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Huang T, Lu Z, Wang Z, Cheng L, Gao L, Gao J, Zhang N, Geng CA, Zhao X, Wang H, Wong CW, Yeung KWK, Pan H, Lu WW, Guan M. Targeting adipocyte ESRRA promotes osteogenesis and vascular formation in adipocyte-rich bone marrow. Nat Commun 2024; 15:3769. [PMID: 38704393 PMCID: PMC11069533 DOI: 10.1038/s41467-024-48255-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2023] [Accepted: 04/23/2024] [Indexed: 05/06/2024] Open
Abstract
Excessive bone marrow adipocytes (BMAds) accumulation often occurs under diverse pathophysiological conditions associated with bone deterioration. Estrogen-related receptor α (ESRRA) is a key regulator responding to metabolic stress. Here, we show that adipocyte-specific ESRRA deficiency preserves osteogenesis and vascular formation in adipocyte-rich bone marrow upon estrogen deficiency or obesity. Mechanistically, adipocyte ESRRA interferes with E2/ESR1 signaling resulting in transcriptional repression of secreted phosphoprotein 1 (Spp1); yet positively modulates leptin expression by binding to its promoter. ESRRA abrogation results in enhanced SPP1 and decreased leptin secretion from both visceral adipocytes and BMAds, concertedly dictating bone marrow stromal stem cell fate commitment and restoring type H vessel formation, constituting a feed-forward loop for bone formation. Pharmacological inhibition of ESRRA protects obese mice against bone loss and high marrow adiposity. Thus, our findings highlight a therapeutic approach via targeting adipocyte ESRRA to preserve bone formation especially in detrimental adipocyte-rich bone milieu.
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Affiliation(s)
- Tongling Huang
- Research Center for Human Tissues and Organs Degeneration, Institute of Biomedicine and Biotechnology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China
| | - Zhaocheng Lu
- Research Center for Human Tissues and Organs Degeneration, Institute of Biomedicine and Biotechnology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China
| | - Zihui Wang
- Research Center for Human Tissues and Organs Degeneration, Institute of Biomedicine and Biotechnology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Lixin Cheng
- Guangdong Provincial Clinical Research Center for Geriatrics, Shenzhen Clinical Research Center for Geriatrics, Shenzhen People's Hospital, Shenzhen, China
| | - Lu Gao
- Research Center for Human Tissues and Organs Degeneration, Institute of Biomedicine and Biotechnology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Jun Gao
- Research Center for Human Tissues and Organs Degeneration, Institute of Biomedicine and Biotechnology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China
| | - Ning Zhang
- Neuroscience Center, Shantou University Medical College, Shantou, China
| | - Chang-An Geng
- State Key Laboratory of Phytochemistry and Plant Resources in West China, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, China
| | - Xiaoli Zhao
- Research Center for Human Tissues and Organs Degeneration, Institute of Biomedicine and Biotechnology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China
| | - Huaiyu Wang
- Research Center for Human Tissues and Organs Degeneration, Institute of Biomedicine and Biotechnology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China
| | | | - Kelvin W K Yeung
- Department of Orthopaedics and Traumatology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, China
| | - Haobo Pan
- Research Center for Human Tissues and Organs Degeneration, Institute of Biomedicine and Biotechnology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China
| | - William Weijia Lu
- Faculty of Pharmaceutical Sciences, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China
| | - Min Guan
- Research Center for Human Tissues and Organs Degeneration, Institute of Biomedicine and Biotechnology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China.
- University of Chinese Academy of Sciences, Beijing, China.
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Ha S, Kim HW, Kim KM, Kim BM, Kim J, Son M, Kim D, Kim MJ, Yoo J, Yu HS, Jung YS, Lee J, Chung HY, Chung KW. PAR2-mediated cellular senescence promotes inflammation and fibrosis in aging and chronic kidney disease. Aging Cell 2024:e14184. [PMID: 38687090 DOI: 10.1111/acel.14184] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2023] [Revised: 03/29/2024] [Accepted: 04/10/2024] [Indexed: 05/02/2024] Open
Abstract
Cellular senescence contributes to inflammatory kidney disease via the secretion of inflammatory and profibrotic factors. Protease-activating receptor 2 (PAR2) is a key regulator of inflammation in kidney diseases. However, the relationship between PAR2 and cellular senescence in kidney disease has not yet been described. In this study, we found that PAR2-mediated metabolic changes in renal tubular epithelial cells induced cellular senescence and increased inflammatory responses. Using an aging and renal injury model, PAR2 expression was shown to be associated with cellular senescence. Under in vitro conditions in NRK52E cells, PAR2 activation induces tubular epithelial cell senescence and senescent cells showed defective fatty acid oxidation (FAO). Cpt1α inhibition showed similar senescent phenotype in the cells, implicating the important role of defective FAO in senescence. Finally, we subjected mice lacking PAR2 to aging and renal injury. PAR2-deficient kidneys are protected from adenine- and cisplatin-induced renal fibrosis and injury, respectively, by reducing senescence and inflammation. Moreover, kidneys lacking PAR2 exhibited reduced numbers of senescent cells and inflammation during aging. These findings offer fresh insights into the mechanisms underlying renal senescence and indicate that targeting PAR2 or FAO may be a promising therapeutic approach for managing kidney injury.
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Affiliation(s)
- Sugyeong Ha
- Department of Pharmacy and Research Institute for Drug Development, College of Pharmacy, Pusan National University, Busan, Korea
| | - Hyun Woo Kim
- Department of Pharmacy and Research Institute for Drug Development, College of Pharmacy, Pusan National University, Busan, Korea
| | - Kyung Mok Kim
- Department of Pharmacy and Research Institute for Drug Development, College of Pharmacy, Pusan National University, Busan, Korea
| | - Byeong Moo Kim
- Department of Pharmacy and Research Institute for Drug Development, College of Pharmacy, Pusan National University, Busan, Korea
| | - Jeongwon Kim
- Department of Pharmacy and Research Institute for Drug Development, College of Pharmacy, Pusan National University, Busan, Korea
| | - Minjung Son
- Department of Pharmacy and Research Institute for Drug Development, College of Pharmacy, Pusan National University, Busan, Korea
| | - Doyeon Kim
- Department of Pharmacy and Research Institute for Drug Development, College of Pharmacy, Pusan National University, Busan, Korea
| | - Mi-Jeong Kim
- Department of Pharmacy and Research Institute for Drug Development, College of Pharmacy, Pusan National University, Busan, Korea
| | - Jian Yoo
- Department of Pharmacy and Research Institute for Drug Development, College of Pharmacy, Pusan National University, Busan, Korea
| | - Hak Sun Yu
- Department of Parasitology and Tropical Medicine, School of Medicine, Pusan National University, Yangsan, Korea
| | - Young-Suk Jung
- Department of Pharmacy and Research Institute for Drug Development, College of Pharmacy, Pusan National University, Busan, Korea
| | - Jaewon Lee
- Department of Pharmacy and Research Institute for Drug Development, College of Pharmacy, Pusan National University, Busan, Korea
| | - Hae Young Chung
- Department of Pharmacy and Research Institute for Drug Development, College of Pharmacy, Pusan National University, Busan, Korea
| | - Ki Wung Chung
- Department of Pharmacy and Research Institute for Drug Development, College of Pharmacy, Pusan National University, Busan, Korea
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3
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Hinze C, Lovric S, Halloran PF, Barasch J, Schmidt-Ott KM. Epithelial cell states associated with kidney and allograft injury. Nat Rev Nephrol 2024:10.1038/s41581-024-00834-0. [PMID: 38632381 DOI: 10.1038/s41581-024-00834-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/27/2024] [Indexed: 04/19/2024]
Abstract
The kidney epithelium, with its intricate arrangement of highly specialized cell types, constitutes the functional core of the organ. Loss of kidney epithelium is linked to the loss of functional nephrons and a subsequent decline in kidney function. In kidney transplantation, epithelial injury signatures observed during post-transplantation surveillance are strong predictors of adverse kidney allograft outcomes. However, epithelial injury is currently neither monitored clinically nor addressed therapeutically after kidney transplantation. Several factors can contribute to allograft epithelial injury, including allograft rejection, drug toxicity, recurrent infections and postrenal obstruction. The injury mechanisms that underlie allograft injury overlap partially with those associated with acute kidney injury (AKI) and chronic kidney disease (CKD) in the native kidney. Studies using advanced transcriptomic analyses of single cells from kidney or urine have identified a role for kidney injury-induced epithelial cell states in exacerbating and sustaining damage in AKI and CKD. These epithelial cell states and their associated expression signatures are also observed in transplanted kidney allografts, suggesting that the identification and characterization of transcriptomic epithelial cell states in kidney allografts may have potential clinical implications for diagnosis and therapy.
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Affiliation(s)
- Christian Hinze
- Department of Nephrology and Hypertension, Hannover Medical School, Hannover, Germany
| | - Svjetlana Lovric
- Department of Nephrology and Hypertension, Hannover Medical School, Hannover, Germany
| | - Philip F Halloran
- Alberta Transplant Applied Genomics Centre, Edmonton, Alberta, Canada
- Department of Medicine, Division of Nephrology and Transplant Immunology, University of Alberta, Edmonton, Alberta, Canada
| | - Jonathan Barasch
- Division of Nephrology, Columbia University, New York City, NY, USA
| | - Kai M Schmidt-Ott
- Department of Nephrology and Hypertension, Hannover Medical School, Hannover, Germany.
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4
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Li H, Humphreys BD. Multimodal characterization of sexual dimorphism in the mammalian kidney. Kidney Int 2024; 105:653-655. [PMID: 38519227 DOI: 10.1016/j.kint.2023.11.017] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2023] [Accepted: 11/01/2023] [Indexed: 03/24/2024]
Affiliation(s)
- Haikuo Li
- Division of Nephrology, Department of Medicine, Washington University in St. Louis, St. Louis, Missouri, USA
| | - Benjamin D Humphreys
- Division of Nephrology, Department of Medicine, Washington University in St. Louis, St. Louis, Missouri, USA; Department of Developmental Biology, Washington University in St. Louis, St. Louis, Missouri, USA.
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5
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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] [What about the content of this article? (0)] [Affiliation(s)] [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.
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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.
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6
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Chen H, You R, Guo J, Zhou W, Chew G, Devapragash N, Loh JZ, Gesualdo L, Li Y, Jiang Y, Tan ELS, Chen S, Pontrelli P, Pesce F, Behmoaras J, Zhang A, Petretto E. WWP2 Regulates Renal Fibrosis and the Metabolic Reprogramming of Profibrotic Myofibroblasts. J Am Soc Nephrol 2024:00001751-990000000-00269. [PMID: 38502123 DOI: 10.1681/asn.0000000000000328] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2023] [Accepted: 02/28/2024] [Indexed: 03/20/2024] Open
Abstract
Key Points
WWP2 expression is elevated in the tubulointerstitium of fibrotic kidneys and contributes to CKD pathogenesis and progression.WWP2 uncouples the profibrotic activation and cell proliferation in renal myofibroblasts.WWP2 controls mitochondrial respiration in renal myofibroblasts through the metabolic regulator peroxisome proliferator-activated receptor gamma coactivator 1-alpha.
Background
Renal fibrosis is a common pathologic end point in CKD that is challenging to reverse, and myofibroblasts are responsible for the accumulation of a fibrillar collagen–rich extracellular matrix. Recent studies have unveiled myofibroblasts' diversity in proliferative and fibrotic characteristics, which are linked to different metabolic states. We previously demonstrated the regulation of extracellular matrix genes and tissue fibrosis by WWP2, a multifunctional E3 ubiquitin–protein ligase. Here, we investigate WWP2 in renal fibrosis and in the metabolic reprograming of myofibroblasts in CKD.
Methods
We used kidney samples from patients with CKD and WWP2-null kidney disease mice models and leveraged single-cell RNA sequencing analysis to detail the cell-specific regulation of WWP2 in fibrotic kidneys. Experiments in primary cultured myofibroblasts by bulk-RNA sequencing, chromatin immunoprecipitation sequencing, metabolomics, and cellular metabolism assays were used to study the metabolic regulation of WWP2 and its downstream signaling.
Results
The tubulointerstitial expression of WWP2 was associated with fibrotic progression in patients with CKD and in murine kidney disease models. WWP2 deficiency promoted myofibroblast proliferation and halted profibrotic activation, reducing the severity of renal fibrosis in vivo. In renal myofibroblasts, WWP2 deficiency increased fatty acid oxidation and activated the pentose phosphate pathway, boosting mitochondrial respiration at the expense of glycolysis. WWP2 suppressed the transcription of peroxisome proliferator-activated receptor gamma coactivator 1-alpha (PGC-1α), a metabolic mediator of fibrotic response, and pharmacologic inhibition of PGC-1α partially abrogated the protective effects of WWP2 deficiency on myofibroblasts.
Conclusions
WWP2 regulates the metabolic reprogramming of profibrotic myofibroblasts by a WWP2-PGC-1α axis, and WWP2 deficiency protects against renal fibrosis in CKD.
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Affiliation(s)
- Huimei Chen
- Programme in Cardiovascular and Metabolic Disorders (CVMD) and Centre for Computational Biology (CCB), Duke-NUS Medical School, Singapore
| | - Ran You
- Department of Nephrology, Children's Hospital of Nanjing Medical University, Nanjing, China
| | - Jing Guo
- Programme in Cardiovascular and Metabolic Disorders (CVMD) and Centre for Computational Biology (CCB), Duke-NUS Medical School, Singapore
| | - Wei Zhou
- Department of Nephrology, Children's Hospital of Nanjing Medical University, Nanjing, China
| | - Gabriel Chew
- Programme in Cardiovascular and Metabolic Disorders (CVMD) and Centre for Computational Biology (CCB), Duke-NUS Medical School, Singapore
| | - Nithya Devapragash
- Programme in Cardiovascular and Metabolic Disorders (CVMD) and Centre for Computational Biology (CCB), Duke-NUS Medical School, Singapore
| | - Jui Zhi Loh
- Programme in Cardiovascular and Metabolic Disorders (CVMD) and Centre for Computational Biology (CCB), Duke-NUS Medical School, Singapore
| | - Loreto Gesualdo
- Nephrology, Dialysis and Transplantation Unit, Department of Precision and Regenerative Medicine and Ionian Area (DiMePRe-J), University of Bari Aldo Moro, Bari, Italy
| | - Yanwei Li
- Department of Nephrology, Children's Hospital of Nanjing Medical University, Nanjing, China
| | - Yuteng Jiang
- Department of Nephrology, Children's Hospital of Nanjing Medical University, Nanjing, China
| | - Elisabeth Li Sa Tan
- Programme in Cardiovascular and Metabolic Disorders (CVMD) and Centre for Computational Biology (CCB), Duke-NUS Medical School, Singapore
| | - Shuang Chen
- Department of Nephrology, Children's Hospital of Nanjing Medical University, Nanjing, China
- School of Science, Institute for Big Data and Artificial Intelligence in Medicine, China Pharmaceutical University, Nanjing, China
| | - Paola Pontrelli
- Nephrology, Dialysis and Transplantation Unit, Department of Precision and Regenerative Medicine and Ionian Area (DiMePRe-J), University of Bari Aldo Moro, Bari, Italy
| | - Francesco Pesce
- Division of Renal Medicine, Fatebenefratelli Isola Tiberina-Gemelli Isola, Rome, Italy
| | - Jacques Behmoaras
- Programme in Cardiovascular and Metabolic Disorders (CVMD) and Centre for Computational Biology (CCB), Duke-NUS Medical School, Singapore
- Centre for Inflammatory Disease, Imperial College London, Hammersmith Hospital, London, United Kingdom
| | - Aihua Zhang
- Department of Nephrology, Children's Hospital of Nanjing Medical University, Nanjing, China
| | - Enrico Petretto
- Programme in Cardiovascular and Metabolic Disorders (CVMD) and Centre for Computational Biology (CCB), Duke-NUS Medical School, Singapore
- School of Science, Institute for Big Data and Artificial Intelligence in Medicine, China Pharmaceutical University, Nanjing, China
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7
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Li H, Li D, Ledru N, Xuanyuan Q, Wu H, Asthana A, Byers LN, Tullius SG, Orlando G, Waikar SS, Humphreys BD. Transcriptomic, epigenomic, and spatial metabolomic cell profiling redefines regional human kidney anatomy. Cell Metab 2024:S1550-4131(24)00061-5. [PMID: 38513647 DOI: 10.1016/j.cmet.2024.02.015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/06/2023] [Revised: 12/20/2023] [Accepted: 02/26/2024] [Indexed: 03/23/2024]
Abstract
A large-scale multimodal atlas that includes major kidney regions is lacking. Here, we employed simultaneous high-throughput single-cell ATAC/RNA sequencing (SHARE-seq) and spatially resolved metabolomics to profile 54 human samples from distinct kidney anatomical regions. We generated transcriptomes of 446,267 cells and chromatin accessibility profiles of 401,875 cells and developed a package to analyze 408,218 spatially resolved metabolomes. We find that the same cell type, including thin limb, thick ascending limb loop of Henle and principal cells, display distinct transcriptomic, chromatin accessibility, and metabolomic signatures, depending on anatomic location. Surveying metabolism-associated gene profiles revealed non-overlapping metabolic signatures between nephron segments and dysregulated lipid metabolism in diseased proximal tubule (PT) cells. Integrating multimodal omics with clinical data identified PLEKHA1 as a disease marker, and its in vitro knockdown increased gene expression in PT differentiation, suggesting possible pathogenic roles. This study highlights previously underrepresented cellular heterogeneity underlying the human kidney anatomy.
