of Medicine, Biology and Health, University of Manchester, Manchester, UK
| | - John Bowes
- Division of Musculoskeletal and Dermatological Sciences, Faculty of Medicine, Biology and Health, University of Manchester, Manchester, UK
| | - Mark Caulfield
- William Harvey Research Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, London, UK.,National Institute for Health Research, Barts Cardiovascular Biomedical Research Centre, Queen Mary University of London, London, UK
| | | | - Joanna Zywiec
- Department of Internal Medicine, Diabetology and Nephrology, Zabrze, Medical University of Silesia, Katowice, Poland
| | - Pawel Bogdanski
- Department of Obesity, Metabolic Disorders Treatment and Clinical Dietetics, Karol Marcinkowski University of Medical Sciences, Poznan, Poland
| | | | - Adrian S Woolf
- Division of Cell Matrix Biology and Regenerative Medicine, Faculty of Biology, Medicine and Health, University of Manchester, Manchester, UK.,Royal Manchester Children's Hospital and Manchester Academic Health Science Centre, Manchester University NHS Foundation Trust, Manchester, UK
| | - David Talavera
- Division of Cardiovascular Sciences, Faculty of Medicine, Biology and Health, University of Manchester, Manchester, UK
| | - Bernard Keavney
- Division of Cardiovascular Sciences, Faculty of Medicine, Biology and Health, University of Manchester, Manchester, UK.,Division of Cardiology and Manchester Academic Health Science Centre, Manchester University NHS Foundation Trust, Manchester, UK
| | - Pasquale Maffia
- Institute of Infection, Immunity and Inflammation, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, UK.,Institute of Cardiovascular and Medical Sciences, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, UK.,Department of Pharmacy, University of Naples Federico II, Naples, Italy
| | - Tomasz J Guzik
- Institute of Cardiovascular and Medical Sciences, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, UK.,Department of Internal and Agricultural Medicine, Jagiellonian University College of Medicine, Kraków, Poland
| | - Raymond T O'Keefe
- Division of Evolution and Genomic Sciences, Faculty of Medicine, Biology and Health, University of Manchester, Manchester, UK
| | - Gosia Trynka
- Department of Human Genetics, Wellcome Sanger Institute, Cambridge, UK.,Open Targets, Wellcome Genome Campus, Cambridge, UK
| | - Nilesh J Samani
- Department of Cardiovascular Sciences, University of Leicester, Leicester, UK.,National Institute for Health Research, Leicester Biomedical Research Centre, Leicester, UK
| | - Aroon Hingorani
- Institute of Cardiovascular Science, University College London, London, UK
| | - Matthew G Sampson
- Division of Nephrology, Boston Children's Hospital, Boston, MA, USA.,The Broad Institute, Cambridge, MA, USA.,Harvard Medical School, Boston, MA, USA
| | - Andrew P Morris
- Division of Musculoskeletal and Dermatological Sciences, Faculty of Medicine, Biology and Health, University of Manchester, Manchester, UK.,Department of Biostatistics, Institute of Translational Medicine, University of Liverpool, Liverpool, UK
| | - Fadi J Charchar
- Health Innovation and Transformation Centre, School of Science, Psychology and Sport, Federation University Australia, Ballarat, Victoria, Australia.,Department of Cardiovascular Sciences, University of Leicester, Leicester, UK.,Department of Physiology, University of Melbourne, Parkville, Victoria, Australia
| | - Maciej Tomaszewski
- Division of Cardiovascular Sciences, Faculty of Medicine, Biology and Health, University of Manchester, Manchester, UK. .,Manchester Heart Centre and Manchester Academic Health Science Centre, Manchester University NHS Foundation Trust, Manchester, UK.
| |
Collapse
|
25
|
Breeze CE, Batorsky A, Lee MK, Szeto MD, Xu X, McCartney DL, Jiang R, Patki A, Kramer HJ, Eales JM, Raffield L, Lange L, Lange E, Durda P, Liu Y, Tracy RP, Van Den Berg D, Evans KL, Kraus WE, Shah S, Tiwari HK, Hou L, Whitsel EA, Jiang X, Charchar FJ, Baccarelli AA, Rich SS, Morris AP, Irvin MR, Arnett DK, Hauser ER, Rotter JI, Correa A, Hayward C, Horvath S, Marioni RE, Tomaszewski M, Beck S, Berndt SI, London SJ, Mychaleckyj JC, Franceschini N. Epigenome-wide association study of kidney function identifies trans-ethnic and ethnic-specific loci. Genome Med 2021; 13:74. [PMID: 33931109 PMCID: PMC8088054 DOI: 10.1186/s13073-021-00877-z] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2020] [Accepted: 03/24/2021] [Indexed: 11/18/2022] Open
Abstract
BACKGROUND DNA methylation (DNAm) is associated with gene regulation and estimated glomerular filtration rate (eGFR), a measure of kidney function. Decreased eGFR is more common among US Hispanics and African Americans. The causes for this are poorly understood. We aimed to identify trans-ethnic and ethnic-specific differentially methylated positions (DMPs) associated with eGFR using an agnostic, genome-wide approach. METHODS The study included up to 5428 participants from multi-ethnic studies for discovery and 8109 participants for replication. We tested the associations between whole blood DNAm and eGFR using beta values from Illumina 450K or EPIC arrays. Ethnicity-stratified analyses were performed using linear mixed models adjusting for age, sex, smoking, and study-specific and technical variables. Summary results were meta-analyzed within and across ethnicities. Findings were assessed using integrative epigenomics methods and pathway analyses. RESULTS We identified 93 DMPs associated with eGFR at an FDR of 0.05 and replicated 13 and 1 DMPs across independent samples in trans-ethnic and African American meta-analyses, respectively. The study also validated 6 previously published DMPs. Identified DMPs showed significant overlap enrichment with DNase I hypersensitive sites in kidney tissue, sites associated with the expression of proximal genes, and transcription factor motifs and pathways associated with kidney tissue and kidney development. CONCLUSIONS We uncovered trans-ethnic and ethnic-specific DMPs associated with eGFR, including DMPs enriched in regulatory elements in kidney tissue and pathways related to kidney development. These findings shed light on epigenetic mechanisms associated with kidney function, bridging the gap between population-specific eGFR-associated DNAm and tissue-specific regulatory context.
Collapse
Affiliation(s)
- Charles E Breeze
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Department Health and Human Services, Bethesda, MD, USA.
- UCL Cancer Institute, University College London, London, WC1E 6BT, UK.
- Altius Institute for Biomedical Sciences, Seattle, WA, 98121, USA.
