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Cao J, Li C, Cui Z, Deng S, Lei T, Liu W, Yang H, Chen P. Spatial Transcriptomics: A Powerful Tool in Disease Understanding and Drug Discovery. Theranostics 2024; 14:2946-2968. [PMID: 38773973 PMCID: PMC11103497 DOI: 10.7150/thno.95908] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2024] [Accepted: 04/25/2024] [Indexed: 05/24/2024] Open
Abstract
Recent advancements in modern science have provided robust tools for drug discovery. The rapid development of transcriptome sequencing technologies has given rise to single-cell transcriptomics and single-nucleus transcriptomics, increasing the accuracy of sequencing and accelerating the drug discovery process. With the evolution of single-cell transcriptomics, spatial transcriptomics (ST) technology has emerged as a derivative approach. Spatial transcriptomics has emerged as a hot topic in the field of omics research in recent years; it not only provides information on gene expression levels but also offers spatial information on gene expression. This technology has shown tremendous potential in research on disease understanding and drug discovery. In this article, we introduce the analytical strategies of spatial transcriptomics and review its applications in novel target discovery and drug mechanism unravelling. Moreover, we discuss the current challenges and issues in this research field that need to be addressed. In conclusion, spatial transcriptomics offers a new perspective for drug discovery.
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Affiliation(s)
- Junxian Cao
- Beijing Key Laboratory of Traditional Chinese Medicine Basic Research on Prevention and Treatment for Major Diseases, Experimental Research Center, China Academy of Chinese Medical Sciences, Beijing 100700, China
- Analysis of Complex Effects of Proprietary Chinese Medicine, Hunan Provincial Key Laboratory, Yongzhou City, Hunan Province, China
| | - Caifeng Li
- Beijing Key Laboratory of Traditional Chinese Medicine Basic Research on Prevention and Treatment for Major Diseases, Experimental Research Center, China Academy of Chinese Medical Sciences, Beijing 100700, China
| | - Zhao Cui
- Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing 100700, China
| | - Shiwen Deng
- Beijing Key Laboratory of Traditional Chinese Medicine Basic Research on Prevention and Treatment for Major Diseases, Experimental Research Center, China Academy of Chinese Medical Sciences, Beijing 100700, China
- Analysis of Complex Effects of Proprietary Chinese Medicine, Hunan Provincial Key Laboratory, Yongzhou City, Hunan Province, China
| | - Tong Lei
- Institute of Basic Theory for Chinese Medicine, China Academy of Chinese Medical Sciences, Beijing 100700, China
| | - Wei Liu
- Beijing Key Laboratory of Traditional Chinese Medicine Basic Research on Prevention and Treatment for Major Diseases, Experimental Research Center, China Academy of Chinese Medical Sciences, Beijing 100700, China
| | - Hongjun Yang
- Beijing Key Laboratory of Traditional Chinese Medicine Basic Research on Prevention and Treatment for Major Diseases, Experimental Research Center, China Academy of Chinese Medical Sciences, Beijing 100700, China
- Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing 100700, China
- Analysis of Complex Effects of Proprietary Chinese Medicine, Hunan Provincial Key Laboratory, Yongzhou City, Hunan Province, China
| | - Peng Chen
- Beijing Key Laboratory of Traditional Chinese Medicine Basic Research on Prevention and Treatment for Major Diseases, Experimental Research Center, China Academy of Chinese Medical Sciences, Beijing 100700, China
- Analysis of Complex Effects of Proprietary Chinese Medicine, Hunan Provincial Key Laboratory, Yongzhou City, Hunan Province, China
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2
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Hinze C, Lovric S, Halloran PF, Barasch J, Schmidt-Ott KM. Epithelial cell states associated with kidney and allograft injury. Nat Rev Nephrol 2024:10.1038/s41581-024-00834-0. [PMID: 38632381 DOI: 10.1038/s41581-024-00834-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/27/2024] [Indexed: 04/19/2024]
Abstract
The kidney epithelium, with its intricate arrangement of highly specialized cell types, constitutes the functional core of the organ. Loss of kidney epithelium is linked to the loss of functional nephrons and a subsequent decline in kidney function. In kidney transplantation, epithelial injury signatures observed during post-transplantation surveillance are strong predictors of adverse kidney allograft outcomes. However, epithelial injury is currently neither monitored clinically nor addressed therapeutically after kidney transplantation. Several factors can contribute to allograft epithelial injury, including allograft rejection, drug toxicity, recurrent infections and postrenal obstruction. The injury mechanisms that underlie allograft injury overlap partially with those associated with acute kidney injury (AKI) and chronic kidney disease (CKD) in the native kidney. Studies using advanced transcriptomic analyses of single cells from kidney or urine have identified a role for kidney injury-induced epithelial cell states in exacerbating and sustaining damage in AKI and CKD. These epithelial cell states and their associated expression signatures are also observed in transplanted kidney allografts, suggesting that the identification and characterization of transcriptomic epithelial cell states in kidney allografts may have potential clinical implications for diagnosis and therapy.
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Affiliation(s)
- Christian Hinze
- Department of Nephrology and Hypertension, Hannover Medical School, Hannover, Germany
| | - Svjetlana Lovric
- Department of Nephrology and Hypertension, Hannover Medical School, Hannover, Germany
| | - Philip F Halloran
- Alberta Transplant Applied Genomics Centre, Edmonton, Alberta, Canada
- Department of Medicine, Division of Nephrology and Transplant Immunology, University of Alberta, Edmonton, Alberta, Canada
| | - Jonathan Barasch
- Division of Nephrology, Columbia University, New York City, NY, USA
| | - Kai M Schmidt-Ott
- Department of Nephrology and Hypertension, Hannover Medical School, Hannover, Germany.
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Li L, Xiang T, Guo J, Guo F, Wu Y, Feng H, Liu J, Tao S, Fu P, Ma L. Inhibition of ACSS2-mediated histone crotonylation alleviates kidney fibrosis via IL-1β-dependent macrophage activation and tubular cell senescence. Nat Commun 2024; 15:3200. [PMID: 38615014 PMCID: PMC11016098 DOI: 10.1038/s41467-024-47315-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2023] [Accepted: 03/25/2024] [Indexed: 04/15/2024] Open
Abstract
Histone lysine crotonylation (Kcr), as a posttranslational modification, is widespread as acetylation (Kac); however, its roles are largely unknown in kidney fibrosis. In this study, we report that histone Kcr of tubular epithelial cells is abnormally elevated in fibrotic kidneys. By screening these crotonylated/acetylated factors, a crotonyl-CoA-producing enzyme ACSS2 (acyl-CoA synthetase short chain family member 2) is found to remarkably increase histone 3 lysine 9 crotonylation (H3K9cr) level without influencing H3K9ac in kidneys and tubular epithelial cells. The integrated analysis of ChIP-seq and RNA-seq of fibrotic kidneys reveal that the hub proinflammatory cytokine IL-1β, which is regulated by H3K9cr, play crucial roles in fibrogenesis. Furthermore, genetic and pharmacologic inhibition of ACSS2 both suppress H3K9cr-mediated IL-1β expression, which thereby alleviate IL-1β-dependent macrophage activation and tubular cell senescence to delay renal fibrosis. Collectively, our findings uncover that H3K9cr exerts a critical, previously unrecognized role in kidney fibrosis, where ACSS2 represents an attractive drug target to slow fibrotic kidney disease progression.
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Affiliation(s)
- Lingzhi Li
- Department of Nephrology, Institute of Kidney Diseases, West China Hospital of Sichuan University, and National Key Laboratory of Kidney Diseases, Chengdu, China
| | - Ting Xiang
- Department of Nephrology, Institute of Kidney Diseases, West China Hospital of Sichuan University, and National Key Laboratory of Kidney Diseases, Chengdu, China
| | - Jingjing Guo
- Department of Urology, Institute of Urology, West China Hospital of Sichuan University, Chengdu, China
| | - Fan Guo
- Department of Nephrology, Institute of Kidney Diseases, West China Hospital of Sichuan University, and National Key Laboratory of Kidney Diseases, Chengdu, China
| | - Yiting Wu
- Department of Nephrology, Institute of Kidney Diseases, West China Hospital of Sichuan University, and National Key Laboratory of Kidney Diseases, Chengdu, China
| | - Han Feng
- Tulane Research and Innovation for Arrhythmia Discoveries-TRIAD Center, Tulane University School of Medicine, New Orleans, LA, USA
| | - Jing Liu
- Department of Nephrology, Institute of Kidney Diseases, West China Hospital of Sichuan University, and National Key Laboratory of Kidney Diseases, Chengdu, China
| | - Sibei Tao
- Department of Nephrology, Institute of Kidney Diseases, West China Hospital of Sichuan University, and National Key Laboratory of Kidney Diseases, Chengdu, China
| | - Ping Fu
- Department of Nephrology, Institute of Kidney Diseases, West China Hospital of Sichuan University, and National Key Laboratory of Kidney Diseases, Chengdu, China.
| | - Liang Ma
- Department of Nephrology, Institute of Kidney Diseases, West China Hospital of Sichuan University, and National Key Laboratory of Kidney Diseases, Chengdu, China.
