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Cui X, Zhou Z, Tu H, Wu J, Zhou J, Yi Q, Liu O, Dai X. Mitophagy in fibrotic diseases: molecular mechanisms and therapeutic applications. Front Physiol 2024; 15:1430230. [PMID: 39183973 PMCID: PMC11341310 DOI: 10.3389/fphys.2024.1430230] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2024] [Accepted: 07/17/2024] [Indexed: 08/27/2024] Open
Abstract
Mitophagy is a highly precise process of selective autophagy, primarily aimed at eliminating excess or damaged mitochondria to maintain the stability of both mitochondrial and cellular homeostasis. In recent years, with in-depth research into the association between mitophagy and fibrotic diseases, it has been discovered that this process may interact with crucial cellular biological processes such as oxidative stress, inflammatory responses, cellular dynamics regulation, and energy metabolism, thereby influencing the occurrence and progression of fibrotic diseases. Consequently, modulating mitophagy holds promise as a therapeutic approach for fibrosis. Currently, various methods have been identified to regulate mitophagy to prevent fibrosis, categorized into three types: natural drug therapy, biological therapy, and physical therapy. This review comprehensively summarizes the current understanding of the mechanisms of mitophagy, delves into its biological roles in fibrotic diseases, and introduces mitophagy modulators effective in fibrosis, aiming to provide new targets and theoretical basis for the investigation of fibrosis-related mechanisms and disease prevention.
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Affiliation(s)
- Xinyan Cui
- Hunan Key Laboratory of Oral Health Research, Hunan Clinical Research Center of Oral Major Diseases, Oral Health and Academician Workstation for Oral-maxilofacial, Regenerative Medicine and Xiangya Stomatological Hospital, Xiangya School of Stomatology, Central South University, Changsha, Hunan, China
| | - Zekun Zhou
- Hunan Key Laboratory of Oral Health Research, Hunan Clinical Research Center of Oral Major Diseases, Oral Health and Academician Workstation for Oral-maxilofacial, Regenerative Medicine and Xiangya Stomatological Hospital, Xiangya School of Stomatology, Central South University, Changsha, Hunan, China
| | - Hua Tu
- Hunan Key Laboratory of Oral Health Research, Hunan Clinical Research Center of Oral Major Diseases, Oral Health and Academician Workstation for Oral-maxilofacial, Regenerative Medicine and Xiangya Stomatological Hospital, Xiangya School of Stomatology, Central South University, Changsha, Hunan, China
| | - Jianjun Wu
- Hunan Key Laboratory of Oral Health Research, Hunan Clinical Research Center of Oral Major Diseases, Oral Health and Academician Workstation for Oral-maxilofacial, Regenerative Medicine and Xiangya Stomatological Hospital, Xiangya School of Stomatology, Central South University, Changsha, Hunan, China
| | - Jian Zhou
- Salivary Gland Disease Center and Beijing Key Laboratory of Tooth Regeneration and Function Reconstruction, Beijing Laboratory of Oral Health and Beijing Stomatological Hospital, Capital Medical University, Beijing, China
- Department of VIP Dental Service, School of Stomatology, Capital Medical University, Beijing, China
- Laboratory for Oral and General Health Integration and Translation, Beijing Tiantan Hospital, Capital Medical University, Beijing, China
| | - Qiao Yi
- Hunan Key Laboratory of Oral Health Research, Hunan Clinical Research Center of Oral Major Diseases, Oral Health and Academician Workstation for Oral-maxilofacial, Regenerative Medicine and Xiangya Stomatological Hospital, Xiangya School of Stomatology, Central South University, Changsha, Hunan, China
| | - Ousheng Liu
- Hunan Key Laboratory of Oral Health Research, Hunan Clinical Research Center of Oral Major Diseases, Oral Health and Academician Workstation for Oral-maxilofacial, Regenerative Medicine and Xiangya Stomatological Hospital, Xiangya School of Stomatology, Central South University, Changsha, Hunan, China
| | - Xiaohan Dai
- Hunan Key Laboratory of Oral Health Research, Hunan Clinical Research Center of Oral Major Diseases, Oral Health and Academician Workstation for Oral-maxilofacial, Regenerative Medicine and Xiangya Stomatological Hospital, Xiangya School of Stomatology, Central South University, Changsha, Hunan, China
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2
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Nauffal V, Klarqvist MDR, Hill MC, Pace DF, Di Achille P, Choi SH, Rämö JT, Pirruccello JP, Singh P, Kany S, Hou C, Ng K, Philippakis AA, Batra P, Lubitz SA, Ellinor PT. Noninvasive assessment of organ-specific and shared pathways in multi-organ fibrosis using T1 mapping. Nat Med 2024; 30:1749-1760. [PMID: 38806679 DOI: 10.1038/s41591-024-03010-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2023] [Accepted: 04/22/2024] [Indexed: 05/30/2024]
Abstract
Fibrotic diseases affect multiple organs and are associated with morbidity and mortality. To examine organ-specific and shared biologic mechanisms that underlie fibrosis in different organs, we developed machine learning models to quantify T1 time, a marker of interstitial fibrosis, in the liver, pancreas, heart and kidney among 43,881 UK Biobank participants who underwent magnetic resonance imaging. In phenome-wide association analyses, we demonstrate the association of increased organ-specific T1 time, reflecting increased interstitial fibrosis, with prevalent diseases across multiple organ systems. In genome-wide association analyses, we identified 27, 18, 11 and 10 independent genetic loci associated with liver, pancreas, myocardial and renal cortex T1 time, respectively. There was a modest genetic correlation between the examined organs. Several loci overlapped across the examined organs implicating genes involved in a myriad of biologic pathways including metal ion transport (SLC39A8, HFE and TMPRSS6), glucose metabolism (PCK2), blood group antigens (ABO and FUT2), immune function (BANK1 and PPP3CA), inflammation (NFKB1) and mitosis (CENPE). Finally, we found that an increasing number of organs with T1 time falling in the top quintile was associated with increased mortality in the population. Individuals with a high burden of fibrosis in ≥3 organs had a 3-fold increase in mortality compared to those with a low burden of fibrosis across all examined organs in multivariable-adjusted analysis (hazard ratio = 3.31, 95% confidence interval 1.77-6.19; P = 1.78 × 10-4). By leveraging machine learning to quantify T1 time across multiple organs at scale, we uncovered new organ-specific and shared biologic pathways underlying fibrosis that may provide therapeutic targets.