| | - Anna Batorsky
- Department of Biostatistics, University of North Carolina, Chapel Hill, NC, 27516, USA
| | - Mi Kyeong Lee
- Epidemiology Branch, National Institute of Environmental Health Sciences, National Institutes of Health, Department of Health and Human Services, Research Triangle Park, NC, 27709, USA
| | - Mindy D Szeto
- Division of Biomedical Informatics and Personalized Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - Xiaoguang Xu
- Division of Cardiovascular Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester, UK
| | - Daniel L McCartney
- Centre for Genomic and Experimental Medicine, Institute of Genetics and Molecular Medicine, University of Edinburgh, Crewe Road, Edinburgh, EH4 2XU, UK
| | - Rong Jiang
- Department of Psychiatry and Behavioral Sciences, Duke University Medical Center, Durham, NC, 27701, USA
| | - Amit Patki
- Department of Biostatistics, University of Alabama, Birmingham, AL, USA
| | - Holly J Kramer
- Department of Public Health Sciences and Medicine, Loyola University Chicago, Maywood, IL, USA
- Division of Nephrology and Hypertension, Loyola University Chicago, Maywood, IL, USA
| | - James M Eales
- Division of Cardiovascular Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester, UK
| | - Laura Raffield
- Department of Genetics, University of North Carolina, Chapel Hill, NC, USA
| | - Leslie Lange
- Division of Biomedical Informatics and Personalized Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - Ethan Lange
- Division of Biomedical Informatics and Personalized Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - Peter Durda
- Department of Pathology & Laboratory Medicine, Larner College of Medicine, University of Vermont, Burlington, VT, USA
| | - Yongmei Liu
- Duke Molecular Physiology Institute, Duke University Medical Center, Durham, NC, USA
| | - Russ P Tracy
- Department of Pathology & Laboratory Medicine, Larner College of Medicine, University of Vermont, Burlington, VT, USA
- Department of Biochemistry, Larner College of Medicine, University of Vermont, Burlington, VT, USA
| | - David Van Den Berg
- Center for Genetic Epidemiology, Department of Preventive Medicine, Keck School of Medicine of USC, University of Southern California, Los Angeles, CA, USA
| | - Kathryn L Evans
- Centre for Genomic and Experimental Medicine, Institute of Genetics and Molecular Medicine, University of Edinburgh, Crewe Road, Edinburgh, EH4 2XU, UK
| | - William E Kraus
- Duke Molecular Physiology Institute, Duke University Medical Center, Durham, NC, USA
- Division of Cardiology, Department of Medicine, School of Medicine, Duke University, Durham, NC, USA
| | - Svati Shah
- Duke Molecular Physiology Institute, Duke University Medical Center, Durham, NC, USA
- Division of Cardiology, Department of Medicine, School of Medicine, Duke University, Durham, NC, USA
| | - Hermant K Tiwari
- Department of Biostatistics, University of Alabama, Birmingham, AL, USA
| | - Lifang Hou
- Department of Preventive Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
- Center for Global Oncology, Institute of Global Health, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
| | - Eric A Whitsel
- Department of Epidemiology, University of North Carolina, Chapel Hill, NC, USA
- Department of Medicine, University of North Carolina, Chapel Hill, NC, 27599, USA
| | - Xiao Jiang
- Division of Cardiovascular Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester, UK
| | - Fadi J Charchar
- School of Health and Life Sciences, Federation University Australia, Ballarat, VIC, Australia
- Department of Physiology, University of Melbourne, Parkville, VIC, Australia
- Department of Cardiovascular Sciences, University of Leicester, Leicester, UK
| | - Andrea A Baccarelli
- Laboratory of Environmental Epigenetics, Departments of Environmental Health Sciences and Epidemiology, Columbia University Mailman School of Public Health, New York, NY, USA
| | - Stephen S Rich
- Center for Public Health Genomics, University of Virginia, Charlottesville, VA, USA
| | - Andrew P Morris
- Centre for Genetics and Genomics Versus Arthritis, Centre for Musculoskeletal Research, The University of Manchester, Manchester, UK
| | - Marguerite R Irvin
- Department of Epidemiology, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Donna K Arnett
- College of Public Health, University of Kentucky, Lexington, KY, USA
| | - Elizabeth R Hauser
- Duke Molecular Physiology Institute, Duke University Medical Center, Durham, NC, USA
- Durham VA Health System, Durham, NC, 27705, USA
| | - 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, CA, USA
| | - Adolfo Correa
- Department of Medicine, University of Mississippi Medical Center, Jackson, MS, USA
| | - Caroline Hayward
- MRC Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Crewe Road, Edinburgh, EH4 2XU, UK
| | - Steve Horvath
- Department of Human Genetics, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA, 90095, USA
- Department of Biostatistics, Fielding School of Public Health, University of California Los Angeles, Los Angeles, CA, 90095, USA
| | - Riccardo E Marioni
- Centre for Genomic and Experimental Medicine, Institute of Genetics and Molecular Medicine, University of Edinburgh, Crewe Road, Edinburgh, EH4 2XU, UK
| | - Maciej Tomaszewski
- Division of Cardiovascular Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester, UK
- Manchester Heart Centre and Manchester Academic Health Science Centre, Manchester University NHS Foundation Trust, Manchester, UK
| | - Stephan Beck
- UCL Cancer Institute, University College London, London, WC1E 6BT, UK
| | - Sonja I Berndt
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Department Health and Human Services, Bethesda, MD, USA
| | - Stephanie J London
- Epidemiology Branch, National Institute of Environmental Health Sciences, National Institutes of Health, Department of Health and Human Services, Research Triangle Park, NC, 27709, USA
| | - Josyf C Mychaleckyj
- Center for Public Health Genomics, University of Virginia, Charlottesville, VA, USA
| | - Nora Franceschini
- Department of Epidemiology, University of North Carolina, Chapel Hill, NC, USA.
| |
Collapse
|
26
|
Rigby MJ, Lawton AJ, Kaur G, Banduseela VC, Kamm WE, Lakkaraju A, Denu JM, Puglielli L. Endoplasmic reticulum acetyltransferases Atase1 and Atase2 differentially regulate reticulophagy, macroautophagy and cellular acetyl-CoA metabolism. Commun Biol 2021; 4:454. [PMID: 33846551 PMCID: PMC8041774 DOI: 10.1038/s42003-021-01992-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2020] [Accepted: 03/17/2021] [Indexed: 12/25/2022] Open
Abstract
Nε-lysine acetylation in the ER lumen is a recently discovered quality control mechanism that ensures proteostasis within the secretory pathway. The acetyltransferase reaction is carried out by two type-II membrane proteins, ATase1/NAT8B and ATase2/NAT8. Prior studies have shown that reducing ER acetylation can induce reticulophagy, increase ER turnover, and alleviate proteotoxic states. Here, we report the generation of Atase1-/- and Atase2-/- mice and show that these two ER-based acetyltransferases play different roles in the regulation of reticulophagy and macroautophagy. Importantly, knockout of Atase1 alone results in activation of reticulophagy and rescue of the proteotoxic state associated with Alzheimer's disease. Furthermore, loss of Atase1 or Atase2 results in widespread adaptive changes in the cell acetylome and acetyl-CoA metabolism. Overall, our study supports a divergent role of Atase1 and Atase2 in cellular biology, emphasizing ATase1 as a valid translational target for diseases characterized by toxic protein aggregation in the secretory pathway.
Collapse
Affiliation(s)
- Michael J Rigby
- Department of Medicine, University of Wisconsin-Madison, Madison, WI, USA
- Neuroscience Training Program, University of Wisconsin-Madison, Madison, WI, USA
- Waisman Center, University of Wisconsin-Madison, Madison, WI, USA
| | - Alexis J Lawton
- Department of Biomolecular Chemistry and the Wisconsin Institute for Discovery, University of Wisconsin-Madison, Madison, WI, USA
| | - Gulpreet Kaur
- Department of Ophthalmology and Visual Sciences, University of Wisconsin-Madison, Madison, WI, USA
| | - Varuna C Banduseela
- Department of Medicine, University of Wisconsin-Madison, Madison, WI, USA
- Department of Pharmacology, University of Michigan, Ann Arbor, MI, USA
| | - William E Kamm
- Department of Medicine, University of Wisconsin-Madison, Madison, WI, USA
- Waisman Center, University of Wisconsin-Madison, Madison, WI, USA
| | - Aparna Lakkaraju
- Department of Ophthalmology and Visual Sciences, University of Wisconsin-Madison, Madison, WI, USA
- Department of Ophthalmology and Anatomy, University of California, San Francisco, CA, USA
| | - John M Denu
- Department of Biomolecular Chemistry and the Wisconsin Institute for Discovery, University of Wisconsin-Madison, Madison, WI, USA
| | - Luigi Puglielli
- Department of Medicine, University of Wisconsin-Madison, Madison, WI, USA.
- Neuroscience Training Program, University of Wisconsin-Madison, Madison, WI, USA.
- Waisman Center, University of Wisconsin-Madison, Madison, WI, USA.
- Geriatric Research Education Clinical Center, Veterans Affairs Medical Center, Madison, WI, USA.
| |
Collapse
|
27
|
Duan A, Wang H, Zhu Y, Wang Q, Zhang J, Hou Q, Xing Y, Shi J, Hou J, Qin Z, Chen Z, Liu Z, Yang J. Chromatin architecture reveals cell type-specific target genes for kidney disease risk variants. BMC Biol 2021; 19:38. [PMID: 33627123 PMCID: PMC7905576 DOI: 10.1186/s12915-021-00977-7] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2020] [Accepted: 02/08/2021] [Indexed: 12/27/2022] Open
Abstract
BACKGROUND Cell type-specific transcriptional programming results from the combinatorial interplay between the repertoire of active regulatory elements. Disease-associated variants disrupt such programming, leading to altered expression of downstream regulated genes and the onset of pathological states. However, due to the non-linear regulatory properties of non-coding elements such as enhancers, which can activate transcription at long distances and in a non-directional way, the identification of causal variants and their target genes remains challenging. Here, we provide a multi-omics analysis to identify regulatory elements associated with functional kidney disease variants, and downstream regulated genes. RESULTS In order to understand the genetic risk of kidney diseases, we generated a comprehensive dataset of the chromatin landscape of human kidney tubule cells, including transcription-centered 3D chromatin organization, histone modifications distribution and transcriptome with HiChIP, ChIP-seq and RNA-seq. We identified genome-wide functional elements and thousands of interactions between the distal elements and target genes. The results revealed that risk variants for renal tumor and chronic kidney disease were enriched in kidney tubule cells. We further pinpointed the target genes for the variants and validated two target genes by CRISPR/Cas9 genome editing techniques in zebrafish, demonstrating that SLC34A1 and MTX1 were indispensable genes to maintain kidney function. CONCLUSIONS Our results provide a valuable multi-omics resource on the chromatin landscape of human kidney tubule cells and establish a bioinformatic pipeline in dissecting functions of kidney disease-associated variants based on cell type-specific epigenome.
