51
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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: 61] [Impact Index Per Article: 30.5] [Reference Citation Analysis] [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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52
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Chromatin accessibility dynamics dictate renal tubular epithelial cell response to injury. Nat Commun 2022; 13:7322. [PMID: 36443310 PMCID: PMC9705299 DOI: 10.1038/s41467-022-34854-w] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [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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53
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Protocol for SARS-CoV-2 infection of kidney organoids derived from human pluripotent stem cells. STAR Protoc 2022; 3:101872. [PMID: 36595951 PMCID: PMC9637521 DOI: 10.1016/j.xpro.2022.101872] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2022] [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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54
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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] [Abstract] [Key Words] [Grants] [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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Affiliation(s)
- John J. Gildea
- Department of Pathology, The University of Virginia, Charlottesville, VA 22903, USA; (J.J.G.); (P.X.); (K.A.S.); (W.Y.)
| | - Peng Xu
- Department of Pathology, The University of Virginia, Charlottesville, VA 22903, USA; (J.J.G.); (P.X.); (K.A.S.); (W.Y.)
| | - Katie A. Schiermeyer
- Department of Pathology, The University of Virginia, Charlottesville, VA 22903, USA; (J.J.G.); (P.X.); (K.A.S.); (W.Y.)
| | - Wei Yue
- Department of Pathology, The University of Virginia, Charlottesville, VA 22903, USA; (J.J.G.); (P.X.); (K.A.S.); (W.Y.)
| | - Robert M. Carey
- Division of Endocrinology and Metabolism, Department of Medicine, The University of Virginia, Charlottesville, VA 22903, USA;
| | - Pedro A. Jose
- Division of Renal Diseases & Hypertension, Department of Medicine, School of Medicine and Health Sciences, The George Washington University, Washington, DC 20052, USA;
- Department of Physiology/Pharmacology, School of Medicine and Health Sciences, The George Washington University, Washington, DC 20052, USA
| | - Robin A. Felder
- Department of Pathology, The University of Virginia, Charlottesville, VA 22903, USA; (J.J.G.); (P.X.); (K.A.S.); (W.Y.)
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55
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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] [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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56
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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: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [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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57
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Immunometabolic alterations in lupus: where do they come from and where do we go from there? Curr Opin Immunol 2022; 78:102245. [PMID: 36122544 PMCID: PMC10161929 DOI: 10.1016/j.coi.2022.102245] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [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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58
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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] [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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59
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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 PMCID: PMC9276703 DOI: 10.1038/s41467-022-31772-9] [Citation(s) in RCA: 78] [Impact Index Per Article: 39.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [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.
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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
| | - Tomohito Doke
- 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
| | - Ya-Wen Yang
- 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
| | - Daniel L Aldridge
- Department of Pathobiology, School of Veterinary Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Hailong Hu
- 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
| | - Hung Mai
- 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
| | - Dhanunjay Mukhi
- 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
| | - Ziyuan Ma
- 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
| | - Rojesh Shrestha
- 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
| | - Matthew B Palmer
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Christopher A Hunter
- Department of Pathobiology, School of Veterinary Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - 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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60
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Immunometabolic rewiring of tubular epithelial cells in kidney disease. Nat Rev Nephrol 2022; 18:588-603. [PMID: 35798902 DOI: 10.1038/s41581-022-00592-x] [Citation(s) in RCA: 30] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [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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61
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Röck R, Rizzo L, Lienkamp SS. Kidney Development: Recent Insights from Technological Advances. Physiology (Bethesda) 2022; 37:0. [PMID: 35253460 DOI: 10.1152/physiol.00041.2021] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
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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62
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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] [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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63
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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. FRONTIERS IN NEPHROLOGY 2022; 2:923068. [PMID: 37674991 PMCID: PMC10479694 DOI: 10.3389/fneph.2022.923068] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/18/2022] [Accepted: 05/30/2022] [Indexed: 09/08/2023]
Abstract
Chronic kidney disease (CKD) was the 12th leading cause of death globally in 2017 with the prevalence of CKD estimated at ~9%. Early detection and intervention for CKD may improve patient outcomes, but standard testing approaches even in developed countries do not facilitate identification of patients at high risk of developing CKD, nor those progressing to end-stage kidney disease (ESKD). Recent advances in CKD research are moving towards a more personalised approach for CKD. Heritability for CKD ranges from 30% to 75%, yet identified genetic risk factors account for only a small proportion of the inherited contribution to CKD. More in depth analysis of genomic sequencing data in large cohorts is revealing new genetic risk factors for common diagnoses of CKD and providing novel diagnoses for rare forms of CKD. Multi-omic approaches are now being harnessed to improve our understanding of CKD and explain some of the so-called 'missing heritability'. The most common omic analyses employed for CKD are genomics, epigenomics, transcriptomics, metabolomics, proteomics and phenomics. While each of these omics have been reviewed individually, considering integrated multi-omic analysis offers considerable scope to improve our understanding and treatment of CKD. This narrative review summarises current understanding of multi-omic research alongside recent experimental and analytical approaches, discusses current challenges and future perspectives, and offers new insights for CKD.
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Affiliation(s)
| | | | | | | | - Amy Jayne McKnight
- Centre for Public Health, Queen’s University Belfast, Belfast, United Kingdom
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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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65
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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 PMCID: PMC9097013 DOI: 10.1016/j.cmet.2022.04.009] [Citation(s) in RCA: 38] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [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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66
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Doke T, Abedini A, Aldridge DL, Yang YW, Park J, Hernandez CM, Balzer MS, Shrestra R, Coppock G, Rico JMI, Han SY, Kim J, Xin S, Piliponsky AM, Angelozzi M, Lefebvre V, Siracusa MC, Hunter CA, Susztak K. Single-cell analysis identifies the interaction of altered renal tubules with basophils orchestrating kidney fibrosis. Nat Immunol 2022; 23:947-959. [PMID: 35552540 DOI: 10.1038/s41590-022-01200-7] [Citation(s) in RCA: 45] [Impact Index Per Article: 22.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2021] [Accepted: 04/01/2022] [Indexed: 02/06/2023]
Abstract
Inflammation is an important component of fibrosis but immune processes that orchestrate kidney fibrosis are not well understood. Here we apply single-cell sequencing to a mouse model of kidney fibrosis. We identify a subset of kidney tubule cells with a profibrotic-inflammatory phenotype characterized by the expression of cytokines and chemokines associated with immune cell recruitment. Receptor-ligand interaction analysis and experimental validation indicate that CXCL1 secreted by profibrotic tubules recruits CXCR2+ basophils. In mice, these basophils are an important source of interleukin-6 and recruitment of the TH17 subset of helper T cells. Genetic deletion or antibody-based depletion of basophils results in reduced renal fibrosis. Human kidney single-cell, bulk gene expression and immunostaining validate a function for basophils in patients with kidney fibrosis. Collectively, these studies identify basophils as contributors to the development of renal fibrosis and suggest that targeting these cells might be a useful clinical strategy to manage chronic kidney disease.
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Affiliation(s)
- Tomohito Doke
- Department of Medicine, Renal Electrolyte and Hypertension Division, University of Pennsylvania, Philadelphia, PA, USA
| | - Amin Abedini
- Department of Medicine, Renal Electrolyte and Hypertension Division, University of Pennsylvania, Philadelphia, PA, USA
| | - Daniel L Aldridge
- Department of Pathobiology, University of Pennsylvania School of Veterinary Medicine, Philadelphia, PA, USA
| | - Ya-Wen Yang
- Department of Medicine, Renal Electrolyte and Hypertension Division, University of Pennsylvania, Philadelphia, PA, USA
| | - Jihwan Park
- Department of Medicine, Renal Electrolyte and Hypertension Division, University of Pennsylvania, Philadelphia, PA, USA
| | - Christina M Hernandez
- Center for Immunity and Inflammation, Department of Medicine, New Jersey Medical School, Rutgers-The State University of New Jersey, Newark, NJ, USA
| | - Michael S Balzer
- Department of Medicine, Renal Electrolyte and Hypertension Division, University of Pennsylvania, Philadelphia, PA, USA
| | - Rojesh Shrestra
- Department of Medicine, Renal Electrolyte and Hypertension Division, University of Pennsylvania, Philadelphia, PA, USA
| | - Gaia Coppock
- Department of Medicine, Renal Electrolyte and Hypertension Division, University of Pennsylvania, Philadelphia, PA, USA
- Department of Pathobiology, University of Pennsylvania School of Veterinary Medicine, Philadelphia, PA, USA
| | - Juan M Inclan Rico
- Center for Immunity and Inflammation, Department of Medicine, New Jersey Medical School, Rutgers-The State University of New Jersey, Newark, NJ, USA
| | - Seung Yub Han
- Department of Biology, University of Pennsylvania, Philadelphia, PA, USA
| | - Junhyong Kim
- Department of Biology, University of Pennsylvania, Philadelphia, PA, USA
| | - Sheng Xin
- Department of Medicine, Renal Electrolyte and Hypertension Division, University of Pennsylvania, Philadelphia, PA, USA
| | - Adrian M Piliponsky
- Center for Immunity and Immunotherapies, Seattle Children's Research Institute, Seattle, WA, USA
| | - Marco Angelozzi
- Division of Orthopaedic Surgery, Department of Surgery, The Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Veronique Lefebvre
- Division of Orthopaedic Surgery, Department of Surgery, The Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Mark C Siracusa
- Center for Immunity and Inflammation, Department of Medicine, New Jersey Medical School, Rutgers-The State University of New Jersey, Newark, NJ, USA
| | - Christopher A Hunter
- Department of Pathobiology, University of Pennsylvania School of Veterinary Medicine, Philadelphia, PA, USA
| | - Katalin Susztak
- Department of Medicine, Renal Electrolyte and Hypertension Division, University of Pennsylvania, Philadelphia, PA, USA.
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67
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Vorperian SK, Moufarrej MN, Quake SR. Cell types of origin of the cell-free transcriptome. Nat Biotechnol 2022; 40:855-861. [PMID: 35132263 PMCID: PMC9200634 DOI: 10.1038/s41587-021-01188-9] [Citation(s) in RCA: 30] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2021] [Accepted: 12/13/2021] [Indexed: 12/12/2022]
Abstract
Cell-free RNA from liquid biopsies can be analyzed to determine disease tissue of origin. We extend this concept to identify cell types of origin using the Tabula Sapiens transcriptomic cell atlas as well as individual tissue transcriptomic cell atlases in combination with the Human Protein Atlas RNA consensus dataset. We define cell type signature scores, which allow the inference of cell types that contribute to cell-free RNA for a variety of diseases.
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Affiliation(s)
- Sevahn K Vorperian
- Department of Chemical Engineering, Stanford University, Stanford, CA, USA
- ChEM-H, Stanford University, Stanford, CA, USA
| | - Mira N Moufarrej
- Department of Bioengineering, Stanford University, Stanford, CA, USA
| | - Stephen R Quake
- Department of Bioengineering, Stanford University, Stanford, CA, USA.