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4
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Cheung MD, Asiimwe R, Erman EN, Fucile CF, Liu S, Sun CW, Hanumanthu VS, Pal HC, Wright ED, Ghajar-Rahimi G, Epstein D, Orandi BJ, Kumar V, Anderson DJ, Greene ME, Bell M, Yates S, Moore KH, LaFontaine J, Killian JT, Baker G, Perry J, Khan Z, Reed R, Little SC, Rosenberg AF, George JF, Locke JE, Porrett PM. Spatiotemporal immune atlas of a clinical-grade gene-edited pig-to-human kidney xenotransplant. Nat Commun 2024; 15:3140. [PMID: 38605083 PMCID: PMC11009229 DOI: 10.1038/s41467-024-47454-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2023] [Accepted: 04/02/2024] [Indexed: 04/13/2024] Open
Abstract
Pig-to-human xenotransplantation is rapidly approaching the clinical arena; however, it is unclear which immunomodulatory regimens will effectively control human immune responses to pig xenografts. Here, we transplant a gene-edited pig kidney into a brain-dead human recipient on pharmacologic immunosuppression and study the human immune response to the xenograft using spatial transcriptomics and single-cell RNA sequencing. Human immune cells are uncommon in the porcine kidney cortex early after xenotransplantation and consist of primarily myeloid cells. Both the porcine resident macrophages and human infiltrating macrophages express genes consistent with an alternatively activated, anti-inflammatory phenotype. No significant infiltration of human B or T cells into the porcine kidney xenograft is detectable. Altogether, these findings provide proof of concept that conventional pharmacologic immunosuppression may be able to restrict infiltration of human immune cells into the xenograft early after compatible pig-to-human kidney xenotransplantation.
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Affiliation(s)
- Matthew D Cheung
- Department of Surgery, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Rebecca Asiimwe
- Department of Surgery, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Elise N Erman
- Department of Surgery, University of Alabama at Birmingham, Birmingham, AL, USA
| | | | - Shanrun Liu
- Department of Biochemistry and Molecular Genetics, University of Alabama at Birmingham, Birmingham, AL, USA
- Flow Cytometry & Single Cell Core Facility, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Chiao-Wang Sun
- Department of Biochemistry and Molecular Genetics, University of Alabama at Birmingham, Birmingham, AL, USA
- Flow Cytometry & Single Cell Core Facility, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Vidya Sagar Hanumanthu
- Flow Cytometry & Single Cell Core Facility, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Harish C Pal
- Flow Cytometry & Single Cell Core Facility, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Emma D Wright
- Department of Surgery, University of Alabama at Birmingham, Birmingham, AL, USA
| | | | - Daniel Epstein
- Department of Surgery, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Babak J Orandi
- Department of Surgery, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Vineeta Kumar
- Department of Medicine, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Douglas J Anderson
- Department of Surgery, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Morgan E Greene
- Department of Surgery, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Markayla Bell
- Department of Surgery, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Stefani Yates
- Department of Surgery, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Kyle H Moore
- Department of Medicine, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Jennifer LaFontaine
- Department of Surgery, University of Alabama at Birmingham, Birmingham, AL, USA
| | - John T Killian
- Department of Surgery, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Gavin Baker
- Department of Surgery, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Jackson Perry
- Department of Surgery, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Zayd Khan
- Department of Surgery, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Rhiannon Reed
- Department of Surgery, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Shawn C Little
- Department of Surgery, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Alexander F Rosenberg
- Informatics Institute, University of Alabama at Birmingham, Birmingham, AL, USA
- Department of Microbiology, University of Alabama at Birmingham, Birmingham, AL, USA
| | - James F George
- Department of Surgery, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Jayme E Locke
- Department of Surgery, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Paige M Porrett
- Department of Surgery, University of Alabama at Birmingham, Birmingham, AL, USA.
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5
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Wu H, Dixon EE, Xuanyuan Q, Guo J, Yoshimura Y, Debashish C, Niesnerova A, Xu H, Rouault M, Humphreys BD. High resolution spatial profiling of kidney injury and repair using RNA hybridization-based in situ sequencing. Nat Commun 2024; 15:1396. [PMID: 38360882 PMCID: PMC10869771 DOI: 10.1038/s41467-024-45752-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2023] [Accepted: 02/02/2024] [Indexed: 02/17/2024] Open
Abstract
Emerging spatially resolved transcriptomics technologies allow for the measurement of gene expression in situ at cellular resolution. We apply direct RNA hybridization-based in situ sequencing (dRNA HybISS, Cartana part of 10xGenomics) to compare male and female healthy mouse kidneys and the male kidney injury and repair timecourse. A pre-selected panel of 200 genes is used to identify cell state dynamics patterns during injury and repair. We develop a new computational pipeline, CellScopes, for the rapid analysis, multi-omic integration and visualization of spatially resolved transcriptomic datasets. The resulting dataset allows us to resolve 13 kidney cell types within distinct kidney niches, dynamic alterations in cell state over the course of injury and repair and cell-cell interactions between leukocytes and kidney parenchyma. At late timepoints after injury, C3+ leukocytes are enriched near pro-inflammatory, failed-repair proximal tubule cells. Integration of snRNA-seq dataset from the same injury and repair samples also allows us to impute the spatial localization of genes not directly measured by dRNA HybISS.
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Affiliation(s)
- Haojia Wu
- Division of Nephrology, Department of Medicine, Washington University in St. Louis School of Medicine, St. Louis, MO, USA
| | - Eryn E Dixon
- Division of Nephrology, Department of Medicine, Washington University in St. Louis School of Medicine, St. Louis, MO, USA
| | - Qiao Xuanyuan
- Division of Nephrology, Department of Medicine, Washington University in St. Louis School of Medicine, St. Louis, MO, USA
| | - Juanru Guo
- Division of Nephrology, Department of Medicine, Washington University in St. Louis School of Medicine, St. Louis, MO, USA
| | - Yasuhiro Yoshimura
- Division of Nephrology, Department of Medicine, Washington University in St. Louis School of Medicine, St. Louis, MO, USA
| | | | | | - Hao Xu
- 10X Genomics, Pleasanton, CA, USA
- Aplex Bio AB, Solna, Sweden
| | | | - Benjamin D Humphreys
- Division of Nephrology, Department of Medicine, Washington University in St. Louis School of Medicine, St. Louis, MO, USA.
- Department of Developmental Biology, Washington University in St. Louis School of Medicine, St. Louis, MO, USA.
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6
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Haug S, Muthusamy S, Li Y, Stewart G, Li X, Treppner M, Köttgen A, Akilesh S. Multi-omic analysis of human kidney tissue identified medulla-specific gene expression patterns. Kidney Int 2024; 105:293-311. [PMID: 37995909 PMCID: PMC10843743 DOI: 10.1016/j.kint.2023.10.024] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2022] [Revised: 09/21/2023] [Accepted: 10/23/2023] [Indexed: 11/25/2023]
Abstract
The kidney medulla is a specialized region with important homeostatic functions. It has been implicated in genetic and developmental disorders along with ischemic and drug-induced injuries. Despite its role in kidney function and disease, the medulla's baseline gene expression and epigenomic signatures have not been well described in the adult human kidney. Here we generated and analyzed gene expression (RNA-seq), chromatin accessibility (ATAC-seq), chromatin conformation (Hi-C) and spatial transcriptomic data from the adult human kidney cortex and medulla. Tissue samples were obtained from macroscopically dissected cortex and medulla of tumor-adjacent normal material in nephrectomy specimens from five male patients. We used these carefully annotated specimens to reassign incorrectly labeled samples in the larger public Genotype-Tissue Expression (GTEx) Project, and to extract meaningful medullary gene expression signatures. Using integrated analysis of gene expression, chromatin accessibility and conformation profiles, we found insights into medulla development and function and then validated this by spatial transcriptomics and immunohistochemistry. Thus, our datasets provide a valuable resource for functional annotation of variants from genome-wide association studies and are freely accessible through an epigenome browser portal.
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Affiliation(s)
- Stefan Haug
- Institute of Genetic Epidemiology, Medical Center-University of Freiburg, Freiburg, Germany
| | - Selvaraj Muthusamy
- Department of Pathology, Virginia Commonwealth University, Richmond, Virginia, USA
| | - Yong Li
- Institute of Genetic Epidemiology, Medical Center-University of Freiburg, Freiburg, Germany
| | - Galen Stewart
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, Washington, USA
| | - Xianwu Li
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, Washington, USA
| | - Martin Treppner
- Institute of Medical Biometry and Statistics, Faculty of Medicine and Medical Center-University of Freiburg, Freiburg, Germany
| | - Anna Köttgen
- Institute of Genetic Epidemiology, Medical Center-University of Freiburg, Freiburg, Germany.
| | - Shreeram Akilesh
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, Washington, USA.
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7
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Chen Z, Ye L, Zhu M, Xia C, Fan J, Chen H, Li Z, Mou S. Single cell multi-omics of fibrotic kidney reveal epigenetic regulation of antioxidation and apoptosis within proximal tubule. Cell Mol Life Sci 2024; 81:56. [PMID: 38270638 PMCID: PMC10811088 DOI: 10.1007/s00018-024-05118-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2023] [Revised: 12/10/2023] [Accepted: 01/07/2024] [Indexed: 01/26/2024]
Abstract
BACKGROUND Until now, there has been no particularly effective treatment for chronic kidney disease (CKD). Fibrosis is a common pathological change that exist in CKD. METHODS To better understand the transcriptional dynamics in fibrotic kidney, we make use of single-nucleus assay for transposase-accessible chromatin sequencing (snATAC-seq) and single-cell RNA sequencing (scRNA-seq) from GEO datasets and perform scRNA-seq of human biopsy to seek possible transcription factors (TFs) regulating target genes in the progress of kidney fibrosis across mouse and human kidneys. RESULTS Our analysis has displayed chromatin accessibility, gene expression pattern and cell-cell communications at single-cell level in kidneys suffering from unilateral ureteral obstruction (UUO) or chronic interstitial nephritis (CIN). Using multimodal data, there exists epigenetic regulation producing less Sod1 and Sod2 mRNA within the proximal tubule which is hard to withstand oxidative stress during fibrosis. Meanwhile, a transcription factor Nfix promoting the apoptosis-related gene Ifi27 expression found by multimodal data was validated by an in vitro study. And the gene Ifi27 upregulated by in situ AAV injection within the kidney cortex aggravates kidney fibrosis. CONCLUSIONS In conclusion, as we know oxidation and apoptosis are traumatic factors during fibrosis, thus enhancing antioxidation and inhibiting the Nfix-Ifi27 pathway to inhibit apoptosis could be a potential treatment for kidney fibrosis.