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Affiliation(s)
- Haikuo Li
- Division of Nephrology, Department of Medicine, Washington University in St. Louis, St. Louis, MO, USA
| | - Dian Li
- Division of Nephrology, Department of Medicine, Washington University in St. Louis, St. Louis, MO, USA
| | - Nicolas Ledru
- Division of Nephrology, Department of Medicine, Washington University in St. Louis, St. Louis, MO, USA
| | - Qiao Xuanyuan
- Division of Nephrology, Department of Medicine, Washington University in St. Louis, St. Louis, MO, USA
| | - Haojia Wu
- Division of Nephrology, Department of Medicine, Washington University in St. Louis, St. Louis, MO, USA
| | - Amish Asthana
- Department of Surgery, Atrium Health Wake Forest Baptist, Wake Forest Institute for Regenerative Medicine, Wake Forest School of Medicine, Winston Salem, NC, USA
| | - Lori N Byers
- Department of Surgery, Atrium Health Wake Forest Baptist, Wake Forest Institute for Regenerative Medicine, Wake Forest School of Medicine, Winston Salem, NC, USA
| | - Stefan G Tullius
- Division of Transplant Surgery and Transplant Surgery Research Laboratory, Department of Surgery, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Giuseppe Orlando
- Department of Surgery, Atrium Health Wake Forest Baptist, Wake Forest Institute for Regenerative Medicine, Wake Forest School of Medicine, Winston Salem, NC, USA
| | - Sushrut S Waikar
- Section of Nephrology, Department of Medicine, Boston University Chobanian & Avedisian School of Medicine, Boston Medical Center, Boston, MA, USA
| | - Benjamin D Humphreys
- Division of Nephrology, Department of Medicine, Washington University in St. Louis, St. Louis, MO, USA; Department of Developmental Biology, Washington University in St. Louis, St. Louis, MO, USA.
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8
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Hu J, Wang SG, Hou Y, Chen Z, Liu L, Li R, Li N, Zhou L, Yang Y, Wang L, Wang L, Yang X, Lei Y, Deng C, Li Y, Deng Z, Ding Y, Kuang Y, Yao Z, Xun Y, Li F, Li H, Hu J, Liu Z, Wang T, Hao Y, Jiao X, Guan W, Tao Z, Ren S, Chen K. Multi-omic profiling of clear cell renal cell carcinoma identifies metabolic reprogramming associated with disease progression. Nat Genet 2024; 56:442-457. [PMID: 38361033 PMCID: PMC10937392 DOI: 10.1038/s41588-024-01662-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2023] [Accepted: 01/10/2024] [Indexed: 02/17/2024]
Abstract
Clear cell renal cell carcinoma (ccRCC) is a complex disease with remarkable immune and metabolic heterogeneity. Here we perform genomic, transcriptomic, proteomic, metabolomic and spatial transcriptomic and metabolomic analyses on 100 patients with ccRCC from the Tongji Hospital RCC (TJ-RCC) cohort. Our analysis identifies four ccRCC subtypes including De-clear cell differentiated (DCCD)-ccRCC, a subtype with distinctive metabolic features. DCCD cancer cells are characterized by fewer lipid droplets, reduced metabolic activity, enhanced nutrient uptake capability and a high proliferation rate, leading to poor prognosis. Using single-cell and spatial trajectory analysis, we demonstrate that DCCD is a common mode of ccRCC progression. Even among stage I patients, DCCD is associated with worse outcomes and higher recurrence rate, suggesting that it cannot be cured by nephrectomy alone. Our study also suggests a treatment strategy based on subtype-specific immune cell infiltration that could guide the clinical management of ccRCC.
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Affiliation(s)
- Junyi Hu
- Department of Urology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Shao-Gang Wang
- Department of Urology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Yaxin Hou
- Department of Urology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Zhaohui Chen
- Department of Urology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Lilong Liu
- Department of Urology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Ruizhi Li
- Shanghai Luming Biotech, Shanghai, China
| | - Nisha Li
- Shanghai Luming Biotech, Shanghai, China
- Shanghai OE Biotech, Shanghai, China
| | - Lijie Zhou
- Department of Urology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Yu Yang
- Department of Pathology and Laboratory Medicine, Indiana University School of Medicine, Indianapolis, IN, USA
| | - Liping Wang
- Department of Pathology, Baylor Scott & White Medical Center, Temple, TX, USA
| | - Liang Wang
- Department of Urology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Xiong Yang
- Department of Urology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Yichen Lei
- Shanghai Institute of Hematology, State Key Laboratory of Medical Genomics, National Research Center for Translational Medicine at Shanghai, Ruijin Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Changqi Deng
- Department of Urology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Yang Li
- Department of Urology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Zhiyao Deng
- Department of Urology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Yuhong Ding
- Department of Urology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Yingchun Kuang
- Department of Urology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Zhipeng Yao
- Department of Urology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Yang Xun
- Department of Urology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Fan Li
- Department of Urology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Heng Li
- Department of Urology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Jia Hu
- Department of Urology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Zheng Liu
- Department of Urology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Tao Wang
- Department of Urology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Yi Hao
- Department of Pathogen Biology, School of Basic Medicine, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Xuanmao Jiao
- Pennsylvania Cancer and Regenerative Medicine Research Center, Baruch S. Blumberg Institute, Philadelphia, PA, USA
| | - Wei Guan
- Department of Urology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China.
| | - Zhen Tao
- Department of Radiation Oncology, Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer; Tianjin's Clinical Research Center for Cancer; Key Laboratory of Cancer Prevention and Therapy, Tianjin, China.
- Department of Oncology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China.
| | - Shancheng Ren
- Department of Urology, Second Affiliated Hospital of Naval Medical University, Shanghai, China.
| | - Ke Chen
- Department of Urology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China.
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9
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Ledru N, Wilson PC, Muto Y, Yoshimura Y, Wu H, Li D, Asthana A, Tullius SG, Waikar SS, Orlando G, Humphreys BD. Predicting proximal tubule failed repair drivers through regularized regression analysis of single cell multiomic sequencing. Nat Commun 2024; 15:1291. [PMID: 38347009 PMCID: PMC10861555 DOI: 10.1038/s41467-024-45706-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2023] [Accepted: 01/31/2024] [Indexed: 02/15/2024] Open
Abstract
Renal proximal tubule epithelial cells have considerable intrinsic repair capacity following injury. However, a fraction of injured proximal tubule cells fails to undergo normal repair and assumes a proinflammatory and profibrotic phenotype that may promote fibrosis and chronic kidney disease. The healthy to failed repair change is marked by cell state-specific transcriptomic and epigenomic changes. Single nucleus joint RNA- and ATAC-seq sequencing offers an opportunity to study the gene regulatory networks underpinning these changes in order to identify key regulatory drivers. We develop a regularized regression approach to construct genome-wide parametric gene regulatory networks using multiomic datasets. We generate a single nucleus multiomic dataset from seven adult human kidney samples and apply our method to study drivers of a failed injury response associated with kidney disease. We demonstrate that our approach is a highly effective tool for predicting key cis- and trans-regulatory elements underpinning the healthy to failed repair transition and use it to identify NFAT5 as a driver of the maladaptive proximal tubule state.
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Affiliation(s)
- Nicolas Ledru
- Division of Nephrology, Department of Medicine, Washington University in St. Louis School of Medicine, St. Louis, MO, USA
| | - Parker C Wilson
- Division of Anatomic and Molecular Pathology, Department of Pathology and Immunology, Washington University in St. Louis, St. Louis, MO, USA
| | - Yoshiharu Muto
- Division of Nephrology, Department of Medicine, Washington University in St. Louis School of Medicine, St. Louis, MO, USA
| | - Yasuhiro Yoshimura
- Division of Nephrology, Department of Medicine, Washington University in St. Louis School of Medicine, St. Louis, MO, USA
| | - Haojia Wu
- Division of Nephrology, Department of Medicine, Washington University in St. Louis School of Medicine, St. Louis, MO, USA
| | - Dian Li
- Division of Nephrology, Department of Medicine, Washington University in St. Louis School of Medicine, St. Louis, MO, USA
| | - Amish Asthana
- Department of Surgery, Wake Forest Baptist Medical Center; Wake Forest Institute for Regenerative Medicine, Wake Forest School of Medicine, Winston Salem, NC, USA
| | - Stefan G Tullius
- Division of Transplant Surgery and Transplant Surgery Research Laboratory, Department of Surgery, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Sushrut S Waikar
- Section of Nephrology, Department of Medicine, Boston University Chobanian and Avedisian School of Medicine, Boston Medical Center, Boston, MA, USA
| | - Giuseppe Orlando
- Department of Surgery, Wake Forest Baptist Medical Center; Wake Forest Institute for Regenerative Medicine, Wake Forest School of Medicine, Winston Salem, NC, USA
| | - Benjamin D Humphreys
- Division of Nephrology, Department of Medicine, Washington University in St. Louis School of Medicine, St. Louis, MO, USA.
- Department of Developmental Biology, Washington University in St. Louis School of Medicine, St. Louis, MO, USA.
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10
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Liu J, Feng L, Jia Q, Meng J, Zhao Y, Ren L, Yan Z, Wang M, Qin J. A comprehensive bioinformatics analysis identifies mitophagy biomarkers and potential Molecular mechanisms in hypertensive nephropathy. J Biomol Struct Dyn 2024:1-20. [PMID: 38334110 DOI: 10.1080/07391102.2024.2311344] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2023] [Accepted: 12/05/2023] [Indexed: 02/10/2024]
Abstract
Mitophagy, the selective removal of damaged mitochondria, plays a critical role in kidney diseases, but its involvement in hypertensive nephropathy (HTN) is not well understood. To address this gap, we investigated mitophagy-related genes in HTN, identifying potential biomarkers for diagnosis and treatment. Transcriptome datasets from the Gene Expression Omnibus database were analyzed, resulting in the identification of seven mitophagy related differentially expressed genes (MR-DEGs), namely PINK1, ULK1, SQSTM1, ATG5, ATG12, MFN2, and UBA52. Further, we explored the correlation between MR-DEGs, immune cells, and inflammatory factors. The identified genes demonstrated a strong correlation with Mast cells, T-cells, TGFβ3, IL13, and CSF3. Machine learning techniques were employed to screen important genes, construct diagnostic models, and evaluate their accuracy. Consensus clustering divided the HTN patients into two mitophagy subgroups, with Subgroup 2 showing higher levels of immune cell infiltration and inflammatory factors. The functions of their proteins primarily involve complement, coagulation, lipids, and vascular smooth muscle contraction. Single-cell RNA sequencing revealed that mitophagy was most significant in proximal tubule cells (PTC) in HTN patients. Pseudotime analysis of PTC confirmed the expression changes observed in the transcriptome. Intercellular communication analysis suggested that mitophagy might regulate PTC's participation in intercellular crosstalk. Notably, specific transcription factors such as HNF4A, PPARA, and STAT3 showed strong correlations with mitophagy-related genes in PTC, indicating their potential role in modulating PTC function and influencing the onset and progression of HTN. This study offers a comprehensive analysis of mitophagy in HTN, enhancing our understanding of the pathogenesis, diagnosis, and treatment of HTN.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Jiayou Liu
- The Second Clinical Medical College, Beijing University of Chinese Medicine, Beijing, China
| | - Luda Feng
- Department of Nephropathy, Dongfang Hospital, Beijing University of Chinese Medicine, Beijing, China
| | - Qi Jia
- Dongzhimen Hospital, Beijing University of Chinese Medicine, Beijing, China
| | - Jia Meng
- Department of Nephropathy, Dongfang Hospital, Beijing University of Chinese Medicine, Beijing, China
| | - Yun Zhao
- Department of Nephropathy, Dongfang Hospital, Beijing University of Chinese Medicine, Beijing, China
| | - Lei Ren
- Department of Nephropathy, Dongfang Hospital, Beijing University of Chinese Medicine, Beijing, China
| | - Ziming Yan
- Department of Nephropathy, Dongfang Hospital, Beijing University of Chinese Medicine, Beijing, China
| | - Manrui Wang
- The Second Clinical Medical College, Beijing University of Chinese Medicine, Beijing, China
| | - Jianguo Qin
- Department of Nephropathy, Dongfang Hospital, Beijing University of Chinese Medicine, Beijing, China
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11
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Yan Y, Liu H, Abedini A, Sheng X, Palmer M, Li H, Susztak K. Unraveling the epigenetic code: human kidney DNA methylation and chromatin dynamics in renal disease development. Nat Commun 2024; 15:873. [PMID: 38287030 PMCID: PMC10824731 DOI: 10.1038/s41467-024-45295-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2023] [Accepted: 01/19/2024] [Indexed: 01/31/2024] Open
Abstract
Epigenetic changes may fill a critical gap in our understanding of kidney disease development, as they not only reflect metabolic changes but are also preserved and transmitted during cell division. We conducted a genome-wide cytosine methylation analysis of 399 human kidney samples, along with single-nuclear open chromatin analysis on over 60,000 cells from 14 subjects, including controls, and diabetes and hypertension attributed chronic kidney disease (CKD) patients. We identified and validated differentially methylated positions associated with disease states, and discovered that nearly 30% of these alterations were influenced by underlying genetic variations, including variants known to be associated with kidney disease in genome-wide association studies. We also identified regions showing both methylation and open chromatin changes. These changes in methylation and open chromatin significantly associated gene expression changes, most notably those playing role in metabolism and expressed in proximal tubules. Our study further demonstrated that methylation risk scores (MRS) can improve disease state annotation and prediction of kidney disease development. Collectively, our results suggest a causal relationship between epigenetic changes and kidney disease pathogenesis, thereby providing potential pathways for the development of novel risk stratification methods.
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Affiliation(s)
- Yu Yan
- Renal, Electrolyte, and Hypertension Division, Department of Medicine, University of Pennsylvania, Perelman School of Medicine, Philadelphia, PA, 19014, USA
- Institute for Diabetes, Obesity, and Metabolism, University of Pennsylvania, Perelman School of Medicine, Philadelphia, PA, 19014, USA
- Department of Genetics, University of Pennsylvania, Perelman School of Medicine, Philadelphia, PA, 19014, USA
- Kidney Innovation Center, University of Pennsylvania, Perelman School of Medicine, Philadelphia, PA, 19014, USA
| | - Hongbo Liu
- Renal, Electrolyte, and Hypertension Division, Department of Medicine, University of Pennsylvania, Perelman School of Medicine, Philadelphia, PA, 19014, USA
- Institute for Diabetes, Obesity, and Metabolism, University of Pennsylvania, Perelman School of Medicine, Philadelphia, PA, 19014, USA
- Department of Genetics, University of Pennsylvania, Perelman School of Medicine, Philadelphia, PA, 19014, USA
- Kidney Innovation Center, University of Pennsylvania, Perelman School of Medicine, Philadelphia, PA, 19014, USA
| | - Amin Abedini
- Renal, Electrolyte, and Hypertension Division, Department of Medicine, University of Pennsylvania, Perelman School of Medicine, Philadelphia, PA, 19014, USA
- Institute for Diabetes, Obesity, and Metabolism, University of Pennsylvania, Perelman School of Medicine, Philadelphia, PA, 19014, USA
- Department of Genetics, University of Pennsylvania, Perelman School of Medicine, Philadelphia, PA, 19014, USA
- Kidney Innovation Center, University of Pennsylvania, Perelman School of Medicine, Philadelphia, PA, 19014, USA
| | - Xin Sheng
- Renal, Electrolyte, and Hypertension Division, Department of Medicine, University of Pennsylvania, Perelman School of Medicine, Philadelphia, PA, 19014, USA
- Institute for Diabetes, Obesity, and Metabolism, University of Pennsylvania, Perelman School of Medicine, Philadelphia, PA, 19014, USA
- Department of Genetics, University of Pennsylvania, Perelman School of Medicine, Philadelphia, PA, 19014, USA
- Kidney Innovation Center, University of Pennsylvania, Perelman School of Medicine, Philadelphia, PA, 19014, USA
| | - Matthew Palmer
- Kidney Innovation Center, University of Pennsylvania, Perelman School of Medicine, Philadelphia, PA, 19014, USA
- Department of Epidemiology and Biostatistics, Perelman School of Medicine, Philadelphia, PA, 19014, USA
| | - Hongzhe Li
- Kidney Innovation Center, University of Pennsylvania, Perelman School of Medicine, Philadelphia, PA, 19014, USA
- Department of Pathology, Perelman School of Medicine, Philadelphia, PA, 19014, USA
| | - Katalin Susztak
- Renal, Electrolyte, and Hypertension Division, Department of Medicine, University of Pennsylvania, Perelman School of Medicine, Philadelphia, PA, 19014, USA.
- Institute for Diabetes, Obesity, and Metabolism, University of Pennsylvania, Perelman School of Medicine, Philadelphia, PA, 19014, USA.
- Department of Genetics, University of Pennsylvania, Perelman School of Medicine, Philadelphia, PA, 19014, USA.