- Department of Applied Physics, Stanford University, Stanford, CA, USA.
- Chan Zuckerberg Biohub, San Francisco, CA, USA.
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68
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Scholtes C, Giguère V. Transcriptional control of energy metabolism by nuclear receptors. Nat Rev Mol Cell Biol 2022; 23:750-770. [DOI: 10.1038/s41580-022-00486-7] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/08/2022] [Indexed: 12/11/2022]
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69
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Abstract
Altered lipid metabolism is a characteristic feature and potential driving factor of acute kidney injury (AKI). Of the lipids that accumulate in injured renal tissues, ceramides are potent regulators of metabolism and cell fate. Up-regulation of ceramide synthesis is a common feature shared across several AKI etiologies in vitro and in vivo. Furthermore, ceramide accumulation is an early event in the natural history of AKI that precedes cell death and organ dysfunction. Emerging evidence suggests that inhibition of ceramide accumulation may improve renal outcomes in several models of AKI. This review examines the landscape of ceramide metabolism and regulation in the healthy and injured kidney. Furthermore, we discuss the body of literature regarding ceramides as therapeutic targets for AKI and consider potential mechanisms by which ceramides drive kidney pathogenesis.
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Affiliation(s)
- Rebekah J Nicholson
- Department of Nutrition and Integrative Physiology, Diabetes and Metabolism Research Center, University of Utah, Salt Lake City, UT
| | - William L Holland
- Department of Nutrition and Integrative Physiology, Diabetes and Metabolism Research Center, University of Utah, Salt Lake City, UT
| | - Scott A Summers
- Department of Nutrition and Integrative Physiology, Diabetes and Metabolism Research Center, University of Utah, Salt Lake City, UT.
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70
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Lidberg KA, Muthusamy S, Adil M, Mahadeo A, Yang J, Patel RS, Wang L, Bammler TK, Reichel J, Yeung CK, Himmelfarb J, Kelly EJ, Akilesh S. Serum Protein Exposure Activates a Core Regulatory Program Driving Human Proximal Tubule Injury. J Am Soc Nephrol 2022; 33:949-965. [PMID: 35197326 PMCID: PMC9063895 DOI: 10.1681/asn.2021060751] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2021] [Accepted: 02/06/2022] [Indexed: 11/03/2022] Open
Abstract
BACKGROUND The kidneys efficiently filter waste products while retaining serum proteins in the circulation. However, numerous diseases compromise this barrier function, resulting in spillage of serum proteins into the urine (proteinuria). Some studies of glomerular filtration suggest that tubules may be physiologically exposed to nephrotic-range protein levels. Therefore, whether serum components can directly injure the downstream tubular portions of the kidney, which in turn can lead to inflammation and fibrosis, remains controversial. METHODS We tested the effects of serum protein exposure in human kidney tubule microphysiologic systems and with orthogonal epigenomic approaches since animal models cannot directly assess the effect of serum components on tubules. RESULTS Serum, but not its major protein component albumin, induced tubular injury and secretion of proinflammatory cytokines. Epigenomic comparison of serum-injured tubules and intact kidney tissue revealed canonical stress-inducible regulation of injury-induced genes. Concordant transcriptional changes in microdissected tubulointerstitium were also observed in an independent cohort of patients with proteinuric kidney disease. CONCLUSIONS Our results demonstrate a causal role for serum proteins in tubular injury and identify regulatory mechanisms and novel pathways for intervention.
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Affiliation(s)
- Kevin A. Lidberg
- Department of Pharmaceutics, University of Washington, Seattle, Washington
| | - Selvaraj Muthusamy
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, Washington
| | - Mohamed Adil
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, Washington
| | - Anish Mahadeo
- Department of Pharmaceutics, University of Washington, Seattle, Washington
| | - Jade Yang
- Department of Pharmaceutics, University of Washington, Seattle, Washington
| | | | - Lu Wang
- Department of Environmental and Occupational Health Sciences, University of Washington, Seattle, Washington
| | - Theo K. Bammler
- Department of Environmental and Occupational Health Sciences, University of Washington, Seattle, Washington
| | - Jonathan Reichel
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, Washington
| | - Catherine K. Yeung
- Department of Pharmacy, University of Washington, Seattle, Washington
- Kidney Research Institute, Seattle, Washington
| | - Jonathan Himmelfarb
- Kidney Research Institute, Seattle, Washington
- Nephrology Division, Department of Medicine, University of Washington, Seattle, Washington
| | - Edward J. Kelly
- Department of Pharmaceutics, University of Washington, Seattle, Washington
- Kidney Research Institute, Seattle, Washington
| | - Shreeram Akilesh
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, Washington
- Kidney Research Institute, Seattle, Washington
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71
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The nuclear receptor ERR cooperates with the cardiogenic factor GATA4 to orchestrate cardiomyocyte maturation. Nat Commun 2022; 13:1991. [PMID: 35418170 PMCID: PMC9008061 DOI: 10.1038/s41467-022-29733-3] [Citation(s) in RCA: 21] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2021] [Accepted: 03/30/2022] [Indexed: 12/19/2022] Open
Abstract
Estrogen-related receptors (ERR) α and γ were shown recently to serve as regulators of cardiac maturation, yet the underlying mechanisms have not been delineated. Herein, we find that ERR signaling is necessary for induction of genes involved in mitochondrial and cardiac-specific contractile processes during human induced pluripotent stem cell-derived cardiomyocyte (hiPSC-CM) differentiation. Genomic interrogation studies demonstrate that ERRγ occupies many cardiomyocyte enhancers/super-enhancers, often co-localizing with the cardiogenic factor GATA4. ERRγ interacts with GATA4 to cooperatively activate transcription of targets involved in cardiomyocyte-specific processes such as contractile function, whereas ERRγ-mediated control of metabolic genes occurs independent of GATA4. Both mechanisms require the transcriptional coregulator PGC-1α. A disease-causing GATA4 mutation is shown to diminish PGC-1α/ERR/GATA4 cooperativity and expression of ERR target genes are downregulated in human heart failure samples suggesting that dysregulation of this circuitry may contribute to congenital and acquired forms of heart failure. Mature cardiac muscle requires high mitochondrial ATP production and specialized contractile proteins. Here the authors demonstrate that cardiomyocyte-specific contractile maturation involves cooperation between the nuclear receptor ERRγ and cardiogenic transcription factor GATA4, but ERRγ controls metabolic genes independently.
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72
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Wu J, Sun Z, Yang S, Fu J, Fan Y, Wang N, Hu J, Ma L, Peng C, Wang Z, Lee K, He JC, Li Q. Kidney single-cell transcriptome profile reveals distinct response of proximal tubule cells to SGLT2i and ARB treatment in diabetic mice. Mol Ther 2022; 30:1741-1753. [PMID: 34678510 PMCID: PMC9077318 DOI: 10.1016/j.ymthe.2021.10.013] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2021] [Revised: 08/30/2021] [Accepted: 10/13/2021] [Indexed: 12/20/2022] Open
Abstract
Angiotensin receptor blockers (ARBs) and sodium-glucose cotransporter 2 inhibitors (SGLT2i) have been used as the standard therapy for patients with diabetic kidney disease (DKD). However, how these two drugs possess additive renoprotective effects remains unclear. Here, we conducted single-cell RNA sequencing to profile the kidney cell transcriptome of db/db mice treated with vehicle, ARBs, SGLT2i, or ARBs plus SGLT2i, using db/m mice as control. We identified 10 distinct clusters of kidney cells with predominant proximal tubular (PT) cells. We found that ARBs had more anti-inflammatory and anti-fibrotic effects, while SGLT2i affected more mitochondrial function in PT. We also identified a new PT subcluster, was increased in DKD, but reversed by the treatments. This new subcluster was also confirmed by immunostaining of mouse and human kidneys with DKD. Together, our study reveals kidney cell-specific gene signatures in response to ARBs and SGLT2i and identifies a new PT subcluster, which provides new insight into the pathogenesis of DKD.
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Affiliation(s)
- Jinshan Wu
- Department of Endocrinology, the First Affiliated Hospital of Chongqing Medical University, Chongqing 400016, China
| | - Zeguo Sun
- Division of Nephrology, Department of Medicine, Icahn School of Medicine at Mount Sinai, NY 10029, USA
| | - Shumin Yang
- Department of Endocrinology, the First Affiliated Hospital of Chongqing Medical University, Chongqing 400016, China
| | - Jia Fu
- Division of Nephrology, Department of Medicine, Icahn School of Medicine at Mount Sinai, NY 10029, USA
| | - Ying Fan
- Department of Nephrology, Shanghai Jiao Tong University Affiliated Sixth People's Hospital, Shanghai 200233, China
| | - Niansong Wang
- Department of Nephrology, Shanghai Jiao Tong University Affiliated Sixth People's Hospital, Shanghai 200233, China
| | - Jinbo Hu
- Department of Endocrinology, the First Affiliated Hospital of Chongqing Medical University, Chongqing 400016, China
| | - Linqiang Ma
- Department of Endocrinology, the First Affiliated Hospital of Chongqing Medical University, Chongqing 400016, China
| | - Chuan Peng
- Department of Endocrinology, the First Affiliated Hospital of Chongqing Medical University, Chongqing 400016, China
| | - Zhihong Wang
- Department of Endocrinology, the First Affiliated Hospital of Chongqing Medical University, Chongqing 400016, China
| | - Kyung Lee
- Division of Nephrology, Department of Medicine, Icahn School of Medicine at Mount Sinai, NY 10029, USA
| | - John Cijiang He
- Division of Nephrology, Department of Medicine, Icahn School of Medicine at Mount Sinai, NY 10029, USA; Renal Program, James J Peters VA Medical Center at Bronx, NY 10468, USA.
| | - Qifu Li
- Department of Endocrinology, the First Affiliated Hospital of Chongqing Medical University, Chongqing 400016, China.
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73
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Abstract
The field of single-cell genomics and spatial technologies is rapidly evolving and has already provided unprecedented insights into complex tissues. Major advances have been made in dissecting the cellular composition and spatiotemporal interactions that mediate developmental processes in the fetal kidney. Single-cell technologies have also provided detailed insights into the heterogeneity of cell types within the healthy adult and shed light on the complex cellular mechanisms that contribute to kidney disease. The in-depth characterization of specific cell types associated with acute kidney injury and glomerular diseases has potential for the development of prognostic biomarkers and new therapeutics. Analyses of pathway activity in clear-cell renal cell carcinoma can predict the sensitivity of tumour cells to specific inhibitors. The identification of the cell of origin of renal cell carcinoma and of new cell types within the tumour microenvironment also has implications for the development of targeted therapeutics. Similarly, single-cell sequencing has provided new insights into the mechanisms underlying kidney fibrosis, specifically our understanding of myofibroblast origins and the contribution of cell crosstalk within the fibrotic niche to disease progression. These and future studies will enable the creation of a map to aid our understanding of the cellular processes and interactions in the developing, healthy and diseased kidney.