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Affiliation(s)
- Zhejun Chen
- Department of Nephrology, The First Affiliated Hospital of Zhejiang Chinese Medical University (Zhejiang Provincial Hospital of Chinese Medicine), Hangzhou, 310000, Zhejiang, China.
| | - Liqing Ye
- Department of Nephrology, The First Affiliated Hospital of Zhejiang Chinese Medical University (Zhejiang Provincial Hospital of Chinese Medicine), Hangzhou, 310000, Zhejiang, China
| | - Minyan Zhu
- Department of Nephrology, Molecular Cell Lab for Kidney Disease, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, No 1630, Dong Fang Road, Shanghai, 200127, China
| | - Cong Xia
- Department of Nephrology, The First Affiliated Hospital of Zhejiang Chinese Medical University (Zhejiang Provincial Hospital of Chinese Medicine), Hangzhou, 310000, Zhejiang, China
| | - Junfen Fan
- Department of Nephrology, The First Affiliated Hospital of Zhejiang Chinese Medical University (Zhejiang Provincial Hospital of Chinese Medicine), Hangzhou, 310000, Zhejiang, China
| | - Hongbo Chen
- Department of Nephrology, The First Affiliated Hospital of Zhejiang Chinese Medical University (Zhejiang Provincial Hospital of Chinese Medicine), Hangzhou, 310000, Zhejiang, China.
| | - Zhijian Li
- Broad Institute of Harvard and MIT, Cambridge, MA, 02142, USA.
| | - Shan Mou
- Department of Nephrology, Molecular Cell Lab for Kidney Disease, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, No 1630, Dong Fang Road, Shanghai, 200127, China.
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8
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Deng Y, Lu Y, Li M, Shen J, Qin S, Zhang W, Zhang Q, Shen Z, Li C, Jia T, Chen P, Peng L, Chen Y, Zhang W, Liu H, Zhang L, Rong L, Wang X, Chen D. SCAN: Spatiotemporal Cloud Atlas for Neural cells. Nucleic Acids Res 2024; 52:D998-D1009. [PMID: 37930842 PMCID: PMC10767991 DOI: 10.1093/nar/gkad895] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2023] [Revised: 09/20/2023] [Accepted: 10/05/2023] [Indexed: 11/08/2023] Open
Abstract
The nervous system is one of the most complicated and enigmatic systems within the animal kingdom. Recently, the emergence and development of spatial transcriptomics (ST) and single-cell RNA sequencing (scRNA-seq) technologies have provided an unprecedented ability to systematically decipher the cellular heterogeneity and spatial locations of the nervous system from multiple unbiased aspects. However, efficiently integrating, presenting and analyzing massive multiomic data remains a huge challenge. Here, we manually collected and comprehensively analyzed high-quality scRNA-seq and ST data from the nervous system, covering 10 679 684 cells. In addition, multi-omic datasets from more than 900 species were included for extensive data mining from an evolutionary perspective. Furthermore, over 100 neurological diseases (e.g. Alzheimer's disease, Parkinson's disease, Down syndrome) were systematically analyzed for high-throughput screening of putative biomarkers. Differential expression patterns across developmental time points, cell types and ST spots were discerned and subsequently subjected to extensive interpretation. To provide researchers with efficient data exploration, we created a new database with interactive interfaces and integrated functions called the Spatiotemporal Cloud Atlas for Neural cells (SCAN), freely accessible at http://47.98.139.124:8799 or http://scanatlas.net. SCAN will benefit the neuroscience research community to better exploit the spatiotemporal atlas of the neural system and promote the development of diagnostic strategies for various neurological disorders.
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Affiliation(s)
- Yushan Deng
- State Key Laboratory of Common Mechanism Research for Major Diseases, Suzhou Institute of Systems Medicine, Chinese Academy of Medical Sciences & Peking Union Medical College, Suzhou 215123, China
| | - Yubao Lu
- Department of Spine Surgery, The Third Affiliated Hospital, Sun Yat-sen University, Guangzhou 510630, China
| | - Mengrou Li
- State Key Laboratory of Common Mechanism Research for Major Diseases, Suzhou Institute of Systems Medicine, Chinese Academy of Medical Sciences & Peking Union Medical College, Suzhou 215123, China
- Institutes of Biology and Medical Sciences (IBMS), Soochow University, Suzhou 215123, China
| | - Jiayi Shen
- State Key Laboratory of Common Mechanism Research for Major Diseases, Suzhou Institute of Systems Medicine, Chinese Academy of Medical Sciences & Peking Union Medical College, Suzhou 215123, China
- Peninsula Cancer Research Center, School of Basic Medical Sciences, Binzhou Medical University, Yantai 264003, China
| | - Siying Qin
- State Key Laboratory of Common Mechanism Research for Major Diseases, Suzhou Institute of Systems Medicine, Chinese Academy of Medical Sciences & Peking Union Medical College, Suzhou 215123, China
| | - Wei Zhang
- Department of Spine Surgery, The Third Affiliated Hospital, Sun Yat-sen University, Guangzhou 510630, China
| | - Qiang Zhang
- State Key Laboratory of Common Mechanism Research for Major Diseases, Suzhou Institute of Systems Medicine, Chinese Academy of Medical Sciences & Peking Union Medical College, Suzhou 215123, China
| | - Zhaoyang Shen
- Life Sciences and Technology College, China Pharmaceutical University, Nanjing 211198, China
| | - Changxiao Li
- State Key Laboratory of Common Mechanism Research for Major Diseases, Suzhou Institute of Systems Medicine, Chinese Academy of Medical Sciences & Peking Union Medical College, Suzhou 215123, China
| | - Tengfei Jia
- State Key Laboratory of Common Mechanism Research for Major Diseases, Suzhou Institute of Systems Medicine, Chinese Academy of Medical Sciences & Peking Union Medical College, Suzhou 215123, China
- Institutes of Biology and Medical Sciences (IBMS), Soochow University, Suzhou 215123, China
| | - Peixin Chen
- State Key Laboratory of Common Mechanism Research for Major Diseases, Suzhou Institute of Systems Medicine, Chinese Academy of Medical Sciences & Peking Union Medical College, Suzhou 215123, China
- Cam-Su Genomic Resource Center, Medical College of Soochow University, Suzhou 215123, China
| | - Lingmin Peng
- State Key Laboratory of Common Mechanism Research for Major Diseases, Suzhou Institute of Systems Medicine, Chinese Academy of Medical Sciences & Peking Union Medical College, Suzhou 215123, China
| | - Yangfeng Chen
- State Key Laboratory of Common Mechanism Research for Major Diseases, Suzhou Institute of Systems Medicine, Chinese Academy of Medical Sciences & Peking Union Medical College, Suzhou 215123, China
| | - Wensheng Zhang
- Peninsula Cancer Research Center, School of Basic Medical Sciences, Binzhou Medical University, Yantai 264003, China
- Cam-Su Genomic Resource Center, Medical College of Soochow University, Suzhou 215123, China
| | - Hebin Liu
- Institutes of Biology and Medical Sciences (IBMS), Soochow University, Suzhou 215123, China
| | - Liangming Zhang
- Department of Spine Surgery, The Third Affiliated Hospital, Sun Yat-sen University, Guangzhou 510630, China
| | - Limin Rong
- Department of Spine Surgery, The Third Affiliated Hospital, Sun Yat-sen University, Guangzhou 510630, China
| | - Xiangdong Wang
- Zhongshan Hospital, Department of Pulmonary and Critical Care Medicine, Institute for Clinical Science, Shanghai Institute of Clinical Bioinformatics, Shanghai 200000, China
| | - Dongsheng Chen
- State Key Laboratory of Common Mechanism Research for Major Diseases, Suzhou Institute of Systems Medicine, Chinese Academy of Medical Sciences & Peking Union Medical College, Suzhou 215123, China
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9
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Yamashita N, Kramann R. Mechanisms of kidney fibrosis and routes towards therapy. Trends Endocrinol Metab 2024; 35:31-48. [PMID: 37775469 DOI: 10.1016/j.tem.2023.09.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/18/2023] [Revised: 09/01/2023] [Accepted: 09/04/2023] [Indexed: 10/01/2023]
Abstract
Kidney fibrosis is the final common pathway of virtually all chronic kidney diseases (CKDs) and is therefore considered to be a promising therapeutic target for these conditions. However, despite great progress in recent years, no targeted antifibrotic therapies for the kidney have been approved, likely because the complex mechanisms that initiate and drive fibrosis are not yet completely understood. Recent single-cell genomic approaches have allowed novel insights into kidney fibrosis mechanisms in mouse and human, particularly the heterogeneity and differentiation processes of myofibroblasts, the role of injured epithelial cells and immune cells, and their crosstalk mechanisms. In this review we summarize the key mechanisms that drive kidney fibrosis, including recent advances in understanding the mechanisms, as well as potential routes for developing novel targeted antifibrotic therapeutics.