- Kidney Innovation Center, University of Pennsylvania, Perelman School of Medicine, Philadelphia, PA, 19014, USA.
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12
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Tang W, Wei Q. The metabolic pathway regulation in kidney injury and repair. Front Physiol 2024; 14:1344271. [PMID: 38283280 PMCID: PMC10811252 DOI: 10.3389/fphys.2023.1344271] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2023] [Accepted: 12/28/2023] [Indexed: 01/30/2024] Open
Abstract
Kidney injury and repair are accompanied by significant disruptions in metabolic pathways, leading to renal cell dysfunction and further contributing to the progression of renal pathology. This review outlines the complex involvement of various energy production pathways in glucose, lipid, amino acid, and ketone body metabolism within the kidney. We provide a comprehensive summary of the aberrant regulation of these metabolic pathways in kidney injury and repair. After acute kidney injury (AKI), there is notable mitochondrial damage and oxygen/nutrient deprivation, leading to reduced activity in glycolysis and mitochondrial bioenergetics. Additionally, disruptions occur in the pentose phosphate pathway (PPP), amino acid metabolism, and the supply of ketone bodies. The subsequent kidney repair phase is characterized by a metabolic shift toward glycolysis, along with decreased fatty acid β-oxidation and continued disturbances in amino acid metabolism. Furthermore, the impact of metabolism dysfunction on renal cell injury, regeneration, and the development of renal fibrosis is analyzed. Finally, we discuss the potential therapeutic strategies by targeting renal metabolic regulation to ameliorate kidney injury and fibrosis and promote kidney repair.
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Affiliation(s)
- Wenbin Tang
- Health Management Center, Xiangya Hospital, Central South University, Changsha, Hunan, China
- Department of Cellular Biology and Anatomy, Medical College of Georgia, Augusta University, Augusta, GA, United States
| | - Qingqing Wei
- Department of Cellular Biology and Anatomy, Medical College of Georgia, Augusta University, Augusta, GA, United States
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13
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Abedini A, Sánchez-Navaro A, Wu J, Klötzer KA, Ma Z, Poudel B, Doke T, Balzer MS, Frederick J, Cernecka H, Liu H, Liang X, Vitale S, Kolkhof P, Susztak K. Single-cell transcriptomics and chromatin accessibility profiling elucidate the kidney-protective mechanism of mineralocorticoid receptor antagonists. J Clin Invest 2024; 134:e157165. [PMID: 37906287 PMCID: PMC10760974 DOI: 10.1172/jci157165] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2021] [Accepted: 10/23/2023] [Indexed: 11/02/2023] Open
Abstract
Mineralocorticoid excess commonly leads to hypertension (HTN) and kidney disease. In our study, we used single-cell expression and chromatin accessibility tools to characterize the mineralocorticoid target genes and cell types. We demonstrated that mineralocorticoid effects were established through open chromatin and target gene expression, primarily in principal and connecting tubule cells and, to a lesser extent, in segments of the distal convoluted tubule cells. We examined the kidney-protective effects of steroidal and nonsteroidal mineralocorticoid antagonists (MRAs), as well as of amiloride, an epithelial sodium channel inhibitor, in a rat model of deoxycorticosterone acetate, unilateral nephrectomy, and high-salt consumption-induced HTN and cardiorenal damage. All antihypertensive therapies protected against cardiorenal damage. However, finerenone was particularly effective in reducing albuminuria and improving gene expression changes in podocytes and proximal tubule cells, even with an equivalent reduction in blood pressure. We noted a strong correlation between the accumulation of injured/profibrotic tubule cells expressing secreted posphoprotein 1 (Spp1), Il34, and platelet-derived growth factor subunit b (Pdgfb) and the degree of fibrosis in rat kidneys. This gene signature also showed a potential for classifying human kidney samples. Our multiomics approach provides fresh insights into the possible mechanisms underlying HTN-associated kidney disease, the target cell types, the protective effects of steroidal and nonsteroidal MRAs, and amiloride.
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Affiliation(s)
- Amin Abedini
- Renal, Electrolyte, and Hypertension Division, Department of Medicine
- Institute for Diabetes, Obesity, and Metabolism, and
- Department of Genetics, University of Pennsylvania, Perelman School of Medicine, Philadelphia, Pennsylvania, USA
| | - Andrea Sánchez-Navaro
- Renal, Electrolyte, and Hypertension Division, Department of Medicine
- Institute for Diabetes, Obesity, and Metabolism, and
- Department of Genetics, University of Pennsylvania, Perelman School of Medicine, Philadelphia, Pennsylvania, USA
| | - Junnan Wu
- Renal, Electrolyte, and Hypertension Division, Department of Medicine
- Institute for Diabetes, Obesity, and Metabolism, and
- Department of Genetics, University of Pennsylvania, Perelman School of Medicine, Philadelphia, Pennsylvania, USA
| | - Konstantin A. Klötzer
- Renal, Electrolyte, and Hypertension Division, Department of Medicine
- Institute for Diabetes, Obesity, and Metabolism, and
- Department of Genetics, University of Pennsylvania, Perelman School of Medicine, Philadelphia, Pennsylvania, USA
| | - Ziyuan Ma
- Renal, Electrolyte, and Hypertension Division, Department of Medicine
- Institute for Diabetes, Obesity, and Metabolism, and
- Department of Genetics, University of Pennsylvania, Perelman School of Medicine, Philadelphia, Pennsylvania, USA
| | - Bibek Poudel
- Renal, Electrolyte, and Hypertension Division, Department of Medicine
- Institute for Diabetes, Obesity, and Metabolism, and
- Department of Genetics, University of Pennsylvania, Perelman School of Medicine, Philadelphia, Pennsylvania, USA
| | - Tomohito Doke
- Renal, Electrolyte, and Hypertension Division, Department of Medicine
- Institute for Diabetes, Obesity, and Metabolism, and
- Department of Genetics, University of Pennsylvania, Perelman School of Medicine, Philadelphia, Pennsylvania, USA
| | - Michael S. Balzer
- Renal, Electrolyte, and Hypertension Division, Department of Medicine
- Institute for Diabetes, Obesity, and Metabolism, and
- Department of Genetics, University of Pennsylvania, Perelman School of Medicine, Philadelphia, Pennsylvania, USA
| | - Julia Frederick
- Renal, Electrolyte, and Hypertension Division, Department of Medicine
- Institute for Diabetes, Obesity, and Metabolism, and
- Department of Genetics, University of Pennsylvania, Perelman School of Medicine, Philadelphia, Pennsylvania, USA
| | - Hana Cernecka
- Bayer AG, Pharmaceuticals, Research and Development, Cardiovascular Research, Wuppertal, Germany
| | - Hongbo Liu
- Renal, Electrolyte, and Hypertension Division, Department of Medicine
- Institute for Diabetes, Obesity, and Metabolism, and
- Department of Genetics, University of Pennsylvania, Perelman School of Medicine, Philadelphia, Pennsylvania, USA
| | - Xiujie Liang
- Renal, Electrolyte, and Hypertension Division, Department of Medicine
- Institute for Diabetes, Obesity, and Metabolism, and
- Department of Genetics, University of Pennsylvania, Perelman School of Medicine, Philadelphia, Pennsylvania, USA
| | - Steven Vitale
- Renal, Electrolyte, and Hypertension Division, Department of Medicine
- Institute for Diabetes, Obesity, and Metabolism, and
- Department of Genetics, University of Pennsylvania, Perelman School of Medicine, Philadelphia, Pennsylvania, USA
| | - Peter Kolkhof
- Bayer AG, Pharmaceuticals, Research and Development, Cardiovascular Research, Wuppertal, Germany
| | - Katalin Susztak
- Renal, Electrolyte, and Hypertension Division, Department of Medicine
- Institute for Diabetes, Obesity, and Metabolism, and
- Department of Genetics, University of Pennsylvania, Perelman School of Medicine, Philadelphia, Pennsylvania, USA
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14
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Hu H, Li W, Hao Y, Peng Z, Zou Z, Liang W. Baicalin ameliorates renal fibrosis by upregulating CPT1α-mediated fatty acid oxidation in diabetic kidney disease. Phytomedicine 2024; 122:155162. [PMID: 37922789 DOI: 10.1016/j.phymed.2023.155162] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/27/2023] [Revised: 09/21/2023] [Accepted: 10/22/2023] [Indexed: 11/07/2023]
Abstract
BACKGROUND Diabetic kidney disease (DKD) is a leading cause of end-stage renal disease (ESRD). The progression of DKD is often marked by heightened renal fibrosis due to hindered fatty acid oxidation within renal tubules. Baicalin (BA), a naturally derived compound, has exhibited the potential to mitigate the advancement of DKD. Delving deeper into the precise targets and mechanisms of BA's effect on DKD is crucial. PURPOSE This study sought to elucidate the specific mechanism through which BA moderates the progression of DKD. METHODS Renal tubular tissues from diabetic (db/db) and control (db/m) mice were subjected to mRNA sequencing to discern BA's influence on DKD. Immunohistochemical staining and Western blot were employed to assess the expression of CPT1α in DKD patients and db/db and db/m mice administered with either BA (50 mg/kg/day) or a vehicle for 12 weeks. In vitro, human proximal renal tubule cells (HK-2) were treated with 40 mM high glucose or 50 μM BA. The potential inhibitory mechanism of BA on renal fibrosis in DKD was evaluated using Oil Red O staining and oxygen consumption rate (OCR) measurements. RESULTS The results demonstrated that BA notably reduced lipid accumulation and renal fibrosis in db/db mice. Moreover, mRNA sequencing pinpointed a significant downregulation of CPT1α in DKD. In vitro assays revealed that both the overexpression of CPT1α and treatment with BA exerted similar influences on mitochondrial respiration, fatty acid oxidation, and renal fibrosis levels. Given the pronounced downregulation of CPT1α in DKD patients and its substantial correlation with clinical indicators, it was evident that CPT1α could serve as a therapeutic target for BA in addressing DKD. CONCLUSION Our findings demonstrated that BA potentially enhances FAO by augmenting the expression of CPT1α, subsequently diminishing renal fibrosis in DKD. As such, CPT1α emerges as a promising therapeutic target for DKD intervention.
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Affiliation(s)
- Hongtu Hu
- Division of Nephrology, Renmin Hospital of Wuhan University, 238 Jiefang Road, Wuhan, Hubei 430060, China; Key Clinical Research Center of Kidney Disease in Hubei, 238 Jiefang Rd, Wuhan, Hubei 430060, China; Central Laboratory, Renmin Hospital of Wuhan University, Wuhan, China
| | - Weiwei Li
- Division of Nephrology, The Central Hospital of Enshi Tujia and Miao Autonomous Prefecture, No.158 Wuyang Avenue, Enshi City, Hubei Province, China
| | - Yiqun Hao
- Division of Nephrology, Renmin Hospital of Wuhan University, 238 Jiefang Road, Wuhan, Hubei 430060, China; Key Clinical Research Center of Kidney Disease in Hubei, 238 Jiefang Rd, Wuhan, Hubei 430060, China
| | - Zhuan Peng
- Division of Nephrology, Renmin Hospital of Wuhan University, 238 Jiefang Road, Wuhan, Hubei 430060, China; Key Clinical Research Center of Kidney Disease in Hubei, 238 Jiefang Rd, Wuhan, Hubei 430060, China
| | - Zhengping Zou
- Division of Nephrology, Qianjiang Hospital Affiliated to Renmin Hospital of Wuhan University, No. 22, Zhanghua Zhong Road, Qianjiang, Hubei 433100, China; Qianjiang Clinical Medical College, Health Science Center, Yangtze University, China.
| | - Wei Liang
- Division of Nephrology, Renmin Hospital of Wuhan University, 238 Jiefang Road, Wuhan, Hubei 430060, China; Key Clinical Research Center of Kidney Disease in Hubei, 238 Jiefang Rd, Wuhan, Hubei 430060, China.
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15
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Yamashita N, Kramann R. Mechanisms of kidney fibrosis and routes towards therapy. Trends Endocrinol Metab 2024; 35:31-48. [PMID: 37775469 DOI: 10.1016/j.tem.2023.09.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/18/2023] [Revised: 09/01/2023] [Accepted: 09/04/2023] [Indexed: 10/01/2023]
Abstract
Kidney fibrosis is the final common pathway of virtually all chronic kidney diseases (CKDs) and is therefore considered to be a promising therapeutic target for these conditions. However, despite great progress in recent years, no targeted antifibrotic therapies for the kidney have been approved, likely because the complex mechanisms that initiate and drive fibrosis are not yet completely understood. Recent single-cell genomic approaches have allowed novel insights into kidney fibrosis mechanisms in mouse and human, particularly the heterogeneity and differentiation processes of myofibroblasts, the role of injured epithelial cells and immune cells, and their crosstalk mechanisms. In this review we summarize the key mechanisms that drive kidney fibrosis, including recent advances in understanding the mechanisms, as well as potential routes for developing novel targeted antifibrotic therapeutics.
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Affiliation(s)
- Noriyuki Yamashita
- Department of Nephrology and Clinical Immunology, RWTH Aachen University, Aachen, Germany; Department of Nephrology, Graduate School of Medical Science, Kyoto Prefectural University of Medicine, Kyoto, Japan
| | - Rafael Kramann
- Department of Nephrology and Clinical Immunology, RWTH Aachen University, Aachen, Germany; Department of Internal Medicine, Nephrology, and Transplantation, Erasmus Medical Center, Rotterdam, The Netherlands.
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Eun M, Kim D, Shin SI, Yang HO, Kim KD, Choi SY, Park S, Kim DK, Jeong CW, Moon KC, Lee H, Park J. Chromatin accessibility analysis and architectural profiling of human kidneys reveal key cell types and a regulator of diabetic kidney disease. Kidney Int 2024; 105:150-164. [PMID: 37925023 DOI: 10.1016/j.kint.2023.09.030] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2023] [Revised: 08/22/2023] [Accepted: 09/25/2023] [Indexed: 11/06/2023]
Abstract
Diabetes is the leading cause of kidney disease that progresses to kidney failure. However, the key molecular and cellular pathways involved in diabetic kidney disease (DKD) pathogenesis are largely unknown. Here, we performed a comparative analysis of adult human kidneys by examining cell type-specific chromatin accessibility by single-nucleus ATAC-seq (snATAC-seq) and analyzing three-dimensional chromatin architecture via high-throughput chromosome conformation capture (Hi-C method) of paired samples. We mapped the cell type-specific and DKD-specific open chromatin landscape and found that genetic variants associated with kidney diseases were significantly enriched in the proximal tubule- (PT) and injured PT-specific open chromatin regions in samples from patients with DKD. BACH1 was identified as a core transcription factor of injured PT cells; its binding target genes were highly associated with fibrosis and inflammation, which were also key features of injured PT cells. Additionally, Hi-C analysis revealed global chromatin architectural changes in DKD, accompanied by changes in local open chromatin patterns. Combining the snATAC-seq and Hi-C data identified direct target genes of BACH1, and indicated that BACH1 binding regions showed increased chromatin contact frequency with promoters of their target genes in DKD. Thus, our multi-omics analysis revealed BACH1 target genes in injured PTs and highlighted the role of BACH1 as a novel regulator of tubular inflammation and fibrosis.
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Affiliation(s)
- Minho Eun
- School of Life Sciences, Gwangju Institute of Science and Technology (GIST), Gwangju, Republic of Korea
| | - Donggun Kim
- School of Life Sciences, Gwangju Institute of Science and Technology (GIST), Gwangju, Republic of Korea
| | - So-I Shin
- School of Life Sciences, Gwangju Institute of Science and Technology (GIST), Gwangju, Republic of Korea
| | - Hyun Oh Yang
- Department of Systems Biotechnology, Chung-Ang University, Anseong, Republic of Korea
| | - Kyoung-Dong Kim
- Department of Systems Biotechnology, Chung-Ang University, Anseong, Republic of Korea
| | - Sin Young Choi
- School of Life Sciences, Gwangju Institute of Science and Technology (GIST), Gwangju, Republic of Korea
| | - Sehoon Park
- Department of Internal Medicine, Seoul National University Hospital, Seoul, Republic of Korea
| | - Dong Ki Kim
- Department of Internal Medicine, Seoul National University Hospital, Seoul, Republic of Korea; Department of Internal Medicine, Seoul National University College of Medicine, Seoul, Republic of Korea
| | - Chang Wook Jeong
- Department of Urology, Seoul National University Hospital, Seoul, Republic of Korea
| | - Kyung Chul Moon
- Department of Pathology, Seoul National University College of Medicine, Seoul, Republic of Korea
| | - Hajeong Lee
- Department of Internal Medicine, Seoul National University Hospital, Seoul, Republic of Korea; Department of Internal Medicine, Seoul National University College of Medicine, Seoul, Republic of Korea.
| | - Jihwan Park
- School of Life Sciences, Gwangju Institute of Science and Technology (GIST), Gwangju, Republic of Korea.