Collapse
Affiliation(s)
- Aiping Duan
- National Clinical Research Center for Kidney Disease, Jinling Hospital, Medical School of Nanjing University, Nanjing, 210002, Jiangsu, China
- Medical School of Nanjing University, Nanjing, 210093, Jiangsu, China
| | - Hong Wang
- Medical School of Nanjing University, Nanjing, 210093, Jiangsu, China
| | - Yan Zhu
- National Clinical Research Center for Kidney Disease, Jinling Hospital, Medical School of Nanjing University, Nanjing, 210002, Jiangsu, China
- Medical School of Nanjing University, Nanjing, 210093, Jiangsu, China
| | - Qi Wang
- Medical School of Nanjing University, Nanjing, 210093, Jiangsu, China
| | - Jing Zhang
- Medical School of Nanjing University, Nanjing, 210093, Jiangsu, China
| | - Qing Hou
- National Clinical Research Center for Kidney Disease, Jinling Hospital, Medical School of Nanjing University, Nanjing, 210002, Jiangsu, China
- Medical School of Nanjing University, Nanjing, 210093, Jiangsu, China
| | - Yuexian Xing
- National Clinical Research Center for Kidney Disease, Jinling Hospital, Medical School of Nanjing University, Nanjing, 210002, Jiangsu, China
- Medical School of Nanjing University, Nanjing, 210093, Jiangsu, China
| | - Jinsong Shi
- National Clinical Research Center for Kidney Disease, Jinling Hospital, Medical School of Nanjing University, Nanjing, 210002, Jiangsu, China
- Medical School of Nanjing University, Nanjing, 210093, Jiangsu, China
| | - Jinhua Hou
- National Clinical Research Center for Kidney Disease, Jinling Hospital, Medical School of Nanjing University, Nanjing, 210002, Jiangsu, China
- Medical School of Nanjing University, Nanjing, 210093, Jiangsu, China
| | - Zhaohui Qin
- Department of Biostatistics and Bioinformatics, Rollins School of Public Health, Emory University, 1518 Clifton Road N.E, Atlanta, GA, 30322, USA
| | - Zhaohong Chen
- National Clinical Research Center for Kidney Disease, Jinling Hospital, Medical School of Nanjing University, Nanjing, 210002, Jiangsu, China
- Medical School of Nanjing University, Nanjing, 210093, Jiangsu, China
| | - Zhihong Liu
- National Clinical Research Center for Kidney Disease, Jinling Hospital, Medical School of Nanjing University, Nanjing, 210002, Jiangsu, China
- Medical School of Nanjing University, Nanjing, 210093, Jiangsu, China
| | - Jingping Yang
- National Clinical Research Center for Kidney Disease, Jinling Hospital, Medical School of Nanjing University, Nanjing, 210002, Jiangsu, China.
- Medical School of Nanjing University, Nanjing, 210093, Jiangsu, China.
| |
Collapse
|
28
|
Lowe M, Payton A, Verma A, Worthington J, Gemmell I, Hamilton P, Ollier W, Augustine T, Poulton K. Associations between human leukocyte antigens and renal function. Sci Rep 2021; 11:3158. [PMID: 33542305 PMCID: PMC7862310 DOI: 10.1038/s41598-021-82361-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2020] [Accepted: 12/09/2020] [Indexed: 02/07/2023] Open
Abstract
Human leukocyte antigens (HLA) have been associated with renal function, but previous studies report contradictory findings with little consensus on the exact nature or impact of this observation. This study included 401,307 white British subjects aged 39–73 when they were recruited by UK Biobank. Subjects’ HLA types were imputed using HLA*IMP:02 software. Regression analysis was used to compare 362 imputed HLA types with estimated glomerular filtration rate (eGFR) as a primary outcome and clinical indications as secondary outcome measures. 22 imputed HLA types were associated with increased eGFR (and therefore increased renal function). Decreased eGFR (decreased renal function) was associated with 11 imputed HLA types, seven of which were also associated with increased risk of end-stage renal disease and/or chronic kidney disease. Many of these HLA types are commonly inherited together in established haplotypes, for example: HLA-A*01:01, B*08:01, C*07:01, DRB1*03:01, DQB1*02:01. This haplotype has a population frequency of 9.5% in England and each allele was associated with decreased renal function. 33 imputed HLA types were associated with kidney function in white British subjects. Linkage disequilibrium in HLA heritance suggests that this is not random and particularly affects carriers of established haplotypes. This could have important applications for the diagnosis and treatment of renal disease and global population health.
Collapse
Affiliation(s)
- Marcus Lowe
- Transplantation Laboratory, Manchester Royal Infirmary, Manchester University NHS Foundation Trust, Manchester, UK. .,Division of Population Health, Health Services Research and Primary Care, University of Manchester, Manchester, UK.
| | - Antony Payton
- Division of Informatics, Imaging and Data Sciences, School of Health Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester, UK
| | - Arpana Verma
- Division of Population Health, Health Services Research and Primary Care, University of Manchester, Manchester, UK
| | - Judith Worthington
- Transplantation Laboratory, Manchester Royal Infirmary, Manchester University NHS Foundation Trust, Manchester, UK
| | - Isla Gemmell
- Division of Population Health, Health Services Research and Primary Care, University of Manchester, Manchester, UK
| | - Patrick Hamilton
- Department of Renal and Pancreatic Transplantation, Manchester Royal Infirmary, Manchester University NHS Foundation Trust, Manchester, UK
| | - William Ollier
- Division of Population Health, Health Services Research and Primary Care, University of Manchester, Manchester, UK.,Centre for Bioscience, Faculty of Science and Engineering, Manchester Metropolitan University, Manchester, UK
| | - Titus Augustine
- Department of Renal and Pancreatic Transplantation, Manchester Royal Infirmary, Manchester University NHS Foundation Trust, Manchester, UK.,Division of Diabetes, Endocrinology and Gastroenterology, University of Manchester, Manchester, UK
| | - Kay Poulton
- Transplantation Laboratory, Manchester Royal Infirmary, Manchester University NHS Foundation Trust, Manchester, UK.,Division of Population Health, Health Services Research and Primary Care, University of Manchester, Manchester, UK
| |
Collapse
|
29
|
Jiang X, Eales JM, Scannali D, Nazgiewicz A, Prestes P, Maier M, Denniff M, Xu X, Saluja S, Cano-Gamez E, Wystrychowski W, Szulinska M, Antczak A, Byars S, Skrypnik D, Glyda M, Król R, Zywiec J, Zukowska-Szczechowska E, Burrell LM, Woolf AS, Greenstein A, Bogdanski P, Keavney B, Morris AP, Heagerty A, Williams B, Harrap SB, Trynka G, Samani NJ, Guzik TJ, Charchar FJ, Tomaszewski M. Hypertension and renin-angiotensin system blockers are not associated with expression of angiotensin-converting enzyme 2 (ACE2) in the kidney. Eur Heart J 2020; 41:4580-4588. [PMID: 33206176 PMCID: PMC7665509 DOI: 10.1093/eurheartj/ehaa794] [Citation(s) in RCA: 38] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/27/2020] [Revised: 07/03/2020] [Accepted: 09/16/2020] [Indexed: 01/08/2023] Open
Abstract
AIMS Angiotensin-converting enzyme 2 (ACE2) is the cellular entry point for severe acute respiratory syndrome coronavirus (SARS-CoV-2)-the cause of coronavirus disease 2019 (COVID-19). However, the effect of renin-angiotensin system (RAS)-inhibition on ACE2 expression in human tissues of key relevance to blood pressure regulation and COVID-19 infection has not previously been reported. METHODS AND RESULTS We examined how hypertension, its major metabolic co-phenotypes, and antihypertensive medications relate to ACE2 renal expression using information from up to 436 patients whose kidney transcriptomes were characterized by RNA-sequencing. We further validated some of the key observations in other human tissues and/or a controlled experimental model. Our data reveal increasing expression of ACE2 with age in both human lungs and the kidney. We show no association between renal expression of ACE2 and either hypertension or common types of RAS inhibiting drugs. We demonstrate that renal abundance of ACE2 is positively associated with a biochemical index of kidney function and show a strong enrichment for genes responsible for kidney health and disease in ACE2 co-expression analysis. CONCLUSION Our results indicate that neither hypertension nor antihypertensive treatment is likely to alter the expression of the key entry receptor for SARS-CoV-2 in the human kidney. Our data further suggest that in the absence of SARS-CoV-2 infection, kidney ACE2 is most likely nephro-protective but the age-related increase in its expression within lungs and kidneys may be relevant to the risk of SARS-CoV-2 infection.