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74
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Verissimo T, Faivre A, Rinaldi A, Lindenmeyer M, Delitsikou V, Veyrat-Durebex C, Heckenmeyer C, Fernandez M, Berchtold L, Dalga D, Cohen C, Naesens M, Ricksten SE, Martin PY, Pugin J, Merlier F, Haupt K, Rutkowski JM, Moll S, Cippà PE, Legouis D, de Seigneux S. Decreased Renal Gluconeogenesis Is a Hallmark of Chronic Kidney Disease. J Am Soc Nephrol 2022; 33:810-827. [PMID: 35273087 PMCID: PMC8970457 DOI: 10.1681/asn.2021050680] [Citation(s) in RCA: 28] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2021] [Accepted: 01/19/2022] [Indexed: 12/12/2022] Open
Abstract
INTRODUCTION CKD is associated with alterations of tubular function. Renal gluconeogenesis is responsible for 40% of systemic gluconeogenesis during fasting, but how and why CKD affects this process and the repercussions of such regulation are unknown. METHODS We used data on the renal gluconeogenic pathway from more than 200 renal biopsies performed on CKD patients and from 43 kidney allograft patients, and studied three mouse models, of proteinuric CKD (POD-ATTAC), of ischemic CKD, and of unilateral urinary tract obstruction. We analyzed a cohort of patients who benefitted from renal catheterization and a retrospective cohort of patients hospitalized in the intensive care unit. RESULTS Renal biopsies of CKD and kidney allograft patients revealed a stage-dependent decrease in the renal gluconeogenic pathway. Two animal models of CKD and one model of kidney fibrosis confirm gluconeogenic downregulation in injured proximal tubule cells. This shift resulted in an alteration of renal glucose production and lactate clearance during an exogenous lactate load. The isolated perfused kidney technique in animal models and renal venous catheterization in CKD patients confirmed decreased renal glucose production and lactate clearance. In CKD patients hospitalized in the intensive care unit, systemic alterations of glucose and lactate levels were more prevalent and associated with increased mortality and a worse renal prognosis at follow-up. Decreased expression of the gluconeogenesis pathway and its regulators predicted faster histologic progression of kidney disease in kidney allograft biopsies. CONCLUSION Renal gluconeogenic function is impaired in CKD. Altered renal gluconeogenesis leads to systemic metabolic changes with a decrease in glucose and increase in lactate level, and is associated with a worse renal prognosis.
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Affiliation(s)
- Thomas Verissimo
- Department of Medicine and Cell Physiology and Metabolism, University of Geneva, Geneva, Switzerland
| | - Anna Faivre
- Department of Medicine and Cell Physiology and Metabolism, University of Geneva, Geneva, Switzerland.,Service of Nephrology, Department of Medicine, Geneva University Hospitals, Geneva, Switzerland
| | - Anna Rinaldi
- Division of Nephrology, Ente Ospedaliero Cantonale, Lugano, Switzerland
| | - Maja Lindenmeyer
- III. Department of Medicine, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Vasiliki Delitsikou
- Department of Medicine and Cell Physiology and Metabolism, University of Geneva, Geneva, Switzerland
| | - Christelle Veyrat-Durebex
- Department of Medicine and Cell Physiology and Metabolism, University of Geneva, Geneva, Switzerland.,Diabetes Center, Faculty of Medicine, University of Geneva, Geneva, Switzerland
| | - Carolyn Heckenmeyer
- Department of Medicine and Cell Physiology and Metabolism, University of Geneva, Geneva, Switzerland
| | - Marylise Fernandez
- Department of Medicine and Cell Physiology and Metabolism, University of Geneva, Geneva, Switzerland
| | - Lena Berchtold
- Department of Medicine and Cell Physiology and Metabolism, University of Geneva, Geneva, Switzerland.,Service of Nephrology, Department of Medicine, Geneva University Hospitals, Geneva, Switzerland
| | - Delal Dalga
- Department of Medicine and Cell Physiology and Metabolism, University of Geneva, Geneva, Switzerland
| | - Clemens Cohen
- Nephrological Center, Medical Clinic and Polyclinic IV, University of Munich, Munich, Germany
| | - Maarten Naesens
- Department of Microbiology, Immunology and Transplantation, KU Leuven, Leuven, Belgium
| | - Sven-Erik Ricksten
- Department of Anesthesiology and Intensive Care, Sahlgrenska Academy, University of Gothenburg, Sahlgrenska University Hospital, Gothenburg, Sweden
| | - Pierre-Yves Martin
- Service of Nephrology, Department of Medicine, Geneva University Hospitals, Geneva, Switzerland
| | - Jérôme Pugin
- Division of Intensive Care, Department of Acute Medicine, Geneva University Hospitals, Geneva, Switzerland
| | - Franck Merlier
- Université de Technologie de Compiègne, CNRS Laboratory for Enzyme and Cell Engineering, Compiègne, France
| | - Karsten Haupt
- Université de Technologie de Compiègne, CNRS Laboratory for Enzyme and Cell Engineering, Compiègne, France
| | - Joseph M Rutkowski
- Department of Medical Physiology, Texas A&M University Health Science Center, Bryan, Texas
| | - Solange Moll
- Service of Clinical Pathology, Department of Pathology and Immunology, University Hospitals and University of Geneva, Geneva, Switzerland
| | - Pietro E Cippà
- Division of Nephrology, Ente Ospedaliero Cantonale, Lugano, Switzerland
| | - David Legouis
- Department of Medicine and Cell Physiology and Metabolism, University of Geneva, Geneva, Switzerland.,Division of Intensive Care, Department of Acute Medicine, Geneva University Hospitals, Geneva, Switzerland
| | - Sophie de Seigneux
- Department of Medicine and Cell Physiology and Metabolism, University of Geneva, Geneva, Switzerland .,Service of Nephrology, Department of Medicine, Geneva University Hospitals, Geneva, Switzerland
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Bell RMB, Conway BR. Macrophages in the kidney in health, injury and repair. INTERNATIONAL REVIEW OF CELL AND MOLECULAR BIOLOGY 2022; 367:101-147. [PMID: 35461656 DOI: 10.1016/bs.ircmb.2022.01.005] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Macrophages are a key component of the renal mononuclear phagocyte system, playing a major role in defense against infection, renal injury and repair. Yolk sac macrophage precursors seed the early embryonic kidney and are important for renal development. Later, renal macrophages are derived from hematopoietic stem cells and in adult life, there is a significant contribution from circulating monocytes, which is enhanced in response to infection or injury. Macrophages are highly plastic and can alter their phenotype in response to cues from parenchymal renal cells. Danger-associated molecules released from injured kidney cells may activate macrophages toward a pro-inflammatory phenotype, mediating further recruitment of inflammatory cells, exacerbating renal injury and activating renal fibroblasts to promote scarring. In acute kidney injury, once the injury stimulus has abated, macrophages may adopt a more reparative phenotype, dampening the immune response and promoting repair of renal tissue. However, in chronic kidney disease ongoing activation of pro-inflammatory monocytes and persistence of reparative macrophages leads to glomerulosclerosis and tubulointerstitial fibrosis, the hallmarks of end-stage kidney disease. Several strategies to inhibit the recruitment, activation and secretory products of pro-inflammatory macrophages have proven beneficial in pre-clinical models and are now undergoing clinical trials in patients with kidney disease. In addition, macrophages may be utilized in cell therapy as a "Trojan Horse" to deliver targeted therapies to the kidney. Single-cell RNA sequencing has identified a previously unappreciated spectrum of macrophage phenotypes, which may be selectively present in injury or repair, and ongoing functional analyses of these subsets may identify more specific targets for therapeutic intervention.
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Affiliation(s)
- Rachel M B Bell
- Centre for Cardiovascular Science, University of Edinburgh, Edinburgh, United Kingdom
| | - Bryan R Conway
- Centre for Cardiovascular Science, University of Edinburgh, Edinburgh, United Kingdom.
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76
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Abstract
The kidney maintains electrolyte, water, and acid-base balance, eliminates foreign and waste compounds, regulates blood pressure, and secretes hormones. There are at least 16 different highly specialized epithelial cell types in the mammalian kidney. The number of specialized endothelial cells, immune cells, and interstitial cell types might even be larger. The concerted interplay between different cell types is critical for kidney function. Traditionally, cells were defined by their function or microscopical morphological appearance. With the advent of new single-cell modalities such as transcriptomics, epigenetics, metabolomics, and proteomics we are entering into a new era of cell type definition. This new technological revolution provides new opportunities to classify cells in the kidney and understand their functions.
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Affiliation(s)
- Michael S Balzer
- Department of Medicine, Renal Electrolyte and Hypertension Division, University of Pennsylvania, Philadelphia, Pennsylvania, USA;
- Institute of Diabetes Obesity and Metabolism, University of Pennsylvania, Philadelphia, Philadelphia, USA
| | - Tibor Rohacs
- Department of Pharmacology, Physiology and Neuroscience, Rutgers New Jersey Medical School, Newark, New Jersey, USA
| | - Katalin Susztak
- Department of Medicine, Renal Electrolyte and Hypertension Division, University of Pennsylvania, Philadelphia, Pennsylvania, USA;
- Institute of Diabetes Obesity and Metabolism, University of Pennsylvania, Philadelphia, Philadelphia, USA
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77
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The Therapeutic Potential of Zinc-Alpha2-Glycoprotein (AZGP1) in Fibrotic Kidney Disease. Int J Mol Sci 2022; 23:ijms23020646. [PMID: 35054830 PMCID: PMC8775758 DOI: 10.3390/ijms23020646] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2021] [Revised: 01/04/2022] [Accepted: 01/06/2022] [Indexed: 11/30/2022] Open
Abstract
Chronic kidney disease (CKD) is characterized by a long-term loss of kidney function and, in most cases, by progressive fibrosis. Zinc-alpha2-glycoprotein (AZGP1) is a secreted protein, which is expressed in many different tissues and has been associated with a variety of functions. In a previous study, we have shown in cell culture and in AZGP1 deficient mice that AZGP1 has protective anti-fibrotic effects. In the present study, we tested the therapeutic potential of an experimental increase in AZGP1 using two different strategies. (1) C57Bl/6J mice were treated systemically with recombinant AZGP1, and (2) a transgenic mouse strain was generated to overexpress AZGP1 conditionally in proximal tubular cells. Mice underwent unilateral uretic obstruction as a pro-fibrotic kidney stress model, and kidneys were examined after 14 days. Recombinant AZGP1 treatment was accompanied by better preservation of tubular integrity, reduced collagen deposition, and lower expression of injury and fibrosis markers. Weaker but similar tendencies were observed in transgenic AZGP1 overexpressing mice. Higher AZGP1 levels led to a significant reduction in stress-induced accumulation of tubular lipid droplets, which was paralleled by improved expression of key players in lipid metabolism and fatty acid oxidation. Together these data show beneficial effects of elevated AZGP1 levels in fibrotic kidney disease and highlight a novel link to tubular cell lipid metabolism, which might open up new opportunities for CKD treatment.