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Pang L, Ding Z, Chai H, Shuang W. The causal relationship between immune cells and different kidney diseases: A Mendelian randomization study. Open Med (Wars) 2023; 18:20230877. [PMID: 38152332 PMCID: PMC10751893 DOI: 10.1515/med-2023-0877] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2023] [Revised: 11/24/2023] [Accepted: 11/24/2023] [Indexed: 12/29/2023] Open
Abstract
Studies have suggested that the progress of most kidney diseases from occurrence to course and subsequent related complications are closely related to inflammatory reaction. Increased common leukocytes count in the family (neutrophils, eosinophils, basophils, lymphocytes, etc.) are also involved in the tissue damage of kidney diseases. However, these studies are only traditional observational studies, which cannot prove whether there is a causal relationship between these four kinds of leukocytes count and kidney diseases. We aim to explore the causal relationship between these four kinds of leukocytes count and kidney diseases by Mendelian randomization (MR). Large sample size of the genome-wide association database of four cell traits (neutrophil, basophil, lymphocyte, and eosinophil cell counts) in the leukocyte family were used as exposure variables. The outcome variables were various renal diseases (including chronic renal failure, acute renal failure, hypertensive heart or/and kidney disease, hypertensive renal disease, disorders resulting from impaired renal tubular function, and type 1 diabetes with renal complications). The covariates used in multivariable MR are also four cell traits related to blood cells (neutrophil, basophil, lymphocyte, and eosinophil cell counts). Instrumental variables and single nucleotide polymorphic loci were identified (P < 5 × 10-8. Linkage disequilibrium R2 < 0.001). The causal relationships were studied by inverse variance weighted (IVW), weighted median, and MR-Egger regression. Sensitivity analysis was also performed. In our study, IVW analysis results showed that increased neutrophil cell count was a risk factor for chronic renal failure (OR = 2.0245861, 95% CI = 1.1231207-3.649606, P = 0.01896524), increased basophil cell count was a risk factor for chronic renal failure (OR = 3.975935, 95% CI = 1.4871198-10.62998, P = 0.005942755). Basophil cell count was not a risk factor for acute renal failure (OR = 1.160434, 95% CI = 0.9455132-1.424207, P = 0.15448828). Increased basophil cell count was a protective factor for hypertensive heart and/or renal disease (OR = 0.7716065, 95% CI = 0.6484979-0.9180856, P = 0.003458707). Increased basophil cell count was a risk factor for disorders resulting from impaired renal tubular function (OR = 1.648131, 95% CI = 1.010116-2.689133, P = 0.04546835). Increased lymphocyte cell count was a risk factor for hypertensive renal disease (OR = 1.372961, 95% CI = 1.0189772-1.849915, P = 0.03719874). Increased eosinophil cell count was a risk factor for type 1 diabetes with renal complications (OR = 1.516454, 95% CI = 1.1826453-1.944482, P = 0.001028964). Macrophage inflammatory protein 1b levels was a protective factor for renal failure (OR = 0.9381862, 95% CI = 0.8860402-0.9934013, P = 0.02874872). After multivariable MR was used to correct covariates (neutrophil, basophil, and lymphocyte cell counts), the correlation effect between increased eosinophil cell counts and type 1 diabetes with renal complications was still statistically significant (P = 0.02201152). After adjusting covariates (neutrophil, basophil, and eosinophil cell counts) with multivariable MR, the correlation effect between increased lymphocyte cell counts and hypertensive renal disease was still statistically significant (P = 0.02050226). This study shows that increased basophils can increase the relative risk of chronic renal failure and renal tubular dysfunction, and reduce the risk of hypertensive heart disease and/or hypertensive nephropathy, while increased basophil cell count will not increase the relative risk of acute renal failure, increased neutrophil cell count can increase the risk of chronic renal failure, increased lymphocyte cell count can increase the relative risk of hypertensive nephropathy, and increased eosinophil cell count can increase the relative risk of type 1 diabetes with renal complications. Macrophage inflammatory protein 1b levels was a protective factor for renal failure.
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Affiliation(s)
- Lei Pang
- Department of Urology, The Fifth Hospital of Shanxi Medical University (Shanxi Provincial People's Hospital), Taiyuan City, 030012, Shanxi Province, China
- The First Clinical Medical College of Shanxi Medical University, Taiyuan City, 030012, Shanxi Province, China
| | - Zijun Ding
- Department of Neonatology, Shanxi Children's Hospital, Taiyuan City, 030013, Shanxi Province, China
| | - Hongqiang Chai
- Department of Urology, The Fifth Hospital of Shanxi Medical University (Shanxi Provincial People's Hospital), Taiyuan City, 030012, Shanxi Province, China
| | - Weibing Shuang
- The First Clinical Medical College of Shanxi Medical University, No. 85, Jiefang South Road, Yingze District, Taiyuan City, 030012, Shanxi Province, China
- Department of Urology, The First Hospital of Shanxi Medical University, No. 85, Jiefang South Road, Yingze District, Taiyuan City, 030012, Shanxi Province, China
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18
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Holcombe J, Weavers H. Functional-metabolic coupling in distinct renal cell types coordinates organ-wide physiology and delays premature ageing. Nat Commun 2023; 14:8405. [PMID: 38110414 PMCID: PMC10728150 DOI: 10.1038/s41467-023-44098-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2023] [Accepted: 11/30/2023] [Indexed: 12/20/2023] Open
Abstract
Precise coupling between cellular physiology and metabolism is emerging as a vital relationship underpinning tissue health and longevity. Nevertheless, functional-metabolic coupling within heterogenous microenvironments in vivo remains poorly understood due to tissue complexity and metabolic plasticity. Here, we establish the Drosophila renal system as a paradigm for linking mechanistic analysis of metabolism, at single-cell resolution, to organ-wide physiology. Kidneys are amongst the most energetically-demanding organs, yet exactly how individual cell types fine-tune metabolism to meet their diverse, unique physiologies over the life-course remains unclear. Integrating live-imaging of metabolite and organelle dynamics with spatio-temporal genetic perturbation within intact functional tissue, we uncover distinct cellular metabolic signatures essential to support renal physiology and healthy ageing. Cell type-specific programming of glucose handling, PPP-mediated glutathione regeneration and FA β-oxidation via dynamic lipid-peroxisomal networks, downstream of differential ERR receptor activity, precisely match cellular energetic demands whilst limiting damage and premature senescence; however, their dramatic dysregulation may underlie age-related renal dysfunction.
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Affiliation(s)
- Jack Holcombe
- School of Biochemistry, Biomedical Sciences, University of Bristol, Bristol, BS8 1TD, UK
| | - Helen Weavers
- School of Biochemistry, Biomedical Sciences, University of Bristol, Bristol, BS8 1TD, UK.
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19
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Zhao L, Hao Y, Tang S, Han X, Li R, Zhou X. Energy metabolic reprogramming regulates programmed cell death of renal tubular epithelial cells and might serve as a new therapeutic target for acute kidney injury. Front Cell Dev Biol 2023; 11:1276217. [PMID: 38054182 PMCID: PMC10694365 DOI: 10.3389/fcell.2023.1276217] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2023] [Accepted: 11/08/2023] [Indexed: 12/07/2023] Open
Abstract
Acute kidney injury (AKI) induces significant energy metabolic reprogramming in renal tubular epithelial cells (TECs), thereby altering lipid, glucose, and amino acid metabolism. The changes in lipid metabolism encompass not only the downregulation of fatty acid oxidation (FAO) but also changes in cell membrane lipids and triglycerides metabolism. Regarding glucose metabolism, AKI leads to increased glycolysis, activation of the pentose phosphate pathway (PPP), inhibition of gluconeogenesis, and upregulation of the polyol pathway. Research indicates that inhibiting glycolysis, promoting the PPP, and blocking the polyol pathway exhibit a protective effect on AKI-affected kidneys. Additionally, changes in amino acid metabolism, including branched-chain amino acids, glutamine, arginine, and tryptophan, play an important role in AKI progression. These metabolic changes are closely related to the programmed cell death of renal TECs, involving autophagy, apoptosis, necroptosis, pyroptosis, and ferroptosis. Notably, abnormal intracellular lipid accumulation can impede autophagic clearance, further exacerbating lipid accumulation and compromising autophagic function, forming a vicious cycle. Recent studies have demonstrated the potential of ameliorating AKI-induced kidney damage through calorie and dietary restriction. Consequently, modifying the energy metabolism of renal TECs and dietary patterns may be an effective strategy for AKI treatment.
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Affiliation(s)
- Limei Zhao
- The Fifth Clinical Medical College of Shanxi Medical University, Taiyuan, Shanxi, China
| | - Yajie Hao
- The Fifth Clinical Medical College of Shanxi Medical University, Taiyuan, Shanxi, China
| | - Shuqin Tang
- The Fifth Clinical Medical College of Shanxi Medical University, Taiyuan, Shanxi, China
| | - Xiutao Han
- The Third Clinical College, Shanxi University of Chinese Medicine, Jinzhong, Shanxi, China
| | - Rongshan Li
- Department of Nephrology, Shanxi Provincial People’s Hospital, The Fifth Clinical Medical College of Shanxi Medical University, Taiyuan, Shanxi, China
| | - Xiaoshuang Zhou
- Department of Nephrology, Shanxi Provincial People’s Hospital, The Fifth Clinical Medical College of Shanxi Medical University, Taiyuan, Shanxi, China
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20
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Cao S, Pan Y, Terker AS, Arroyo Ornelas JP, Wang Y, Tang J, Niu A, Kar SA, Jiang M, Luo W, Dong X, Fan X, Wang S, Wilson MH, Fogo A, Zhang MZ, Harris RC. Epidermal growth factor receptor activation is essential for kidney fibrosis development. Nat Commun 2023; 14:7357. [PMID: 37963889 PMCID: PMC10645887 DOI: 10.1038/s41467-023-43226-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2023] [Accepted: 11/03/2023] [Indexed: 11/16/2023] Open
Abstract
Fibrosis is the progressive accumulation of excess extracellular matrix and can cause organ failure. Fibrosis can affect nearly every organ including kidney and there is no specific treatment currently. Although Epidermal Growth Factor Receptor (EGFR) signaling pathway has been implicated in development of kidney fibrosis, underlying mechanisms by which EGFR itself mediates kidney fibrosis have not been elucidated. We find that EGFR expression increases in interstitial myofibroblasts in human and mouse fibrotic kidneys. Selective EGFR deletion in the fibroblast/pericyte population inhibits interstitial fibrosis in response to unilateral ureteral obstruction, ischemia or nephrotoxins. In vivo and in vitro studies and single-nucleus RNA sequencing analysis demonstrate that EGFR activation does not induce myofibroblast transformation but is necessary for the initial pericyte/fibroblast migration and proliferation prior to subsequent myofibroblast transformation by TGF-ß or other profibrotic factors. These findings may also provide insight into development of fibrosis in other organs and in other conditions.
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Affiliation(s)
- Shirong Cao
- Division of Nephrology and Hypertension, Department of Medicine, Nashville, TN, USA
- Vanderbilt Center for Kidney Disease, Nashville, TN, USA
| | - Yu Pan
- Division of Nephrology and Hypertension, Department of Medicine, Nashville, TN, USA
- Vanderbilt Center for Kidney Disease, Nashville, TN, USA
- Division of Nephrology, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Andrew S Terker
- Division of Nephrology and Hypertension, Department of Medicine, Nashville, TN, USA
- Vanderbilt Center for Kidney Disease, Nashville, TN, USA
| | - Juan Pablo Arroyo Ornelas
- Division of Nephrology and Hypertension, Department of Medicine, Nashville, TN, USA
- Vanderbilt Center for Kidney Disease, Nashville, TN, USA
| | - Yinqiu Wang
- Division of Nephrology and Hypertension, Department of Medicine, Nashville, TN, USA
- Vanderbilt Center for Kidney Disease, Nashville, TN, USA
| | - Jiaqi Tang
- Division of Nephrology and Hypertension, Department of Medicine, Nashville, TN, USA
- Vanderbilt Center for Kidney Disease, Nashville, TN, USA
| | - Aolei Niu
- Division of Nephrology and Hypertension, Department of Medicine, Nashville, TN, USA
- Vanderbilt Center for Kidney Disease, Nashville, TN, USA
| | - Sarah Abu Kar
- Division of Nephrology and Hypertension, Department of Medicine, Nashville, TN, USA
- Vanderbilt Center for Kidney Disease, Nashville, TN, USA
| | - Mengdi Jiang
- Division of Nephrology and Hypertension, Department of Medicine, Nashville, TN, USA
- Vanderbilt Center for Kidney Disease, Nashville, TN, USA
| | - Wentian Luo
- Division of Nephrology and Hypertension, Department of Medicine, Nashville, TN, USA
- Vanderbilt Center for Kidney Disease, Nashville, TN, USA
| | - Xinyu Dong
- Division of Nephrology and Hypertension, Department of Medicine, Nashville, TN, USA
- Vanderbilt Center for Kidney Disease, Nashville, TN, USA
| | - Xiaofeng Fan
- Division of Nephrology and Hypertension, Department of Medicine, Nashville, TN, USA
- Vanderbilt Center for Kidney Disease, Nashville, TN, USA
| | - Suwan Wang
- Division of Nephrology and Hypertension, Department of Medicine, Nashville, TN, USA
- Vanderbilt Center for Kidney Disease, Nashville, TN, USA
| | - Matthew H Wilson
- Division of Nephrology and Hypertension, Department of Medicine, Nashville, TN, USA
- Vanderbilt Center for Kidney Disease, Nashville, TN, USA
- Veterans Affairs, Nashville, TN, USA
| | - Agnes Fogo
- Department of Pathology, Microbiology and Immunology, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Ming-Zhi Zhang
- Division of Nephrology and Hypertension, Department of Medicine, Nashville, TN, USA.
- Vanderbilt Center for Kidney Disease, Nashville, TN, USA.
| | - Raymond C Harris
- Division of Nephrology and Hypertension, Department of Medicine, Nashville, TN, USA.
- Vanderbilt Center for Kidney Disease, Nashville, TN, USA.
- Veterans Affairs, Nashville, TN, USA.
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21
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Latt KZ, Yoshida T, Shrivastav S, Abedini A, Reece JM, Sun Z, Lee H, Okamoto K, Dagur P, Heymann J, Zhao Y, Chung JY, Hewitt S, Jose PA, Lee K, He JC, Winkler CA, Knepper MA, Kino T, Rosenberg AZ, Susztak K, Kopp JB. HIV viral protein R induces loss of DCT1-type renal tubules. bioRxiv 2023:2023.02.02.526686. [PMID: 36945458 PMCID: PMC10028744 DOI: 10.1101/2023.02.02.526686] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Hyponatremia and salt wasting is a common occurance in patients with HIV/AIDS, however, the understanding of its contributing factors is limited. HIV viral protein R (Vpr) contributes to HIV-associated nephropathy. To investigate the effects of Vpr on the expression level of the Slc12a3 gene, encoding the Na-Cl cotransporter, which is responsible for sodium reabsorption in distal nephron segments, we performed single-nucleus RNA sequencing of kidney cortices from three wild-type (WT) and three Vpr-transgenic (Vpr Tg) mice. The results showed that the percentage of distal convoluted tubule (DCT) cells was significantly lower in Vpr Tg mice compared with WT mice (P < 0.05), and that in Vpr Tg mice, Slc12a3 expression was not different in DCT cell cluster. The Pvalb + DCT1 subcluster had fewer cells in Vpr Tg mice compared with WT (P < 0.01). Immunohistochemistry demonstrated fewer Slc12a3 + Pvalb + DCT1 segments in Vpr Tg mice. Differential gene expression analysis comparing Vpr Tg and WT in the DCT cluster showed Ier3 , an inhibitor of apoptosis, to be the most downregulated gene. These observations demonstrate that the salt-wasting effect of Vpr in Vpr Tg mice is mediated by loss of Slc12a3 + Pvalb + DCT1 segments via apoptosis dysregulation.
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Zhang F, Hanif Q, Luo X, Jin X, Zhang J, He Z, Lei C, Liu J, Huang B, Qu K. Muscle transcriptome analysis reveal candidate genes and pathways related to fat and lipid metabolism in Yunling cattle. Anim Biotechnol 2023; 34:1022-1029. [PMID: 34874232 DOI: 10.1080/10495398.2021.2009846] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Abstract
Yunling cattle (YL) is a recently developed beef breed harboring a quarter of Yunnan ancestral cattle genome, spanning over past 30 years. Compared with Diqing cattle (DQ), a Yunnan native cattle breed, YL presents various advantages, including rapid growth and exquisite meat quality. However, the molecular mechanisms underlying these phenotypic differences are not clearly understood. To further identify the candidate genes responsible for the quality of the meat in the muscle, longissimus dorsi (LD) muscle was used for RNA-Seq analysis. A total of 508 differentially expressed genes (DEGs) were identified in YL (adjusted p-value <0.01 and log2FoldChange >1), of which 243 were up-regulated and 265 were down-regulated. Functional association analysis showed that the identified DEGs mainly enriched the lipid and fat metabolism pathways. Moreover, it was also observed that several fat-related genes were differentially expressed in both cattle breeds, including three up-regulated genes (MOGAT1, ACSM3, PLPP2) and two down-regulated genes (ADIG, GPAT3). In addition, alternative splice analysis was also performed revealing an important 9-11 exon skipping variation of GPAM gene (crucial for beef marbling) in YL, which is three times higher than that in DQ, suggesting that this variation might have played the central role in the 'snow beef' effect in YL. We believe that our results will help in understanding the mechanism of muscle development and promote the further breeding programs in YL cattle.