Collapse
Affiliation(s)
- Xiao Jiang
- Division of Cardiovascular Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester, UK
| | - James M Eales
- Division of Cardiovascular Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester, UK
| | - David Scannali
- Division of Cardiovascular Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester, UK
| | - Alicja Nazgiewicz
- Division of Cardiovascular Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester, UK
| | - Priscilla Prestes
- School of Health and Life Sciences, Federation University Australia, Ballarat, VIC, Australia
| | - Michelle Maier
- School of Health and Life Sciences, Federation University Australia, Ballarat, VIC, Australia
| | - Matthew Denniff
- Department of Cardiovascular Sciences, University of Leicester, Leicester, UK
| | - Xiaoguang Xu
- Division of Cardiovascular Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester, UK
| | - Sushant Saluja
- Division of Cardiovascular Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester, UK
| | - Eddie Cano-Gamez
- Department of Cellular Genetics, Wellcome Sanger Institute, Cambridge, UK
| | - Wojciech Wystrychowski
- Department of General, Vascular and Transplant Surgery, Medical University of Silesia, Katowice, Poland
| | - Monika Szulinska
- Department of Treatment of Obesity, Metabolic Disorders and Clinical Dietetics, Poznan University of Medical Sciences, Poznan, Poland
| | - Andrzej Antczak
- Department of Urology and Uro-oncology, Karol Marcinkowski University of Medical Sciences, Poznan, Poland
| | - Sean Byars
- Centre for Systems Genomics, School of BioSciences, The University of Melbourne, Parkville, VIC, Australia
- Department of Pathology, The University of Melbourne, Parkville, VIC, Australia
| | - Damian Skrypnik
- Department of Treatment of Obesity, Metabolic Disorders and Clinical Dietetics, Poznan University of Medical Sciences, Poznan, Poland
| | - Maciej Glyda
- Department of Transplantology and General Surgery Poznan, Collegium Medicum, Nicolaus Copernicus University, Bydgoszcz, Poland
| | - Robert Król
- Department of General, Vascular and Transplant Surgery, Medical University of Silesia, Katowice, Poland
| | - Joanna Zywiec
- Department of Internal Medicine, Diabetology and Nephrology, Medical University of Silesia, Zabrze, Poland
| | | | - Louise M Burrell
- Department of Medicine and Cardiology, University of Melbourne, Melbourne, VIC, Australia
| | - Adrian S Woolf
- Division of Cell Matrix Biology and Regenerative Medicine, Faculty of Biology, Medicine and Health, University of Manchester, Manchester, UK
- Royal Manchester Children’s Hospital and Manchester Academic Health Science Centre, Manchester University NHS Foundation Trust, Manchester, UK
| | - Adam Greenstein
- Division of Cardiovascular Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester, UK
- Division of Medicine and Manchester Academic Health Science Centre, Manchester University NHS Foundation Trust Manchester, Manchester, UK
| | - Pawel Bogdanski
- Department of Treatment of Obesity, Metabolic Disorders and Clinical Dietetics, Poznan University of Medical Sciences, Poznan, Poland
| | - Bernard Keavney
- Division of Cardiovascular Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester, UK
- Division of Medicine and Manchester Academic Health Science Centre, Manchester University NHS Foundation Trust Manchester, Manchester, UK
| | - Andrew P Morris
- Division of Musculoskeletal & Dermatological Sciences, Faculty of Medicine, Biology and Health, University of Manchester, Manchester, UK
| | - Anthony Heagerty
- Division of Cardiovascular Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester, UK
- Division of Medicine and Manchester Academic Health Science Centre, Manchester University NHS Foundation Trust Manchester, Manchester, UK
| | - Bryan Williams
- Institute of Cardiovascular Sciences, University College London, London, UK
| | - Stephen B Harrap
- Department of Physiology, University of Melbourne, Melbourne, VIC, Australia
| | - Gosia Trynka
- Department of Cellular Genetics, Wellcome Sanger Institute, Cambridge, UK
| | - Nilesh J Samani
- Department of Cardiovascular Sciences, University of Leicester, Leicester, UK
- Leicester Biomedical Research Centre, National Institute for Health Research, Leicester, UK
| | - Tomasz J Guzik
- Institute of Cardiovascular and Medical Sciences, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, UK
- Department of Internal and Agricultural Medicine, Jagiellonian University College of Medicine, Kraków, Poland
| | - Fadi J Charchar
- School of Health and Life Sciences, Federation University Australia, Ballarat, VIC, Australia
- Department of Cardiovascular Sciences, University of Leicester, Leicester, UK
- Department of Physiology, University of Melbourne, Melbourne, VIC, Australia
| | - Maciej Tomaszewski
- Division of Cardiovascular Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester, UK
- Division of Medicine and Manchester Academic Health Science Centre, Manchester University NHS Foundation Trust Manchester, Manchester, UK
| |
Collapse
|
30
|
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.
Collapse
|
31
|
Schroth J, Thiemermann C, Henson SM. Senescence and the Aging Immune System as Major Drivers of Chronic Kidney Disease. Front Cell Dev Biol 2020; 8:564461. [PMID: 33163486 PMCID: PMC7581911 DOI: 10.3389/fcell.2020.564461] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2020] [Accepted: 09/16/2020] [Indexed: 12/20/2022] Open
Abstract
Chronic kidney disease (CKD) presents an ever-growing disease burden for the world's aging population. It is characterized by numerous changes to the kidney, including a decrease in renal mass, renal fibrosis, and a diminished glomerular filtration rate. The premature aging phenotype observed in CKD is associated with cellular senescence, particularly of renal tubular epithelial cells (TECs), which contributes to chronic inflammation through the production of a proinflammatory senescence associated secretory phenotype (SASP). When coupled with changes in immune system composition and progressive immune dysfunction, the accumulation of senescent kidney cells acts as a driver for the progression of CKD. The targeting of senescent cells may well present an attractive therapeutic avenue for the treatment of CKD. We propose that the targeting of senescent cells either by direct inhibition of pro-survival pathways (senolytics) or through the inhibition of their proinflammatory secretory profile (senomorphics) together with immunomodulation to enhance immune system surveillance of senescent cells could be of benefit to patients with CKD.
Collapse
Affiliation(s)
| | | | - Siân M. Henson
- Translational Medicine and Therapeutics, William Harvey Research Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, London, United Kingdom
| |
Collapse
|
32
|
Lowe M, Payton A, Verma A, Gemmell I, Worthington J, Hamilton P, Ollier W, Augustine T, Poulton K. Human leukocyte antigen associations with renal function among ethnic minorities in the United Kingdom. HLA 2020; 96:697-708. [PMID: 32985786 DOI: 10.1111/tan.14078] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2020] [Revised: 09/10/2020] [Accepted: 09/21/2020] [Indexed: 01/10/2023]
Abstract
Human leukocyte antigens (HLA) have been associated with renal function, but previous studies report contradictory findings. There has been a lack of research into how HLA affects renal function in Black, Asian and Minority Ethnic (BAME) people in the UK, despite BAME people being disproportionately affected by renal dysfunction. This study included >27 000 UK Biobank subjects of six ethnicities (>12 100 Irish, >5400 Indian, >4000 Black Caribbean, >3000 Black African, >1600 Pakistani, and >1400 Chinese) aged 39 to 73. Subjects' high-resolution HLA genotypes were imputed using HLA*IMP:02 software. Regression analysis was used to compare 108 imputed HLA alleles with two measures of estimated glomerular filtration rate (eGFR): one based on serum creatinine; one based on serum cystatin. Secondary analysis compared CKD stage 2 subjects to healthy controls. Nine imputed HLA alleles were associated with eGFR (adjusted P < .05). Six associations were based on creatinine in Black African subjects: HLA-B*53:01 (beta = -2.628, adjusted P = 4.69 × 10-4 ); C*04:01 (beta = -1.667, adjusted P = .0269); DPA1*02:01 (beta = -1.569, adjusted P = .0182); and DPA1*02:02 (beta = -1.716, adjusted P = .0251) were linked to decreased renal function, while DRB1*03:01 (beta = 3.200, adjusted P = 3.99 × 10-3 ) and DPA1*01:03 (beta = 2.276, adjusted P = 2.31 × 10-5 ) were linked to increased renal function. Two of these (HLA-B*53:01 and C*04:01) are commonly inherited together. In Irish subjects, HLA-DRB1*04:01 (beta = 1.075, adjusted P = .0138) was linked to increased eGFR (based on cystatin); in Indian subjects, HLA-DRB1*03:01 (beta = -1.72, adjusted P = 4.78 × 10-3 ) and DQB1*02:01 (beta = -1.755, adjusted P = 2.26 × 10-3 )were associated with decreased eGFR (based on cystatin). No associations were found in the other three ethnic groups. Nine HLA alleles appear to be associated with kidney function in BAME people in the UK. This could have applications for the diagnosis and treatment of renal disease and could help reduce health inequalities in the UK.