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Affiliation(s)
- Victor Nauffal
- Cardiovascular Division, Brigham and Women's Hospital, Boston, MA, USA
- Cardiovascular Disease Initiative, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | | | - Matthew C Hill
- Cardiovascular Disease Initiative, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Cardiovascular Research Center, Massachusetts General Hospital, Boston, MA, USA
| | - Danielle F Pace
- Cardiovascular Disease Initiative, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Data Sciences Platform, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Paolo Di Achille
- Data Sciences Platform, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Seung Hoan Choi
- Cardiovascular Disease Initiative, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Joel T Rämö
- Cardiovascular Disease Initiative, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - James P Pirruccello
- Cardiovascular Disease Initiative, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Cardiology Division, Massachusetts General Hospital, Boston, MA, USA
- Division of Cardiology, University of California, San Francisco, San Francisco, CA, USA
| | - Pulkit Singh
- Data Sciences Platform, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Shinwan Kany
- Cardiovascular Disease Initiative, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Cardiology, University Heart and Vascular Center Hamburg-Eppendorf, Hamburg, Germany
| | - Cody Hou
- Cardiovascular Disease Initiative, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Kenney Ng
- Center for Computational Health, IBM Research, Cambridge, MA, USA
| | - Anthony A Philippakis
- Cardiovascular Disease Initiative, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Data Sciences Platform, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Eric and Wendy Schmidt Center, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Puneet Batra
- Data Sciences Platform, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Steven A Lubitz
- Demoulas Center for Cardiac Arrhythmias, Massachusetts General Hospital, Boston, MA, USA
| | - Patrick T Ellinor
- Cardiovascular Disease Initiative, Broad Institute of MIT and Harvard, Cambridge, MA, USA.
- Demoulas Center for Cardiac Arrhythmias, Massachusetts General Hospital, Boston, MA, USA.
- Cardiovascular Research Center, Massachusetts General Hospital, Boston, MA, USA.
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Lu YQ, Wang Y. Multi-Omic Analysis Reveals Genetic Determinants and Therapeutic Targets of Chronic Kidney Disease and Kidney Function. Int J Mol Sci 2024; 25:6033. [PMID: 38892221 PMCID: PMC11172763 DOI: 10.3390/ijms25116033] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2024] [Revised: 05/20/2024] [Accepted: 05/29/2024] [Indexed: 06/21/2024] Open
Abstract
Chronic kidney disease (CKD) presents a significant global health challenge, characterized by complex pathophysiology. This study utilized a multi-omic approach, integrating genomic data from the CKDGen consortium alongside transcriptomic, metabolomic, and proteomic data to elucidate the genetic underpinnings and identify therapeutic targets for CKD and kidney function. We employed a range of analytical methods including cross-tissue transcriptome-wide association studies (TWASs), Mendelian randomization (MR), summary-based MR (SMR), and molecular docking. These analyses collectively identified 146 cross-tissue genetic associations with CKD and kidney function. Key Golgi apparatus-related genes (GARGs) and 41 potential drug targets were highlighted, with MAP3K11 emerging as a significant gene from the TWAS and MR data, underscoring its potential as a therapeutic target. Capsaicin displayed promising drug-target interactions in molecular docking analyses. Additionally, metabolome- and proteome-wide MR (PWMR) analyses revealed 33 unique metabolites and critical inflammatory proteins such as FGF5 that are significantly linked to and colocalized with CKD and kidney function. These insights deepen our understanding of CKD pathogenesis and highlight novel targets for treatment and prevention.
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Affiliation(s)
| | - Yirong Wang
- School of Biology & Basic Medical Sciences, Suzhou Medical College of Soochow University, Suzhou 215123, China;
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4
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von Mässenhausen A, Schlecht MN, Beer K, Maremonti F, Tonnus W, Belavgeni A, Gavali S, Flade K, Riley JS, Zamora Gonzalez N, Brucker A, Becker JN, Tmava M, Meyer C, Peitzsch M, Hugo C, Gembardt F, Angeli JPF, Bornstein SR, Tait SWG, Linkermann A. Treatment with siRNAs is commonly associated with GPX4 up-regulation and target knockdown-independent sensitization to ferroptosis. SCIENCE ADVANCES 2024; 10:eadk7329. [PMID: 38489367 PMCID: PMC10942120 DOI: 10.1126/sciadv.adk7329] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/07/2023] [Accepted: 02/09/2024] [Indexed: 03/17/2024]
Abstract
Small interfering RNAs (siRNAs) are widely used in biomedical research and in clinical trials. Here, we demonstrate that siRNA treatment is commonly associated with significant sensitization to ferroptosis, independently of the target protein knockdown. Genetically targeting mitochondrial antiviral-signaling protein (MAVS) reversed the siRNA-mediated sensitizing effect, but no activation of canonical MAVS signaling, which involves phosphorylation of IkBα and interferon regulatory transcription factor 3 (IRF3), was observed. In contrast, MAVS mediated a noncanonical signal resulting in a prominent increase in mitochondrial ROS levels, and increase in the BACH1/pNRF2 transcription factor ratio and GPX4 up-regulation, which was associated with a 50% decrease in intracellular glutathione levels. We conclude that siRNAs commonly sensitize to ferroptosis and may severely compromise the conclusions drawn from silencing approaches in biomedical research. Finally, as ferroptosis contributes to a variety of pathophysiological processes, we cannot exclude side effects in human siRNA-based therapeutical concepts that should be clinically tested.