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Affiliation(s)
- Fengwei Zhang
- Academy of Science and Technology, Chuxiong Normal University, Chuxiong, Yunnan, China
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, China
| | - Quratulain Hanif
- National Institute for Biotechnology and Genetic Engineering, Pakistan Institute of Engineering and Applied Sciences, Faisalabad, Pakistan
| | - Xiaoyu Luo
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, China
| | - Xiandong Jin
- Yunnan Animal Husbandry Station, Kunming, Yunnan, China
| | - Jicai Zhang
- Yunnan Academy of Grassland and Animal Science, Kunming, Yunnan, China
| | - Zhanxing He
- Yunnan Academy of Grassland and Animal Science, Kunming, Yunnan, China
| | - Chuzhao Lei
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, China
| | - Jianyong Liu
- Yunnan Academy of Grassland and Animal Science, Kunming, Yunnan, China
| | - Bizhi Huang
- Yunnan Academy of Grassland and Animal Science, Kunming, Yunnan, China
| | - Kaixing Qu
- Academy of Science and Technology, Chuxiong Normal University, Chuxiong, Yunnan, China
- Yunnan Academy of Grassland and Animal Science, Kunming, Yunnan, China
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23
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Zhou J, Abedini A, Balzer MS, Shrestha R, Dhillon P, Liu H, Hu H, Susztak K. Unified Mouse and Human Kidney Single-Cell Expression Atlas Reveal Commonalities and Differences in Disease States. J Am Soc Nephrol 2023; 34:1843-1862. [PMID: 37639336 PMCID: PMC10631616 DOI: 10.1681/asn.0000000000000217] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2023] [Accepted: 08/09/2023] [Indexed: 08/31/2023] Open
Abstract
SIGNIFICANCE STATEMENT Mouse models have been widely used to understand kidney disease pathomechanisms and play an important role in drug discovery. However, these models have not been systematically analyzed and compared. The authors characterized 18 different mouse kidney disease models at both bulk and single-cell gene expression levels and compared single-cell gene expression data from diabetic kidney disease (DKD) mice and from patients with DKD. Although single cell-level gene expression changes were mostly model-specific, different disease models showed similar changes when compared at a pathway level. The authors also found that changes in fractions of cell types are major drivers of bulk gene expression differences. Although the authors found only a small overlap of single cell-level gene expression changes between the mouse DKD model and patients, they observed consistent pathway-level changes. BACKGROUND Mouse models have been widely used to understand kidney disease pathomechanisms and play an important role in drug discovery. However, these models have not been systematically analyzed and compared. METHODS We analyzed single-cell RNA sequencing data (36 samples) and bulk gene expression data (42 samples) from 18 commonly used mouse kidney disease models. We compared single-nucleus RNA sequencing data from a mouse diabetic kidney disease model with data from patients with diabetic kidney disease and healthy controls. RESULTS We generated a uniformly processed mouse single-cell atlas containing information for nearly 300,000 cells, identifying all major kidney cell types and states. Our analysis revealed that changes in fractions of cell types are major drivers of differences in bulk gene expression. Although gene expression changes at the single-cell level were mostly model-specific, different disease models showed similar changes when compared at a pathway level. Tensor decomposition analysis highlighted the important changes in proximal tubule cells in disease states. Specifically, we identified important alterations in expression of metabolic and inflammation-associated pathways. The mouse diabetic kidney disease model and patients with diabetic kidney disease shared only a small number of conserved cell type-specific differentially expressed genes, but we observed pathway-level activation patterns conserved between mouse and human diabetic kidney disease samples. CONCLUSIONS This study provides a comprehensive mouse kidney single-cell atlas and defines gene expression commonalities and differences in disease states in mice. The results highlight the key role of cell heterogeneity in driving changes in bulk gene expression and the limited overlap of single-cell gene expression changes between animal models and patients, but they also reveal consistent pathway-level changes.
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Affiliation(s)
- Jianfu Zhou
- Renal, Electrolyte, and Hypertension Division, Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania
- Institute for Diabetes, Obesity, and Metabolism, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania
- Kidney Innovation Center, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania
| | - Amin Abedini
- Renal, Electrolyte, and Hypertension Division, Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania
- Institute for Diabetes, Obesity, and Metabolism, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania
- Kidney Innovation Center, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania
| | - Michael S. Balzer
- Renal, Electrolyte, and Hypertension Division, Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania
- Institute for Diabetes, Obesity, and Metabolism, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania
- Kidney Innovation Center, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania
| | - Rojesh Shrestha
- Renal, Electrolyte, and Hypertension Division, Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania
- Institute for Diabetes, Obesity, and Metabolism, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania
- Kidney Innovation Center, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania
| | - Poonam Dhillon
- Renal, Electrolyte, and Hypertension Division, Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania
- Institute for Diabetes, Obesity, and Metabolism, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania
- Kidney Innovation Center, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania
| | - Hongbo Liu
- Renal, Electrolyte, and Hypertension Division, Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania
- Institute for Diabetes, Obesity, and Metabolism, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania
- Kidney Innovation Center, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania
| | - Hailong Hu
- Renal, Electrolyte, and Hypertension Division, Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania
- Institute for Diabetes, Obesity, and Metabolism, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania
- Kidney Innovation Center, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania
| | - Katalin Susztak
- Renal, Electrolyte, and Hypertension Division, Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania
- Institute for Diabetes, Obesity, and Metabolism, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania
- Kidney Innovation Center, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania
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24
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Szrok-Jurga S, Czumaj A, Turyn J, Hebanowska A, Swierczynski J, Sledzinski T, Stelmanska E. The Physiological and Pathological Role of Acyl-CoA Oxidation. Int J Mol Sci 2023; 24:14857. [PMID: 37834305 PMCID: PMC10573383 DOI: 10.3390/ijms241914857] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2023] [Revised: 09/27/2023] [Accepted: 09/30/2023] [Indexed: 10/15/2023] Open
Abstract
Fatty acid metabolism, including β-oxidation (βOX), plays an important role in human physiology and pathology. βOX is an essential process in the energy metabolism of most human cells. Moreover, βOX is also the source of acetyl-CoA, the substrate for (a) ketone bodies synthesis, (b) cholesterol synthesis, (c) phase II detoxication, (d) protein acetylation, and (d) the synthesis of many other compounds, including N-acetylglutamate-an important regulator of urea synthesis. This review describes the current knowledge on the importance of the mitochondrial and peroxisomal βOX in various organs, including the liver, heart, kidney, lung, gastrointestinal tract, peripheral white blood cells, and other cells. In addition, the diseases associated with a disturbance of fatty acid oxidation (FAO) in the liver, heart, kidney, lung, alimentary tract, and other organs or cells are presented. Special attention was paid to abnormalities of FAO in cancer cells and the diseases caused by mutations in gene-encoding enzymes involved in FAO. Finally, issues related to α- and ω- fatty acid oxidation are discussed.
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Affiliation(s)
- Sylwia Szrok-Jurga
- Department of Biochemistry, Faculty of Medicine, Medical University of Gdansk, 80-211 Gdansk, Poland; (S.S.-J.); (J.T.); (A.H.)
| | - Aleksandra Czumaj
- Department of Pharmaceutical Biochemistry, Faculty of Pharmacy, Medical University of Gdansk, 80-211 Gdansk, Poland;
| | - Jacek Turyn
- Department of Biochemistry, Faculty of Medicine, Medical University of Gdansk, 80-211 Gdansk, Poland; (S.S.-J.); (J.T.); (A.H.)
| | - Areta Hebanowska
- Department of Biochemistry, Faculty of Medicine, Medical University of Gdansk, 80-211 Gdansk, Poland; (S.S.-J.); (J.T.); (A.H.)
| | - Julian Swierczynski
- Institue of Nursing and Medical Rescue, State University of Applied Sciences in Koszalin, 75-582 Koszalin, Poland;
| | - Tomasz Sledzinski
- Department of Pharmaceutical Biochemistry, Faculty of Pharmacy, Medical University of Gdansk, 80-211 Gdansk, Poland;
| | - Ewa Stelmanska
- Department of Biochemistry, Faculty of Medicine, Medical University of Gdansk, 80-211 Gdansk, Poland; (S.S.-J.); (J.T.); (A.H.)
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25
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Abstract
Chronic kidney disease (CKD) is a global health problem with rising incidence and prevalence. Among several pathogenetic mechanisms responsible for disease progression, lipid accumulation in the kidney parenchyma might drive inflammation and fibrosis, as has been described in fatty liver diseases. Lipids and their metabolites have several important structural and functional roles, as they are constituents of cell and organelle membranes, serve as signalling molecules and are used for energy production. However, although lipids can be stored in lipid droplets to maintain lipid homeostasis, lipid accumulation can become pathogenic. Understanding the mechanisms linking kidney parenchymal lipid accumulation to CKD of metabolic or non-metabolic origin is challenging, owing to the tremendous variety of lipid species and their functional diversity across different parenchymal cells. Nonetheless, multiple research reports have begun to emphasize the effect of dysregulated kidney lipid metabolism in CKD progression. For example, altered cholesterol and fatty acid metabolism contribute to glomerular and tubular cell injury. Newly developed lipid-targeting agents are being tested in clinical trials in CKD, raising expectations for further therapeutic development in this field.
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Affiliation(s)
- Alla Mitrofanova
- Katz Family Division of Nephrology and Hypertension, Department of Medicine, University of Miami, Miller School of Medicine, Miami, FL, USA
- Peggy and Harold Katz Family Drug Discovery Center, University of Miami, Miller School of Medicine, Miami, FL, USA
| | - Sandra Merscher
- Katz Family Division of Nephrology and Hypertension, Department of Medicine, University of Miami, Miller School of Medicine, Miami, FL, USA
- Peggy and Harold Katz Family Drug Discovery Center, University of Miami, Miller School of Medicine, Miami, FL, USA
| | - Alessia Fornoni
- Katz Family Division of Nephrology and Hypertension, Department of Medicine, University of Miami, Miller School of Medicine, Miami, FL, USA.
- Peggy and Harold Katz Family Drug Discovery Center, University of Miami, Miller School of Medicine, Miami, FL, USA.
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26
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Berquez M, Chen Z, Festa BP, Krohn P, Keller SA, Parolo S, Korzinkin M, Gaponova A, Laczko E, Domenici E, Devuyst O, Luciani A. Lysosomal cystine export regulates mTORC1 signaling to guide kidney epithelial cell fate specialization. Nat Commun 2023; 14:3994. [PMID: 37452023 PMCID: PMC10349091 DOI: 10.1038/s41467-023-39261-3] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2022] [Accepted: 06/06/2023] [Indexed: 07/18/2023] Open
Abstract
Differentiation is critical for cell fate decisions, but the signals involved remain unclear. The kidney proximal tubule (PT) cells reabsorb disulphide-rich proteins through endocytosis, generating cystine via lysosomal proteolysis. Here we report that defective cystine mobilization from lysosomes through cystinosin (CTNS), which is mutated in cystinosis, diverts PT cells towards growth and proliferation, disrupting their functions. Mechanistically, cystine storage stimulates Ragulator-Rag GTPase-dependent recruitment of mechanistic target of rapamycin complex 1 (mTORC1) and its constitutive activation. Re-introduction of CTNS restores nutrient-dependent regulation of mTORC1 in knockout cells, whereas cell-permeant analogues of L-cystine, accumulating within lysosomes, render wild-type cells resistant to nutrient withdrawal. Therapeutic mTORC1 inhibition corrects lysosome and differentiation downstream of cystine storage, and phenotypes in preclinical models of cystinosis. Thus, cystine serves as a lysosomal signal that tailors mTORC1 and metabolism to direct epithelial cell fate decisions. These results identify mechanisms and therapeutic targets for dysregulated homeostasis in cystinosis.
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Affiliation(s)
- Marine Berquez
- Institute of Physiology, University of Zurich, 8057, Zurich, Switzerland
| | - Zhiyong Chen
- Institute of Physiology, University of Zurich, 8057, Zurich, Switzerland
| | | | - Patrick Krohn
- Institute of Physiology, University of Zurich, 8057, Zurich, Switzerland
| | | | - Silvia Parolo
- Fondazione The Microsoft Research University of Trento-Centre for Computational and Systems Biology (COSBI), 38068, Rovereto, Italy
| | - Mikhail Korzinkin
- Insilico Medicine Hong Kong Ltd., Hong Kong Science and Technology Park, Hong Kong, Hong Kong SAR, China
| | - Anna Gaponova
- Insilico Medicine Hong Kong Ltd., Hong Kong Science and Technology Park, Hong Kong, Hong Kong SAR, China
| | - Endre Laczko
- Functional Genomics Center Zurich, University of Zurich, Winterthurerstrasse 190, CH-8057, Zurich, Switzerland
| | - Enrico Domenici
- Fondazione The Microsoft Research University of Trento-Centre for Computational and Systems Biology (COSBI), 38068, Rovereto, Italy
- Department of Cellular, Computational and Integrative Biology (CIBIO), University of Trento, 38123, Trento, Italy
| | - Olivier Devuyst
- Institute of Physiology, University of Zurich, 8057, Zurich, Switzerland.
- Institute for Rare Diseases, UCLouvain Medical School, 1200, Brussels, Belgium.
| | - Alessandro Luciani
- Institute of Physiology, University of Zurich, 8057, Zurich, Switzerland.
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27
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Miguel V, Kramann R. Metabolic reprogramming heterogeneity in chronic kidney disease. FEBS Open Bio 2023; 13:1154-1163. [PMID: 36723270 PMCID: PMC10315765 DOI: 10.1002/2211-5463.13568] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2022] [Revised: 01/25/2023] [Accepted: 01/31/2023] [Indexed: 02/02/2023] Open
Abstract
Fibrosis driven by excessive accumulation of extracellular matrix (ECM) is the hallmark of chronic kidney disease (CKD). Myofibroblasts, which are the cells responsible for ECM production, are activated by cross talk with injured proximal tubule and immune cells. Emerging evidence suggests that alterations in metabolism are not only a feature of but also play an influential role in the pathogenesis of renal fibrosis. The application of omics technologies to cell-tracing animal models and follow-up functional data suggest that cell-type-specific metabolic shifts have particular roles in the fibrogenic response. In this review, we cover the main metabolic reprogramming outcomes in renal fibrosis and provide a future perspective on the field of renal fibrometabolism.
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Affiliation(s)
- Verónica Miguel
- Institute of Experimental Medicine and Systems BiologyRWTH Aachen University HospitalAachenGermany
| | - Rafael Kramann
- Institute of Experimental Medicine and Systems BiologyRWTH Aachen University HospitalAachenGermany
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28
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Li KY, Tam CHT, Liu H, Day S, Lim CKP, So WY, Huang C, Jiang G, Shi M, Lee HM, Lan HY, Szeto CC, Hanson RL, Nelson RG, Susztak K, Chan JCN, Yip KY, Ma RCW. DNA methylation markers for kidney function and progression of diabetic kidney disease. Nat Commun 2023; 14:2543. [PMID: 37188670 DOI: 10.1038/s41467-023-37837-7] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2022] [Accepted: 04/03/2023] [Indexed: 05/17/2023] Open
Abstract
Epigenetic markers are potential biomarkers for diabetes and related complications. Using a prospective cohort from the Hong Kong Diabetes Register, we perform two independent epigenome-wide association studies to identify methylation markers associated with baseline estimated glomerular filtration rate (eGFR) and subsequent decline in kidney function (eGFR slope), respectively, in 1,271 type 2 diabetes subjects. Here we show 40 (30 previously unidentified) and eight (all previously unidentified) CpG sites individually reach epigenome-wide significance for baseline eGFR and eGFR slope, respectively. We also develop a multisite analysis method, which selects 64 and 37 CpG sites for baseline eGFR and eGFR slope, respectively. These models are validated in an independent cohort of Native Americans with type 2 diabetes. Our identified CpG sites are near genes enriched for functional roles in kidney diseases, and some show association with renal damage. This study highlights the potential of methylation markers in risk stratification of kidney disease among type 2 diabetes individuals.