Collapse
Affiliation(s)
- Marcus Lowe
- Transplantation Laboratory, Manchester Royal Infirmary, Manchester University NHS Foundation Trust, Manchester, UK.,Division of Population Health, Health Services Research and Primary Care, University of Manchester, Manchester, UK
| | - Antony Payton
- Faculty of Biology, Medicine and Health, Division of Informatics, Imaging & Data Sciences, School of Health Sciences, University of Manchester, Manchester, UK
| | - Arpana Verma
- Division of Population Health, Health Services Research and Primary Care, University of Manchester, Manchester, UK
| | - Isla Gemmell
- Division of Population Health, Health Services Research and Primary Care, University of Manchester, Manchester, UK
| | - Judith Worthington
- Transplantation Laboratory, Manchester Royal Infirmary, Manchester University NHS Foundation Trust, Manchester, UK
| | - Patrick Hamilton
- Department of Renal and Pancreas Transplantation, Manchester Royal Infirmary, Manchester University NHS Foundation Trust, Manchester, UK
| | - William Ollier
- Division of Population Health, Health Services Research and Primary Care, University of Manchester, Manchester, UK.,Faculty of Science and Engineering, Centre for Bioscience, Manchester Metropolitan University, Manchester, UK
| | - Titus Augustine
- Department of Renal and Pancreas Transplantation, Manchester Royal Infirmary, Manchester University NHS Foundation Trust, Manchester, UK.,Division of Diabetes, Endocrinology and Gastroenterology, University of Manchester, Manchester, UK
| | - Kay Poulton
- Transplantation Laboratory, Manchester Royal Infirmary, Manchester University NHS Foundation Trust, Manchester, UK.,Division of Population Health, Health Services Research and Primary Care, University of Manchester, Manchester, UK
| |
Collapse
|
33
|
Lin J, Susztak K. Complexities of Understanding Function from CKD-Associated DNA Variants. Clin J Am Soc Nephrol 2020; 15:1028-1040. [PMID: 32513823 PMCID: PMC7341770 DOI: 10.2215/cjn.15771219] [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] [Indexed: 11/23/2022]
Abstract
Genome-wide association studies (GWASs) have facilitated the unbiased discovery of hundreds of genomic loci associated with CKD and kidney function. The vast majority of disease-associated DNA variants are noncoding. Those that are causal in CKD pathogenesis likely modulate transcription of target genes in a cell type-specific manner. To gain novel biological insights into mechanisms driving the development of CKD, the causal variants (which are usually not the most significant variant reported in a GWAS), their target genes, and causal cell types need to be identified. This functional validation requires a large number of new data sets, complex bioinformatics analyses, and experimental cellular and in vivo studies. Here, we review the basic principles and some of the current approaches being leveraged to assign functional significance to a genotype-phenotype association.
Collapse
Affiliation(s)
- Jennie Lin
- Division of Nephrology and Hypertension, Feinberg Cardiovascular and Renal Research Institute, Department of Medicine, Northwestern University, Chicago, Illinois
- Jesse Brown Veterans Affairs Medical Center, Chicago, Illinois
| | - Katalin Susztak
- Renal, Electrolyte, and Hypertension Division, Department of Medicine, Perelman School of Medicine of the University of Pennsylvania, Philadelphia, Pennsylvania
- Department of Genetics, Perelman School of Medicine of the University of Pennsylvania, Philadelphia, Pennsylvania
| |
Collapse
|
34
|
Schmidt AF, Finan C, Gordillo-Marañón M, Asselbergs FW, Freitag DF, Patel RS, Tyl B, Chopade S, Faraway R, Zwierzyna M, Hingorani AD. Genetic drug target validation using Mendelian randomisation. Nat Commun 2020; 11:3255. [PMID: 32591531 PMCID: PMC7320010 DOI: 10.1038/s41467-020-16969-0] [Citation(s) in RCA: 162] [Impact Index Per Article: 40.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2019] [Accepted: 06/02/2020] [Indexed: 02/06/2023] Open
Abstract
Mendelian randomisation (MR) analysis is an important tool to elucidate the causal relevance of environmental and biological risk factors for disease. However, causal inference is undermined if genetic variants used to instrument a risk factor also influence alternative disease-pathways (horizontal pleiotropy). Here we report how the 'no horizontal pleiotropy assumption' is strengthened when proteins are the risk factors of interest. Proteins are typically the proximal effectors of biological processes encoded in the genome. Moreover, proteins are the targets of most medicines, so MR studies of drug targets are becoming a fundamental tool in drug development. To enable such studies, we introduce a mathematical framework that contrasts MR analysis of proteins with that of risk factors located more distally in the causal chain from gene to disease. We illustrate key model decisions and introduce an analytical framework for maximising power and evaluating the robustness of analyses.
Collapse
Affiliation(s)
- Amand F Schmidt
- Institute of Cardiovascular Science, Faculty of Population Health, University College London, London, WC1E 6BT, UK.
- UCL BHF Research Accelerator Centre, London, UK.
- Department of Cardiology, Division Heart and Lungs, University Medical Center Utrecht, Heidelberglaan 100, 3584 CX, Utrecht, The Netherlands.
| | - Chris Finan
- Institute of Cardiovascular Science, Faculty of Population Health, University College London, London, WC1E 6BT, UK
- UCL BHF Research Accelerator Centre, London, UK
| | - Maria Gordillo-Marañón
- Institute of Cardiovascular Science, Faculty of Population Health, University College London, London, WC1E 6BT, UK
| | - Folkert W Asselbergs
- Institute of Cardiovascular Science, Faculty of Population Health, University College London, London, WC1E 6BT, UK
- Department of Cardiology, Division Heart and Lungs, University Medical Center Utrecht, Heidelberglaan 100, 3584 CX, Utrecht, The Netherlands
- Health Data Research UK, 222 Euston Road, London, UK
| | - Daniel F Freitag
- Bayer AG Pharmaceuticals, Open Innovation & Digital Technologies, Aprather Weg 18a, Wuppertal, 42096, Germany
| | - Riyaz S Patel
- Institute of Cardiovascular Science, Faculty of Population Health, University College London, London, WC1E 6BT, UK
- UCL BHF Research Accelerator Centre, London, UK
| | - Benoît Tyl
- Center for Therapeutic Innovation, Cardiovascular and Metabolic Disease, Institut de Recherches Internationales Servier, 50 Rue Carnot, 92284, Suresnes Cedex, France
| | - Sandesh Chopade
- Institute of Cardiovascular Science, Faculty of Population Health, University College London, London, WC1E 6BT, UK
- UCL BHF Research Accelerator Centre, London, UK
| | - Rupert Faraway
- Institute of Cardiovascular Science, Faculty of Population Health, University College London, London, WC1E 6BT, UK
- UCL BHF Research Accelerator Centre, London, UK
- The Francis Crick Institute, 1 Midland Rd, London, NW1 1AT, UK
| | - Magdalena Zwierzyna
- Institute of Cardiovascular Science, Faculty of Population Health, University College London, London, WC1E 6BT, UK
- UCL BHF Research Accelerator Centre, London, UK
| | - Aroon D Hingorani
- Institute of Cardiovascular Science, Faculty of Population Health, University College London, London, WC1E 6BT, UK
- UCL BHF Research Accelerator Centre, London, UK
- Health Data Research UK, 222 Euston Road, London, UK
| |
Collapse
|
35
|
Moeller MJ, Kuppe C, D'Agati VD. The authors reply. Kidney Int 2020; 96:1241. [PMID: 31648701 DOI: 10.1016/j.kint.2019.08.016] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2019] [Accepted: 08/22/2019] [Indexed: 11/26/2022]
Affiliation(s)
- Marcus J Moeller
- Division of Nephrology and Clinical Immunology, Rheinisch-Westfälische Technische Hochschule (RWTH) Aachen University, Aachen, Germany.
| | - Christoph Kuppe
- Division of Nephrology and Clinical Immunology, Rheinisch-Westfälische Technische Hochschule (RWTH) Aachen University, Aachen, Germany
| | - Vivette D D'Agati
- Department of Pathology and Cell Biology, Renal Pathology Division, Columbia University Medical Center, New York, New York, USA
| |
Collapse
|
36
|
The Future of Paediatric Nephrology—Genomics and Personalised Precision Medicine. CURRENT PEDIATRICS REPORTS 2020. [DOI: 10.1007/s40124-020-00218-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
|
37
|
Sullivan KM, Susztak K. Unravelling the complex genetics of common kidney diseases: from variants to mechanisms. Nat Rev Nephrol 2020; 16:628-640. [PMID: 32514149 DOI: 10.1038/s41581-020-0298-1] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/23/2020] [Indexed: 12/20/2022]
Abstract
Genome-wide association studies (GWAS) have identified hundreds of loci associated with kidney-related traits such as glomerular filtration rate, albuminuria, hypertension, electrolyte and metabolite levels. However, these impressive, large-scale mapping approaches have not always translated into an improved understanding of disease or development of novel therapeutics. GWAS have several important limitations. Nearly all disease-associated risk loci are located in the non-coding region of the genome and therefore, their target genes, affected cell types and regulatory mechanisms remain unknown. Genome-scale approaches can be used to identify associations between DNA sequence variants and changes in gene expression (quantified through bulk and single-cell methods), gene regulation and other molecular quantitative trait studies, such as chromatin accessibility, DNA methylation, protein expression and metabolite levels. Data obtained through these approaches, used in combination with robust computational methods, can deliver robust mechanistic inferences for translational exploitation. Understanding the genetic basis of common kidney diseases means having a comprehensive picture of the genes that have a causal role in disease development and progression, of the cells, tissues and organs in which these genes act to affect the disease, of the cellular pathways and mechanisms that drive disease, and of potential targets for disease prevention, detection and therapy.