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Affiliation(s)
- Anne von Mässenhausen
- Division of Nephrology, Department of Internal Medicine III, University Hospital Carl Gustav Carus at the Technische Universität Dresden, 01307 Dresden, Germany
- Institute of Clinical Chemistry and Clinical Pharmacology, University Hospital Bonn, 53127 Bonn, Germany
| | - Marlena Nastassja Schlecht
- Division of Nephrology, Department of Internal Medicine III, University Hospital Carl Gustav Carus at the Technische Universität Dresden, 01307 Dresden, Germany
| | - Kristina Beer
- Division of Nephrology, Department of Internal Medicine III, University Hospital Carl Gustav Carus at the Technische Universität Dresden, 01307 Dresden, Germany
| | - Francesca Maremonti
- Division of Nephrology, Department of Internal Medicine III, University Hospital Carl Gustav Carus at the Technische Universität Dresden, 01307 Dresden, Germany
| | - Wulf Tonnus
- Division of Nephrology, Department of Internal Medicine III, University Hospital Carl Gustav Carus at the Technische Universität Dresden, 01307 Dresden, Germany
| | - Alexia Belavgeni
- Division of Nephrology, Department of Internal Medicine III, University Hospital Carl Gustav Carus at the Technische Universität Dresden, 01307 Dresden, Germany
| | - Shubhangi Gavali
- Division of Nephrology, Department of Internal Medicine III, University Hospital Carl Gustav Carus at the Technische Universität Dresden, 01307 Dresden, Germany
| | - Karolin Flade
- Division of Nephrology, Department of Internal Medicine III, University Hospital Carl Gustav Carus at the Technische Universität Dresden, 01307 Dresden, Germany
| | - Joel S. Riley
- Cancer Research UK Beatson Institute, Switchback Road, Glasgow G61 1BD, UK
- School of Cancer Sciences, University of Glasgow, Switchback Road, Glasgow G61 1BD, UK
- Biocenter Innsbruck (CCB), Medical University Innsbruck, Division of Developmental Immunology, Innrain 80, 6020 Innsbruck, Austria
| | - Nadia Zamora Gonzalez
- Division of Nephrology, Department of Internal Medicine III, University Hospital Carl Gustav Carus at the Technische Universität Dresden, 01307 Dresden, Germany
| | - Anne Brucker
- Division of Nephrology, Department of Internal Medicine III, University Hospital Carl Gustav Carus at the Technische Universität Dresden, 01307 Dresden, Germany
| | - Jorunn Naila Becker
- Division of Nephrology, Department of Internal Medicine III, University Hospital Carl Gustav Carus at the Technische Universität Dresden, 01307 Dresden, Germany
| | - Mirela Tmava
- Division of Nephrology, Department of Internal Medicine III, University Hospital Carl Gustav Carus at the Technische Universität Dresden, 01307 Dresden, Germany
| | - Claudia Meyer
- Division of Nephrology, Department of Internal Medicine III, University Hospital Carl Gustav Carus at the Technische Universität Dresden, 01307 Dresden, Germany
| | - Mirko Peitzsch
- Institute of Clinical Chemistry and Laboratory Medicine, University Hospital Carl Gustav Carus at the Technische Universität Dresden, 01307 Dresden, Germany
| | - Christian Hugo
- Division of Nephrology, Department of Internal Medicine III, University Hospital Carl Gustav Carus at the Technische Universität Dresden, 01307 Dresden, Germany
| | - Florian Gembardt
- Division of Nephrology, Department of Internal Medicine III, University Hospital Carl Gustav Carus at the Technische Universität Dresden, 01307 Dresden, Germany
| | - Jose Pedro Friedmann Angeli
- Rudolf Virchow Center for Integrative and Translational Bioimaging, Chair of Translational Cell Biology, University of Würzburg, 97080 Würzburg, Germany
| | - Stefan R. Bornstein
- Department of Internal Medicine 3, University Hospital Carl Gustav Carus at the Technische Universität Dresden, Dresden, Germany
- Diabetes and Nutritional Sciences, King's College London, London, UK
- Center for Regenerative Therapies, Technische Universität Dresden, Dresden, Germany
- Paul Langerhans Institute Dresden of Helmholtz Centre Munich at University Clinic Carl Gustav Carus of TU Dresden Faculty of Medicine, Dresden, Germany
- Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore, Singapore
| | - Stephen W. G. Tait
- Cancer Research UK Beatson Institute, Switchback Road, Glasgow G61 1BD, UK
- School of Cancer Sciences, University of Glasgow, Switchback Road, Glasgow G61 1BD, UK
| | - Andreas Linkermann
- Division of Nephrology, Department of Internal Medicine III, University Hospital Carl Gustav Carus at the Technische Universität Dresden, 01307 Dresden, Germany
- Division of Nephrology, Department of Medicine, Albert Einstein College of Medicine, Bronx, NY, USA
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Fountoglou A, Deltas C, Siomou E, Dounousi E. Genome-wide association studies reconstructing chronic kidney disease. Nephrol Dial Transplant 2024; 39:395-402. [PMID: 38124660 PMCID: PMC10899781 DOI: 10.1093/ndt/gfad209] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2023] [Indexed: 12/23/2023] Open
Abstract
Chronic kidney disease (CKD) is a major health problem with an increasing epidemiological burden, and is the 16th leading cause of years of life lost worldwide. It is estimated that more than 10% of the population have a variable stage of CKD, while about 850 million people worldwide are affected. Nevertheless, public awareness remains low, clinical access is inappropriate in many circumstances and medication is still ineffective due to the lack of clear therapeutic targets. One of the main issues that drives these problems is the fact that CKD remains a clinical entity with significant causal ambiguity. Beyond diabetes mellitus and hypertension, which are the two major causes of kidney disease, there are still many gray areas in the diagnostic context of CKD. Genetics nowadays emerges as a promising field in nephrology. The role of genetic factors in CKD's causes and predisposition is well documented and thousands of genetic variants are well established to contribute to the high burden of disease. Next-generation sequencing is increasingly revealing old and new rare variants that cause Mendelian forms of chronic nephropathy while genome-wide association studies (GWAS) uncover common variants associated with CKD-defining traits in the general population. In this article we review how GWAS has revolutionized-and continues to revolutionize-the old concept of CKD. Furthermore, we present how the investigation of common genetic variants with previously unknown kidney significance has begun to expand our knowledge on disease understanding, providing valuable insights into disease mechanisms and perhaps paving the way for novel therapeutic targets.
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Affiliation(s)
- Anastasios Fountoglou
- Department of Nephrology, Faculty of Medicine, School of Health Sciences, University of Ioannina, Ioannina, Greece
| | - Constantinos Deltas
- School of Medicine and biobank.cy Center of Excellence in Biobanking and Biomedical Research, University of Cyprus, Nicosia 2109, Cyprus
| | - Ekaterini Siomou
- Department of Pediatrics, Faculty of Medicine, School of Health Sciences, University of Ioannina, Ioannina, Greece
| | - Evangelia Dounousi
- Department of Nephrology, Faculty of Medicine, School of Health Sciences, University of Ioannina, Ioannina, Greece
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6
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Bai F, Han L, Yang J, Liu Y, Li X, Wang Y, Jiang R, Zeng Z, Gao Y, Zhang H. Integrated analysis reveals crosstalk between pyroptosis and immune regulation in renal fibrosis. Front Immunol 2024; 15:1247382. [PMID: 38343546 PMCID: PMC10853448 DOI: 10.3389/fimmu.2024.1247382] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2023] [Accepted: 01/09/2024] [Indexed: 02/15/2024] Open
Abstract
Purpose The pathogenesis of renal fibrosis (RF) involves intricate interactions between profibrotic processes and immune responses. This study aimed to explore the potential involvement of the pyroptosis signaling pathway in immune microenvironment regulation within the context of RF. Through comprehensive bioinformatics analysis and experimental validation, we investigated the influence of pyroptosis on the immune landscape in RF. Methods We obtained RNA-seq datasets from Gene Expression Omnibus (GEO) databases and identified Pyroptosis-Associated Regulators (PARs) through literature reviews. Systematic evaluation of alterations in 27 PARs was performed in RF and normal kidney samples, followed by relevant functional analyses. Unsupervised cluster analysis revealed distinct pyroptosis modification patterns. Using single-sample gene set enrichment analysis (ssGSEA), we examined the correlation between pyroptosis and immune infiltration. Hub regulators were identified via weighted gene coexpression network analysis (WGCNA) and further validated in a single-cell RNA-seq dataset. We also established a unilateral ureteral obstruction-induced RF mouse model to verify the expression of key regulators at the mRNA and protein levels. Results Our comprehensive analysis revealed altered expression of 19 PARs in RF samples compared to normal samples. Five hub regulators, namely PYCARD, CASP1, AIM2, NOD2, and CASP9, exhibited potential as biomarkers for RF. Based on these regulators, a classifier capable of distinguishing normal samples from RF samples was developed. Furthermore, we identified correlations between immune features and PARs expression, with PYCARD positively associated with regulatory T cells abundance in fibrotic tissues. Unsupervised clustering of RF samples yielded two distinct subtypes (Subtype A and Subtype B), with Subtype B characterized by active immune responses against RF. Subsequent WGCNA analysis identified PYCARD, CASP1, and NOD2 as hub PARs in the pyroptosis modification patterns. Single-cell level validation confirmed PYCARD expression in myofibroblasts, implicating its significance in the stress response of myofibroblasts to injury. In vivo experimental validation further demonstrated elevated PYCARD expression in RF, accompanied by infiltration of Foxp3+ regulatory T cells. Conclusions Our findings suggest that pyroptosis plays a pivotal role in orchestrating the immune microenvironment of RF. This study provides valuable insights into the pathogenesis of RF and highlights potential targets for future therapeutic interventions.