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Affiliation(s)
- Kelly Yichen Li
- Department of Computer Science and Engineering, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong
- Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA, USA
| | - Claudia Ha Ting Tam
- Department of Medicine and Therapeutics, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong
- Hong Kong Institute of Diabetes and Obesity, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong
- Laboratory for Molecular Epidemiology in Diabetes, Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong
| | - Hongbo Liu
- Department of Medicine, Renal Electrolyte and Hypertension Division, University of Pennsylvania, Philadelphia, PA, USA
- Institute of Diabetes Obesity and Metabolism, University of Pennsylvania, Philadelphia, PA, USA
| | - Samantha Day
- Phoenix Epidemiology and Clinical Research Branch, National Institute of Diabetes and Digestive and Kidney Diseases, Phoenix, AZ, USA
- Department of Biochemistry and Molecular Genetics, College of Graduate Studies and Arizona College of Osteopathic Medicine, Midwestern University, Glendale, AZ, USA
| | - Cadmon King Poo Lim
- Department of Medicine and Therapeutics, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong
- Laboratory for Molecular Epidemiology in Diabetes, Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong
| | - Wing Yee So
- Department of Medicine and Therapeutics, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong
- Hong Kong Institute of Diabetes and Obesity, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong
| | - Chuiguo Huang
- Department of Medicine and Therapeutics, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong
| | - Guozhi Jiang
- Department of Medicine and Therapeutics, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong
- School of Public Health (Shenzhen), Sun Yat-sen University, Shenzhen, Guangdong, China
| | - Mai Shi
- Department of Medicine and Therapeutics, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong
| | - Heung Man Lee
- Department of Medicine and Therapeutics, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong
| | - Hui-Yao Lan
- Department of Medicine and Therapeutics, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong
- Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong
| | - Cheuk-Chun Szeto
- Department of Medicine and Therapeutics, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong
- Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong
| | - Robert L Hanson
- Phoenix Epidemiology and Clinical Research Branch, National Institute of Diabetes and Digestive and Kidney Diseases, Phoenix, AZ, USA
| | - Robert G Nelson
- Phoenix Epidemiology and Clinical Research Branch, National Institute of Diabetes and Digestive and Kidney Diseases, Phoenix, AZ, USA
| | - Katalin Susztak
- Department of Medicine, Renal Electrolyte and Hypertension Division, University of Pennsylvania, Philadelphia, PA, USA
- Institute of Diabetes Obesity and Metabolism, University of Pennsylvania, Philadelphia, PA, USA
| | - Juliana C N Chan
- Department of Medicine and Therapeutics, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong
- Hong Kong Institute of Diabetes and Obesity, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong
- Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong
| | - Kevin Y Yip
- Department of Computer Science and Engineering, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong.
- Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA, USA.
- Hong Kong Institute of Diabetes and Obesity, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong.
- Hong Kong Bioinformatics Centre, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong.
| | - Ronald C W Ma
- Department of Medicine and Therapeutics, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong.
- Hong Kong Institute of Diabetes and Obesity, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong.
- Laboratory for Molecular Epidemiology in Diabetes, Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong.
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29
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Wen Y, Xu L, Melchinger I, Thiessen-Philbrook H, Moledina DG, Coca SG, Hsu CY, Go AS, Liu KD, Siew ED, Ikizler TA, Chinchilli VM, Kaufman JS, Kimmel PL, Himmelfarb J, Cantley LG, Parikh CR. Longitudinal biomarkers and kidney disease progression after acute kidney injury. JCI Insight 2023; 8:e167731. [PMID: 36951957 PMCID: PMC10243801 DOI: 10.1172/jci.insight.167731] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2022] [Accepted: 03/15/2023] [Indexed: 03/24/2023] Open
Abstract
BACKGROUNDLongitudinal investigations of murine acute kidney injury (AKI) suggest that injury and inflammation may persist long after the initial insult. However, the evolution of these processes and their prognostic values are unknown in patients with AKI.METHODSIn a prospective cohort of 656 participants hospitalized with AKI, we measured 7 urine and 2 plasma biomarkers of kidney injury, inflammation, and tubular health at multiple time points from the diagnosis to 12 months after AKI. We used linear mixed-effect models to estimate biomarker changes over time, and we used Cox proportional hazard regressions to determine their associations with a composite outcome of chronic kidney disease (CKD) incidence and progression. We compared the gene expression kinetics of biomarkers in murine models of repair and atrophy after ischemic reperfusion injury (IRI).RESULTSAfter 4.3 years, 106 and 52 participants developed incident CKD and CKD progression, respectively. Each SD increase in the change of urine KIM-1, MCP-1, and plasma TNFR1 from baseline to 12 months was associated with 2- to 3-fold increased risk for CKD, while the increase in urine uromodulin was associated with 40% reduced risk for CKD. The trajectories of these biological processes were associated with progression to kidney atrophy in mice after IRI.CONCLUSIONSustained tissue injury and inflammation, and slower restoration of tubular health, are associated with higher risk of kidney disease progression. Further investigation into these ongoing biological processes may help researchers understand and prevent the AKI-to-CKD transition.FUNDINGNIH and NIDDK (grants U01DK082223, U01DK082185, U01DK082192, U01DK082183, R01DK098233, R01DK101507, R01DK114014, K23DK100468, R03DK111881, K01DK120783, and R01DK093771).
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Affiliation(s)
- Yumeng Wen
- Division of Nephrology, Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Leyuan Xu
- Section of Nephrology, Department of Medicine, Yale School of Medicine, New Haven, Connecticut, USA
| | - Isabel Melchinger
- Section of Nephrology, Department of Medicine, Yale School of Medicine, New Haven, Connecticut, USA
| | - Heather Thiessen-Philbrook
- Division of Nephrology, Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Dennis G. Moledina
- Section of Nephrology, Department of Medicine, Yale School of Medicine, New Haven, Connecticut, USA
| | - Steven G. Coca
- Division of Nephrology, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Chi-yuan Hsu
- Division of Nephrology, University of California, San Francisco, San Francisco, California, USA
- Kaiser Permanente Division of Research, Oakland, California, USA
| | - Alan S. Go
- Kaiser Permanente Division of Research, Oakland, California, USA
| | - Kathleen D. Liu
- Division of Nephrology, University of California, San Francisco, San Francisco, California, USA
| | - Edward D. Siew
- Division of Nephrology, Vanderbilt University, Nashville, Tennessee, USA
| | - T. Alp Ikizler
- Division of Nephrology, Vanderbilt University, Nashville, Tennessee, USA
| | - Vernon M. Chinchilli
- Division of Nephrology, Pennsylvania State University College of Medicine, Hershey, Pennsylvania, USA
| | - James S. Kaufman
- Division of Nephrology, New York University School of Medicine and VA New York Harbor Healthcare System, New York, New York, USA
| | - Paul L. Kimmel
- National Institute of Diabetes and Digestive and Kidney Diseases (NIDDK), National Institutes of Health (NIH), Bethesda, Maryland, USA
| | | | - Lloyd G. Cantley
- Section of Nephrology, Department of Medicine, Yale School of Medicine, New Haven, Connecticut, USA
| | - Chirag R. Parikh
- Division of Nephrology, Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
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30
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Li M, Yu Y, Xue K, Li J, Son G, Wang J, Qian W, Wang S, Zheng J, Yang C, Ge J. Genistein mitigates senescence of bone marrow mesenchymal stem cells via ERRα-mediated mitochondrial biogenesis and mitophagy in ovariectomized rats. Redox Biol 2023; 61:102649. [PMID: 36871183 PMCID: PMC9995482 DOI: 10.1016/j.redox.2023.102649] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2023] [Revised: 02/25/2023] [Accepted: 02/25/2023] [Indexed: 03/02/2023] Open
Abstract
Senescence of bone marrow mesenchymal stem cells (BMMSCs) induced by chronic oxidative stress is an important factor contributes to the postmenopausal osteoporosis (PMOP). Mitochondrial quality control takes a pivotal role in regulating oxidative stress and cell senescence. Genistein is a major isoflavone in soy products, which is best known for its ability to inhibit bone loss in both postmenopausal women and ovariectomized (OVX) rodents. Here we show that OVX-BMMSCs displayed premature senescence, elevated reactive oxygen species (ROS) level and mitochondria dysfunction, while genistein rescued these phenotypes. Using network pharmacology and molecular docking, we identified estrogen-related receptor α (ERRα) as the potential target of genistein. Knockdown of ERRα greatly abolished the anti-senescence effect of genistein on OVX-BMMSCs. Further, the mitochondrial biogenesis and mitophagy induced by genistein were inhibited by ERRα knockdown in OVX-BMMSCs. In vivo, genistein inhibited trabecular bone loss and p16INK4a expression, upregulated sirtuin 3 (SIRT3) and peroxisome proliferator-activated receptor gamma coactivator one alpha (PGC1α) expression in the trabecular bone area of proximal tibia in OVX rats. Together, this study revealed that genistein ameliorates senescence of OVX-BMMSCs through ERRα-mediated mitochondrial biogenesis and mitophagy, which provided a molecular basis for advancement and development of therapeutic strategies against PMOP.
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Affiliation(s)
- Mengyu Li
- Department of Oral Surgery, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, College of Stomatology, Shanghai Jiao Tong University, National Center for Stomatology, National Clinical Research Center for Oral Diseases, Shanghai Key Laboratory of Stomatology, Shanghai Research Institute of Stomatology, Shanghai, China
| | - Yejia Yu
- Department of Oral Surgery, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, College of Stomatology, Shanghai Jiao Tong University, National Center for Stomatology, National Clinical Research Center for Oral Diseases, Shanghai Key Laboratory of Stomatology, Shanghai Research Institute of Stomatology, Shanghai, China
| | - Ke Xue
- Department of Pastic and Reconstructive Surgery, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Jiayi Li
- Department of Oral Surgery, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, College of Stomatology, Shanghai Jiao Tong University, National Center for Stomatology, National Clinical Research Center for Oral Diseases, Shanghai Key Laboratory of Stomatology, Shanghai Research Institute of Stomatology, Shanghai, China
| | - Geehun Son
- Department of Oral Surgery, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, College of Stomatology, Shanghai Jiao Tong University, National Center for Stomatology, National Clinical Research Center for Oral Diseases, Shanghai Key Laboratory of Stomatology, Shanghai Research Institute of Stomatology, Shanghai, China
| | - Jiajia Wang
- Department of Oral Surgery, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, College of Stomatology, Shanghai Jiao Tong University, National Center for Stomatology, National Clinical Research Center for Oral Diseases, Shanghai Key Laboratory of Stomatology, Shanghai Research Institute of Stomatology, Shanghai, China
| | - Wentao Qian
- Department of Oral Surgery, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, College of Stomatology, Shanghai Jiao Tong University, National Center for Stomatology, National Clinical Research Center for Oral Diseases, Shanghai Key Laboratory of Stomatology, Shanghai Research Institute of Stomatology, Shanghai, China
| | - Shaoyi Wang
- Department of Oral Surgery, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, College of Stomatology, Shanghai Jiao Tong University, National Center for Stomatology, National Clinical Research Center for Oral Diseases, Shanghai Key Laboratory of Stomatology, Shanghai Research Institute of Stomatology, Shanghai, China
| | - Jiawei Zheng
- Department of Oromaxillofacial Head and Neck Surgery, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, College of Stomatology, Shanghai Jiao Tong University, National Center for Stomatology, National Clinical Research Center for Oral Diseases, Shanghai Key Laboratory of Stomatology, Shanghai Research Institute of Stomatology, Shanghai, China
| | - Chi Yang
- Department of Oral Surgery, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, College of Stomatology, Shanghai Jiao Tong University, National Center for Stomatology, National Clinical Research Center for Oral Diseases, Shanghai Key Laboratory of Stomatology, Shanghai Research Institute of Stomatology, Shanghai, China.
| | - Jing Ge
- Department of Oral Surgery, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, College of Stomatology, Shanghai Jiao Tong University, National Center for Stomatology, National Clinical Research Center for Oral Diseases, Shanghai Key Laboratory of Stomatology, Shanghai Research Institute of Stomatology, Shanghai, China.
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31
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Balzer MS, Pavkovic M, Frederick J, Abedini A, Freyberger A, Vienenkötter J, Mathar I, Siudak K, Eitner F, Sandner P, Grundmann M, Susztak K. Treatment effects of soluble guanylate cyclase modulation on diabetic kidney disease at single-cell resolution. Cell Rep Med 2023; 4:100992. [PMID: 37023747 PMCID: PMC10140477 DOI: 10.1016/j.xcrm.2023.100992] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2022] [Revised: 01/29/2023] [Accepted: 03/14/2023] [Indexed: 04/08/2023]
Abstract
Diabetic kidney disease (DKD) is the most common cause of renal failure. Therapeutics development is hampered by our incomplete understanding of animal models on a cellular level. We show that ZSF1 rats recapitulate human DKD on a phenotypic and transcriptomic level. Tensor decomposition prioritizes proximal tubule (PT) and stroma as phenotype-relevant cell types exhibiting a continuous lineage relationship. As DKD features endothelial dysfunction, oxidative stress, and nitric oxide depletion, soluble guanylate cyclase (sGC) is a promising DKD drug target. sGC expression is specifically enriched in PT and stroma. In ZSF1 rats, pharmacological sGC activation confers considerable benefits over stimulation and is mechanistically related to improved oxidative stress regulation, resulting in enhanced downstream cGMP effects. Finally, we define sGC gene co-expression modules, which allow stratification of human kidney samples by DKD prevalence and disease-relevant measures such as kidney function, proteinuria, and fibrosis, underscoring the relevance of the sGC pathway to patients.
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Affiliation(s)
- Michael S Balzer
- Renal, Electrolyte, and Hypertension Division, Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; Institute for Diabetes, Obesity and Metabolism, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; Department of Nephrology and Medical Intensive Care, Charité - Universitätsmedizin Berlin, 10117 Berlin, Germany; Berlin Institute of Health at Charité - Universitätsmedizin Berlin, BIH Biomedical Innovation Academy, BIH Charité Clinician Scientist Program, 10117 Berlin, Germany
| | - Mira Pavkovic
- Bayer AG, Research and Early Development, Pharma Research Center, 42096 Wuppertal, Germany
| | - Julia Frederick
- Renal, Electrolyte, and Hypertension Division, Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; Institute for Diabetes, Obesity and Metabolism, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Amin Abedini
- Renal, Electrolyte, and Hypertension Division, Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; Institute for Diabetes, Obesity and Metabolism, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Alexius Freyberger
- Bayer AG, Research and Early Development, Pharma Research Center, 42096 Wuppertal, Germany
| | - Julia Vienenkötter
- Bayer AG, Research and Early Development, Pharma Research Center, 42096 Wuppertal, Germany
| | - Ilka Mathar
- Bayer AG, Research and Early Development, Pharma Research Center, 42096 Wuppertal, Germany
| | - Krystyna Siudak
- Bayer AG, Research and Early Development, Pharma Research Center, 42096 Wuppertal, Germany
| | - Frank Eitner
- Bayer AG, Research and Early Development, Pharma Research Center, 42096 Wuppertal, Germany; Division of Nephrology and Clinical Immunology, RWTH Aachen University, 52062 Aachen, Germany
| | - Peter Sandner
- Bayer AG, Research and Early Development, Pharma Research Center, 42096 Wuppertal, Germany; Department of Pharmacology, Hannover Medical School, 30625 Hannover, Germany
| | - Manuel Grundmann
- Bayer AG, Research and Early Development, Pharma Research Center, 42096 Wuppertal, Germany
| | - Katalin Susztak
- Renal, Electrolyte, and Hypertension Division, Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; Institute for Diabetes, Obesity and Metabolism, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA.
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32
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Abstract
Diseases of the heart and the kidney, including heart failure and chronic kidney disease, can dramatically impair life expectancy and the quality of life of patients. The heart and kidney form a functional axis; therefore, functional impairment of 1 organ will inevitably affect the function of the other. Fibrosis represents the common final pathway of diseases of both organs, regardless of the disease entity. Thus, inhibition of fibrosis represents a promising therapeutic approach to treat diseases of both organs and to resolve functional impairment. However, despite the growing knowledge in this field, the exact pathomechanisms that drive fibrosis remain elusive. RNA-sequencing approaches, particularly single-cell RNA-sequencing, have revolutionized the investigation of pathomechanisms at a molecular level and facilitated the discovery of disease-associated cell types and mechanisms. In this review, we give a brief overview over the evolution of RNA-sequencing techniques, summarize most recent insights into the pathogenesis of heart and kidney fibrosis, and discuss how transcriptomic data can be used, to identify new drug targets and to develop novel therapeutic strategies.
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Affiliation(s)
- Felix Schreibing
- Institute of Experimental Medicine and Systems Biology (F.S., T.M.A., R.K.), RWTH Aachen University, Medical Faculty, Aachen, Germany
- Division of Nephrology and Clinical Immunology (F.S., T.M.A., R.K.), RWTH Aachen University, Medical Faculty, Aachen, Germany
| | - Teresa M Anslinger
- Institute of Experimental Medicine and Systems Biology (F.S., T.M.A., R.K.), RWTH Aachen University, Medical Faculty, Aachen, Germany
- Division of Nephrology and Clinical Immunology (F.S., T.M.A., R.K.), RWTH Aachen University, Medical Faculty, Aachen, Germany
| | - Rafael Kramann
- Institute of Experimental Medicine and Systems Biology (F.S., T.M.A., R.K.), RWTH Aachen University, Medical Faculty, Aachen, Germany
- Division of Nephrology and Clinical Immunology (F.S., T.M.A., R.K.), RWTH Aachen University, Medical Faculty, Aachen, Germany
- Department of Internal Medicine, Nephrology and Transplantation, Erasmus Medical Center, Rotterdam, The Netherlands (R.K.)