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Affiliation(s)
- Noriyuki Yamashita
- Department of Nephrology and Clinical Immunology, RWTH Aachen University, Aachen, Germany; Department of Nephrology, Graduate School of Medical Science, Kyoto Prefectural University of Medicine, Kyoto, Japan
| | - Rafael Kramann
- Department of Nephrology and Clinical Immunology, RWTH Aachen University, Aachen, Germany; Department of Internal Medicine, Nephrology, and Transplantation, Erasmus Medical Center, Rotterdam, The Netherlands.
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10
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Smith KD, Prince DK, MacDonald JW, Bammler TK, Akilesh S. Challenges and Opportunities for the Clinical Translation of Spatial Transcriptomics Technologies. GLOMERULAR DISEASES 2024; 4:49-63. [PMID: 38600956 PMCID: PMC11006413 DOI: 10.1159/000538344] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/05/2024] [Accepted: 03/10/2024] [Indexed: 04/12/2024]
Abstract
Background The first spatially resolved transcriptomics platforms, GeoMx (Nanostring) and Visium (10x Genomics) were launched in 2019 and were recognized as the method of the year by Nature Methods in 2020. The subsequent refinement and expansion of these and other technologies to increase -plex, work with formalin-fixed paraffin-embedded tissue, and analyze protein in addition to gene expression have only added to their significance and impact on the biomedical sciences. In this perspective, we focus on two platforms for spatial transcriptomics, GeoMx and Visium, and how these platforms have been used to provide novel insight into kidney disease. The choice of platform will depend largely on experimental questions and design. The application of these technologies to clinically sourced biopsies presents the opportunity to identify specific tissue biomarkers that help define disease etiology and more precisely target therapeutic interventions in the future. Summary In this review, we provide a description of the existing and emerging technologies that can be used to capture spatially resolved gene and protein expression data from tissue. These technologies have provided new insight into the spatial heterogeneity of diseases, how reactions to disease are distributed within a tissue, which cells are affected, and molecular pathways that predict disease and response to therapy. Key Message The upcoming years will see intense use of spatial transcriptomics technologies to better define the pathophysiology of kidney diseases and develop novel diagnostic tests to guide personalized treatments for patients.
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Affiliation(s)
- Kelly D. Smith
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA, USA
| | | | - James W. MacDonald
- Department of Environmental and Occupational Health Sciences, University of Washington, Seattle, WA, USA
| | - Theo K. Bammler
- Department of Environmental and Occupational Health Sciences, University of Washington, Seattle, WA, USA
| | - Shreeram Akilesh
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA, USA
- Kidney Research Institute, Seattle, WA, USA
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11
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Curtis LM. Sex and Gender Differences in AKI. KIDNEY360 2024; 5:160-167. [PMID: 37990360 PMCID: PMC10833607 DOI: 10.34067/kid.0000000000000321] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/27/2023] [Accepted: 11/14/2023] [Indexed: 11/23/2023]
Abstract
Sex differences in AKI continue to be identified. Generally, women are protected from AKI when compared to men. Much of the protection exhibited in women is diminished after menopause. These sex and age effects have also been noted in animal models of AKI. Gonadal hormones, as modifiers of incidence, severity, and progression of AKI, have been offered as likely contributors to this sex and age effect. In animal models of AKI, estrogen and testosterone seem to modulate susceptibility. Questions remain however regarding cellular and molecular changes that are initiated by modulation of these hormones because both estrogen and testosterone have effects across cell types that play a role in AKI. Although findings have largely been informed by studies in males, molecular pathways that are involved in the initiation and progression of AKI may be modulated by gonadal hormones. Compounding the hormone-receptor effects are developmental effects of sex chromosomal complement and epigenetic influences that may confer sex-based baseline differences in gene and protein expression, and gene dosage effects of X inactivation and escape on molecular pathways. Elucidation of sex-based protection may afford a more complete view of AKI and potential therapeutic interventions. Furthermore, the effect on susceptibility to AKI in transgender patients, who receive life-altering and essential gender-affirming hormone therapy, requires greater attention. In this review, several potential contributors to the sex differences observed in humans and animal models are discussed.
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Affiliation(s)
- Lisa M Curtis
- Division of Nephrology, University of Alabama at Birmingham, Birmingham, Alabama
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12
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Li Z, Lu Y, Yang L. Imaging and spatial omics of kidney injury: significance, challenges, advances and perspectives. MEDICAL REVIEW (2021) 2023; 3:514-520. [PMID: 38282803 PMCID: PMC10808090 DOI: 10.1515/mr-2023-0046] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/20/2023] [Accepted: 12/11/2023] [Indexed: 01/30/2024]
Abstract
The kidneys are susceptible to a range of insults that can cause damage to them. Early diagnosis, timely prevention, and proper treatment are crucial for improving the outcome of kidney injury. However, the complexity of renal structure and function makes it difficult to reach the demand of early detection and comprehensive evaluation of kidney injury. No successful drug therapy caused by the elaborate pathogenesis mechanism network of kidney injury calls for a systematical interpretation in mechanism researches. Recent advances in renal imaging and omics studies have provided novel views and deeper insights into kidney injury, but also raise challenges in reaching a comprehensive cellular and molecular atlas of kidney injury. Progresses in imaging and omics of kidney injury are being made in various directions, with the initiative of construction a high-resolution structural atlas of kidney, dynamic and non-invasive evaluation of renal function, and systematic establishment of spatially resolved molecular atlas by transcriptomics and metabolomics. With the limitations of a single modality, novel multimodal integration technologies of imaging and omics are being attempted to achieve a systematic description of nephropathy mechanisms. Further extensive efforts in renal multimodal imaging and omics studies are extremely required to deepen our understanding on kidney injury in the context of diagnostic, mechanistic and therapeutic perspectives.
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Affiliation(s)
- Zehua Li
- Renal Division, Peking University Institute of Nephrology, Peking University First Hospital, Beijing, China
- Key Laboratory of Renal Disease-Ministry of Health of China, Key Laboratory of CKD Prevention and Treatment (Peking University)-Ministry of Education of China, Peking University First Hospital, Beijing, China
- Research Units of Diagnosis and Treatment of Immune-mediated Kidney Diseases-Chinese Academy of Medical Sciences, Peking University First Hospital, Beijing, China
| | - Yao Lu
- Renal Division, Peking University Institute of Nephrology, Peking University First Hospital, Beijing, China
- Key Laboratory of Renal Disease-Ministry of Health of China, Key Laboratory of CKD Prevention and Treatment (Peking University)-Ministry of Education of China, Peking University First Hospital, Beijing, China
- Research Units of Diagnosis and Treatment of Immune-mediated Kidney Diseases-Chinese Academy of Medical Sciences, Peking University First Hospital, Beijing, China
| | - Li Yang
- Renal Division, Peking University Institute of Nephrology, Peking University First Hospital, Beijing, China
- Key Laboratory of Renal Disease-Ministry of Health of China, Key Laboratory of CKD Prevention and Treatment (Peking University)-Ministry of Education of China, Peking University First Hospital, Beijing, China
- Research Units of Diagnosis and Treatment of Immune-mediated Kidney Diseases-Chinese Academy of Medical Sciences, Peking University First Hospital, Beijing, China
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13
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Cross AR, Gartner L, Hester J, Issa F. Opportunities for High-plex Spatial Transcriptomics in Solid Organ Transplantation. Transplantation 2023; 107:2464-2472. [PMID: 36944604 DOI: 10.1097/tp.0000000000004587] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/23/2023]
Abstract
The last 5 y have seen the development and widespread adoption of high-plex spatial transcriptomic technology. This technique detects and quantifies mRNA transcripts in situ, meaning that transcriptomic signatures can be sampled from specific cells, structures, lesions, or anatomical regions while conserving the physical relationships that exist within complex tissues. These methods now frequently implement next-generation sequencing, enabling the simultaneous measurement of many targets, up to and including the whole mRNA transcriptome. To date, spatial transcriptomics has been foremost used in the fields of neuroscience and oncology, but there is potential for its use in transplantation sciences. Transplantation has a clear dependence on biopsies for diagnosis, monitoring, and research. Transplant patients represent a unique cohort with multiple organs of interest, clinical courses, demographics, and immunosuppressive regimens. Obtaining high complexity data on the disease processes underlying rejection, tolerance, infection, malignancy, and injury could identify new opportunities for therapeutic intervention and biomarker identification. In this review, we discuss currently available spatial transcriptomic technologies and how they can be applied to transplantation.