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Affiliation(s)
- Fengxia Bai
- School of Clinical Medicine, Hebei University, Affiliated Hospital of Hebei University, Baoding, China
- Hebei Provincial Key Laboratory of Skeletal Metabolic Physiology of Chronic Kidney Disease, Affiliated Hospital of Hebei University, Baoding, China
| | - Longchao Han
- Department of Gastrointestinal Oncology, Affiliated Xingtai People's Hospital of Hebei Medical University, Xingtai, China
| | - Jifeng Yang
- School of Clinical Medicine, Hebei University, Affiliated Hospital of Hebei University, Baoding, China
- Hebei Provincial Key Laboratory of Skeletal Metabolic Physiology of Chronic Kidney Disease, Affiliated Hospital of Hebei University, Baoding, China
| | - Yuxiu Liu
- School of Clinical Medicine, Hebei University, Affiliated Hospital of Hebei University, Baoding, China
- Hebei Provincial Key Laboratory of Skeletal Metabolic Physiology of Chronic Kidney Disease, Affiliated Hospital of Hebei University, Baoding, China
| | - Xiangmeng Li
- School of Clinical Medicine, Hebei University, Affiliated Hospital of Hebei University, Baoding, China
- Hebei Provincial Key Laboratory of Skeletal Metabolic Physiology of Chronic Kidney Disease, Affiliated Hospital of Hebei University, Baoding, China
| | - Yaqin Wang
- Department of Critical Care Medicine, The First Hospital of Hebei Medical University, Shijiazhuang, China
| | - Ruijian Jiang
- School of Clinical Medicine, Hebei University, Affiliated Hospital of Hebei University, Baoding, China
- Hebei Provincial Key Laboratory of Skeletal Metabolic Physiology of Chronic Kidney Disease, Affiliated Hospital of Hebei University, Baoding, China
| | - Zhaomu Zeng
- Department of Neurosurgery, Jiangxi Provincial People's Hospital, The First Affiliated Hospital of Nanchang Medical College, Nanchang, China
| | - Yan Gao
- School of Clinical Medicine, Hebei University, Affiliated Hospital of Hebei University, Baoding, China
- Hebei Provincial Key Laboratory of Skeletal Metabolic Physiology of Chronic Kidney Disease, Affiliated Hospital of Hebei University, Baoding, China
| | - Haisong Zhang
- School of Clinical Medicine, Hebei University, Affiliated Hospital of Hebei University, Baoding, China
- Hebei Provincial Key Laboratory of Skeletal Metabolic Physiology of Chronic Kidney Disease, Affiliated Hospital of Hebei University, Baoding, China
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7
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Gisch DL, Brennan M, Lake BB, Basta J, Keller MS, Melo Ferreira R, Akilesh S, Ghag R, Lu C, Cheng YH, Collins KS, Parikh SV, Rovin BH, Robbins L, Stout L, Conklin KY, Diep D, Zhang B, Knoten A, Barwinska D, Asghari M, Sabo AR, Ferkowicz MJ, Sutton TA, Kelly KJ, De Boer IH, Rosas SE, Kiryluk K, Hodgin JB, Alakwaa F, Winfree S, Jefferson N, Türkmen A, Gaut JP, Gehlenborg N, Phillips CL, El-Achkar TM, Dagher PC, Hato T, Zhang K, Himmelfarb J, Kretzler M, Mollah S, Jain S, Rauchman M, Eadon MT. The chromatin landscape of healthy and injured cell types in the human kidney. Nat Commun 2024; 15:433. [PMID: 38199997 PMCID: PMC10781985 DOI: 10.1038/s41467-023-44467-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2023] [Accepted: 12/14/2023] [Indexed: 01/12/2024] Open
Abstract
There is a need to define regions of gene activation or repression that control human kidney cells in states of health, injury, and repair to understand the molecular pathogenesis of kidney disease and design therapeutic strategies. Comprehensive integration of gene expression with epigenetic features that define regulatory elements remains a significant challenge. We measure dual single nucleus RNA expression and chromatin accessibility, DNA methylation, and H3K27ac, H3K4me1, H3K4me3, and H3K27me3 histone modifications to decipher the chromatin landscape and gene regulation of the kidney in reference and adaptive injury states. We establish a spatially-anchored epigenomic atlas to define the kidney's active, silent, and regulatory accessible chromatin regions across the genome. Using this atlas, we note distinct control of adaptive injury in different epithelial cell types. A proximal tubule cell transcription factor network of ELF3, KLF6, and KLF10 regulates the transition between health and injury, while in thick ascending limb cells this transition is regulated by NR2F1. Further, combined perturbation of ELF3, KLF6, and KLF10 distinguishes two adaptive proximal tubular cell subtypes, one of which manifested a repair trajectory after knockout. This atlas will serve as a foundation to facilitate targeted cell-specific therapeutics by reprogramming gene regulatory networks.