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Huang R, Fu P, Ma L. Kidney fibrosis: from mechanisms to therapeutic medicines. Signal Transduct Target Ther 2023; 8:129. [PMID: 36932062 PMCID: PMC10023808 DOI: 10.1038/s41392-023-01379-7] [Citation(s) in RCA: 54] [Impact Index Per Article: 54.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2022] [Revised: 02/12/2023] [Accepted: 02/20/2023] [Indexed: 03/19/2023] Open
Abstract
Chronic kidney disease (CKD) is estimated to affect 10-14% of global population. Kidney fibrosis, characterized by excessive extracellular matrix deposition leading to scarring, is a hallmark manifestation in different progressive CKD; However, at present no antifibrotic therapies against CKD exist. Kidney fibrosis is identified by tubule atrophy, interstitial chronic inflammation and fibrogenesis, glomerulosclerosis, and vascular rarefaction. Fibrotic niche, where organ fibrosis initiates, is a complex interplay between injured parenchyma (like tubular cells) and multiple non-parenchymal cell lineages (immune and mesenchymal cells) located spatially within scarring areas. Although the mechanisms of kidney fibrosis are complicated due to the kinds of cells involved, with the help of single-cell technology, many key questions have been explored, such as what kind of renal tubules are profibrotic, where myofibroblasts originate, which immune cells are involved, and how cells communicate with each other. In addition, genetics and epigenetics are deeper mechanisms that regulate kidney fibrosis. And the reversible nature of epigenetic changes including DNA methylation, RNA interference, and chromatin remodeling, gives an opportunity to stop or reverse kidney fibrosis by therapeutic strategies. More marketed (e.g., RAS blockage, SGLT2 inhibitors) have been developed to delay CKD progression in recent years. Furthermore, a better understanding of renal fibrosis is also favored to discover biomarkers of fibrotic injury. In the review, we update recent advances in the mechanism of renal fibrosis and summarize novel biomarkers and antifibrotic treatment for CKD.
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Affiliation(s)
- Rongshuang Huang
- Kidney Research Institute, Division of Nephrology, West China Hospital, Sichuan University, Chengdu, 610041, China
| | - Ping Fu
- Kidney Research Institute, Division of Nephrology, West China Hospital, Sichuan University, Chengdu, 610041, China.
| | - Liang Ma
- Kidney Research Institute, Division of Nephrology, West China Hospital, Sichuan University, Chengdu, 610041, China.
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34
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Abstract
Kidney disease is a major driver of mortality among patients with diabetes and diabetic kidney disease (DKD) is responsible for close to half of all chronic kidney disease cases. DKD usually develops in a genetically susceptible individual as a result of poor metabolic (glycemic) control. Molecular and genetic studies indicate the key role of podocytes and endothelial cells in driving albuminuria and early kidney disease in diabetes. Proximal tubule changes show a strong association with the glomerular filtration rate. Hyperglycemia represents a key cellular stress in the kidney by altering cellular metabolism in endothelial cells and podocytes and by imposing an excess workload requiring energy and oxygen for proximal tubule cells. Changes in metabolism induce early adaptive cellular hypertrophy and reorganization of the actin cytoskeleton. Later, mitochondrial defects contribute to increased oxidative stress and activation of inflammatory pathways, causing progressive kidney function decline and fibrosis. Blockade of the renin-angiotensin system or the sodium-glucose cotransporter is associated with cellular protection and slowing kidney function decline. Newly identified molecular pathways could provide the basis for the development of much-needed novel therapeutics.
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Affiliation(s)
- Samer Mohandes
- Renal, Electrolyte, and Hypertension Division, Department of Medicine;,Institute for Diabetes, Obesity, and Metabolism;,Department of Genetics; and,Kidney Innovation Center; Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Tomohito Doke
- Renal, Electrolyte, and Hypertension Division, Department of Medicine;,Institute for Diabetes, Obesity, and Metabolism;,Department of Genetics; and,Kidney Innovation Center; Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Hailong Hu
- Renal, Electrolyte, and Hypertension Division, Department of Medicine;,Institute for Diabetes, Obesity, and Metabolism;,Department of Genetics; and,Kidney Innovation Center; Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Dhanunjay Mukhi
- Renal, Electrolyte, and Hypertension Division, Department of Medicine;,Institute for Diabetes, Obesity, and Metabolism;,Department of Genetics; and,Kidney Innovation Center; Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Poonam Dhillon
- Renal, Electrolyte, and Hypertension Division, Department of Medicine;,Institute for Diabetes, Obesity, and Metabolism;,Department of Genetics; and,Kidney Innovation Center; Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Katalin Susztak
- Renal, Electrolyte, and Hypertension Division, Department of Medicine;,Institute for Diabetes, Obesity, and Metabolism;,Department of Genetics; and,Kidney Innovation Center; Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
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35
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Dhillon P, Mulholland KA, Hu H, Park J, Sheng X, Abedini A, Liu H, Vassalotti A, Wu J, Susztak K. Increased levels of endogenous retroviruses trigger fibroinflammation and play a role in kidney disease development. Nat Commun 2023; 14:559. [PMID: 36732547 PMCID: PMC9895454 DOI: 10.1038/s41467-023-36212-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2022] [Accepted: 01/20/2023] [Indexed: 02/04/2023] Open
Abstract
Inflammation is a common feature of all forms of chronic kidney disease; however, the underlying mechanism remains poorly understood. Evolutionarily inherited endogenous retroviruses (ERVs) have the potential to trigger an immune reaction. Comprehensive RNA-sequencing of control and diseased kidneys from human and mouse disease models indicated higher expression of transposable elements (TEs) and ERVs in diseased kidneys. Loss of cytosine methylation causing epigenetic derepression likely contributes to an increase in ERV levels. Genetic deletion/pharmacological inhibition of DNA methyltransferase 1 (DNMT1) induces ERV expression. In cultured kidney tubule cells, ERVs elicit the activation of cytosolic nucleotide sensors such as RIG-I, MDA5, and STING. ERVs expressions in kidney tubules trigger RIG-I/STING, and cytokine expression, and correlate with the presence of immune cells. Genetic deletion of RIG-I or STING or treatment with reverse transcriptase inhibitor ameliorates kidney fibroinflammation. Our data indicate an important role of epigenetic derepression-induced ERV activation triggering renal fibroinflammation.
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Affiliation(s)
- Poonam Dhillon
- Renal, Electrolyte, and Hypertension Division, Department of Medicine, University of Pennsylvania, Perelman School of Medicine, Philadelphia, PA, 19014, USA
- Institute for Diabetes, Obesity, and Metabolism, University of Pennsylvania, Perelman School of Medicine, Philadelphia, PA, 19014, USA
| | - Kelly Ann Mulholland
- Renal, Electrolyte, and Hypertension Division, Department of Medicine, University of Pennsylvania, Perelman School of Medicine, Philadelphia, PA, 19014, USA
- Institute for Diabetes, Obesity, and Metabolism, University of Pennsylvania, Perelman School of Medicine, Philadelphia, PA, 19014, USA
| | - Hailong Hu
- Renal, Electrolyte, and Hypertension Division, Department of Medicine, University of Pennsylvania, Perelman School of Medicine, Philadelphia, PA, 19014, USA
- Institute for Diabetes, Obesity, and Metabolism, University of Pennsylvania, Perelman School of Medicine, Philadelphia, PA, 19014, USA
| | - Jihwan Park
- Renal, Electrolyte, and Hypertension Division, Department of Medicine, University of Pennsylvania, Perelman School of Medicine, Philadelphia, PA, 19014, USA
- Institute for Diabetes, Obesity, and Metabolism, University of Pennsylvania, Perelman School of Medicine, Philadelphia, PA, 19014, USA
| | - Xin Sheng
- Renal, Electrolyte, and Hypertension Division, Department of Medicine, University of Pennsylvania, Perelman School of Medicine, Philadelphia, PA, 19014, USA
- Institute for Diabetes, Obesity, and Metabolism, University of Pennsylvania, Perelman School of Medicine, Philadelphia, PA, 19014, USA
| | - Amin Abedini
- Renal, Electrolyte, and Hypertension Division, Department of Medicine, University of Pennsylvania, Perelman School of Medicine, Philadelphia, PA, 19014, USA
- Institute for Diabetes, Obesity, and Metabolism, University of Pennsylvania, Perelman School of Medicine, Philadelphia, PA, 19014, USA
| | - Hongbo Liu
- Renal, Electrolyte, and Hypertension Division, Department of Medicine, University of Pennsylvania, Perelman School of Medicine, Philadelphia, PA, 19014, USA
- Institute for Diabetes, Obesity, and Metabolism, University of Pennsylvania, Perelman School of Medicine, Philadelphia, PA, 19014, USA
| | - Allison Vassalotti
- Renal, Electrolyte, and Hypertension Division, Department of Medicine, University of Pennsylvania, Perelman School of Medicine, Philadelphia, PA, 19014, USA
- Institute for Diabetes, Obesity, and Metabolism, University of Pennsylvania, Perelman School of Medicine, Philadelphia, PA, 19014, USA
| | - Junnan Wu
- Renal, Electrolyte, and Hypertension Division, Department of Medicine, University of Pennsylvania, Perelman School of Medicine, Philadelphia, PA, 19014, USA
- Institute for Diabetes, Obesity, and Metabolism, University of Pennsylvania, Perelman School of Medicine, Philadelphia, PA, 19014, USA
| | - Katalin Susztak
- Renal, Electrolyte, and Hypertension Division, Department of Medicine, University of Pennsylvania, Perelman School of Medicine, Philadelphia, PA, 19014, USA.
- Institute for Diabetes, Obesity, and Metabolism, University of Pennsylvania, Perelman School of Medicine, Philadelphia, PA, 19014, USA.
- Department of Genetics, University of Pennsylvania, Perelman School of Medicine, Philadelphia, PA, 19014, USA.
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36
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Li H, Dixon EE, Wu H, Humphreys BD. Comprehensive single-cell transcriptional profiling defines shared and unique epithelial injury responses during kidney fibrosis. Cell Metab 2022; 34:1977-1998.e9. [PMID: 36265491 PMCID: PMC9742301 DOI: 10.1016/j.cmet.2022.09.026] [Citation(s) in RCA: 43] [Impact Index Per Article: 21.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/03/2022] [Revised: 07/19/2022] [Accepted: 09/28/2022] [Indexed: 01/12/2023]
Abstract
The underlying cellular events driving kidney fibrogenesis and metabolic dysfunction are incompletely understood. Here, we employed single-cell combinatorial indexing RNA sequencing to analyze 24 mouse kidneys from two fibrosis models. We profiled 309,666 cells in one experiment, representing 50 cell types/states encompassing epithelial, endothelial, immune, and stromal populations. Single-cell analysis identified diverse injury states of the proximal tubule, including two distinct early-phase populations with dysregulated lipid and amino acid metabolism, respectively. Lipid metabolism was defective in the chronic phase but was transiently activated in the very early stages of ischemia-induced injury, where we discovered increased lipid deposition and increased fatty acid β-oxidation. Perilipin 2 was identified as a surface marker of intracellular lipid droplets, and its knockdown in vitro disrupted cell energy state maintenance during lipid accumulation. Surveying epithelial cells across nephron segments identified shared and unique injury responses. Stromal cells exhibited high heterogeneity and contributed to fibrogenesis by epithelial-stromal crosstalk.
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Affiliation(s)
- Haikuo Li
- Division of Nephrology, Department of Medicine, Washington University in St. Louis, St. Louis, MO, USA
| | - Eryn E Dixon
- Division of Nephrology, Department of Medicine, Washington University in St. Louis, St. Louis, MO, USA
| | - Haojia Wu
- Division of Nephrology, Department of Medicine, Washington University in St. Louis, St. Louis, MO, USA
| | - Benjamin D Humphreys
- Division of Nephrology, Department of Medicine, Washington University in St. Louis, St. Louis, MO, USA; Department of Developmental Biology, Washington University in St. Louis, St. Louis, MO, USA.
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37
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Cao X, Wang J, Zhang T, Liu Z, Liu L, Chen Y, Li Z, Zhao Y, Yu Q, Liu T, Nie J, Niu Y, Chen Y, Yang L, Zhang L. Chromatin accessibility dynamics dictate renal tubular epithelial cell response to injury. Nat Commun 2022; 13:7322. [PMID: 36443310 DOI: 10.1038/s41467-022-34854-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2022] [Accepted: 11/09/2022] [Indexed: 11/29/2022] Open
Abstract
Renal tubular epithelial cells (TECs) can initiate an adaptive response to completely recover from mild acute kidney injury (AKI), whereas severe injury often leads to persistence of maladaptive repair and progression to kidney fibrosis. Through profiling of active DNA regulatory elements by ATAC-seq, we reveal widespread, dynamic changes in the chromatin accessibility of TECs after ischemia-reperfusion injury. We show that injury-specific domains of regulatory chromatin become accessible prior to gene activation, creating poised chromatin states to activate the consequent gene expression program and injury response. We further identify RXRα as a key transcription factor in promoting adaptive repair. Activation of RXRα by bexarotene, an FDA-approved RXRα agonist, restores the chromatin state and gene expression program to protect TECs against severe kidney injury. Together, our findings elucidate a chromatin-mediated mechanism underlying differential responses of TECs to varying injuries and identify RXRα as a therapeutic target of acute kidney injury.
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38
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Garreta E, Moya-Rull D, Stanifer ML, Monteil V, Prado P, Marco A, Tarantino C, Gallo M, Jonsson G, Hagelkruys A, Mirazimi A, Boulant S, Penninger JM, Montserrat N. Protocol for SARS-CoV-2 infection of kidney organoids derived from human pluripotent stem cells. STAR Protoc 2022; 3:101872. [PMID: 36595951 DOI: 10.1016/j.xpro.2022.101872] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2022] [Revised: 09/30/2022] [Accepted: 11/01/2022] [Indexed: 11/09/2022] Open
Abstract
This protocol presents the use of SARS-CoV-2 isolates to infect human kidney organoids, enabling exploration of the impact of SARS-CoV-2 infection in a human multicellular in vitro system. We detail steps to generate kidney organoids from human pluripotent stem cells (hPSCs) and emulate a diabetic milieu via organoids exposure to diabetogenic-like cell culture conditions. We further describe preparation and titration steps of SARS-CoV-2 virus stocks, their subsequent use to infect the kidney organoids, and assessment of the infection via immunofluorescence. For complete details on the use and execution of this protocol, please refer to Garreta et al. (2022).1.
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39
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Gildea JJ, Xu P, Schiermeyer KA, Yue W, Carey RM, Jose PA, Felder RA. Inverse Salt Sensitivity of Blood Pressure Is Associated with an Increased Renin-Angiotensin System Activity. Biomedicines 2022; 10:2811. [PMID: 36359330 PMCID: PMC9687845 DOI: 10.3390/biomedicines10112811] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2022] [Revised: 10/30/2022] [Accepted: 10/31/2022] [Indexed: 11/06/2022] Open
Abstract
High and low sodium diets are associated with increased blood pressure and cardiovascular morbidity and mortality. The paradoxical response of elevated BP in low salt diets, aka inverse salt sensitivity (ISS), is an understudied vulnerable 11% of the adult population with yet undiscovered etiology. A linear relationship between the number of single nucleotide polymorphisms (SNPs) in the dopamine D2 receptor (DRD2, rs6276 and 6277), and the sodium myo-inositol cotransporter 2 (SLC5A11, rs11074656), as well as decreased expression of these two genes in urine-derived renal proximal tubule cells (uRPTCs) isolated from clinical study participants suggest involvement of these cells in ISS. Insight into this newly discovered paradoxical response to sodium is found by incubating cells in low sodium (LS) conditions that unveil cell physiologic differences that are then reversed by mir-485-5p miRNA blocker transfection and bypassing the genetic defect by DRD2 re-expression. The renin-angiotensin system (RAS) is an important counter-regulatory mechanism to prevent hyponatremia under LS conditions. Oversensitive RAS under LS conditions could partially explain the increased mortality in ISS. Angiotensin-II (AngII, 10 nmol/L) increased sodium transport in uRPTCs to a greater extent in individuals with ISS than SR. Downstream signaling of AngII is verified by identifying lowered expression of nuclear factor erythroid 2-related factor 2 (NRF2), CCCTC-binding factor (CTCF), and manganese-dependent mitochondrial superoxide dismutase (SOD2) only in ISS-derived uRPTCs and not SR-derived uRPTCs when incubated in LS conditions. We conclude that DRD2 and SLC5A11 variants in ISS may cause an increased low sodium sensitivity to AngII and renal sodium reabsorption which can contribute to inverse salt-sensitive hypertension.
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40
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Wang G, Heijs B, Kostidis S, Rietjens RG, Koning M, Yuan L, Tiemeier GL, Mahfouz A, Dumas SJ, Giera M, Kers J, Chuva de Sousa Lopes SM, van den Berg CW, van den Berg BM, Rabelink TJ. Spatial dynamic metabolomics identifies metabolic cell fate trajectories in human kidney differentiation. Cell Stem Cell 2022; 29:1580-1593.e7. [DOI: 10.1016/j.stem.2022.10.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2022] [Revised: 10/07/2022] [Accepted: 10/17/2022] [Indexed: 11/06/2022]
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41
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Wei X, Hou Y, Long M, Jiang L, Du Y. Advances in energy metabolism in renal fibrosis. Life Sci 2022; 312:121033. [PMID: 36270427 DOI: 10.1016/j.lfs.2022.121033] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2022] [Revised: 09/22/2022] [Accepted: 09/30/2022] [Indexed: 11/05/2022]
Abstract
Renal fibrosis is a common pathway toward chronic kidney disease (CKD) and is the main pathological predecessor for end-stage renal disease; thus, preventing progressive CKD and renal fibrosis is essential to reducing their consequential morbidity and mortality. Emerging evidence has connected renal fibrosis to metabolic reprogramming; abnormalities in energy metabolism pathways, such as glycolysis, the tricarboxylic acid cycle, and lipid metabolism, are known to cause diseases of diverse etiologies. Cytokine interventions in affected metabolic pathways may significantly reduce the degree of fibrosis, highlighting therapeutic targets for drug development for renal fibrosis. Here, we discuss the relationship between glycolysis, lipid metabolism, mitochondrial and peroxisome dysfunction, and renal fibrosis in detail and propose that targeted therapies for specific metabolic pathways are expected to represent the next generation of treatments for renal fibrosis.