Collapse
Affiliation(s)
- Katie Marie Sullivan
- Department of Medicine, Renal Electrolyte and Hypertension Division, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | - Katalin Susztak
- Department of Medicine, Renal Electrolyte and Hypertension Division, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA.
| |
Collapse
|
38
|
Abstract
PURPOSE OF REVIEW Accurate risk stratification in patients with chronic kidney disease (CKD) is highly desirable to help guide earlier, targeted treatment in high-risk individuals. In this review, we report recent developments in our understanding of risk factors and risk prediction in patients with CKD. RECENT FINDINGS A large meta-analysis has shown that conventional cardiovascular risk factors continue to play an important role in disease progression and adverse outcomes in patients with advanced CKD where the estimated glomerular filtration rate (eGFR) is < 30 ml/min/1.73 m). Several studies have shed light on novel biomarkers in CKD, including peptides (LG1 M), genes (MUC1) and metabolic factors (urinary oxalate excretion). Cortical oxygenation measured by BOLD-MRI also provides a novel radiological measure predictive of future eGFR decline. A new risk prediction score for patients with CKD G4-5 has been developed, offering an aid to decision-making in these patients. SUMMARY Ongoing work across various disciplines continues to unravel the determinants of CKD progression. A few notable risk prediction tools in CKD have now surfaced but whether they can be utilised to offer improved care remains a key unanswered question.
Collapse
|
39
|
Garrett MR, Korstanje R. Using Genetic and Species Diversity to Tackle Kidney Disease. Trends Genet 2020; 36:499-509. [PMID: 32362446 DOI: 10.1016/j.tig.2020.04.001] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2020] [Revised: 03/26/2020] [Accepted: 04/03/2020] [Indexed: 12/18/2022]
Abstract
Progress in the identification of causal genes and understanding of the mechanism underlying kidney disease is hindered by the almost exclusive use of a few animal models with restrictive monogenic backgrounds that may be more resistant to kidney disease compared with humans and, therefore, poor models. Exploring the large genetic diversity in classical animal models, such as mice and rats, and leveraging species diversity will allow us to use the genetic advantages of zebrafish, Drosophila, and other species, to develop both new animal models that are more relevant to the study of human kidney disease and potential therapies.
Collapse
Affiliation(s)
- Michael R Garrett
- Department of Pharmacology, University of Mississippi Medical Center, Jackson, MS, USA; Department of Medicine (Nephrology), University of Mississippi Medical Center, Jackson, MS, USA; Department of Pediatrics (Genetics), University of Mississippi Medical Center, Jackson, MS, USA
| | - Ron Korstanje
- The Jackson Laboratory for Mammalian Genetics, Bar Harbor, Maine, ME, USA; Mount Desert Island Biological Laboratory, Bar Harbor, Maine, ME, USA.
| |
Collapse
|
40
|
The genetic architecture of membranous nephropathy and its potential to improve non-invasive diagnosis. Nat Commun 2020; 11:1600. [PMID: 32231244 PMCID: PMC7105485 DOI: 10.1038/s41467-020-15383-w] [Citation(s) in RCA: 112] [Impact Index Per Article: 28.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2019] [Accepted: 03/03/2020] [Indexed: 02/06/2023] Open
Abstract
Membranous Nephropathy (MN) is a rare autoimmune cause of kidney failure. Here we report a genome-wide association study (GWAS) for primary MN in 3,782 cases and 9,038 controls of East Asian and European ancestries. We discover two previously unreported loci, NFKB1 (rs230540, OR = 1.25, P = 3.4 × 10−12) and IRF4 (rs9405192, OR = 1.29, P = 1.4 × 10−14), fine-map the PLA2R1 locus (rs17831251, OR = 2.25, P = 4.7 × 10−103) and report ancestry-specific effects of three classical HLA alleles: DRB1*1501 in East Asians (OR = 3.81, P = 2.0 × 10−49), DQA1*0501 in Europeans (OR = 2.88, P = 5.7 × 10−93), and DRB1*0301 in both ethnicities (OR = 3.50, P = 9.2 × 10−23 and OR = 3.39, P = 5.2 × 10−82, respectively). GWAS loci explain 32% of disease risk in East Asians and 25% in Europeans, and correctly re-classify 20–37% of the cases in validation cohorts that are antibody-negative by the serum anti-PLA2R ELISA diagnostic test. Our findings highlight an unusual genetic architecture of MN, with four loci and their interactions accounting for nearly one-third of the disease risk. Membranous nephropathy (MN) is a rare autoimmune disease of podocyte-directed antibodies, such as anti-phospholipase A2 receptor. Here, the authors report a genome-wide association study for MN and identify two previously unreported loci encompassing the NFKB1 and IRF4 genes and additional ancestry-specific effects.
Collapse
|
41
|
Abstract
PURPOSE OF REVIEW Comprehensive analyses of the genome, transcriptome, proteome and metabolome are instrumental in identifying biomarkers of disease, to gain insight into mechanisms underlying the development of cardiovascular disease, and show promise for better stratifying patients according to disease subtypes. This review highlights recent 'omics' studies, including integration of multiple 'omics' that have advanced mechanistic understanding and diagnosis in humans and animal models. RECENT FINDINGS Transcriptome-based discovery continues to be a primary method to obtain data for hypothesis generation and the understanding of disease pathogenesis has been enhanced by single cell-based methods capable of revealing heterogeneity in cellular responses. Advances in proteome coverage and quantitation of individual protein species, together with enhanced methods for detecting posttranslational modifications, have improved discovery of protein-based biomarkers. SUMMARY High-throughput assays capable of quantitating the vast majority of any particular type of biomolecule within a tissue sample, isolated cells or plasma are now available. In order to make best use of the large amount of data that can be generated on given molecule types, as well as their interrelationships in disease, continued development of pattern-recognition algorithms ('machine learning') will be required and the subclassification of disease that is made possible by such algorithms will be likely to inform clinical practice, and vice versa.
Collapse
|
42
|
Kanbay M, Yerlikaya A, Sag AA, Ortiz A, Kuwabara M, Covic A, Wiecek A, Stenvinkel P, Afsar B. A journey from microenvironment to macroenvironment: the role of metaflammation and epigenetic changes in cardiorenal disease. Clin Kidney J 2019; 12:861-870. [PMID: 31807301 PMCID: PMC6885688 DOI: 10.1093/ckj/sfz106] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2019] [Indexed: 12/11/2022] Open
Abstract
Chronic non-communicable diseases have become a pandemic public problem in the 21st century, causing enormous burden on the economy, health and quality of life of societies. The role of a chronic inflammatory state in the pathogenesis of chronic disease has been more comprehensively recognized by recent findings. The new paradigm ‘metaflammation’ focuses on metabolism-induced (high fat or fructose-based diet or excessive calorie intake) chronic inflammation. There is a close correlation between the increased incidence of chronic kidney disease (CKD) and chronic heart failure with both increased inflammatory marker levels and western-type diet. In this review we describe the concept of metaflammation, its role in the development of CKD and chronic heart disease, the molecular and signalling pathways involved and the therapeutic consequences.