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Affiliation(s)
- Amy R Cross
- Translational Research and Immunology Group, Nuffield Department of Surgical Sciences, University of Oxford, Oxford, United Kingdom
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14
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Clark AJ, Saade MC, Vemireddy V, Vu KQ, Flores BM, Etzrodt V, Ciampa EJ, Huang H, Takakura A, Zandi-Nejad K, Zsengellér ZK, Parikh SM. Hepatocyte nuclear factor 4α mediated quinolinate phosphoribosylltransferase (QPRT) expression in the kidney facilitates resilience against acute kidney injury. Kidney Int 2023; 104:1150-1163. [PMID: 37783445 PMCID: PMC10843022 DOI: 10.1016/j.kint.2023.09.013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2023] [Revised: 08/23/2023] [Accepted: 09/07/2023] [Indexed: 10/04/2023]
Abstract
Nicotinamide adenine dinucleotide (NAD+) levels decline in experimental models of acute kidney injury (AKI). Attenuated enzymatic conversion of tryptophan to NAD+ in tubular epithelium may contribute to adverse cellular and physiological outcomes. Mechanisms underlying defense of tryptophan-dependent NAD+ production are incompletely understood. Here we show that regulation of a bottleneck enzyme in this pathway, quinolinate phosphoribosyltransferase (QPRT) may contribute to kidney resilience. Expression of QPRT declined in two unrelated models of AKI. Haploinsufficient mice developed worse outcomes compared to littermate controls whereas novel, conditional gain-of-function mice were protected from injury. Applying these findings, we then identified hepatocyte nuclear factor 4 alpha (HNF4α) as a candidate transcription factor regulating QPRT expression downstream of the mitochondrial biogenesis regulator and NAD+ biosynthesis inducer PPARgamma coactivator-1-alpha (PGC1α). This was verified by chromatin immunoprecipitation. A PGC1α - HNF4α -QPRT axis controlled NAD+ levels across cellular compartments and modulated cellular ATP. These results propose that tryptophan-dependent NAD+ biosynthesis via QPRT and induced by HNF4α may be a critical determinant of kidney resilience to noxious stressors.
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Affiliation(s)
- Amanda J Clark
- Division of Nephrology, Department of Medicine, University of Texas Southwestern, Dallas, Texas, USA; Division of Nephrology, Department of Pediatrics, University of Texas Southwestern, Dallas, Texas, USA
| | - Marie Christelle Saade
- Division of Nephrology, Department of Medicine, University of Texas Southwestern, Dallas, Texas, USA
| | - Vamsidhara Vemireddy
- Division of Nephrology, Department of Medicine, University of Texas Southwestern, Dallas, Texas, USA
| | - Kyle Q Vu
- Division of Nephrology, Department of Medicine, University of Texas Southwestern, Dallas, Texas, USA
| | - Brenda Mendoza Flores
- Division of Nephrology, Department of Medicine, University of Texas Southwestern, Dallas, Texas, USA
| | - Valerie Etzrodt
- Division of Nephrology, Department of Medicine, University of Texas Southwestern, Dallas, Texas, USA
| | - Erin J Ciampa
- Department of Anesthesia, Critical Care, and Pain Medicine, Beth Israel Deaconess Medical Center, Boston, Massachusetts, USA
| | - Huihui Huang
- Division of Nephrology, Department of Medicine, Beth Israel Deaconess Medical Center, Boston, Massachusetts, USA
| | - Ayumi Takakura
- Renal Division, Department of Medicine, Brigham and Women's Hospital, Boston, Massachusetts, USA
| | - Kambiz Zandi-Nejad
- Division of Nephrology, Department of Medicine, Beth Israel Deaconess Medical Center, Boston, Massachusetts, USA
| | - Zsuzsanna K Zsengellér
- Division of Nephrology, Department of Medicine, Beth Israel Deaconess Medical Center, Boston, Massachusetts, USA
| | - Samir M Parikh
- Division of Nephrology, Department of Medicine, University of Texas Southwestern, Dallas, Texas, USA; Department of Pharmacology, University of Texas Southwestern, Dallas, Texas, USA.
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15
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Gharaie S, Lee K, Noller K, Lo EK, Miller B, Jung HJ, Newman-Rivera AM, Kurzhagen JT, Singla N, Welling PA, Fan J, Cahan P, Noel S, Rabb H. Single cell and spatial transcriptomics analysis of kidney double negative T lymphocytes in normal and ischemic mouse kidneys. Sci Rep 2023; 13:20888. [PMID: 38017015 PMCID: PMC10684868 DOI: 10.1038/s41598-023-48213-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2023] [Accepted: 11/23/2023] [Indexed: 11/30/2023] Open
Abstract
T cells are important in the pathogenesis of acute kidney injury (AKI), and TCR+CD4-CD8- (double negative-DN) are T cells that have regulatory properties. However, there is limited information on DN T cells compared to traditional CD4+ and CD8+ cells. To elucidate the molecular signature and spatial dynamics of DN T cells during AKI, we performed single-cell RNA sequencing (scRNA-seq) on sorted murine DN, CD4+, and CD8+ cells combined with spatial transcriptomic profiling of normal and post AKI mouse kidneys. scRNA-seq revealed distinct transcriptional profiles for DN, CD4+, and CD8+ T cells of mouse kidneys with enrichment of Kcnq5, Klrb1c, Fcer1g, and Klre1 expression in DN T cells compared to CD4+ and CD8+ T cells in normal kidney tissue. We validated the expression of these four genes in mouse kidney DN, CD4+ and CD8+ T cells using RT-PCR and Kcnq5, Klrb1, and Fcer1g genes with the NIH human kidney precision medicine project (KPMP). Spatial transcriptomics in normal and ischemic mouse kidney tissue showed a localized cluster of T cells in the outer medulla expressing DN T cell genes including Fcer1g. These results provide a template for future studies in DN T as well as CD4+ and CD8+ cells in normal and diseased kidneys.
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Affiliation(s)
- Sepideh Gharaie
- Department of Medicine, Johns Hopkins University, School of Medicine, Ross 965, 720 Rutland Ave, Baltimore, MD, 21205, USA
| | - Kyungho Lee
- Department of Medicine, Johns Hopkins University, School of Medicine, Ross 965, 720 Rutland Ave, Baltimore, MD, 21205, USA
| | - Kathleen Noller
- Department of Biomedical Engineering, Johns Hopkins University, School of Medicine, Baltimore, MD, 21205, USA
| | - Emily K Lo
- Department of Biomedical Engineering, Johns Hopkins University, School of Medicine, Baltimore, MD, 21205, USA
| | - Brendan Miller
- Department of Biomedical Engineering, Johns Hopkins University, School of Medicine, Baltimore, MD, 21205, USA
| | - Hyun Jun Jung
- Department of Medicine, Johns Hopkins University, School of Medicine, Ross 965, 720 Rutland Ave, Baltimore, MD, 21205, USA
| | - Andrea M Newman-Rivera
- Department of Medicine, Johns Hopkins University, School of Medicine, Ross 965, 720 Rutland Ave, Baltimore, MD, 21205, USA
| | - Johanna T Kurzhagen
- Department of Medicine, Johns Hopkins University, School of Medicine, Ross 965, 720 Rutland Ave, Baltimore, MD, 21205, USA
| | - Nirmish Singla
- Department of Urology, Johns Hopkins University, School of Medicine, Baltimore, MD, 21205, USA
| | - Paul A Welling
- Department of Medicine, Johns Hopkins University, School of Medicine, Ross 965, 720 Rutland Ave, Baltimore, MD, 21205, USA
- Department of Physiology, Johns Hopkins University, School of Medicine, Baltimore, MD, 21205, USA
| | - Jean Fan
- Department of Biomedical Engineering, Johns Hopkins University, School of Medicine, Baltimore, MD, 21205, USA
| | - Patrick Cahan
- Department of Biomedical Engineering, Johns Hopkins University, School of Medicine, Baltimore, MD, 21205, USA
| | - Sanjeev Noel
- Department of Medicine, Johns Hopkins University, School of Medicine, Ross 965, 720 Rutland Ave, Baltimore, MD, 21205, USA
| | - Hamid Rabb
- Department of Medicine, Johns Hopkins University, School of Medicine, Ross 965, 720 Rutland Ave, Baltimore, MD, 21205, USA.
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16
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Polonsky M, Gerhardt LMS, Yun J, Koppitch K, Colón KL, Amrhein H, Zheng S, Yuan GC, Thomson M, Cai L, McMahon AP. Spatial transcriptomics defines injury-specific microenvironments in the adult mouse kidney and novel cellular interactions in regeneration and disease. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.11.22.568217. [PMID: 38045285 PMCID: PMC10690238 DOI: 10.1101/2023.11.22.568217] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/05/2023]
Abstract
Kidney injury disrupts the intricate renal architecture and triggers limited regeneration, and injury-invoked inflammation and fibrosis. Deciphering molecular pathways and cellular interactions driving these processes is challenging due to the complex renal architecture. Here, we applied single cell spatial transcriptomics to examine ischemia-reperfusion injury in the mouse kidney. Spatial transcriptomics revealed injury-specific and spatially-dependent gene expression patterns in distinct cellular microenvironments within the kidney and predicted Clcf1-Crfl1 in a molecular interplay between persistently injured proximal tubule cells and neighboring fibroblasts. Immune cell types play a critical role in organ repair. Spatial analysis revealed cellular microenvironments resembling early tertiary lymphoid structures and identified associated molecular pathways. Collectively, this study supports a focus on molecular interactions in cellular microenvironments to enhance understanding of injury, repair and disease. One-Sentence Summary: Spatial transcriptomics predicted a molecular interplay amongst neighboring cell-types in the injured mammalian kidney Main Text.