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Piret SE, Attallah AA, Gu X, Guo Y, Gujarati NA, Henein J, Zollman A, Hato T, Ma'ayan A, Revelo MP, Dickman KG, Chen CH, Shun CT, Rosenquist TA, He JC, Mallipattu SK. Loss of proximal tubular transcription factor Krüppel-like factor 15 exacerbates kidney injury through loss of fatty acid oxidation. Kidney Int 2021; 100:1250-1267. [PMID: 34634362 PMCID: PMC8608748 DOI: 10.1016/j.kint.2021.08.031] [Citation(s) in RCA: 32] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2021] [Revised: 08/06/2021] [Accepted: 08/20/2021] [Indexed: 11/24/2022]
Abstract
Loss of fatty acid β-oxidation (FAO) in the proximal tubule is a critical mediator of acute kidney injury and eventual fibrosis. However, transcriptional mediators of FAO in proximal tubule injury remain understudied. Krüppel-like factor 15 (KLF15), a highly enriched zinc-finger transcription factor in the proximal tubule, was significantly reduced in proximal tubule cells after aristolochic acid I (AAI) treatment, a proximal tubule-specific injury model. Proximal tubule specific knockout of Klf15 exacerbated proximal tubule injury and kidney function decline compared to control mice during the active phase of AAI treatment, and after ischemia-reperfusion injury. Furthermore, along with worsening proximal tubule injury and kidney function decline, knockout mice exhibited increased kidney fibrosis as compared to control mice during the remodeling phase after AAI treatment. RNA-sequencing of kidney cortex demonstrated increased transcripts involved in immune system and integrin signaling pathways and decreased transcripts encompassing metabolic pathways, specifically FAO, and PPARα signaling, in knockout versus control mice after AAI treatment. In silico and experimental chromatin immunoprecipitation studies collectively demonstrated that KLF15 occupied the promoter region of key FAO genes, CPT1A and ACAA2, in close proximity to transcription factor PPARα binding sites. While the loss of Klf15 reduced the expression of Cpt1a and Acaa2 and led to compromised FAO, induction of KLF15 partially rescued loss of FAO in AAI-treated cells. Klf15, Ppara, Cpt1a, and Acaa2 expression was also decreased in other mouse kidney injury models. Tubulointerstitial KLF15 independently correlated with eGFR, PPARA and CPT1A appearance in expression arrays from human kidney biopsies. Thus, proximal tubule-specific loss of Klf15 exacerbates acute kidney injury and fibrosis, likely due to loss of interaction with PPARα leading to loss of FAO gene transcription.
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Affiliation(s)
- Sian E Piret
- Division of Nephrology, Department of Medicine, Stony Brook University, Stony Brook, New York, USA
| | - Ahmed A Attallah
- Division of Nephrology, Department of Medicine, Stony Brook University, Stony Brook, New York, USA
| | - Xiangchen Gu
- Division of Nephrology, Department of Medicine, Stony Brook University, Stony Brook, New York, USA; Department of Nephrology, Yueyang Hospital of Integrated Traditional Chinese and Western Medicine, Shanghai, China
| | - Yiqing Guo
- Division of Nephrology, Department of Medicine, Stony Brook University, Stony Brook, New York, USA
| | - Nehaben A Gujarati
- Division of Nephrology, Department of Medicine, Stony Brook University, Stony Brook, New York, USA
| | - Justina Henein
- Division of Nephrology, Department of Medicine, Stony Brook University, Stony Brook, New York, USA
| | - Amy Zollman
- Department of Medicine, Indiana University, Indianapolis, Indiana, USA
| | - Takashi Hato
- Department of Medicine, Indiana University, Indianapolis, Indiana, USA
| | - Avi Ma'ayan
- Department of Pharmacological Sciences, Mount Sinai Center for Bioinformatics, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Monica P Revelo
- Department of Pathology, University of Utah, Salt Lake City, Utah, USA
| | - Kathleen G Dickman
- Department of Pharmacological Sciences, Stony Brook University, Stony Brook, New York, USA
| | - Chung-Hsin Chen
- Department of Urology, National Taiwan University Hospital, Taipei, Taiwan
| | - Chia-Tung Shun
- Department of Forensic Medicine and Pathology, National Taiwan University Hospital, Taipei, Taiwan
| | - Thomas A Rosenquist
- Department of Pharmacological Sciences, Stony Brook University, Stony Brook, New York, USA
| | - John C He
- Department of Pharmacological Sciences, Mount Sinai Center for Bioinformatics, Icahn School of Medicine at Mount Sinai, New York, New York, USA; Division of Nephrology, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Sandeep K Mallipattu
- Division of Nephrology, Department of Medicine, Stony Brook University, Stony Brook, New York, USA; Renal Division, Northport VA Medical Center, Northport, New York, USA.
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Gerhardt LMS, McMahon AP. Multi-omic approaches to acute kidney injury and repair. CURRENT OPINION IN BIOMEDICAL ENGINEERING 2021; 20:100344. [PMID: 35005326 PMCID: PMC8740908 DOI: 10.1016/j.cobme.2021.100344] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Abstract
The kidney has a remarkable regenerative capacity. In response to ischemic or toxic injury, proximal tubule cells can proliferate to rebuild damaged tubules and restore kidney function. However, severe acute kidney injury (AKI) or recurrent AKI events can lead to maladaptive repair and disease progression from AKI to chronic kidney disease (CKD). The application of single cell technologies has identified injured proximal tubule cell states weeks after AKI, distinguished by a pro-inflammatory senescent molecular signature. Epigenetic studies highlighted dynamic changes in the chromatin landscape of the kidney following AKI and described key transcription factors linked to the AKI response. The integration of multi-omic technologies opens new possibilities to improve our understanding of AKI and the driving forces behind the AKI-to-CKD transition, with the ultimate goal of designing tailored diagnostic and therapeutic strategies to improve AKI outcomes and prevent kidney disease progression.
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Affiliation(s)
- Louisa M. S. Gerhardt
- Department of Stem Cell Biology and Regenerative Medicine, Eli and Edythe Broad Center for Regenerative Medicine and Stem Cell Research, Keck School of Medicine of the University of Southern California, Los Angeles, CA 90033, USA
| | - Andrew P. McMahon
- Department of Stem Cell Biology and Regenerative Medicine, Eli and Edythe Broad Center for Regenerative Medicine and Stem Cell Research, Keck School of Medicine of the University of Southern California, Los Angeles, CA 90033, USA
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80
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Pou Casellas C, Rookmaaker MB, Verhaar MC. Controlling cellular plasticity to improve in vitro models for kidney regeneration. CURRENT OPINION IN BIOMEDICAL ENGINEERING 2021. [DOI: 10.1016/j.cobme.2021.100345] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
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81
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Human induced pluripotent stem cell-derived kidney organoids toward clinical implementations. CURRENT OPINION IN BIOMEDICAL ENGINEERING 2021. [DOI: 10.1016/j.cobme.2021.100346] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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Bell RM, Denby L. Myeloid Heterogeneity in Kidney Disease as Revealed through Single-Cell RNA Sequencing. KIDNEY360 2021; 2:1844-1851. [PMID: 35372996 PMCID: PMC8785845 DOI: 10.34067/kid.0003682021] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/02/2021] [Accepted: 08/27/2021] [Indexed: 02/04/2023]
Abstract
Kidney disease represents a global health burden of increasing prevalence and is an independent risk factor for cardiovascular disease. Myeloid cells are a major cellular compartment of the immune system; they are found in the healthy kidney and in increased numbers in the damaged and/or diseased kidney, where they act as key players in the progression of injury, inflammation, and fibrosis. They possess enormous plasticity and heterogeneity, adopting different phenotypic and functional characteristics in response to stimuli in the local milieu. Although this inherent complexity remains to be fully understood in the kidney, advances in single-cell genomics promise to change this. Specifically, single-cell RNA sequencing (scRNA-seq) has had a transformative effect on kidney research, enabling the profiling and analysis of the transcriptomes of single cells at unprecedented resolution and throughput, and subsequent generation of cell atlases. Moving forward, combining scRNA- and single-nuclear RNA-seq with greater-resolution spatial transcriptomics will allow spatial mapping of kidney disease of varying etiology to further reveal the patterning of immune cells and nonimmune renal cells. This review summarizes the roles of myeloid cells in kidney health and disease, the experimental workflow in currently available scRNA-seq technologies, and published findings using scRNA-seq in the context of myeloid cells and the kidney.
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Affiliation(s)
- Rachel M.B. Bell
- Centre for Cardiovascular Science, Queen’s Medical Research Institute, University of Edinburgh, Edinburgh, United Kingdom
| | - Laura Denby
- Centre for Cardiovascular Science, Queen’s Medical Research Institute, University of Edinburgh, Edinburgh, United Kingdom
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Hu X, Ono M, Chimge NO, Chosa K, Nguyen C, Melendez E, Lou CH, Lim P, Termini J, Lai KKY, Fueger PT, Teo JL, Higuchi Y, Kahn M. Differential Kat3 Usage Orchestrates the Integration of Cellular Metabolism with Differentiation. Cancers (Basel) 2021; 13:cancers13235884. [PMID: 34884992 PMCID: PMC8656857 DOI: 10.3390/cancers13235884] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2021] [Revised: 11/12/2021] [Accepted: 11/19/2021] [Indexed: 11/29/2022] Open
Abstract
Simple Summary The coupling of metabolism with cellular status is critically important and highly evolutionarily conserved. However, how cells coordinate metabolism with transcription as they change their status is not clear. Utilizing multiomic and functional studies, we now demonstrate the dichotomous roles of the Kat3 coactivators CBP and p300 and, in particular, their extreme N-termini, in coordinating cellular metabolism with cell differentiation. Using multiple in vitro and in vivo systems, our study sheds new light on metabolic regulation in homeostasis and disease, including cancer. Abstract The integration of cellular status with metabolism is critically important and the coupling of energy production and cellular function is highly evolutionarily conserved. This has been demonstrated in stem cell biology, organismal, cellular and tissue differentiation and in immune cell biology. However, a molecular mechanism delineating how cells coordinate and couple metabolism with transcription as they navigate quiescence, growth, proliferation, differentiation and migration remains in its infancy. The extreme N-termini of the Kat3 coactivator family members, CBP and p300, by far the least homologous regions with only 66% identity, interact with members of the nuclear receptor family, interferon activated Stat1 and transcriptionally competent β-catenin, a critical component of the Wnt signaling pathway. We now wish to report based on multiomic and functional investigations, utilizing p300 knockdown, N-terminal p300 edited and p300 S89A edited cell lines and p300 S89A knockin mice, that the N-termini of the Kat3 coactivators provide a highly evolutionarily conserved hub to integrate multiple signaling cascades to coordinate cellular metabolism with the regulation of cellular status and function.