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Affiliation(s)
- Debora L Gisch
- Indiana University School of Medicine, Indianapolis, IN, 46202, USA
| | | | - Blue B Lake
- Department of Bioengineering, University of California, San Diego, La Jolla, CA, USA
- San Diego Institute of Science, Altos Labs, San Diego, CA, USA
| | - Jeannine Basta
- Washington University in Saint Louis, St. Louis, MO, 63103, USA
| | | | | | | | - Reetika Ghag
- Washington University in Saint Louis, St. Louis, MO, 63103, USA
| | - Charles Lu
- Washington University in Saint Louis, St. Louis, MO, 63103, USA
| | - Ying-Hua Cheng
- Indiana University School of Medicine, Indianapolis, IN, 46202, USA
| | | | - Samir V Parikh
- Ohio State University Wexner Medical Center, Columbus, OH, 43210, USA
| | - Brad H Rovin
- Ohio State University Wexner Medical Center, Columbus, OH, 43210, USA
| | - Lynn Robbins
- St. Louis Veteran Affairs Medical Center, St. Louis, MO, 63106, USA
| | - Lisa Stout
- Washington University in Saint Louis, St. Louis, MO, 63103, USA
| | - Kimberly Y Conklin
- Department of Bioengineering, University of California, San Diego, La Jolla, CA, USA
| | - Dinh Diep
- Department of Bioengineering, University of California, San Diego, La Jolla, CA, USA
| | - Bo Zhang
- Washington University in Saint Louis, St. Louis, MO, 63103, USA
| | - Amanda Knoten
- Washington University in Saint Louis, St. Louis, MO, 63103, USA
| | - Daria Barwinska
- Indiana University School of Medicine, Indianapolis, IN, 46202, USA
| | - Mahla Asghari
- Indiana University School of Medicine, Indianapolis, IN, 46202, USA
| | - Angela R Sabo
- Indiana University School of Medicine, Indianapolis, IN, 46202, USA
| | | | - Timothy A Sutton
- Indiana University School of Medicine, Indianapolis, IN, 46202, USA
| | | | | | - Sylvia E Rosas
- Joslin Diabetes Center, Harvard Medical School, Boston, MA, 02215, USA
| | | | | | | | - Seth Winfree
- University of Nebraska Medical Center, Omaha, NE, 68198, USA
| | - Nichole Jefferson
- Kidney Precision Medicine Project Community Engagement Committee, Dallas, TX, USA
| | - Aydın Türkmen
- Istanbul School of Medicine, Division of Nephrology, Istanbul, Turkey
| | - Joseph P Gaut
- Department of Bioengineering, University of California, San Diego, La Jolla, CA, USA
| | | | | | | | - Pierre C Dagher
- Indiana University School of Medicine, Indianapolis, IN, 46202, USA
| | - Takashi Hato
- Indiana University School of Medicine, Indianapolis, IN, 46202, USA
| | - Kun Zhang
- Department of Bioengineering, University of California, San Diego, La Jolla, CA, USA
| | | | | | - Shamim Mollah
- Washington University in Saint Louis, St. Louis, MO, 63103, USA
| | - Sanjay Jain
- Washington University in Saint Louis, St. Louis, MO, 63103, USA.
| | - Michael Rauchman
- Washington University in Saint Louis, St. Louis, MO, 63103, USA.
| | - Michael T Eadon
- Indiana University School of Medicine, Indianapolis, IN, 46202, USA.
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8
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Mukhi D, Li L, Liu H, Doke T, Kolligundla LP, Ha E, Kloetzer K, Abedini A, Mukherjee S, Wu J, Dhillon P, Hu H, Guan D, Funai K, Uehara K, Titchenell PM, Baur JA, Wellen KE, Susztak K. ACSS2 gene variants determine kidney disease risk by controlling de novo lipogenesis in kidney tubules. J Clin Invest 2023; 134:e172963. [PMID: 38051585 PMCID: PMC10866669 DOI: 10.1172/jci172963] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2023] [Accepted: 11/28/2023] [Indexed: 12/07/2023] Open
Abstract
Worldwide, over 800 million people are affected by kidney disease, yet its pathogenesis remains elusive, hindering the development of novel therapeutics. In this study, we used kidney-specific expression of quantitative traits and single-nucleus open chromatin analysis to show that genetic variants linked to kidney dysfunction on chromosome 20 target the acyl-CoA synthetase short-chain family 2 (ACSS2). By generating ACSS2-KO mice, we demonstrated their protection from kidney fibrosis in multiple disease models. Our analysis of primary tubular cells revealed that ACSS2 regulated de novo lipogenesis (DNL), causing NADPH depletion and increasing ROS levels, ultimately leading to NLRP3-dependent pyroptosis. Additionally, we discovered that pharmacological inhibition or genetic ablation of fatty acid synthase safeguarded kidney cells against profibrotic gene expression and prevented kidney disease in mice. Lipid accumulation and the expression of genes related to DNL were elevated in the kidneys of patients with fibrosis. Our findings pinpoint ACSS2 as a critical kidney disease gene and reveal the role of DNL in kidney disease.
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Affiliation(s)
- Dhanunjay Mukhi
- Renal Electrolyte and Hypertension Division
- Institutes for Diabetes, Obesity and Metabolism
- Department of Genetics, and
| | - Lingzhi Li
- Renal Electrolyte and Hypertension Division
- Institutes for Diabetes, Obesity and Metabolism
- Department of Genetics, and
| | - Hongbo Liu
- Renal Electrolyte and Hypertension Division
- Institutes for Diabetes, Obesity and Metabolism
- Department of Genetics, and
| | - Tomohito Doke
- Renal Electrolyte and Hypertension Division
- Institutes for Diabetes, Obesity and Metabolism
- Department of Genetics, and
| | - Lakshmi P. Kolligundla
- Renal Electrolyte and Hypertension Division
- Institutes for Diabetes, Obesity and Metabolism
- Department of Genetics, and
| | - Eunji Ha
- Renal Electrolyte and Hypertension Division
- Institutes for Diabetes, Obesity and Metabolism
- Department of Genetics, and
| | - Konstantin Kloetzer
- Renal Electrolyte and Hypertension Division
- Institutes for Diabetes, Obesity and Metabolism
- Department of Genetics, and
| | - Amin Abedini
- Renal Electrolyte and Hypertension Division
- Institutes for Diabetes, Obesity and Metabolism
- Department of Genetics, and
| | - Sarmistha Mukherjee
- Institutes for Diabetes, Obesity and Metabolism
- Department of Physiology, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Junnan Wu
- Renal Electrolyte and Hypertension Division
- Institutes for Diabetes, Obesity and Metabolism
- Department of Genetics, and
| | - Poonam Dhillon
- Renal Electrolyte and Hypertension Division
- Institutes for Diabetes, Obesity and Metabolism
- Department of Genetics, and
| | - Hailong Hu
- Renal Electrolyte and Hypertension Division
- Institutes for Diabetes, Obesity and Metabolism
- Department of Genetics, and
| | - Dongyin Guan
- Division of Endocrinology, Baylor College of Medicine, Houston, Texas, USA
| | - Katsuhiko Funai
- Diabetes and Metabolism Research Center, University of Utah, Salt Lake City, Utah, USA
| | - Kahealani Uehara
- Institutes for Diabetes, Obesity and Metabolism
- Department of Physiology, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Paul M. Titchenell
- Institutes for Diabetes, Obesity and Metabolism
- Department of Physiology, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Joseph A. Baur
- Institutes for Diabetes, Obesity and Metabolism
- Department of Physiology, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Kathryn E. Wellen
- Department of Cancer Biology
- Abramson Family Cancer Research Institute, and
| | - Katalin Susztak
- Renal Electrolyte and Hypertension Division
- Institutes for Diabetes, Obesity and Metabolism
- Department of Genetics, and
- Penn-CHOP Kidney Innovation Center, University of Pennsylvania, Philadelphia, Pennsylvania, USA
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9
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Naas S, Schiffer M, Schödel J. Hypoxia and renal fibrosis. Am J Physiol Cell Physiol 2023; 325:C999-C1016. [PMID: 37661918 DOI: 10.1152/ajpcell.00201.2023] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2023] [Revised: 08/25/2023] [Accepted: 08/25/2023] [Indexed: 09/05/2023]
Abstract
Renal fibrosis is the final stage of most progressive kidney diseases. Chronic kidney disease (CKD) is associated with high comorbidity and mortality. Thus, preventing fibrosis and thereby preserving kidney function increases the quality of life and prolongs the survival of patients with CKD. Many processes such as inflammation or metabolic stress modulate the progression of kidney fibrosis. Hypoxia has also been implicated in the pathogenesis of renal fibrosis, and oxygen sensing in the kidney is of outstanding importance for the body. The dysregulation of oxygen sensing in the diseased kidney is best exemplified by the loss of stimulation of erythropoietin production from interstitial cells in the fibrotic kidney despite anemia. Furthermore, hypoxia is present in acute or chronic kidney diseases and may affect all cell types present in the kidney including tubular and glomerular cells as well as resident immune cells. Pro- and antifibrotic effects of the transcription factors hypoxia-inducible factors 1 and 2 have been described in a plethora of animal models of acute and chronic kidney diseases, but recent advances in sequencing technologies now allow for novel and deeper insights into the role of hypoxia and its cell type-specific effects on the progression of renal fibrosis, especially in humans. Here, we review existing literature on how hypoxia impacts the development and progression of renal fibrosis.