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Affiliation(s)
- Xuejiao Wei
- Department of Nephrology, The First Hospital of Jilin University, Changchun, China
| | - Yue Hou
- Department of Nephrology, The First Hospital of Jilin University, Changchun, China
| | - Mengtuan Long
- Department of Nephrology, The First Hospital of Jilin University, Changchun, China
| | - Lili Jiang
- Department of Physical Examination Center, The First Hospital of Jilin University, Changchun, China
| | - Yujun Du
- Department of Nephrology, The First Hospital of Jilin University, Changchun, China.
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42
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Ma L, Roach T, Morel L. Immunometabolic alterations in lupus: where do they come from and where do we go from there? Curr Opin Immunol 2022; 78:102245. [PMID: 36122544 DOI: 10.1016/j.coi.2022.102245] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2022] [Accepted: 08/23/2022] [Indexed: 01/28/2023]
Abstract
Systemic lupus erythematosus (SLE) is an autoimmune disease in which the overactivation of the immune system has been associated with metabolic alterations. Targeting the altered immunometabolism has been proposed to treat SLE patients based on their results obtained and mouse models of the disease. Here, we review the recent literature to discuss the possible origins of the alterations in the metabolism of immune cells in lupus, the dominant role of mitochondrial defects, technological advances that may move the field forward, as well as how targeting lupus immunometabolism may have therapeutic potential.
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43
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Zhu M, Zhang Z, Chen Z, Xu Y, Wu J, Che X, Ying L, Shao X, Tang L, Zhou W, Zhang M, Zhang M, Mou S. Single-cell RNA landscape of cell fate decision of renal proximal tubular epithelial cells and immune-microenvironment in kidney fibrosis. Clin Transl Med 2022; 12:e1010. [PMID: 36082701 PMCID: PMC9460484 DOI: 10.1002/ctm2.1010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2022] [Revised: 07/20/2022] [Accepted: 07/26/2022] [Indexed: 11/16/2022] Open
Affiliation(s)
- Minyan Zhu
- Department of Nephrology, Molecular Cell Lab for Kidney Disease, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Zhenhua Zhang
- School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou, Guangdong, China
| | - Zhejun Chen
- Department of Nephrology, Molecular Cell Lab for Kidney Disease, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Yao Xu
- Department of Nephrology, Molecular Cell Lab for Kidney Disease, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Jiajin Wu
- Department of Urology, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China.,Transplantation Center of Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Xiajing Che
- Department of Nephrology, Molecular Cell Lab for Kidney Disease, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Liang Ying
- Department of Urology, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China.,Transplantation Center of Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Xinghua Shao
- Department of Nephrology, Molecular Cell Lab for Kidney Disease, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Lumin Tang
- Department of Nephrology, Molecular Cell Lab for Kidney Disease, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Wenyan Zhou
- Department of Nephrology, Molecular Cell Lab for Kidney Disease, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Minfang Zhang
- Department of Nephrology, Molecular Cell Lab for Kidney Disease, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Ming Zhang
- Department of Urology, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China.,Transplantation Center of Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Shan Mou
- Department of Nephrology, Molecular Cell Lab for Kidney Disease, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
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44
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Balzer MS, Doke T, Yang YW, Aldridge DL, Hu H, Mai H, Mukhi D, Ma Z, Shrestha R, Palmer MB, Hunter CA, Susztak K. Single-cell analysis highlights differences in druggable pathways underlying adaptive or fibrotic kidney regeneration. Nat Commun 2022; 13:4018. [PMID: 35821371 DOI: 10.1038/s41467-022-31772-9] [Citation(s) in RCA: 38] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2021] [Accepted: 07/01/2022] [Indexed: 01/14/2023] Open
Abstract
The kidney has tremendous capacity to repair after acute injury, however, pathways guiding adaptive and fibrotic repair are poorly understood. We developed a model of adaptive and fibrotic kidney regeneration by titrating ischemic injury dose. We performed detailed biochemical and histological analysis and profiled transcriptomic changes at bulk and single-cell level (> 110,000 cells) over time. Our analysis highlights kidney proximal tubule cells as key susceptible cells to injury. Adaptive proximal tubule repair correlated with fatty acid oxidation and oxidative phosphorylation. We identify a specific maladaptive/profibrotic proximal tubule cluster after long ischemia, which expresses proinflammatory and profibrotic cytokines and myeloid cell chemotactic factors. Druggability analysis highlights pyroptosis/ferroptosis as vulnerable pathways in these profibrotic cells. Pharmacological targeting of pyroptosis/ferroptosis in vivo pushed cells towards adaptive repair and ameliorates fibrosis. In summary, our single-cell analysis defines key differences in adaptive and fibrotic repair and identifies druggable pathways for pharmacological intervention to prevent kidney fibrosis. After acute injury, kidneys either successfully repair/regenerate or become fibrotic. Here the authors use scRNA-seq to study adaptive/maladaptive kidney regeneration and identify proinflammatory/fibrotic proximal tubule cells with pharmacologically targetable pyroptosis/ferroptosis signatures.
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45
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van der Rijt S, Leemans JC, Florquin S, Houtkooper RH, Tammaro A. Immunometabolic rewiring of tubular epithelial cells in kidney disease. Nat Rev Nephrol 2022. [PMID: 35798902 DOI: 10.1038/s41581-022-00592-x] [Citation(s) in RCA: 26] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/25/2022] [Indexed: 12/20/2022]
Abstract
Kidney tubular epithelial cells (TECs) have a crucial role in the damage and repair response to acute and chronic injury. To adequately respond to constant changes in the environment, TECs have considerable bioenergetic needs, which are supported by metabolic pathways. Although little is known about TEC metabolism, a number of ground-breaking studies have shown that defective glucose metabolism or fatty acid oxidation in the kidney has a key role in the response to kidney injury. Imbalanced use of these metabolic pathways can predispose TECs to apoptosis and dedifferentiation, and contribute to lipotoxicity and kidney injury. The accumulation of lipids and aberrant metabolic adaptations of TECs during kidney disease can also be driven by receptors of the innate immune system. Similar to their actions in innate immune cells, pattern recognition receptors regulate the metabolic rewiring of TECs, causing cellular dysfunction and lipid accumulation. TECs should therefore be considered a specialized cell type - like cells of the innate immune system - that is subject to regulation by immunometabolism. Targeting energy metabolism in TECs could represent a strategy for metabolically reprogramming the kidney and promoting kidney repair.
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Abstract
The kidney is a complex organ, and how it forms is a fascinating process. New technologies, such as single-cell transcriptomics, and enhanced imaging modalities are offering new approaches to understand the complex and intertwined processes during embryonic kidney development.
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Affiliation(s)
- Ruth Röck
- Institute of Anatomy, University of Zurich, Zurich, Switzerland.,Swiss National Centres of Competence in Research (NCCR) Kidney Control of Homeostasis (Kidney.CH), Zurich, Switzerland
| | - Ludovica Rizzo
- Institute of Anatomy, University of Zurich, Zurich, Switzerland.,Swiss National Centres of Competence in Research (NCCR) Kidney Control of Homeostasis (Kidney.CH), Zurich, Switzerland.,PhD program "Molecular and Translational Biomedicine," Life Science Zurich Graduate School, Zurich, Switzerland
| | - Soeren S Lienkamp
- Institute of Anatomy, University of Zurich, Zurich, Switzerland.,Swiss National Centres of Competence in Research (NCCR) Kidney Control of Homeostasis (Kidney.CH), Zurich, Switzerland
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Keppner A, Maric D, Orlando IMC, Falquet L, Hummler E, Hoogewijs D. Analysis of the Hypoxic Response in a Mouse Cortical Collecting Duct-Derived Cell Line Suggests That Esrra Is Partially Involved in Hif1α-Mediated Hypoxia-Inducible Gene Expression in mCCD cl1 Cells. Int J Mol Sci 2022; 23:7262. [PMID: 35806266 PMCID: PMC9267015 DOI: 10.3390/ijms23137262] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2022] [Revised: 06/22/2022] [Accepted: 06/27/2022] [Indexed: 11/16/2022] Open
Abstract
The kidney is strongly dependent on a continuous oxygen supply, and is conversely highly sensitive to hypoxia. Controlled oxygen gradients are essential for renal control of solutes and urine-concentrating mechanisms, which also depend on various hormones including aldosterone. The cortical collecting duct (CCD) is part of the aldosterone-sensitive distal nephron and possesses a key function in fine-tuned distal salt handling. It is well known that aldosterone is consistently decreased upon hypoxia. Furthermore, a recent study reported a hypoxia-dependent down-regulation of sodium currents within CCD cells. We thus investigated the possibility that cells from the cortical collecting duct are responsive to hypoxia, using the mouse cortical collecting duct cell line mCCDcl1 as a model. By analyzing the hypoxia-dependent transcriptome of mCCDcl1 cells, we found a large number of differentially-expressed genes (3086 in total logFC< −1 or >1) following 24 h of hypoxic conditions (0.2% O2). A gene ontology analysis of the differentially-regulated pathways revealed a strong decrease in oxygen-linked processes such as ATP metabolic functions, oxidative phosphorylation, and cellular and aerobic respiration, while pathways associated with hypoxic responses were robustly increased. The most pronounced regulated genes were confirmed by RT-qPCR. The low expression levels of Epas1 under both normoxic and hypoxic conditions suggest that Hif-1α, rather than Hif-2α, mediates the hypoxic response in mCCDcl1 cells. Accordingly, we generated shRNA-mediated Hif-1α knockdown cells and found Hif-1α to be responsible for the hypoxic induction of established hypoxically-induced genes. Interestingly, we could show that following shRNA-mediated knockdown of Esrra, Hif-1α protein levels were unaffected, but the gene expression levels of Egln3 and Serpine1 were significantly reduced, indicating that Esrra might contribute to the hypoxia-mediated expression of these and possibly other genes. Collectively, mCCDcl1 cells display a broad response to hypoxia and represent an adequate cellular model to study additional factors regulating the response to hypoxia.
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Affiliation(s)
- Anna Keppner
- Section of Medicine, Department of Endocrinology, Metabolism and Cardiovascular System (EMC), Faculty of Science and Medicine, University of Fribourg, Chemin du Musée 5, CH-1700 Fribourg, Switzerland; (A.K.); (D.M.); (I.M.C.O.)
- National Center of Competence in Research Kidney Control of Homeostasis (NCCR Kidney.CH), University of Zurich, CH-8006 Zürich, Switzerland
| | - Darko Maric
- Section of Medicine, Department of Endocrinology, Metabolism and Cardiovascular System (EMC), Faculty of Science and Medicine, University of Fribourg, Chemin du Musée 5, CH-1700 Fribourg, Switzerland; (A.K.); (D.M.); (I.M.C.O.)
- National Center of Competence in Research Kidney Control of Homeostasis (NCCR Kidney.CH), University of Zurich, CH-8006 Zürich, Switzerland
| | - Ilaria Maria Christina Orlando
- Section of Medicine, Department of Endocrinology, Metabolism and Cardiovascular System (EMC), Faculty of Science and Medicine, University of Fribourg, Chemin du Musée 5, CH-1700 Fribourg, Switzerland; (A.K.); (D.M.); (I.M.C.O.)
| | - Laurent Falquet
- Section of Science, Department of Biology, Faculty of Science and Medicine, University of Fribourg, CH-1700 Fribourg, Switzerland;
| | - Edith Hummler
- Department of Biomedical Sciences, University of Lausanne, CH-1011 Lausanne, Switzerland;
| | - David Hoogewijs
- Section of Medicine, Department of Endocrinology, Metabolism and Cardiovascular System (EMC), Faculty of Science and Medicine, University of Fribourg, Chemin du Musée 5, CH-1700 Fribourg, Switzerland; (A.K.); (D.M.); (I.M.C.O.)
- National Center of Competence in Research Kidney Control of Homeostasis (NCCR Kidney.CH), University of Zurich, CH-8006 Zürich, Switzerland
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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. Front Nephrol 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] [What about the content of this article? (0)] [Affiliation(s)] [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.
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Affiliation(s)
| | | | | | | | - Amy Jayne McKnight
- Centre for Public Health, Queen’s University Belfast, Belfast, United Kingdom
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49
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Abstract
Cellular hypoxia occurs when the demand for sufficient molecular oxygen needed to produce the levels of ATP required to perform physiological functions exceeds the vascular supply, thereby leading to a state of oxygen depletion with the associated risk of bioenergetic crisis. To protect against the threat of hypoxia, eukaryotic cells have evolved the capacity to elicit oxygen-sensitive adaptive transcriptional responses driven primarily (although not exclusively) by the hypoxia-inducible factor (HIF) pathway. In addition to the canonical regulation of HIF by oxygen-dependent hydroxylases, multiple other input signals, including gasotransmitters, non-coding RNAs, histone modifiers and post-translational modifications, modulate the nature of the HIF response in discreet cell types and contexts. Activation of HIF induces various effector pathways that mitigate the effects of hypoxia, including metabolic reprogramming and the production of erythropoietin. Drugs that target the HIF pathway to induce erythropoietin production are now approved for the treatment of chronic kidney disease-related anaemia. However, HIF-dependent changes in cell metabolism also have profound implications for functional responses in innate and adaptive immune cells, and thereby heavily influence immunity and the inflammatory response. Preclinical studies indicate a potential use of HIF therapeutics to treat inflammatory diseases, such as inflammatory bowel disease. Understanding the links between HIF, cellular metabolism and immunity is key to unlocking the full therapeutic potential of drugs that target the HIF pathway. Hypoxia-dependent changes in cellular metabolism have important implications for the effective functioning of multiple immune cell subtypes. This Review describes the inputs that shape the hypoxic response in individual cell types and contexts, and the implications of this response for cellular metabolism and associated alterations in immune cell function. Hypoxia is a common feature of particular microenvironments and at sites of immunity and inflammation, resulting in increased activity of the hypoxia-inducible factor (HIF). In addition to hypoxia, multiple inputs modulate the activity of the HIF pathway, allowing nuanced downstream responses in discreet cell types and contexts. HIF-dependent changes in cellular metabolism mitigate the effects of hypoxia and ensure that energy needs are met under conditions in which oxidative phosphorylation is reduced. HIF-dependent changes in metabolism also profoundly affect the phenotype and function of immune cells. The immunometabolic effects of HIF have important implications for targeting the HIF pathway in inflammatory disease.
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Affiliation(s)
- Cormac T Taylor
- School of Medicine, The Conway Institute & Systems Biology Ireland, University College Dublin, Belfield, Dublin, Ireland.
| | - Carsten C Scholz
- Institute of Physiology, University of Zurich, Zurich, Switzerland.,Institute of Physiology, University Medicine Greifswald, Greifswald, Germany
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50
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Garreta E, Prado P, Stanifer ML, Monteil V, Marco A, Ullate-Agote A, Moya-Rull D, Vilas-Zornoza A, Tarantino C, Romero JP, Jonsson G, Oria R, Leopoldi A, Hagelkruys A, Gallo M, González F, Domingo-Pedrol P, Gavaldà A, Del Pozo CH, Hasan Ali O, Ventura-Aguiar P, Campistol JM, Prosper F, Mirazimi A, Boulant S, Penninger JM, Montserrat N. A diabetic milieu increases ACE2 expression and cellular susceptibility to SARS-CoV-2 infections in human kidney organoids and patient cells. Cell Metab 2022; 34:857-873.e9. [PMID: 35561674 DOI: 10.1016/j.cmet.2022.04.009] [Citation(s) in RCA: 32] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/02/2021] [Revised: 02/02/2022] [Accepted: 04/19/2022] [Indexed: 12/14/2022]
Abstract
It is not well understood why diabetic individuals are more prone to develop severe COVID-19. To this, we here established a human kidney organoid model promoting early hallmarks of diabetic kidney disease development. Upon SARS-CoV-2 infection, diabetic-like kidney organoids exhibited higher viral loads compared with their control counterparts. Genetic deletion of the angiotensin-converting enzyme 2 (ACE2) in kidney organoids under control or diabetic-like conditions prevented viral detection. Moreover, cells isolated from kidney biopsies from diabetic patients exhibited altered mitochondrial respiration and enhanced glycolysis, resulting in higher SARS-CoV-2 infections compared with non-diabetic cells. Conversely, the exposure of patient cells to dichloroacetate (DCA), an inhibitor of aerobic glycolysis, resulted in reduced SARS-CoV-2 infections. Our results provide insights into the identification of diabetic-induced metabolic programming in the kidney as a critical event increasing SARS-CoV-2 infection susceptibility, opening the door to the identification of new interventions in COVID-19 pathogenesis targeting energy metabolism.
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