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Affiliation(s)
- Xiaohui Hu
- Department of Pathology, School of Basic Medical Sciences, Anhui Medical University, Hefei 230032, China;
- Department of Molecular Medicine, Beckman Research Institute of City of Hope, Duarte, CA 91010, USA; (N.-O.C.); (K.C.); (C.N.); (E.M.); (P.L.); (J.T.); (K.K.Y.L.); (J.-L.T.); (Y.H.)
| | - Masaya Ono
- Department of Clinical Proteomics, National Cancer Center Research Institute, Tokyo 104-0045, Japan;
| | - Nyam-Osor Chimge
- Department of Molecular Medicine, Beckman Research Institute of City of Hope, Duarte, CA 91010, USA; (N.-O.C.); (K.C.); (C.N.); (E.M.); (P.L.); (J.T.); (K.K.Y.L.); (J.-L.T.); (Y.H.)
| | - Keisuke Chosa
- Department of Molecular Medicine, Beckman Research Institute of City of Hope, Duarte, CA 91010, USA; (N.-O.C.); (K.C.); (C.N.); (E.M.); (P.L.); (J.T.); (K.K.Y.L.); (J.-L.T.); (Y.H.)
| | - Cu Nguyen
- Department of Molecular Medicine, Beckman Research Institute of City of Hope, Duarte, CA 91010, USA; (N.-O.C.); (K.C.); (C.N.); (E.M.); (P.L.); (J.T.); (K.K.Y.L.); (J.-L.T.); (Y.H.)
| | - Elizabeth Melendez
- Department of Molecular Medicine, Beckman Research Institute of City of Hope, Duarte, CA 91010, USA; (N.-O.C.); (K.C.); (C.N.); (E.M.); (P.L.); (J.T.); (K.K.Y.L.); (J.-L.T.); (Y.H.)
| | - Chih-Hong Lou
- Gene Editing and Viral Vector Core, Beckman Research Institute of City of Hope, Duarte, CA 91010, USA;
- City of Hope Comprehensive Cancer Center, Duarte, CA 91010, USA;
| | - Punnajit Lim
- Department of Molecular Medicine, Beckman Research Institute of City of Hope, Duarte, CA 91010, USA; (N.-O.C.); (K.C.); (C.N.); (E.M.); (P.L.); (J.T.); (K.K.Y.L.); (J.-L.T.); (Y.H.)
| | - John Termini
- Department of Molecular Medicine, Beckman Research Institute of City of Hope, Duarte, CA 91010, USA; (N.-O.C.); (K.C.); (C.N.); (E.M.); (P.L.); (J.T.); (K.K.Y.L.); (J.-L.T.); (Y.H.)
- City of Hope Comprehensive Cancer Center, Duarte, CA 91010, USA;
| | - Keane K. Y. Lai
- Department of Molecular Medicine, Beckman Research Institute of City of Hope, Duarte, CA 91010, USA; (N.-O.C.); (K.C.); (C.N.); (E.M.); (P.L.); (J.T.); (K.K.Y.L.); (J.-L.T.); (Y.H.)
- City of Hope Comprehensive Cancer Center, Duarte, CA 91010, USA;
| | - Patrick T. Fueger
- City of Hope Comprehensive Cancer Center, Duarte, CA 91010, USA;
- Department of Molecular and Cellular Endocrinology, Beckman Research Institute of City of Hope, Duarte, CA 91010, USA
| | - Jia-Ling Teo
- Department of Molecular Medicine, Beckman Research Institute of City of Hope, Duarte, CA 91010, USA; (N.-O.C.); (K.C.); (C.N.); (E.M.); (P.L.); (J.T.); (K.K.Y.L.); (J.-L.T.); (Y.H.)
| | - Yusuke Higuchi
- Department of Molecular Medicine, Beckman Research Institute of City of Hope, Duarte, CA 91010, USA; (N.-O.C.); (K.C.); (C.N.); (E.M.); (P.L.); (J.T.); (K.K.Y.L.); (J.-L.T.); (Y.H.)
| | - Michael Kahn
- Department of Molecular Medicine, Beckman Research Institute of City of Hope, Duarte, CA 91010, USA; (N.-O.C.); (K.C.); (C.N.); (E.M.); (P.L.); (J.T.); (K.K.Y.L.); (J.-L.T.); (Y.H.)
- City of Hope Comprehensive Cancer Center, Duarte, CA 91010, USA;
- Correspondence:
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84
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Dissecting nephron morphogenesis using kidney organoids from human pluripotent stem cells. Curr Opin Genet Dev 2021; 72:22-29. [PMID: 34781071 DOI: 10.1016/j.gde.2021.10.002] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2021] [Revised: 10/05/2021] [Accepted: 10/17/2021] [Indexed: 11/21/2022]
Abstract
During kidney development the emergence of complex multicellular shapes such as the nephron (the functional unit of the kidney) rely on spatiotemporally coordinated developmental programs. These involve gene regulatory networks, signaling pathways and mechanical forces, that work in concert to shape and form the nephron(s). The generation of kidney organoids from human pluripotent stem cells now represent an unprecedented experimental set up to study these processes. Here we discuss the potential applications of kidney organoids to advance our knowledge of how mechanical forces and cell fate specification spatiotemporally interact to orchestrate nephron patterning and morphogenesis in humans. Progress in innovative techniques for quantifying and perturbing these processes in a controlled manner will be crucial. A mechanistic understanding of the multicellular dynamic processes occurring during nephrogenesis will pave the way to unveil new mechanisms of human kidney disease.
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85
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Miao Z, Humphreys BD, McMahon AP, Kim J. Multi-omics integration in the age of million single-cell data. Nat Rev Nephrol 2021; 17:710-724. [PMID: 34417589 PMCID: PMC9191639 DOI: 10.1038/s41581-021-00463-x] [Citation(s) in RCA: 74] [Impact Index Per Article: 24.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/25/2021] [Indexed: 02/06/2023]
Abstract
An explosion in single-cell technologies has revealed a previously underappreciated heterogeneity of cell types and novel cell-state associations with sex, disease, development and other processes. Starting with transcriptome analyses, single-cell techniques have extended to multi-omics approaches and now enable the simultaneous measurement of data modalities and spatial cellular context. Data are now available for millions of cells, for whole-genome measurements and for multiple modalities. Although analyses of such multimodal datasets have the potential to provide new insights into biological processes that cannot be inferred with a single mode of assay, the integration of very large, complex, multimodal data into biological models and mechanisms represents a considerable challenge. An understanding of the principles of data integration and visualization methods is required to determine what methods are best applied to a particular single-cell dataset. Each class of method has advantages and pitfalls in terms of its ability to achieve various biological goals, including cell-type classification, regulatory network modelling and biological process inference. In choosing a data integration strategy, consideration must be given to whether the multi-omics data are matched (that is, measured on the same cell) or unmatched (that is, measured on different cells) and, more importantly, the overall modelling and visualization goals of the integrated analysis.
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Affiliation(s)
- Zhen Miao
- Department of Biology, University of Pennsylvania, Philadelphia, PA, USA
- Graduate Group in Genomics and Computational Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Benjamin D Humphreys
- Division of Nephrology, Department of Medicine, Washington University in St. Louis, St. Louis, MO, USA
| | - Andrew P McMahon
- Department of Stem Cell Biology and Regenerative Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Junhyong Kim
- Department of Biology, University of Pennsylvania, Philadelphia, PA, USA.
- Graduate Group in Genomics and Computational Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA.
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86
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Hwang S, Chung KW. Targeting fatty acid metabolism for fibrotic disorders. Arch Pharm Res 2021; 44:839-856. [PMID: 34664210 DOI: 10.1007/s12272-021-01352-4] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2021] [Accepted: 10/11/2021] [Indexed: 02/06/2023]
Abstract
Fibrosis is defined by abnormal accumulation of extracellular matrix, which can affect virtually every organ system under diseased conditions. Fibrotic tissue remodeling often leads to organ dysfunction and is highly associated with increased morbidity and mortality. The disease burden caused by fibrosis is substantial, and the medical need for effective antifibrotic therapies is essential. Significant progress has been made in understanding the molecular mechanism and pathobiology of fibrosis, such as transforming growth factor-β (TGF-β)-mediated signaling pathways. However, owing to the complex and dynamic properties of fibrotic disorders, there are currently no therapeutic options that can prevent or reverse fibrosis. Recent studies have revealed that alterations in fatty acid metabolic processes are common mechanisms and core pathways that play a central role in different fibrotic disorders. Excessive lipid accumulation or defective fatty acid oxidation is associated with increased lipotoxicity, which directly contributes to the development of fibrosis. Genetic alterations or pharmacologic targeting of fatty acid metabolic processes have great potential for the inhibition of fibrosis development. Furthermore, mechanistic studies have revealed active interactions between altered metabolic processes and fibrosis development. Several well-known fibrotic factors change the lipid metabolic processes, while altered metabolic processes actively participate in fibrosis development. This review summarizes the recent evidence linking fatty acid metabolism and fibrosis, and provides new insights into the pathogenesis of fibrotic diseases for the development of drugs for fibrosis prevention and treatment.
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Affiliation(s)
- Seonghwan Hwang
- College of Pharmacy, Pusan National University, Busan, 46214, Republic of Korea
| | - Ki Wung Chung
- College of Pharmacy, Pusan National University, Busan, 46214, Republic of Korea.