Collapse
Affiliation(s)
- Mehmet Kanbay
- Department of Medicine, Division of Nephrology, Koc University School of Medicine, Istanbul, Turkey
| | - Aslihan Yerlikaya
- Department of Medicine, Koc University School of Medicine, Istanbul, Turkey
| | - Alan A Sag
- Department of Radiology, Division of Vascular and Interventional Radiology, Duke University Medical Center, Durham, NC, USA
| | - Alberto Ortiz
- Dialysis Unit, School of Medicine, IIS-Fundacion Jimenez Diaz, Universidad Autónoma de Madrid, Madrid, Spain
| | | | - Adrian Covic
- Nephrology Department, Dialysis and Renal Transplant Center, "Dr. C.I. Parhon" University Hospital, "Grigore T. Popa" University of Medicine and Pharmacy, Iasi, Romania
| | - Andrzej Wiecek
- Department of Nephrology, Transplantation and Internal Medicine, Medical University of Silesia, Katowice, Poland
| | - Peter Stenvinkel
- Department of Clinical Science Intervention and Technology, Division of Renal Medicine and Baxter Novum, Karolinska Institutet, Stockholm, Sweden
| | - Baris Afsar
- Department of Medicine, Division of Nephrology, Suleyman Demirel University School of Medicine, Isparta, Turkey
| |
Collapse
|
43
|
Eales JM, Maan AA, Xu X, Michoel T, Hallast P, Batini C, Zadik D, Prestes PR, Molina E, Denniff M, Schroeder J, Bjorkegren JLM, Thompson J, Maffia P, Guzik TJ, Keavney B, Jobling MA, Samani NJ, Charchar FJ, Tomaszewski M. Human Y Chromosome Exerts Pleiotropic Effects on Susceptibility to Atherosclerosis. Arterioscler Thromb Vasc Biol 2019; 39:2386-2401. [PMID: 31644355 PMCID: PMC6818981 DOI: 10.1161/atvbaha.119.312405] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
Supplemental Digital Content is available in the text. The male-specific region of the Y chromosome (MSY) remains one of the most unexplored regions of the genome. We sought to examine how the genetic variants of the MSY influence male susceptibility to coronary artery disease (CAD) and atherosclerosis.
Collapse
Affiliation(s)
- James M Eales
- From the Division of Cardiovascular Sciences, Faculty of Biology, Medicine and Health, University of Manchester, United Kingdom (J.M.E., A.A.M., X.X., B.K., M.T.)
| | - Akhlaq A Maan
- From the Division of Cardiovascular Sciences, Faculty of Biology, Medicine and Health, University of Manchester, United Kingdom (J.M.E., A.A.M., X.X., B.K., M.T.)
| | - Xiaoguang Xu
- From the Division of Cardiovascular Sciences, Faculty of Biology, Medicine and Health, University of Manchester, United Kingdom (J.M.E., A.A.M., X.X., B.K., M.T.)
| | - Tom Michoel
- The Roslin Institute, The University of Edinburgh, United Kingdom (T.M.).,Computational Biology Unit and Department of Informatics, University of Bergen, Norway (T.M.)
| | - Pille Hallast
- Institute of Biomedicine and Translational Medicine, University of Tartu, Estonia (P.H.)
| | - Chiara Batini
- Department of Health Sciences (C.B., J.T.), University of Leicester, United Kingdom
| | - Daniel Zadik
- Department of Genetics and Genome Biology (D.Z., M.A.J.), University of Leicester, United Kingdom
| | - Priscilla R Prestes
- School of Health and Life Sciences, Federation University Australia, Ballarat, Victoria (P.R.P., E.M., F.J.C.)
| | - Elsa Molina
- School of Health and Life Sciences, Federation University Australia, Ballarat, Victoria (P.R.P., E.M., F.J.C.)
| | - Matthew Denniff
- Department of Cardiovascular Sciences (M.D., N.J.S., F.J.C.), University of Leicester, United Kingdom
| | - Juliane Schroeder
- Centre for Immunobiology, Institute of Infection, Immunity and Inflammation (J.S., P.M.), College of Medical, Veterinary and Life Sciences, University of Glasgow, United Kingdom.,Institute of Cardiovascular and Medical Sciences (J.S., P.M., T.J.G.), College of Medical, Veterinary and Life Sciences, University of Glasgow, United Kingdom
| | - Johan L M Bjorkegren
- Department of Genetics and Genomic Sciences, Icahn Institute for Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, NY (J.L.M.B.)
| | - John Thompson
- Department of Health Sciences (C.B., J.T.), University of Leicester, United Kingdom
| | - Pasquale Maffia
- Centre for Immunobiology, Institute of Infection, Immunity and Inflammation (J.S., P.M.), College of Medical, Veterinary and Life Sciences, University of Glasgow, United Kingdom.,Institute of Cardiovascular and Medical Sciences (J.S., P.M., T.J.G.), College of Medical, Veterinary and Life Sciences, University of Glasgow, United Kingdom.,Department of Pharmacy, University of Naples Federico II, Italy (P.M.)
| | - Tomasz J Guzik
- Institute of Cardiovascular and Medical Sciences (J.S., P.M., T.J.G.), College of Medical, Veterinary and Life Sciences, University of Glasgow, United Kingdom.,Jagiellonian University College of Medicine, Kraków, Poland (T.J.G.)
| | - Bernard Keavney
- From the Division of Cardiovascular Sciences, Faculty of Biology, Medicine and Health, University of Manchester, United Kingdom (J.M.E., A.A.M., X.X., B.K., M.T.).,Division of Medicine, Manchester University NHS Foundation Trust, Manchester Academic Health Science Centre, United Kingdom (B.K., M.T.)
| | - Mark A Jobling
- Department of Genetics and Genome Biology (D.Z., M.A.J.), University of Leicester, United Kingdom
| | - Nilesh J Samani
- Department of Cardiovascular Sciences (M.D., N.J.S., F.J.C.), University of Leicester, United Kingdom.,NIHR Leicester Biomedical Research Centre, United Kingdom (N.J.S.)
| | - Fadi J Charchar
- Department of Cardiovascular Sciences (M.D., N.J.S., F.J.C.), University of Leicester, United Kingdom.,School of Health and Life Sciences, Federation University Australia, Ballarat, Victoria (P.R.P., E.M., F.J.C.).,Department of Physiology, University of Melbourne, Parkville, Victoria, Australia (F.J.C.)
| | - Maciej Tomaszewski
- From the Division of Cardiovascular Sciences, Faculty of Biology, Medicine and Health, University of Manchester, United Kingdom (J.M.E., A.A.M., X.X., B.K., M.T.).,Division of Medicine, Manchester University NHS Foundation Trust, Manchester Academic Health Science Centre, United Kingdom (B.K., M.T.)
| |
Collapse
|
44
|
Chen YY, Yu XY, Chen L, Vaziri ND, Ma SC, Zhao YY. Redox signaling in aging kidney and opportunity for therapeutic intervention through natural products. Free Radic Biol Med 2019; 141:141-149. [PMID: 31199964 DOI: 10.1016/j.freeradbiomed.2019.06.012] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/14/2019] [Revised: 06/04/2019] [Accepted: 06/10/2019] [Indexed: 02/06/2023]
Abstract
Kidney diseases are serious public problems with high morbidity and mortality in the general population and heavily retard renal function with aging regardless of the cause. Although myriad strategies have been assigned to prevent or harness disease progression, unfortunately, thus far, there is a paucity of effective therapies partly due to an insufficient knowledge of underlying pathological mechanisms, indicating deeper studies are urgently needed. Additionally, natural products are increasingly recognized as an alternative source for disease intervention owing to the potent safety and efficacy, which might be exploited for novel drug discovery. In this review, we primarily expatiate the new advances on mediators that might be amenable to targeting aging kidney and kidney diseases, including nicotinamide adenine dinucleotide phosphate oxidase (NOX), transforming growth factor-β (TGF-β), renin-angiotensin system (RAS), nuclear factor-erythroid 2 related factor 2 (Nrf2), peroxisome proliferator-activated γ receptor (PPARγ), advanced glycation endproducts (AGEs) as well as microRNAs and vitagenes. Of note, we conclude by highlighting some natural products which have the potential to facilitate the development of novel treatment for patients with myriad renal diseases.
Collapse
Affiliation(s)
- Yuan-Yuan Chen
- School of Pharmacy, Faculty of Life Science & Medicine, Northwest University, No. 229 Taibai North Road, Xi'an, Shaanxi, 710069, China
| | - Xiao-Yong Yu
- Department of Nephrology, Shaanxi Traditional Chinese Medicine Hospital, No. 2 Xihuamen, Xi'an, Shaanxi, 710003, China
| | - Lin Chen
- School of Pharmacy, Faculty of Life Science & Medicine, Northwest University, No. 229 Taibai North Road, Xi'an, Shaanxi, 710069, China
| | - Nosratola D Vaziri
- Division of Nephrology and Hypertension, School of Medicine, University of California Irvine, Irvine, CA, 92897, USA
| | - Shuang-Cheng Ma
- National Institutes for Food and Drug Control, State Food and Drug Administration, No. 2 Tiantan Xili, Beijing, 100050, China.
| | - Ying-Yong Zhao
- School of Pharmacy, Faculty of Life Science & Medicine, Northwest University, No. 229 Taibai North Road, Xi'an, Shaanxi, 710069, China.
| |
Collapse
|
45
|
Chronic kidney disease: Biomarker diagnosis to therapeutic targets. Clin Chim Acta 2019; 499:54-63. [PMID: 31476302 DOI: 10.1016/j.cca.2019.08.030] [Citation(s) in RCA: 58] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2019] [Revised: 08/29/2019] [Accepted: 08/29/2019] [Indexed: 12/12/2022]
Abstract
Chronic kidney disease (CKD), characterized as renal dysfunction, is recognized as a major public health problem with high morbidity and mortality worldwide. Unfortunately, there are no obvious clinical symptoms in early stage disease until severe damage has occurred. Further complicating early diagnosis and treatment is the lack of sensitive and specific biomarkers. As such, novel biomarkers are urgently needed. Metabolomics has shown an increasing potential for identifying underlying disease mechanisms, facilitating clinical diagnosis and developing pharmaceutical treatments for CKD. Recent advances in metabolomics revealed that CKD was closely associated with the dysregulation of numerous metabolites, such as amino acids, lipids, nucleotides and glycoses, that might be exploited as potential biomarkers. In this review, we summarize recent metabolomic applications based on animal model studies and in patients with CKD and highlight several biomarkers that may play important roles in diagnosis, intervention and development of new therapeutic strategies.