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17
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Vanrobaeys Y, Peterson ZJ, Walsh EN, Chatterjee S, Lin LC, Lyons LC, Nickl-Jockschat T, Abel T. Spatial transcriptomics reveals unique gene expression changes in different brain regions after sleep deprivation. Nat Commun 2023; 14:7095. [PMID: 37925446 PMCID: PMC10625558 DOI: 10.1038/s41467-023-42751-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2023] [Accepted: 10/20/2023] [Indexed: 11/06/2023] Open
Abstract
Sleep deprivation has far-reaching consequences on the brain and behavior, impacting memory, attention, and metabolism. Previous research has focused on gene expression changes in individual brain regions, such as the hippocampus or cortex. Therefore, it is unclear how uniformly or heterogeneously sleep loss affects the brain. Here, we use spatial transcriptomics to define the impact of a brief period of sleep deprivation across the brain in male mice. We find that sleep deprivation induced pronounced differences in gene expression across the brain, with the greatest changes in the hippocampus, neocortex, hypothalamus, and thalamus. Both the differentially expressed genes and the direction of regulation differed markedly across regions. Importantly, we developed bioinformatic tools to register tissue sections and gene expression data into a common anatomical space, allowing a brain-wide comparison of gene expression patterns between samples. Our results suggest that distinct molecular mechanisms acting in discrete brain regions underlie the biological effects of sleep deprivation.
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Affiliation(s)
- Yann Vanrobaeys
- Interdisciplinary Graduate Program in Genetics, University of Iowa, 357 Medical Research Center Iowa City, Iowa, IA, USA
- Iowa Neuroscience Institute, Carver College of Medicine, University of Iowa, 169 Newton Road, 2312 Pappajohn Biomedical Discovery Building, Iowa City, IA, USA
- Department of Neuroscience and Pharmacology, Carver College of Medicine, University of Iowa, 51 Newton Road, 2-417B Bowen Science Building, Iowa City, IA, USA
| | - Zeru J Peterson
- Iowa Neuroscience Institute, Carver College of Medicine, University of Iowa, 169 Newton Road, 2312 Pappajohn Biomedical Discovery Building, Iowa City, IA, USA
- Department of Psychiatry, University of Iowa, Iowa City, IA, USA
| | - Emily N Walsh
- Iowa Neuroscience Institute, Carver College of Medicine, University of Iowa, 169 Newton Road, 2312 Pappajohn Biomedical Discovery Building, Iowa City, IA, USA
- Department of Neuroscience and Pharmacology, Carver College of Medicine, University of Iowa, 51 Newton Road, 2-417B Bowen Science Building, Iowa City, IA, USA
- Interdisciplinary Graduate Program in Neuroscience, University of Iowa, 356 Medical Research Center, Iowa City, IA, USA
| | - Snehajyoti Chatterjee
- Iowa Neuroscience Institute, Carver College of Medicine, University of Iowa, 169 Newton Road, 2312 Pappajohn Biomedical Discovery Building, Iowa City, IA, USA
- Department of Neuroscience and Pharmacology, Carver College of Medicine, University of Iowa, 51 Newton Road, 2-417B Bowen Science Building, Iowa City, IA, USA
| | - Li-Chun Lin
- Iowa Neuroscience Institute, Carver College of Medicine, University of Iowa, 169 Newton Road, 2312 Pappajohn Biomedical Discovery Building, Iowa City, IA, USA
- Department of Neuroscience and Pharmacology, Carver College of Medicine, University of Iowa, 51 Newton Road, 2-417B Bowen Science Building, Iowa City, IA, USA
- Department of Neurology, University of Iowa, Iowa City, IA, USA
| | - Lisa C Lyons
- Program in Neuroscience, Department of Biological Science, Florida State University, Tallahassee, FL, USA
| | - Thomas Nickl-Jockschat
- Iowa Neuroscience Institute, Carver College of Medicine, University of Iowa, 169 Newton Road, 2312 Pappajohn Biomedical Discovery Building, Iowa City, IA, USA.
- Department of Neuroscience and Pharmacology, Carver College of Medicine, University of Iowa, 51 Newton Road, 2-417B Bowen Science Building, Iowa City, IA, USA.
- Department of Psychiatry, University of Iowa, Iowa City, IA, USA.
| | - Ted Abel
- Iowa Neuroscience Institute, Carver College of Medicine, University of Iowa, 169 Newton Road, 2312 Pappajohn Biomedical Discovery Building, Iowa City, IA, USA.
- Department of Neuroscience and Pharmacology, Carver College of Medicine, University of Iowa, 51 Newton Road, 2-417B Bowen Science Building, Iowa City, IA, USA.
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18
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Marques E, Alves Teixeira M, Nguyen C, Terzi F, Gallazzini M. Lipocalin-2 induces mitochondrial dysfunction in renal tubular cells via mTOR pathway activation. Cell Rep 2023; 42:113032. [PMID: 37624695 DOI: 10.1016/j.celrep.2023.113032] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2023] [Revised: 07/03/2023] [Accepted: 08/09/2023] [Indexed: 08/27/2023] Open
Abstract
Mitochondrial dysfunction is a critical process in renal epithelial cells upon kidney injury. While its implication in kidney disease progression is established, the mechanisms modulating it remain unclear. Here, we describe the role of Lipocalin-2 (LCN2), a protein expressed in injured tubular cells, in mitochondrial dysfunction. We show that LCN2 expression decreases mitochondrial mass and function and induces mitochondrial fragmentation. Importantly, while LCN2 expression favors DRP1 mitochondrial recruitment, DRP1 inhibition antagonizes LCN2's effect on mitochondrial shape. Remarkably, LCN2 promotes mitochondrial fragmentation independently of its secretion or transport iron activity. Mechanistically, intracellular LCN2 expression increases mTOR activity, and rapamycin inhibits LCN2's effect on mitochondrial shape. In vivo, Lcn2 gene inactivation prevents mTOR activation and mitochondrial length decrease observed upon ischemia-reperfusion-induced kidney injury (IRI) in Lcn2+/+ mice. Our data identify LCN2 as a key regulator of mitochondrial dynamics and further elucidate the mechanisms leading to mitochondrial dysfunction.
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Affiliation(s)
- Eloïse Marques
- Mechanisms and Therapeutic Strategies of Chronic Kidney Disease, INSERM U1151-CNRS UMR 8253, Université Paris Cité, Institut Necker Enfants Malades, 160 Rue de Vaugirard, 75015 Paris, France
| | - Maraiza Alves Teixeira
- Mechanisms and Therapeutic Strategies of Chronic Kidney Disease, INSERM U1151-CNRS UMR 8253, Université Paris Cité, Institut Necker Enfants Malades, 160 Rue de Vaugirard, 75015 Paris, France
| | - Clément Nguyen
- Mechanisms and Therapeutic Strategies of Chronic Kidney Disease, INSERM U1151-CNRS UMR 8253, Université Paris Cité, Institut Necker Enfants Malades, 160 Rue de Vaugirard, 75015 Paris, France
| | - Fabiola Terzi
- Mechanisms and Therapeutic Strategies of Chronic Kidney Disease, INSERM U1151-CNRS UMR 8253, Université Paris Cité, Institut Necker Enfants Malades, 160 Rue de Vaugirard, 75015 Paris, France
| | - Morgan Gallazzini
- Mechanisms and Therapeutic Strategies of Chronic Kidney Disease, INSERM U1151-CNRS UMR 8253, Université Paris Cité, Institut Necker Enfants Malades, 160 Rue de Vaugirard, 75015 Paris, France.
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19
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Li C, Ma QY, Liu XQ, Li HD, Yu MJ, Xie SS, Ma WX, Chen Y, Wang JN, He RB, Bian HG, He Y, Gao L, Deng SS, Zang HM, Gong Q, Wen JG, Liu MM, Yang C, Chen HY, Li J, Lan HY, Jin J, Yao RS, Meng XM. Genetic and pharmacological inhibition of GRPR protects against acute kidney injury via attenuating renal inflammation and necroptosis. Mol Ther 2023; 31:2734-2754. [PMID: 37415332 PMCID: PMC10492025 DOI: 10.1016/j.ymthe.2023.06.016] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2023] [Revised: 05/16/2023] [Accepted: 06/28/2023] [Indexed: 07/08/2023] Open
Abstract
Gastrin-releasing peptide (GRP) binds to its receptor (GRP receptor [GRPR]) to regulate multiple biological processes, but the function of GRP/GRPR axis in acute kidney injury (AKI) remains unknown. In the present study, GRPR is highly expressed by tubular epithelial cells (TECs) in patients or mice with AKI, while histone deacetylase 8 may lead to the transcriptional activation of GRPR. Functionally, we uncovered that GRPR was pathogenic in AKI, as genetic deletion of GRPR was able to protect mice from cisplatin- and ischemia-induced AKI. This was further confirmed by specifically deleting the GRPR gene from TECs in GRPRFlox/Flox//KspCre mice. Mechanistically, we uncovered that GRPR was able to interact with Toll-like receptor 4 to activate STAT1 that bound the promoter of MLKL and CCL2 to induce TEC necroptosis, necroinflammation, and macrophages recruitment. This was further confirmed by overexpressing STAT1 to restore renal injury in GRPRFlox/Flox/KspCre mice. Concurrently, STAT1 induced GRP synthesis to enforce the GRP/GRPR/STAT1 positive feedback loop. Importantly, targeting GRPR by lentivirus-packaged small hairpin RNA or by treatment with a novel GRPR antagonist RH-1402 was able to inhibit cisplatin-induced AKI. In conclusion, GRPR is pathogenic in AKI and mediates AKI via the STAT1-dependent mechanism. Thus, targeting GRPR may be a novel therapeutic strategy for AKI.