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Bai Y, Kim JY, Bisunke B, Jayne LA, Silvaroli JA, Balzer MS, Gandhi M, Huang KM, Sander V, Prosek J, Cianciolo RE, Baker SD, Sparreboom A, Jhaveri KD, Susztak K, Bajwa A, Pabla NS. Kidney toxicity of the BRAF-kinase inhibitor vemurafenib is driven by off-target ferrochelatase inhibition. Kidney Int 2021; 100:1214-1226. [PMID: 34534550 DOI: 10.1016/j.kint.2021.08.022] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2021] [Revised: 07/21/2021] [Accepted: 08/13/2021] [Indexed: 12/29/2022]
Abstract
A multitude of disease and therapy related factors drive the frequent development of kidney disorders in cancer patients. Along with chemotherapy, the newer targeted therapeutics can also cause kidney dysfunction through on and off-target mechanisms. Interestingly, among the small molecule inhibitors approved for the treatment of cancers that harbor BRAF-kinase activating mutations, vemurafenib can trigger tubular damage and acute kidney injury. BRAF is a proto-oncogene involved in cell growth. To investigate the underlying mechanisms, we developed cell culture and mouse models of vemurafenib kidney toxicity. At clinically relevant concentrations vemurafenib induces cell-death in transformed and primary mouse and human kidney tubular epithelial cells. In mice, two weeks of daily vemurafenib treatment causes moderate acute kidney injury with histopathological characteristics of kidney tubular epithelial cells injury. Importantly, kidney tubular epithelial cell-specific BRAF gene deletion did not influence kidney function under normal conditions or alter the severity of vemurafenib-associated kidney impairment. Instead, we found that inhibition of ferrochelatase, an enzyme involved in heme biosynthesis contributes to vemurafenib kidney toxicity. Ferrochelatase overexpression protected kidney tubular epithelial cells and conversely ferrochelatase knockdown increased the sensitivity to vemurafenib-induced kidney toxicity. Thus, our studies suggest that vemurafenib-associated kidney tubular epithelial cell dysfunction and kidney toxicity is BRAF-independent and caused, in part, by off-target ferrochelatase inhibition.
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Affiliation(s)
- Yuntao Bai
- Division of Pharmaceutics and Pharmacology, College of Pharmacy and Comprehensive Cancer Center, The Ohio State University, Columbus, Ohio, USA
| | - Ji Young Kim
- Division of Pharmaceutics and Pharmacology, College of Pharmacy and Comprehensive Cancer Center, The Ohio State University, Columbus, Ohio, USA
| | - Bijay Bisunke
- Department of Genetics, Genomics, and Informatics, College of Medicine, The University of Tennessee Health Science Center, Memphis, Tennessee, USA
| | - Laura A Jayne
- Division of Pharmaceutics and Pharmacology, College of Pharmacy and Comprehensive Cancer Center, The Ohio State University, Columbus, Ohio, USA
| | - Josie A Silvaroli
- Division of Pharmaceutics and Pharmacology, College of Pharmacy and Comprehensive Cancer Center, The Ohio State University, Columbus, Ohio, USA
| | - Michael S Balzer
- Department of Medicine and Genetics, Renal Electrolyte and Hypertension Division, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Megha Gandhi
- Division of Pharmaceutics and Pharmacology, College of Pharmacy and Comprehensive Cancer Center, The Ohio State University, Columbus, Ohio, USA
| | - Kevin M Huang
- Division of Pharmaceutics and Pharmacology, College of Pharmacy and Comprehensive Cancer Center, The Ohio State University, Columbus, Ohio, USA
| | - Veronika Sander
- Department of Molecular Medicine and Pathology, University of Auckland, Auckland, New Zealand
| | - Jason Prosek
- Department of Internal Medicine, The Ohio State University Wexner Medical Center, Columbus, Ohio, USA
| | - Rachel E Cianciolo
- Department of Veterinary Biosciences, College of Veterinary Medicine, The Ohio State University, Columbus, Ohio, USA
| | - Sharyn D Baker
- Division of Pharmaceutics and Pharmacology, College of Pharmacy and Comprehensive Cancer Center, The Ohio State University, Columbus, Ohio, USA
| | - Alex Sparreboom
- Division of Pharmaceutics and Pharmacology, College of Pharmacy and Comprehensive Cancer Center, The Ohio State University, Columbus, Ohio, USA
| | - Kenar D Jhaveri
- Division of Kidney Diseases and Hypertension, Donald and Barbara Zucker School of Medicine at Hofstra-Northwell, Northwell Health, Great Neck, New York, USA
| | - Katalin Susztak
- Department of Medicine and Genetics, Renal Electrolyte and Hypertension Division, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Amandeep Bajwa
- Department of Genetics, Genomics, and Informatics, College of Medicine, The University of Tennessee Health Science Center, Memphis, Tennessee, USA; Department of Microbiology, Immunology, and Biochemistry, College of Medicine, The University of Tennessee Health Science Center, Memphis, Tennessee, USA; Transplant Research Institute, James D. Eason Transplant Institute, Department of Surgery, College of Medicine, The University of Tennessee Health Science Center, Memphis, Tennessee, USA
| | - Navjot Singh Pabla
- Division of Pharmaceutics and Pharmacology, College of Pharmacy and Comprehensive Cancer Center, The Ohio State University, Columbus, Ohio, USA.
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88
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Pou Casellas C, Jansen K, Rookmaaker MB, Clevers H, Verhaar MC, Masereeuw R. Regulation of Solute Carriers OCT2 and OAT1/3 in the Kidney: A Phylogenetic, Ontogenetic and Cell Dynamic Perspective. Physiol Rev 2021; 102:993-1024. [PMID: 34486394 DOI: 10.1152/physrev.00009.2021] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Over the course of more than 500 million years, the kidneys have undergone a remarkable evolution from primitive nephric tubes to intricate filtration-reabsorption systems that maintain homeostasis and remove metabolic end products from the body. The evolutionarily conserved solute carriers Organic Cation Transporter 2 (OCT2), and Organic Anion Transporters 1 and 3 (OAT1/3) coordinate the active secretion of a broad range of endogenous and exogenous substances, many of which accumulate in the blood of patients with kidney failure despite dialysis. Harnessing OCT2 and OAT1/3 through functional preservation or regeneration could alleviate the progression of kidney disease. Additionally, it would improve current in vitro test models that lose their expression in culture. With this review, we explore OCT2 and OAT1/3 regulation using different perspectives: phylogenetic, ontogenetic and cell dynamic. Our aim is to identify possible molecular targets to both help prevent or compensate for the loss of transport activity in patients with kidney disease, and to enable endogenous OCT2 and OAT1/3 induction in vitro in order to develop better models for drug development.
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Affiliation(s)
- Carla Pou Casellas
- Department of Nephrology and Hypertension, University Medical Center Utrecht, Utrecht, Netherlands.,Hubrecht Institute - Royal Netherlands Academy of Arts and Sciences, Utrecht, The Netherlands
| | - Katja Jansen
- Division of Pharmacology, Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Utrecht, The Netherlands
| | - Maarten B Rookmaaker
- Department of Nephrology and Hypertension, University Medical Center Utrecht, Utrecht, Netherlands
| | - Hans Clevers
- Hubrecht Institute - Royal Netherlands Academy of Arts and Sciences, Utrecht, The Netherlands
| | - Marianne C Verhaar
- Department of Nephrology and Hypertension, University Medical Center Utrecht, Utrecht, Netherlands
| | - Rosalinde Masereeuw
- Division of Pharmacology, Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Utrecht, The Netherlands
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89
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Sheng X, Guan Y, Ma Z, Wu J, Liu H, Qiu C, Vitale S, Miao Z, Seasock MJ, Palmer M, Shin MK, Duffin KL, Pullen SS, Edwards TL, Hellwege JN, Hung AM, Li M, Voight BF, Coffman TM, Brown CD, Susztak K. Mapping the genetic architecture of human traits to cell types in the kidney identifies mechanisms of disease and potential treatments. Nat Genet 2021; 53:1322-1333. [PMID: 34385711 PMCID: PMC9338440 DOI: 10.1038/s41588-021-00909-9] [Citation(s) in RCA: 79] [Impact Index Per Article: 26.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2020] [Accepted: 06/30/2021] [Indexed: 02/07/2023]
Abstract
The functional interpretation of genome-wide association studies (GWAS) is challenging due to the cell-type-dependent influences of genetic variants. Here, we generated comprehensive maps of expression quantitative trait loci (eQTLs) for 659 microdissected human kidney samples and identified cell-type-eQTLs by mapping interactions between cell type abundances and genotypes. By partitioning heritability using stratified linkage disequilibrium score regression to integrate GWAS with single-cell RNA sequencing and single-nucleus assay for transposase-accessible chromatin with high-throughput sequencing data, we prioritized proximal tubules for kidney function and endothelial cells and distal tubule segments for blood pressure pathogenesis. Bayesian colocalization analysis nominated more than 200 genes for kidney function and hypertension. Our study clarifies the mechanism of commonly used antihypertensive and renal-protective drugs and identifies drug repurposing opportunities for kidney disease.
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Affiliation(s)
- Xin Sheng
- 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
- Department of Genetics, University of Pennsylvania, Philadelphia, PA, USA
| | - Yuting Guan
- 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
- Department of Genetics, University of Pennsylvania, Philadelphia, PA, USA
| | - Ziyuan Ma
- 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
- Department of Genetics, University of Pennsylvania, Philadelphia, PA, USA
| | - Junnan Wu
- 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
- Department of Genetics, University of Pennsylvania, Philadelphia, PA, USA
| | - 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
- Department of Genetics, University of Pennsylvania, Philadelphia, PA, USA
| | - Chengxiang Qiu
- 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
- Department of Genetics, University of Pennsylvania, Philadelphia, PA, USA
| | - Steven Vitale
- 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
- Department of Genetics, University of Pennsylvania, Philadelphia, PA, USA
| | - Zhen Miao
- 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
- Department of Genetics, University of Pennsylvania, Philadelphia, PA, USA
| | - Matthew J Seasock
- 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
- Department of Genetics, University of Pennsylvania, Philadelphia, PA, USA
| | - Matthew Palmer
- Department of Pathology and Laboratory Medicine, Hospital of the University of Pennsylvania, Philadelphia, PA, USA
| | | | - Kevin L Duffin
- Eli Lilly and Company Lilly Corporate Center, Indianapolis, IN, USA
| | - Steven S Pullen
- Department of Cardiometabolic Diseases Research, Boehringer Ingelheim Pharmaceuticals, Ridgefield, CT, USA
| | - Todd L Edwards
- Division of Epidemiology, Department of Medicine, Vanderbilt Genetics Institute, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Jacklyn N Hellwege
- Division of Epidemiology, Department of Medicine, Vanderbilt Genetics Institute, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Adriana M Hung
- Division of Nephrology and Hypertension, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Mingyao Li
- Department of Epidemiology and Biostatistics, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | - Benjamin F Voight
- Institute of Diabetes, Obesity and Metabolism, University of Pennsylvania, Philadelphia, PA, USA
- Department of Genetics, University of Pennsylvania, Philadelphia, PA, USA
- Department of Systems Pharmacology and Translational Therapeutics, University of Pennsylvania, Philadelphia, PA, USA
- Institute of Translational Medicine and Therapeutics, University of Pennsylvania, Philadelphia, PA, USA
| | - Thomas M Coffman
- Cardiovascular and Metabolic Disorders Program, Duke-National University of Singapore Medical School, Singapore, Singapore
| | | | - 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.
- Department of Genetics, University of Pennsylvania, Philadelphia, PA, USA.