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Affiliation(s)
- Stephanie Naas
- Department of Nephrology and Hypertension, Uniklinikum Erlangen und Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, Germany
| | - Mario Schiffer
- Department of Nephrology and Hypertension, Uniklinikum Erlangen und Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, Germany
| | - Johannes Schödel
- Department of Nephrology and Hypertension, Uniklinikum Erlangen und Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, Germany
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10
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Gisch DL, Brennan M, Lake BB, Basta J, Keller M, Ferreira RM, Akilesh S, Ghag R, Lu C, Cheng YH, Collins KS, Parikh SV, Rovin BH, Robbins L, Conklin KY, Diep D, Zhang B, Knoten A, Barwinska D, Asghari M, Sabo AR, Ferkowicz MJ, Sutton TA, Kelly KJ, Boer IHD, Rosas SE, Kiryluk K, Hodgin JB, Alakwaa F, Jefferson N, Gaut JP, Gehlenborg N, Phillips CL, El-Achkar TM, Dagher PC, Hato T, Zhang K, Himmelfarb J, Kretzler M, Mollah S, Jain S, Rauchman M, Eadon MT. The chromatin landscape of healthy and injured cell types in the human kidney. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.06.07.543965. [PMID: 37333123 PMCID: PMC10274789 DOI: 10.1101/2023.06.07.543965] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/20/2023]
Abstract
There is a need to define regions of gene activation or repression that control human kidney cells in states of health, injury, and repair to understand the molecular pathogenesis of kidney disease and design therapeutic strategies. However, comprehensive integration of gene expression with epigenetic features that define regulatory elements remains a significant challenge. We measured dual single nucleus RNA expression and chromatin accessibility, DNA methylation, and H3K27ac, H3K4me1, H3K4me3, and H3K27me3 histone modifications to decipher the chromatin landscape and gene regulation of the kidney in reference and adaptive injury states. We established a comprehensive and spatially-anchored epigenomic atlas to define the kidney's active, silent, and regulatory accessible chromatin regions across the genome. Using this atlas, we noted distinct control of adaptive injury in different epithelial cell types. A proximal tubule cell transcription factor network of ELF3 , KLF6 , and KLF10 regulated the transition between health and injury, while in thick ascending limb cells this transition was regulated by NR2F1 . Further, combined perturbation of ELF3 , KLF6 , and KLF10 distinguished two adaptive proximal tubular cell subtypes, one of which manifested a repair trajectory after knockout. This atlas will serve as a foundation to facilitate targeted cell-specific therapeutics by reprogramming gene regulatory networks.
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11
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Fabo T, Khavari P. Functional characterization of human genomic variation linked to polygenic diseases. Trends Genet 2023; 39:462-490. [PMID: 36997428 PMCID: PMC11025698 DOI: 10.1016/j.tig.2023.02.014] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2022] [Revised: 02/22/2023] [Accepted: 02/23/2023] [Indexed: 03/30/2023]
Abstract
The burden of human disease lies predominantly in polygenic diseases. Since the early 2000s, genome-wide association studies (GWAS) have identified genetic variants and loci associated with complex traits. These have ranged from variants in coding sequences to mutations in regulatory regions, such as promoters and enhancers, as well as mutations affecting mediators of mRNA stability and other downstream regulators, such as 5' and 3'-untranslated regions (UTRs), long noncoding RNA (lncRNA), and miRNA. Recent research advances in genetics have utilized a combination of computational techniques, high-throughput in vitro and in vivo screening modalities, and precise genome editing to impute the function of diverse classes of genetic variants identified through GWAS. In this review, we highlight the vastness of genomic variants associated with polygenic disease risk and address recent advances in how genetic tools can be used to functionally characterize them.
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Affiliation(s)
- Tania Fabo
- Program in Epithelial Biology, Stanford University, Stanford, CA, USA; Stanford Cancer Institute, Stanford University, Stanford, CA, USA; Graduate Program in Genetics, Stanford University, Stanford, CA, USA; Stanford University School of Medicine, Stanford University, Stanford, CA, USA
| | - Paul Khavari
- Program in Epithelial Biology, Stanford University, Stanford, CA, USA; Stanford Cancer Institute, Stanford University, Stanford, CA, USA; Graduate Program in Genetics, Stanford University, Stanford, CA, USA; Stanford University School of Medicine, Stanford University, Stanford, CA, USA; Veterans Affairs Palo Alto Healthcare System, Palo Alto, CA, USA.
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12
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Pregizer S, Vreven T, Mathur M, Robinson LN. Multi-omic single cell sequencing: Overview and opportunities for kidney disease therapeutic development. Front Mol Biosci 2023; 10:1176856. [PMID: 37091871 PMCID: PMC10113659 DOI: 10.3389/fmolb.2023.1176856] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2023] [Accepted: 03/21/2023] [Indexed: 04/09/2023] Open
Abstract
Single cell sequencing technologies have rapidly advanced in the last decade and are increasingly applied to gain unprecedented insights by deconstructing complex biology to its fundamental unit, the individual cell. First developed for measurement of gene expression, single cell sequencing approaches have evolved to allow simultaneous profiling of multiple additional features, including chromatin accessibility within the nucleus and protein expression at the cell surface. These multi-omic approaches can now further be applied to cells in situ, capturing the spatial context within which their biology occurs. To extract insights from these complex datasets, new computational tools have facilitated the integration of information across different data types and the use of machine learning approaches. Here, we summarize current experimental and computational methods for generation and integration of single cell multi-omic datasets. We focus on opportunities for multi-omic single cell sequencing to augment therapeutic development for kidney disease, including applications for biomarkers, disease stratification and target identification.