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Affiliation(s)
- Chao Li
- Inflammation and Immune Mediated Diseases Laboratory of Anhui Province, The Key Laboratory of Anti-inflammatory of Immune Medicines, Ministry of Education, Anhui Institute of Innovative Drugs, School of Pharmacy, Anhui Medical University, Hefei 230032, China
| | - Qiu-Ying Ma
- Department of Pharmacy, The First Affiliated Hospital of Anhui Medical University, Anhui Public Health Clinical Center, No. 100 Huaihai Road, Hefei 230012, China
| | - Xue-Qi Liu
- Department of Nephrology, The First Affiliated Hospital of Anhui Medical University, Hefei 230022, China
| | - Hai-di Li
- Inflammation and Immune Mediated Diseases Laboratory of Anhui Province, The Key Laboratory of Anti-inflammatory of Immune Medicines, Ministry of Education, Anhui Institute of Innovative Drugs, School of Pharmacy, Anhui Medical University, Hefei 230032, China
| | - Ming-Jun Yu
- School of Food and Biological Engineering, Hefei University of Technology, Hefei 230009, China
| | - Shuai-Shuai Xie
- Inflammation and Immune Mediated Diseases Laboratory of Anhui Province, The Key Laboratory of Anti-inflammatory of Immune Medicines, Ministry of Education, Anhui Institute of Innovative Drugs, School of Pharmacy, Anhui Medical University, Hefei 230032, China
| | - Wen-Xian Ma
- Inflammation and Immune Mediated Diseases Laboratory of Anhui Province, The Key Laboratory of Anti-inflammatory of Immune Medicines, Ministry of Education, Anhui Institute of Innovative Drugs, School of Pharmacy, Anhui Medical University, Hefei 230032, China
| | - Ying Chen
- Inflammation and Immune Mediated Diseases Laboratory of Anhui Province, The Key Laboratory of Anti-inflammatory of Immune Medicines, Ministry of Education, Anhui Institute of Innovative Drugs, School of Pharmacy, Anhui Medical University, Hefei 230032, China
| | - Jia-Nan Wang
- Inflammation and Immune Mediated Diseases Laboratory of Anhui Province, The Key Laboratory of Anti-inflammatory of Immune Medicines, Ministry of Education, Anhui Institute of Innovative Drugs, School of Pharmacy, Anhui Medical University, Hefei 230032, China
| | - Ruo-Bing He
- Inflammation and Immune Mediated Diseases Laboratory of Anhui Province, The Key Laboratory of Anti-inflammatory of Immune Medicines, Ministry of Education, Anhui Institute of Innovative Drugs, School of Pharmacy, Anhui Medical University, Hefei 230032, China
| | - He-Ge Bian
- Department of Pharmacology, School of Basic Medical Sciences, Key Laboratory of Anti-inflammatory and Immunopharmacology, Ministry of Education, Anhui Medical University, Hefei 230032, China
| | - Yuan He
- Inflammation and Immune Mediated Diseases Laboratory of Anhui Province, The Key Laboratory of Anti-inflammatory of Immune Medicines, Ministry of Education, Anhui Institute of Innovative Drugs, School of Pharmacy, Anhui Medical University, Hefei 230032, China
| | - Li Gao
- Department of Nephrology, The First Affiliated Hospital of Anhui Medical University, Hefei 230022, China
| | - Sheng-Song Deng
- School of Food and Biological Engineering, Hefei University of Technology, Hefei 230009, China
| | - Hong-Mei Zang
- Inflammation and Immune Mediated Diseases Laboratory of Anhui Province, The Key Laboratory of Anti-inflammatory of Immune Medicines, Ministry of Education, Anhui Institute of Innovative Drugs, School of Pharmacy, Anhui Medical University, Hefei 230032, China
| | - Qian Gong
- Department of Cardiovascular Surgery, The First Affiliated Hospital of Anhui Medical University, Hefei 230022, Anhui, China
| | - Jia-Gen Wen
- Inflammation and Immune Mediated Diseases Laboratory of Anhui Province, The Key Laboratory of Anti-inflammatory of Immune Medicines, Ministry of Education, Anhui Institute of Innovative Drugs, School of Pharmacy, Anhui Medical University, Hefei 230032, China
| | - Ming-Ming Liu
- Inflammation and Immune Mediated Diseases Laboratory of Anhui Province, The Key Laboratory of Anti-inflammatory of Immune Medicines, Ministry of Education, Anhui Institute of Innovative Drugs, School of Pharmacy, Anhui Medical University, Hefei 230032, China
| | - Chen Yang
- Institute of Nephrology, Affiliated Hospital of Guangdong Medical University, 57 Renmin Road, Zhanjiang 524001, China
| | - Hai-Yong Chen
- Department of Chinese Medicine, The University of Hong Kong-Shenzhen Hospital, The University of Hong Kong, Shenzhen 518009, China
| | - Jun Li
- Inflammation and Immune Mediated Diseases Laboratory of Anhui Province, The Key Laboratory of Anti-inflammatory of Immune Medicines, Ministry of Education, Anhui Institute of Innovative Drugs, School of Pharmacy, Anhui Medical University, Hefei 230032, China
| | - Hui-Yao Lan
- Department of Medicine and Therapeutics, Li Ka Shing Institute of Health Sciences, and Liu Che Woo Institute of Innovative Medicine, Chinese University of Hong Kong, Shatin, Hong Kong 999077, China
| | - Juan Jin
- Department of Pharmacology, School of Basic Medical Sciences, Key Laboratory of Anti-inflammatory and Immunopharmacology, Ministry of Education, Anhui Medical University, Hefei 230032, China.
| | - Ri-Sheng Yao
- School of Food and Biological Engineering, Hefei University of Technology, Hefei 230009, China.
| | - Xiao-Ming Meng
- Inflammation and Immune Mediated Diseases Laboratory of Anhui Province, The Key Laboratory of Anti-inflammatory of Immune Medicines, Ministry of Education, Anhui Institute of Innovative Drugs, School of Pharmacy, Anhui Medical University, Hefei 230032, China.
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20
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Martin-Cleary C, Sanz AB, Avello A, Sanchez-Niño MD, Ortiz A. NephroCheck at 10: addressing unmet needs in AKI diagnosis and risk stratification. Clin Kidney J 2023; 16:1359-1366. [PMID: 37664563 PMCID: PMC10468756 DOI: 10.1093/ckj/sfad146] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2023] [Indexed: 09/05/2023] Open
Abstract
Despite its name, the current diagnosis of acute kidney injury (AKI) still depends on markers of decreased kidney function and not on markers of injury. This results in a delayed diagnosis: AKI is diagnosed based on serum creatinine criteria only when the severity of injury is enough to decrease glomerular filtration rate. Moreover, by the time AKI is diagnosed, the insult may have already ceased, and even appropriate therapy targeted at the specific insult and its associated pathogenic pathways may no longer be effective. Biomarkers of injury are needed that allow the diagnosis of AKI based on injury criteria. At least three commercially available immunoassays assessing urinary or plasma neutrophil gelatinase-associated lipocalin and urinary tissue inhibitor of metalloproteinases-2 × insulin-like growth factor-binding protein-7 ([TIMP2]*[IGFBP7]) (NephroCheck®) have generated promising data regarding prediction and early diagnosis of AKI, although their relative performance may depend on clinical context. Recently, a urinary peptidomics classifier (PeptAKI) was reported to predict AKI better than current biomarkers. Focusing on [TIMP2]*[IGFBP7], the cellular origin of urinary TIMP2 and IGFBP7 remains unclear, especially under the most common predisposing condition for AKI, i.e. chronic kidney disease. We now discuss novel data on the kidney cell expression of TIMP2 and IGFBP7 and its clinical implications.
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Affiliation(s)
- Catalina Martin-Cleary
- Department of Nephrology and Hypertension, IIS-Fundacion Jimenez Diaz UAM, Madrid, Spain
- RICORS2040, Madrid, Spain
- Departamento de Medicina, Facultad de Medicina, Universidad Autónoma de Madrid, Madrid, Spain
| | - Ana Belen Sanz
- Department of Nephrology and Hypertension, IIS-Fundacion Jimenez Diaz UAM, Madrid, Spain
- RICORS2040, Madrid, Spain
- Departamento de Medicina, Facultad de Medicina, Universidad Autónoma de Madrid, Madrid, Spain
| | - Alejandro Avello
- Department of Nephrology and Hypertension, IIS-Fundacion Jimenez Diaz UAM, Madrid, Spain
- RICORS2040, Madrid, Spain
- Departamento de Medicina, Facultad de Medicina, Universidad Autónoma de Madrid, Madrid, Spain
| | - Maria Dolores Sanchez-Niño
- Department of Nephrology and Hypertension, IIS-Fundacion Jimenez Diaz UAM, Madrid, Spain
- RICORS2040, Madrid, Spain
- Departamento de Farmacología, Facultad de Medicina, Universidad Autónoma de Madrid, Madrid, Spain
| | - Alberto Ortiz
- Department of Nephrology and Hypertension, IIS-Fundacion Jimenez Diaz UAM, Madrid, Spain
- RICORS2040, Madrid, Spain
- Departamento de Medicina, Facultad de Medicina, Universidad Autónoma de Madrid, Madrid, Spain
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21
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DiKun KM, Gudas LJ. Vitamin A and retinoid signaling in the kidneys. Pharmacol Ther 2023; 248:108481. [PMID: 37331524 PMCID: PMC10528136 DOI: 10.1016/j.pharmthera.2023.108481] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2023] [Revised: 05/18/2023] [Accepted: 06/14/2023] [Indexed: 06/20/2023]
Abstract
Vitamin A (VA, retinol) and its metabolites (commonly called retinoids) are required for the proper development of the kidney during embryogenesis, but retinoids also play key roles in the function and repair of the kidney in adults. Kidneys filter 180-200 liters of blood per day and each kidney contains approximately 1 million nephrons, which are often referred to as the 'functional units' of the kidney. Each nephron consists of a glomerulus and a series of tubules (proximal tubule, loop of Henle, distal tubule, and collecting duct) surrounded by a network of capillaries. VA is stored in the liver and converted to active metabolites, most notably retinoic acid (RA), which acts as an agonist for the retinoic acid receptors ((RARs α, β, and γ) to regulate gene transcription. In this review we discuss some of the actions of retinoids in the kidney after injury. For example, in an ischemia-reperfusion model in mice, injury-associated loss of proximal tubule (PT) differentiation markers occurs, followed by re-expression of these differentiation markers during PT repair. Notably, healthy proximal tubules express ALDH1a2, the enzyme that metabolizes retinaldehyde to RA, but transiently lose ALDH1a2 expression after injury, while nearby myofibroblasts transiently acquire RA-producing capabilities after injury. These results indicate that RA is important for renal tubular injury repair and that compensatory mechanisms exist for the generation of endogenous RA by other cell types upon proximal tubule injury. ALDH1a2 levels also increase in podocytes, epithelial cells of the glomeruli, after injury, and RA promotes podocyte differentiation. We also review the ability of exogenous, pharmacological doses of RA and receptor selective retinoids to treat numerous kidney diseases, including kidney cancer and diabetic kidney disease, and the emerging genetic evidence for the importance of retinoids and their receptors in maintaining or restoring kidney function after injury. In general, RA has a protective effect on the kidney after various types of injuries (eg. ischemia, cytotoxic actions of chemicals, hyperglycemia related to diabetes). As more research into the actions of each of the three RARs in the kidney is carried out, a greater understanding of the actions of vitamin A is likely to lead to new insights into the pathology of kidney disorders and the development of new therapies for kidney diseases.