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90
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Kahn M. Taking the road less traveled - the therapeutic potential of CBP/β-catenin antagonists. Expert Opin Ther Targets 2021; 25:701-719. [PMID: 34633266 PMCID: PMC8745629 DOI: 10.1080/14728222.2021.1992386] [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: 10/06/2021] [Accepted: 10/08/2021] [Indexed: 10/20/2022]
Abstract
AREAS COVERED This perspective discusses the challenges of targeting the Wnt signaling cascade, the safety, efficacy, and therapeutic potential of specific CBP/β-catenin antagonists and a rationale for the pleiotropic effects of CBP/β-catenin antagonists beyond Wnt signaling. EXPERT OPINION CBP/β-catenin antagonists can correct lineage infidelity, enhance wound healing, both normal and aberrant (e.g. fibrosis) and force the differentiation and lineage commitment of stem cells and cancer stem cells by regulating enhancer and super-enhancer coactivator occupancy. Small molecule CBP/β-catenin antagonists rebalance the equilibrium between CBP/β-catenin versus p300/β-catenin dependent transcription and may be able to treat or prevent many diseases of aging, via maintenance of our somatic stem cell pool, and regulating mitochondrial function and metabolism involved in differentiation and immune cell function.
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Affiliation(s)
- Michael Kahn
- Department of Molecular Medicine, City of Hope, Beckman Research Institute, 1500 East Duarte Road Flower Building, Duarte, CA, USA
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91
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Yuan Q, Lv Y, Ding H, Ke Q, Shi C, Luo J, Jiang L, Yang J, Zhou Y. CPT1α maintains phenotype of tubules via mitochondrial respiration during kidney injury and repair. Cell Death Dis 2021; 12:792. [PMID: 34392303 PMCID: PMC8364553 DOI: 10.1038/s41419-021-04085-w] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2021] [Revised: 07/29/2021] [Accepted: 08/06/2021] [Indexed: 12/24/2022]
Abstract
Impaired energy metabolism in proximal tubular epithelial cells (PTECs) is strongly associated with various kidney diseases. Here, we characterized proximal tubular phenotype alternations during kidney injury and repair in a mouse model of folic acid nephropathy, in parallel, identified carnitine palmitoyltransferase 1α (CPT1α) as an energy stress response accompanied by renal tubular dedifferentiation. Genetic ablation of Cpt1α aggravated the tubular injury and interstitial fibrosis and hampered kidney repair indicate that CPT1α is vital for the preservation and recovery of tubular phenotype. Our data showed that the lipid accumulation and mitochondrial mass reduction induced by folic acid were persistent and became progressively more severe in PTECs without CPT1α. Interference of CPT1α reduced capacities of mitochondrial respiration and ATP production in PTECs, and further sensitized cells to folic acid-induced phenotypic changes. On the contrary, overexpression of CPT1α protected mitochondrial respiration and prevented against folic acid-induced tubular cell damage. These findings link CPT1α to intrinsic mechanisms regulating the mitochondrial respiration and phenotype of kidney tubules that may contribute to renal pathology during injury and repair.
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Affiliation(s)
- Qi Yuan
- Center for Kidney Disease, Second Affiliated Hospital of Nanjing Medical University, Nanjing, China
- Department of Nephrology, The Affiliated Suzhou Hospital of Nanjing Medical University, Suzhou Municipal Hospital, Gusu School, Nanjing Medical University, Suzhou, China
| | - Yunhui Lv
- Center for Kidney Disease, Second Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Hao Ding
- Center for Kidney Disease, Second Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Qingqing Ke
- Center for Kidney Disease, Second Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Caifeng Shi
- Center for Kidney Disease, Second Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Jing Luo
- Center for Kidney Disease, Second Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Lei Jiang
- Center for Kidney Disease, Second Affiliated Hospital of Nanjing Medical University, Nanjing, China.
| | - Junwei Yang
- Center for Kidney Disease, Second Affiliated Hospital of Nanjing Medical University, Nanjing, China.
| | - Yang Zhou
- Center for Kidney Disease, Second Affiliated Hospital of Nanjing Medical University, Nanjing, China.
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92
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Deleersnijder D, Callemeyn J, Arijs I, Naesens M, Van Craenenbroeck AH, Lambrechts D, Sprangers B. Current Methodological Challenges of Single-Cell and Single-Nucleus RNA-Sequencing in Glomerular Diseases. J Am Soc Nephrol 2021; 32:1838-1852. [PMID: 34140401 PMCID: PMC8455274 DOI: 10.1681/asn.2021020157] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023] Open
Abstract
Single-cell RNA sequencing (scRNA-seq) and single-nucleus RNA-seq (snRNA-seq) allow transcriptomic profiling of thousands of cells from a renal biopsy specimen at a single-cell resolution. Both methods are promising tools to unravel the underlying pathophysiology of glomerular diseases. This review provides an overview of the technical challenges that should be addressed when designing single-cell transcriptomics experiments that focus on glomerulopathies. The isolation of glomerular cells from core needle biopsy specimens for single-cell transcriptomics remains difficult and depends upon five major factors. First, core needle biopsies generate little tissue material, and several samples are required to identify glomerular cells. Second, both fresh and frozen tissue samples may yield glomerular cells, although every experimental pipeline has different (dis)advantages. Third, enrichment for glomerular cells in human tissue before single-cell analysis is challenging because no effective standardized pipelines are available. Fourth, the current warm cell-dissociation protocols may damage glomerular cells and induce transcriptional artifacts, which can be minimized by using cold dissociation techniques at the cost of less efficient cell dissociation. Finally, snRNA-seq methods may be superior to scRNA-seq in isolating glomerular cells; however, the efficacy of snRNA-seq on core needle biopsy specimens remains to be proven. The field of single-cell omics is rapidly evolving, and the integration of these techniques in multiomics assays will undoubtedly create new insights in the complex pathophysiology of glomerular diseases.
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Affiliation(s)
- Dries Deleersnijder
- Department of Microbiology, Immunology and Transplantation, Laboratory of Molecular Immunology, Rega Institute, KU Leuven, Leuven, Belgium
- Division of Nephrology, University Hospitals Leuven, Leuven, Belgium
| | - Jasper Callemeyn
- Division of Nephrology, University Hospitals Leuven, Leuven, Belgium
- Department of Microbiology, Immunology and Transplantation, Nephrology and Renal Transplantation Research Group, KU Leuven, Leuven, Belgium
| | - Ingrid Arijs
- Laboratory for Translational Genetics, Department of Human Genetics, KU Leuven, Leuven, Belgium
- Vlaams Instituut voor Biotechnologie Center for Cancer Biology, Leuven, Belgium
| | - Maarten Naesens
- Division of Nephrology, University Hospitals Leuven, Leuven, Belgium
- Department of Microbiology, Immunology and Transplantation, Nephrology and Renal Transplantation Research Group, KU Leuven, Leuven, Belgium
| | - Amaryllis H. Van Craenenbroeck
- Division of Nephrology, University Hospitals Leuven, Leuven, Belgium
- Department of Microbiology, Immunology and Transplantation, Nephrology and Renal Transplantation Research Group, KU Leuven, Leuven, Belgium
| | - Diether Lambrechts
- Laboratory for Translational Genetics, Department of Human Genetics, KU Leuven, Leuven, Belgium
- Vlaams Instituut voor Biotechnologie Center for Cancer Biology, Leuven, Belgium
| | - Ben Sprangers
- Department of Microbiology, Immunology and Transplantation, Laboratory of Molecular Immunology, Rega Institute, KU Leuven, Leuven, Belgium
- Division of Nephrology, University Hospitals Leuven, Leuven, Belgium
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93
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Ranea-Robles P, Portman K, Bender A, Lee K, He JC, Mulholland DJ, Argmann C, Houten SM. Peroxisomal L-bifunctional protein (EHHADH) deficiency causes male-specific kidney hypertrophy and proximal tubular injury in mice. KIDNEY360 2021; 2:1441-1454. [PMID: 34651140 PMCID: PMC8513500 DOI: 10.34067/kid.0003772021] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
BACKGROUND Proximal tubular (PT) cells are enriched in mitochondria and peroxisomes. Whereas mitochondrial fatty acid oxidation (FAO) plays an important role in kidney function by supporting the high-energy requirements of PT cells, the role of peroxisomal metabolism remains largely unknown. EHHADH, also known as L-bifunctional protein, catalyzes the second and third step of peroxisomal FAO. METHODS We studied kidneys of WT and Ehhadh KO mice on a C57BL/6N background using histology, immunohistochemistry, immunofluorescence, immunoblot, RNA-sequencing, and metabolomics. To assess the role of androgens in the kidney phenotype of Ehhadh KO mice, mice underwent orchiectomy. RESULTS We observed male-specific kidney hypertrophy and glomerular filtration rate reduction in adult Ehhadh KO mice. Transcriptome analysis unveiled a gene expression signature similar to PT injury in acute kidney injury mouse models. This was further illustrated by the presence of KIM-1 (kidney injury molecule-1), SOX-9, and Ki67-positive cells in the PT of male Ehhadh KO kidneys. Male Ehhadh KO kidneys had metabolite changes consistent with peroxisomal dysfunction as well as an elevation in glycosphingolipid levels. Orchiectomy of Ehhadh KO mice decreased the number of KIM-1 positive cells to WT levels. We revealed a pronounced sexual dimorphism in the expression of peroxisomal FAO proteins in mouse kidney, underlining a role of androgens in the kidney phenotype of Ehhadh KO mice. CONCLUSIONS Our data highlight the importance of EHHADH and peroxisomal metabolism in male kidney physiology and reveal peroxisomal FAO as a sexual dimorphic metabolic pathway in mouse kidneys.
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Affiliation(s)
- Pablo Ranea-Robles
- Department of Genetics and Genomic Sciences, Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Kensey Portman
- Division of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Aaron Bender
- Department of Genetics and Genomic Sciences, Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Kyung Lee
- Department of Medicine, Division of Nephrology, Icahn School of Medicine at Mount Sinai, New York, New York
| | - John Cijiang He
- Department of Medicine, Division of Nephrology, Icahn School of Medicine at Mount Sinai, New York, New York
| | - David J. Mulholland
- Division of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Carmen Argmann
- Department of Genetics and Genomic Sciences, Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Sander M. Houten
- Department of Genetics and Genomic Sciences, Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, New York, New York
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94
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Nicholson RJ, Ramkumar N, Summers SA. Gain of 'FAOnction', Loss of Fibrosis. Trends Endocrinol Metab 2021; 32:333-334. [PMID: 33773899 PMCID: PMC8947942 DOI: 10.1016/j.tem.2021.03.005] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/06/2021] [Accepted: 03/16/2021] [Indexed: 11/22/2022]
Abstract
Recent research by Miguel et al. and Dhillon et al. reveals associations between impaired lipid metabolism and kidney fibrosis. Kidney tubule fatty acid oxidation (FAO) gain-of-function in mouse models of kidney disease stimulated cellular respiration, mitochondrial dynamics, and tubular epithelial cell (TEC) differentiation, while upregulation of FAO in kidney tubules provided protection from kidney fibrosis and functional decline.