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13
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Doke T, Mukherjee S, Mukhi D, Dhillon P, Abedini A, Davis JG, Chellappa K, Chen B, Baur JA, Susztak K. NAD + precursor supplementation prevents mtRNA/RIG-I-dependent inflammation during kidney injury. Nat Metab 2023; 5:414-430. [PMID: 36914909 PMCID: PMC10230446 DOI: 10.1038/s42255-023-00761-7] [Citation(s) in RCA: 23] [Impact Index Per Article: 23.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/10/2022] [Accepted: 02/09/2023] [Indexed: 03/16/2023]
Abstract
Our understanding of how global changes in cellular metabolism contribute to human kidney disease remains incompletely understood. Here we show that nicotinamide adenine dinucleotide (NAD+) deficiency drives mitochondrial dysfunction causing inflammation and kidney disease development. Using unbiased global metabolomics in healthy and diseased human kidneys, we identify NAD+ deficiency as a disease signature. Furthermore using models of cisplatin- or ischaemia-reperfusion induced kidney injury in male mice we observed NAD+ depletion Supplemental nicotinamide riboside or nicotinamide mononucleotide restores NAD+ levels and improved kidney function. We find that cisplatin exposure causes cytosolic leakage of mitochondrial RNA (mtRNA) and activation of the cytosolic pattern recognition receptor retinoic acid-inducible gene I (RIG-I), both of which can be ameliorated by restoring NAD+. Male mice with RIG-I knock-out (KO) are protected from cisplatin-induced kidney disease. In summary, we demonstrate that the cytosolic release of mtRNA and RIG-I activation is an NAD+-sensitive mechanism contributing to kidney disease.
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Affiliation(s)
- Tomohito Doke
- Department of Medicine, Renal Electrolyte and Hypertension Division, University of Pennsylvania, Philadelphia, PA, USA
- Institute for Diabetes, Obesity and Metabolism, University of Pennsylvania, Philadelphia, PA, USA
| | - Sarmistha Mukherjee
- Institute for Diabetes, Obesity and Metabolism, University of Pennsylvania, Philadelphia, PA, USA
- Department of Physiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Dhanunjay Mukhi
- Department of Medicine, Renal Electrolyte and Hypertension Division, University of Pennsylvania, Philadelphia, PA, USA
- Institute for Diabetes, Obesity and Metabolism, University of Pennsylvania, Philadelphia, PA, USA
| | - Poonam Dhillon
- Department of Medicine, Renal Electrolyte and Hypertension Division, University of Pennsylvania, Philadelphia, PA, USA
- Institute for Diabetes, Obesity and Metabolism, University of Pennsylvania, Philadelphia, PA, USA
| | - Amin Abedini
- Department of Medicine, Renal Electrolyte and Hypertension Division, University of Pennsylvania, Philadelphia, PA, USA
- Institute for Diabetes, Obesity and Metabolism, University of Pennsylvania, Philadelphia, PA, USA
| | - James G Davis
- Institute for Diabetes, Obesity and Metabolism, University of Pennsylvania, Philadelphia, PA, USA
- Department of Physiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Karthikeyani Chellappa
- Institute for Diabetes, Obesity and Metabolism, University of Pennsylvania, Philadelphia, PA, USA
- Department of Physiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Beishan Chen
- Institute for Diabetes, Obesity and Metabolism, University of Pennsylvania, Philadelphia, PA, USA
- Department of Physiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Joseph A Baur
- Institute for Diabetes, Obesity and Metabolism, University of Pennsylvania, Philadelphia, PA, USA.
- Department of Physiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA.
| | - Katalin Susztak
- Department of Medicine, Renal Electrolyte and Hypertension Division, University of Pennsylvania, Philadelphia, PA, USA.
- Institute for Diabetes, Obesity and Metabolism, University of Pennsylvania, Philadelphia, PA, USA.
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14
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Brown M, Greenwood E, Zeng B, Powell JE, Gibson G. Effect of all-but-one conditional analysis for eQTL isolation in peripheral blood. Genetics 2023; 223:iyac162. [PMID: 36321965 PMCID: PMC9836021 DOI: 10.1093/genetics/iyac162] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2022] [Accepted: 10/13/2022] [Indexed: 11/13/2022] Open
Abstract
Expression quantitative trait locus detection has become increasingly important for understanding how noncoding variants contribute to disease susceptibility and complex traits. The major challenges in expression quantitative trait locus fine-mapping and causal variant discovery relate to the impact of linkage disequilibrium on signals due to one or multiple functional variants that lie within a credible set. We perform expression quantitative trait locus fine-mapping using the all-but-one approach, conditioning each signal on all others detected in an interval, on the Consortium for the Architecture of Gene Expression cohorts of microarray-based peripheral blood gene expression in 2,138 European-ancestry human adults. We contrast these results with traditional forward stepwise conditional analysis and a Bayesian localization method. All-but-one conditioning significantly modifies effect-size estimates for 51% of 2,351 expression quantitative trait locus peaks, but only modestly affects credible set size and location. On the other hand, both conditioning approaches result in unexpectedly low overlap with Bayesian credible sets, with just 57% peak concordance and between 50% and 70% SNP sharing, leading us to caution against the assumption that any one localization method is superior to another. We also cross reference our results with ATAC-seq data, cell-type-specific expression quantitative trait locus, and activity-by-contact-enhancers, leading to the proposal of a 5-tier approach to further reduce credible set sizes and prioritize likely causal variants for all known inflammatory bowel disease risk loci active in immune cells.
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Affiliation(s)
- Margaret Brown
- Center for Integrative Genomics, School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA 30332, USA
| | - Emily Greenwood
- Center for Integrative Genomics, School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA 30332, USA
| | - Biao Zeng
- Present address for Biao Zeng: Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Joseph E Powell
- Present address for Joseph E Powell: Garvan-Weizmann Center for Cellular Genomics, Sydney, NSW 2010, Australia
| | - Greg Gibson
- Center for Integrative Genomics, School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA 30332, USA
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15
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Levinsohn J, Li S, Ha E, Susztak K. Combing Genome-Wide Association Studies and Single-Cell Analysis to Elucidate the Mechanisms of Kidney Disease: Proceedings of the Henry Shavelle Professorship. GLOMERULAR DISEASES 2023; 3:258-265. [PMID: 38033715 PMCID: PMC10686632 DOI: 10.1159/000534678] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/05/2023] [Accepted: 10/13/2023] [Indexed: 12/02/2023]
Abstract
Background Kidney diseases pose a significant global health burden; there is an urgent need to deepen our understanding of their underlying mechanisms. Summary This review focuses on new innovative approaches that merge genome-wide association studies (GWAS) and single-cell omics (including transcriptomics) in kidney disease research. We begin by detailing how GWAS has identified numerous genetic risk factors, offering valuable insight into disease susceptibility. Then, we explore the application of scRNA-seq, highlighting its ability to unravel how genetic variants influence cellular phenotypes. Through a synthesis of recent studies, we illuminate the synergy between these two powerful methodologies, demonstrating their potential in elucidating the complex etiology of kidney diseases. Moreover, we discuss how this integrative approach could pave the way for precise diagnostics and personalized treatments. Key Message This review underscores the transformative potential of combining GWAS and scRNA-seq in the journey toward a deeper understanding of kidney diseases.