Collapse
|
46
|
Huang S, Sheng X, Susztak K. The kidney transcriptome, from single cells to whole organs and back. Curr Opin Nephrol Hypertens 2019; 28:219-226. [PMID: 30844884 PMCID: PMC6761926 DOI: 10.1097/mnh.0000000000000495] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
PURPOSE OF REVIEW Transcriptome analysis of human kidney samples provides an integrated output of genetic, physiological, or environmental inputs. This review summarizes recent findings including gene expression and genetic variation integration, bulk and single cell gene expression analysis, and describes how such studies have improved our understanding of kidney disease development. RECENT FINDINGS Bulk or whole tissue analysis of patient kidney samples identified a large number of genes, whose levels correlate with kidney function and/or structural damage. These genes were enriched for metabolic and immune functions. Using expression quantitative trait analysis, genetic variations-driven gene expression can be identified. Recent developments in single cell sequencing defined cell-type-specific gene expression changes and highlighted specific cell types for disease development. SUMMARY Recent advancement in whole tissue transcriptomics, specifically incorporating genotype information and single cell data have been powerful to identify kidney disease-associated genes, pathways, and cell types.
Collapse
Affiliation(s)
- Shizheng Huang
- Department of Medicine, Renal Electrolyte and Hypertension Division, University of Pennsylvania, Philadelphia, PA, USA
| | - Xin Sheng
- Department of Medicine, Renal Electrolyte and Hypertension Division, University of Pennsylvania, Philadelphia, PA, USA
| | - Katalin Susztak
- Department of Medicine, Renal Electrolyte and Hypertension Division, University of Pennsylvania, Philadelphia, PA, USA
| |
Collapse
|
47
|
Graham SE, Nielsen JB, Zawistowski M, Zhou W, Fritsche LG, Gabrielsen ME, Skogholt AH, Surakka I, Hornsby WE, Fermin D, Larach DB, Kheterpal S, Brummett CM, Lee S, Kang HM, Abecasis GR, Romundstad S, Hallan S, Sampson MG, Hveem K, Willer CJ. Sex-specific and pleiotropic effects underlying kidney function identified from GWAS meta-analysis. Nat Commun 2019; 10:1847. [PMID: 31015462 PMCID: PMC6478837 DOI: 10.1038/s41467-019-09861-z] [Citation(s) in RCA: 42] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2018] [Accepted: 04/03/2019] [Indexed: 12/19/2022] Open
Abstract
Chronic kidney disease (CKD) is a growing health burden currently affecting 10–15% of adults worldwide. Estimated glomerular filtration rate (eGFR) as a marker of kidney function is commonly used to diagnose CKD. We analyze eGFR data from the Nord-Trøndelag Health Study and Michigan Genomics Initiative and perform a GWAS meta-analysis with public summary statistics, more than doubling the sample size of previous meta-analyses. We identify 147 loci (53 novel) associated with eGFR, including genes involved in transcriptional regulation, kidney development, cellular signaling, metabolism, and solute transport. Additionally, sex-stratified analysis identifies one locus with more significant effects in women than men. Using genetic risk scores constructed from these eGFR meta-analysis results, we show that associated variants are generally predictive of CKD with only modest improvements in detection compared with other known clinical risk factors. Collectively, these results yield additional insight into the genetic factors underlying kidney function and progression to CKD. Estimated glomerular filtration rate (eGFR) is a measure of kidney function and used to characterize chronic kidney disease. Here, Graham et al. identify 53 novel loci for eGFR in a GWAS meta-analysis, a subset of which are associated with other common diseases, such as diabetes and hypertension, based on PheWAS.
Collapse
Affiliation(s)
- Sarah E Graham
- Department of Internal Medicine: Cardiology, University of Michigan, Ann Arbor, 48109, MI, USA
| | - Jonas B Nielsen
- Department of Internal Medicine: Cardiology, University of Michigan, Ann Arbor, 48109, MI, USA
| | - Matthew Zawistowski
- Department of Biostatistics: Center for Statistical Genetics, University of Michigan, Ann Arbor, 48109, MI, USA
| | - Wei Zhou
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, 48109, MI, USA
| | - Lars G Fritsche
- Department of Biostatistics: Center for Statistical Genetics, University of Michigan, Ann Arbor, 48109, MI, USA
| | - Maiken E Gabrielsen
- K.G. Jebsen Center for Genetic Epidemiology, Faculty of Medicine and Health Sciences, Norwegian University of Science and Technology, Trondheim, 7491, Norway.,Department of Public Health and Nursing, Faculty of Medicine and Health Sciences, Norwegian University of Science and Technology, Trondheim, 7491, Norway
| | - Anne Heidi Skogholt
- K.G. Jebsen Center for Genetic Epidemiology, Faculty of Medicine and Health Sciences, Norwegian University of Science and Technology, Trondheim, 7491, Norway.,Department of Public Health and Nursing, Faculty of Medicine and Health Sciences, Norwegian University of Science and Technology, Trondheim, 7491, Norway.,Department of Clinical and Molecular Medicine, Faculty of Medicine and Health Sciences, Norwegian University of Science and Technology, Trondheim, 7491, Norway
| | - Ida Surakka
- Department of Internal Medicine: Cardiology, University of Michigan, Ann Arbor, 48109, MI, USA
| | - Whitney E Hornsby
- Department of Internal Medicine: Cardiology, University of Michigan, Ann Arbor, 48109, MI, USA
| | - Damian Fermin
- Department of Pediatrics: Pediatric Nephrology, University of Michigan, Ann Arbor, 48109, MI, USA
| | - Daniel B Larach
- Department of Anesthesiology, University of Michigan, Ann Arbor, 48109, MI, USA
| | - Sachin Kheterpal
- Department of Anesthesiology, University of Michigan, Ann Arbor, 48109, MI, USA
| | - Chad M Brummett
- Department of Anesthesiology, University of Michigan, Ann Arbor, 48109, MI, USA
| | - Seunggeun Lee
- Department of Biostatistics: Center for Statistical Genetics, University of Michigan, Ann Arbor, 48109, MI, USA
| | - Hyun Min Kang
- Department of Biostatistics: Center for Statistical Genetics, University of Michigan, Ann Arbor, 48109, MI, USA
| | - Goncalo R Abecasis
- Department of Biostatistics: Center for Statistical Genetics, University of Michigan, Ann Arbor, 48109, MI, USA
| | - Solfrid Romundstad
- Department of Clinical and Molecular Medicine, Faculty of Medicine and Health Sciences, Norwegian University of Science and Technology, Trondheim, 7491, Norway.,Department of Internal Medicine, Levanger Hospital, Health Trust Nord-Trøndelag, Levanger, 7600, Norway
| | - Stein Hallan
- Department of Clinical and Molecular Medicine, Faculty of Medicine and Health Sciences, Norwegian University of Science and Technology, Trondheim, 7491, Norway.,Department of Nephrology, St Olav Hospital, Trondheim, 7491, Norway
| | - Matthew G Sampson
- Department of Pediatrics: Pediatric Nephrology, University of Michigan, Ann Arbor, 48109, MI, USA
| | - Kristian Hveem
- K.G. Jebsen Center for Genetic Epidemiology, Faculty of Medicine and Health Sciences, Norwegian University of Science and Technology, Trondheim, 7491, Norway. .,Department of Public Health and Nursing, Faculty of Medicine and Health Sciences, Norwegian University of Science and Technology, Trondheim, 7491, Norway. .,HUNT Research Centre, Department of Public Health and General Practice, Norwegian University of Science and Technology, Levanger, 7600, Norway.
| | - Cristen J Willer
- Department of Internal Medicine: Cardiology, University of Michigan, Ann Arbor, 48109, MI, USA. .,Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, 48109, MI, USA. .,Department of Human Genetics, University of Michigan, Ann Arbor, 48109, MI, USA.
| |
Collapse
|