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Affiliation(s)
- Rebekah J Nicholson
- Department of Nutrition and Integrative Physiology, University of Utah, Salt Lake City, UT, USA
| | - Nirupama Ramkumar
- Division of Nephrology and Hypertension, University of Utah Health Center, Salt Lake City, UT, USA
| | - Scott A Summers
- Department of Nutrition and Integrative Physiology, University of Utah, Salt Lake City, UT, USA.
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95
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Balzer MS, Ma Z, Zhou J, Abedini A, Susztak K. How to Get Started with Single Cell RNA Sequencing Data Analysis. J Am Soc Nephrol 2021; 32:1279-1292. [PMID: 33722930 PMCID: PMC8259643 DOI: 10.1681/asn.2020121742] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023] Open
Abstract
Over the last 5 years, single cell methods have enabled the monitoring of gene and protein expression, genetic, and epigenetic changes in thousands of individual cells in a single experiment. With the improved measurement and the decreasing cost of the reactions and sequencing, the size of these datasets is increasing rapidly. The critical bottleneck remains the analysis of the wealth of information generated by single cell experiments. In this review, we give a simplified overview of the analysis pipelines, as they are typically used in the field today. We aim to enable researchers starting out in single cell analysis to gain an overview of challenges and the most commonly used analytical tools. In addition, we hope to empower others to gain an understanding of how typical readouts from single cell datasets are presented in the published literature.
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Affiliation(s)
- Michael S. Balzer
- Renal Electrolyte and Hypertension Division, Department of Medicine, University of Pennsylvania, Perelman School of Medicine, Philadelphia, Pennsylvania,Department of Genetics, University of Pennsylvania, Perelman School of Medicine, Philadelphia, Pennsylvania,Institute for Diabetes, Obesity and Metabolism, University of Pennsylvania, Perelman School of Medicine, Philadelphia, Pennsylvania
| | - Ziyuan Ma
- Renal Electrolyte and Hypertension Division, Department of Medicine, University of Pennsylvania, Perelman School of Medicine, Philadelphia, Pennsylvania,Department of Genetics, University of Pennsylvania, Perelman School of Medicine, Philadelphia, Pennsylvania,Institute for Diabetes, Obesity and Metabolism, University of Pennsylvania, Perelman School of Medicine, Philadelphia, Pennsylvania
| | - Jianfu Zhou
- Renal Electrolyte and Hypertension Division, Department of Medicine, University of Pennsylvania, Perelman School of Medicine, Philadelphia, Pennsylvania,Department of Genetics, University of Pennsylvania, Perelman School of Medicine, Philadelphia, Pennsylvania,Institute for Diabetes, Obesity and Metabolism, University of Pennsylvania, Perelman School of Medicine, Philadelphia, Pennsylvania
| | - Amin Abedini
- Renal Electrolyte and Hypertension Division, Department of Medicine, University of Pennsylvania, Perelman School of Medicine, Philadelphia, Pennsylvania,Department of Genetics, University of Pennsylvania, Perelman School of Medicine, Philadelphia, Pennsylvania,Institute for Diabetes, Obesity and Metabolism, University of Pennsylvania, Perelman School of Medicine, Philadelphia, Pennsylvania
| | - Katalin Susztak
- Renal Electrolyte and Hypertension Division, Department of Medicine, University of Pennsylvania, Perelman School of Medicine, Philadelphia, Pennsylvania,Department of Genetics, University of Pennsylvania, Perelman School of Medicine, Philadelphia, Pennsylvania,Institute for Diabetes, Obesity and Metabolism, University of Pennsylvania, Perelman School of Medicine, Philadelphia, Pennsylvania
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96
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Hasegawa S, Inagi R. Harnessing Metabolomics to Describe the Pathophysiology Underlying Progression in Diabetic Kidney Disease. Curr Diab Rep 2021; 21:21. [PMID: 33974145 PMCID: PMC8113300 DOI: 10.1007/s11892-021-01390-8] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 04/27/2021] [Indexed: 02/06/2023]
Abstract
PURPOSE OF REVIEW Diabetic kidney disease (DKD), a leading cause of end-stage kidney disease, is the result of metabolic network alterations in the kidney. Therefore, metabolomics is an effective tool for understanding its pathophysiology, finding key biomarkers, and developing a new treatment strategy. In this review, we summarize the application of metabolomics to DKD research. RECENT FINDINGS Alterations in renal energy metabolism including the accumulation of tricarboxylic acid cycle and glucose metabolites are observed in the early stage of DKD, and they finally lead to mitochondrial dysfunction in advanced DKD. Mitochondrial fission-fusion imbalance and dysregulated organelle crosstalk might contribute to this process. Moreover, metabolomics has identified several uremic toxins including phenyl sulfate and tryptophan derivatives as promising biomarkers that mediate DKD progression. Recent advances in metabolomics have clarified the role of dysregulated energy metabolism and uremic toxins in DKD pathophysiology. Integration of multi-omics data will provide additional information for identifying critical drivers of DKD.
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Affiliation(s)
- Sho Hasegawa
- Division of Chronic Kidney Disease Pathophysiology, The University of Tokyo Graduate School of Medicine, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-8655 Japan
- Division of Nephrology and Endocrinology, The University of Tokyo Graduate School of Medicine, Tokyo, Japan
| | - Reiko Inagi
- Division of Chronic Kidney Disease Pathophysiology, The University of Tokyo Graduate School of Medicine, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-8655 Japan
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97
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Miao Z, Balzer MS, Ma Z, Liu H, Wu J, Shrestha R, Aranyi T, Kwan A, Kondo A, Pontoglio M, Kim J, Li M, Kaestner KH, Susztak K. Single cell regulatory landscape of the mouse kidney highlights cellular differentiation programs and disease targets. Nat Commun 2021; 12:2277. [PMID: 33859189 PMCID: PMC8050063 DOI: 10.1038/s41467-021-22266-1] [Citation(s) in RCA: 118] [Impact Index Per Article: 39.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2020] [Accepted: 02/28/2021] [Indexed: 12/19/2022] Open
Abstract
Determining the epigenetic program that generates unique cell types in the kidney is critical for understanding cell-type heterogeneity during tissue homeostasis and injury response. Here, we profile open chromatin and gene expression in developing and adult mouse kidneys at single cell resolution. We show critical reliance of gene expression on distal regulatory elements (enhancers). We reveal key cell type-specific transcription factors and major gene-regulatory circuits for kidney cells. Dynamic chromatin and expression changes during nephron progenitor differentiation demonstrates that podocyte commitment occurs early and is associated with sustained Foxl1 expression. Renal tubule cells follow a more complex differentiation, where Hfn4a is associated with proximal and Tfap2b with distal fate. Mapping single nucleotide variants associated with human kidney disease implicates critical cell types, developmental stages, genes, and regulatory mechanisms. The single cell multi-omics atlas reveals key chromatin remodeling events and gene expression dynamics associated with kidney development.
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Affiliation(s)
- Zhen Miao
- Renal, Electrolyte, and Hypertension Division, Department of Medicine, University of Pennsylvania, Perelman School of Medicine, Philadelphia, PA, USA
- Institute for Diabetes, Obesity, and Metabolism, University of Pennsylvania, Perelman School of Medicine, Philadelphia, PA, USA
- Graduate Group in Genomics and Computational Biology, University of Pennsylvania, Perelman School of Medicine, Philadelphia, PA, USA
| | - Michael S Balzer
- Renal, Electrolyte, and Hypertension Division, Department of Medicine, University of Pennsylvania, Perelman School of Medicine, Philadelphia, PA, USA
- Institute for Diabetes, Obesity, and Metabolism, University of Pennsylvania, Perelman School of Medicine, Philadelphia, PA, USA
| | - Ziyuan Ma
- Renal, Electrolyte, and Hypertension Division, Department of Medicine, University of Pennsylvania, Perelman School of Medicine, Philadelphia, PA, USA
- Institute for Diabetes, Obesity, and Metabolism, University of Pennsylvania, Perelman School of Medicine, Philadelphia, PA, USA
| | - Hongbo Liu
- Renal, Electrolyte, and Hypertension Division, Department of Medicine, University of Pennsylvania, Perelman School of Medicine, Philadelphia, PA, USA
- Institute for Diabetes, Obesity, and Metabolism, University of Pennsylvania, Perelman School of Medicine, Philadelphia, PA, USA
| | - Junnan Wu
- Renal, Electrolyte, and Hypertension Division, Department of Medicine, University of Pennsylvania, Perelman School of Medicine, Philadelphia, PA, USA
- Institute for Diabetes, Obesity, and Metabolism, University of Pennsylvania, Perelman School of Medicine, Philadelphia, PA, USA
| | - Rojesh Shrestha
- Renal, Electrolyte, and Hypertension Division, Department of Medicine, University of Pennsylvania, Perelman School of Medicine, Philadelphia, PA, USA
- Institute for Diabetes, Obesity, and Metabolism, University of Pennsylvania, Perelman School of Medicine, Philadelphia, PA, USA
| | - Tamas Aranyi
- Renal, Electrolyte, and Hypertension Division, Department of Medicine, University of Pennsylvania, Perelman School of Medicine, Philadelphia, PA, USA
- Institute for Diabetes, Obesity, and Metabolism, University of Pennsylvania, Perelman School of Medicine, Philadelphia, PA, USA
| | - Amy Kwan
- Department of Genetics, University of Pennsylvania, Perelman School of Medicine, Philadelphia, PA, USA
| | - Ayano Kondo
- Department of Genetics, University of Pennsylvania, Perelman School of Medicine, Philadelphia, PA, USA
| | - Marco Pontoglio
- Epigenetics and Development Laboratory, Université de Paris Inserm U1151/CNRS UMR 8253, Institut Necker Enfants Malades, Paris, France
| | - Junhyong Kim
- Department of Biology, University of Pennsylvania, Philadelphia, PA, USA
| | - Mingyao Li
- Department of Epidemiology and Biostatistics, University of Pennsylvania, Perelman School of Medicine, Philadelphia, PA, USA
| | - Klaus H Kaestner
- Institute for Diabetes, Obesity, and Metabolism, University of Pennsylvania, Perelman School of Medicine, Philadelphia, PA, USA
- Department of Genetics, University of Pennsylvania, Perelman School of Medicine, Philadelphia, PA, USA
| | - Katalin Susztak
- Renal, Electrolyte, and Hypertension Division, Department of Medicine, University of Pennsylvania, Perelman School of Medicine, Philadelphia, PA, USA.
- Institute for Diabetes, Obesity, and Metabolism, University of Pennsylvania, Perelman School of Medicine, Philadelphia, PA, USA.
- Department of Genetics, University of Pennsylvania, Perelman School of Medicine, Philadelphia, PA, USA.
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