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Affiliation(s)
- Jonathan Levinsohn
- Division of Nephrology, Department of Medicine, University of Pennsylvania, Perelman School of Medicine, Philadelphia, PA, USA
- Children’s Hospital of Philadelphia, Philadelphia, PA, USA
- Penn/CHOP Kidney Innovation Center, Philadelphia, PA, USA
| | - Shen Li
- Division of Nephrology, Department of Medicine, University of Pennsylvania, Perelman School of Medicine, Philadelphia, PA, USA
- Penn/CHOP Kidney Innovation Center, Philadelphia, PA, USA
| | - Eunji Ha
- Division of Nephrology, Department of Medicine, University of Pennsylvania, Perelman School of Medicine, Philadelphia, PA, USA
- Penn/CHOP Kidney Innovation Center, Philadelphia, PA, USA
| | - Katalin Susztak
- Division of Nephrology, Department of Medicine, University of Pennsylvania, Perelman School of Medicine, Philadelphia, PA, USA
- Penn/CHOP Kidney Innovation Center, Philadelphia, PA, USA
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16
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Wang Y, Liu Z, Ma J, Xv Q, Gao H, Yin H, Yan G, Jiang X, Yu W. Lycopene attenuates the inflammation and apoptosis in aristolochic acid nephropathy by targeting the Nrf2 antioxidant system. Redox Biol 2022; 57:102494. [PMID: 36198206 PMCID: PMC9530962 DOI: 10.1016/j.redox.2022.102494] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2022] [Revised: 09/26/2022] [Accepted: 09/27/2022] [Indexed: 10/31/2022] Open
Abstract
Lycopene (LYC) is a carotenoid, has antioxidant properties. This study investigated whether lycopene attenuates aristolochic acids (AAs) -induced chronic kidney disease. In this experiment, lycopene was used to intervene C57BL/6 mice with renal injury induced by aristolochic acid exposure. The histomorphological changes and serological parameters of the kidney were measured in order to assess the alleviating effect of lycopene on renal injury in aristolochic acid nephropathy. In vitro and in vivo experiments were carried out to verify the main mechanism of action and drug targets of lycopene in improving aristolochic acid nephropathy (AAN) and by various experimental methods such as ELISA, immunohistochemistry, immunofluorescence, Western-blot and qRT-PCR. The results showed that oxidative stress injury was induced in the kidney of mice after AAI exposure, resulting in inflammatory response and tubular epithelial cell apoptosis. The results showed that the Nrf2/HO-1 antioxidant signaling pathway was inhibited after AAI exposure. AAI induces oxidative stress injury in the kidney, which ultimately leads to inflammation and tubular epithelial cell apoptosis. After LYC intervened in the body, it activated Nrf2 nuclear translocation and its downstream HO-1 and NQO1 antioxidant signaling pathways. LYC inhibited ROS production by renal tubular epithelial cells, and alleviated mitochondrial damage. LYC further modulated the TNF-α/NF-κB signaling cascade, thereby reduced the accumulation of inflammatory factors in the renal interstitium. Moreover, LYC was able to up-regulate the expression of Bcl-2, down-regulate Bax expression and inhibit the activation of cleaved forms of Caspase-9 and Caspase-3, which finally attenuated the apoptosis of the mitochondrial pathway induced by AAI exposure. It was concluded that lycopene was able to activate the Nrf2 antioxidant signaling pathway to maintain the homeostasis of renal oxidative stress and ultimately attenuated renal inflammatory response and apoptosis. These results suggested that lycopene can be used as a drug to relieve AAN.
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Affiliation(s)
- Yu Wang
- Department of Veterinary Medicine, Northeast Agricultural University, Harbin, 150030, China.
| | - Zhihui Liu
- Department of Veterinary Medicine, Northeast Agricultural University, Harbin, 150030, China
| | - Jun Ma
- Department of Veterinary Medicine, Northeast Agricultural University, Harbin, 150030, China
| | - Qingyang Xv
- Department of Veterinary Medicine, Northeast Agricultural University, Harbin, 150030, China
| | - Hongxin Gao
- Department of Veterinary Medicine, Northeast Agricultural University, Harbin, 150030, China
| | - Hang Yin
- Department of Veterinary Medicine, Northeast Agricultural University, Harbin, 150030, China
| | - Ge Yan
- Department of Veterinary Medicine, Northeast Agricultural University, Harbin, 150030, China
| | - Xiaowen Jiang
- Department of Veterinary Medicine, Northeast Agricultural University, Harbin, 150030, China.
| | - Wenhui Yu
- Department of Veterinary Medicine, Northeast Agricultural University, Harbin, 150030, China; Heilongjiang Provincial Key Laboratory for Prevention and Control of Common Animal Diseases, Northeast Agricultural University, Harbin, 150030, China; Institute of Chinese Veterinary Medicine, Northeast Agricultural University, Harbin, 150030, China.
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17
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Doke T, Susztak K. The multifaceted role of kidney tubule mitochondrial dysfunction in kidney disease development. Trends Cell Biol 2022; 32:841-853. [PMID: 35473814 PMCID: PMC9464682 DOI: 10.1016/j.tcb.2022.03.012] [Citation(s) in RCA: 47] [Impact Index Per Article: 23.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2022] [Revised: 03/27/2022] [Accepted: 03/30/2022] [Indexed: 12/24/2022]
Abstract
More than 800 million people suffer from kidney disease. Genetic studies and follow-up animal models and cell biological experiments indicate the key role of proximal tubule metabolism. Kidneys have one of the highest mitochondrial densities. Mitochondrial biogenesis, mitochondrial fusion and fission, and mitochondrial recycling, such as mitophagy are critical for proper mitochondrial function. Mitochondrial dysfunction can lead to an energetic crisis, orchestrate different types of cell death (apoptosis, necroptosis, pyroptosis, and ferroptosis), and influence cellular calcium levels and redox status. Collectively, mitochondrial defects in renal tubules contribute to epithelial atrophy, inflammation, or cell death, orchestrating kidney disease development.
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Affiliation(s)
- Tomohito Doke
- Department of Medicine, Renal Electrolyte and Hypertension Division, University of Pennsylvania, Philadelphia, PA, USA; Department of Genetics, University of Pennsylvania, Perelman School of Medicine, Philadelphia, PA 19104, USA.
| | - Katalin Susztak
- Department of Medicine, Renal Electrolyte and Hypertension Division, University of Pennsylvania, Philadelphia, PA, USA; Department of Genetics, University of Pennsylvania, Perelman School of Medicine, Philadelphia, PA 19104, USA.
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