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Affiliation(s)
- Krysta M DiKun
- Department of Pharmacology, Weill Cornell Medical College of Cornell University, New York, NY, USA; New York Presbyterian Hospital, New York, NY, USA; Weill Cornell Graduate School of Medical Sciences, New York, NY, USA
| | - Lorraine J Gudas
- Department of Pharmacology, Weill Cornell Medical College of Cornell University, New York, NY, USA; Department of Urology, Weill Cornell Medicine, New York, NY, USA; New York Presbyterian Hospital, New York, NY, USA; Weill Cornell Graduate School of Medical Sciences, New York, NY, USA.
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22
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Chen Y, Liu A, Liu H, Cai G, Lu N, Chen J. Identification and validation of the diagnostic signature associated with immune microenvironment of acute kidney injury based on ferroptosis-related genes through integrated bioinformatics analysis and machine learning. Front Cell Dev Biol 2023; 11:1210714. [PMID: 37576602 PMCID: PMC10413118 DOI: 10.3389/fcell.2023.1210714] [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: 04/23/2023] [Accepted: 07/14/2023] [Indexed: 08/15/2023] Open
Abstract
Background: Acute kidney injury (AKI) is a common and severe disease, which poses a global health burden with high morbidity and mortality. In recent years, ferroptosis has been recognized as being deeply related to Acute kidney injury. Our aim is to develop a diagnostic signature for Acute kidney injury based on ferroptosis-related genes (FRGs) through integrated bioinformatics analysis and machine learning. Methods: Our previously uploaded mouse Acute kidney injury dataset GSE192883 and another dataset, GSE153625, were downloaded to identify commonly expressed differentially expressed genes (coDEGs) through bioinformatic analysis. The FRGs were then overlapped with the coDEGs to identify differentially expressed FRGs (deFRGs). Immune cell infiltration was used to investigate immune cell dysregulation in Acute kidney injury. Functional enrichment analysis and protein-protein interaction network analysis were applied to identify candidate hub genes for Acute kidney injury. Then, receiver operator characteristic curve analysis and machine learning analysis (Lasso) were used to screen for diagnostic markers in two human datasets. Finally, these potential biomarkers were validated by quantitative real-time PCR in an Acute kidney injury model and across multiple datasets. Results: A total of 885 coDEGs and 33 deFRGs were commonly identified as differentially expressed in both GSE192883 and GSE153625 datasets. In cluster 1 of the coDEGs PPI network, we found a group of 20 genes clustered together with deFRGs, resulting in a total of 48 upregulated hub genes being identified. After ROC analysis, we discovered that 25 hub genes had an area under the curve (AUC) greater than 0.7; Lcn2, Plin2, and Atf3 all had AUCs over than this threshold in both human datasets GSE217427 and GSE139061. Through Lasso analysis, four hub genes (Lcn2, Atf3, Pir, and Mcm3) were screened for building a nomogram and evaluating diagnostic value. Finally, the expression of these four genes was validated in Acute kidney injury datasets and laboratory investigations, revealing that they may serve as ideal ferroptosis markers for Acute kidney injury. Conclusion: Four hub genes (Lcn2, Atf3, Pir, and Mcm3) were identified. After verification, the signature's versatility was confirmed and a nomogram model based on these four genes effectively distinguished Acute kidney injury samples. Our findings provide critical insight into the progression of Acute kidney injury and can guide individualized diagnosis and treatment.
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Affiliation(s)
- Yalei Chen
- Department of Critical Care Medicine, Capital Medical University Electric Power Teaching Hospital/State Grid Beijing Electric Power Hospital, Beijing, China
| | - Anqi Liu
- Department of Critical Care Medicine, Capital Medical University Electric Power Teaching Hospital/State Grid Beijing Electric Power Hospital, Beijing, China
| | - Hunan Liu
- Department of Critical Care Medicine, Capital Medical University Electric Power Teaching Hospital/State Grid Beijing Electric Power Hospital, Beijing, China
| | - Guangyan Cai
- State Key Laboratory of Kidney Diseases, Beijing Key Laboratory of Kidney Disease Research, Department of Nephrology, First Medical Center of Chinese PLA General Hospital, National Clinical Research Center for Kidney Diseases, Nephrology Institute of the Chinese People’s Liberation Army, Beijing, China
| | - Nianfang Lu
- Department of Critical Care Medicine, Capital Medical University Electric Power Teaching Hospital/State Grid Beijing Electric Power Hospital, Beijing, China
| | - Jianwen Chen
- State Key Laboratory of Kidney Diseases, Beijing Key Laboratory of Kidney Disease Research, Department of Nephrology, First Medical Center of Chinese PLA General Hospital, National Clinical Research Center for Kidney Diseases, Nephrology Institute of the Chinese People’s Liberation Army, Beijing, China
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23
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Yu Z, Zhou Y, Zhang Y, Ning X, Li T, Wei L, Wang Y, Bai X, Sun S. Cell Profiling of Acute Kidney Injury to Chronic Kidney Disease Reveals Novel Oxidative Stress Characteristics in the Failed Repair of Proximal Tubule Cells. Int J Mol Sci 2023; 24:11617. [PMID: 37511374 PMCID: PMC10380716 DOI: 10.3390/ijms241411617] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2023] [Revised: 06/16/2023] [Accepted: 06/27/2023] [Indexed: 07/30/2023] Open
Abstract
Chronic kidney disease (CKD) is a major public health issue around the world. A significant number of CKD patients originates from acute kidney injury (AKI) patients, namely "AKI-CKD". CKD is significantly related to the consequences of AKI. Damaged renal proximal tubular (PT) cell repair has been widely confirmed to indicate the renal prognosis of AKI. Oxidative stress is a key damage-associated factor and plays a significant role throughout the development of AKI and CKD. However, the relationships between AKI-CKD progression and oxidative stress are not totally clear and the underlying mechanisms in "AKI-CKD" remain indistinct. In this research, we constructed unilateral ischemia-reperfusion injury (UIRI)-model mice and performed single-nucleus RNA sequencing (snRNA-seq) of the kidney samples from UIRI and sham mice. We obtained our snRNA-seq data and validated the findings based on the joint analysis of public databases, as well as a series of fundamental experiments. Proximal tubular cells associated with failed repair express more complete senescence and oxidative stress characteristics compared to other subgroups. Furthermore, oxidative stress-related transcription factors, including Stat3 and Dnmt3a, are significantly more active under the circumstance of failed repair. What is more, we identified abnormally active intercellular communication between PT cells associated with failed repair and macrophages through the APP-CD74 pathway. More notably, we observed that the significantly increased expression of CD74 in hypoxia-treated TECs (tubular epithelial cells) was dependent on adjacently infiltrated macrophages, which was essential for the further deterioration of failed repair in PT cells. This research provides a novel understanding of the process of AKI to CKD progression, and the oxidative stress-related characteristics that we identified might represent a potentially novel therapeutic strategy against AKI.
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Affiliation(s)
- Zhixiang Yu
- Department of Nephrology, Xijing Hospital, Fourth Military Medical University, Xi'an 710032, China
| | - Ying Zhou
- Department of Nephrology, Xijing Hospital, Fourth Military Medical University, Xi'an 710032, China
| | - Yuzhan Zhang
- Department of Nephrology, Xijing Hospital, Fourth Military Medical University, Xi'an 710032, China
| | - Xiaoxuan Ning
- Department of Geriatrics, Xijing Hospital, Fourth Military Medical University, Xi'an 710032, China
| | - Tian Li
- School of Basic Medicine, Fourth Military Medical University, Xi'an 710032, China
| | - Lei Wei
- Department of Nephrology, Xijing Hospital, Fourth Military Medical University, Xi'an 710032, China
| | - Yingxue Wang
- National Local Joint Engineering Research Center for Precision Surgery & Regenerative Medicine, Shaanxi Provincial Center for Regenerative Medicine and Surgical Engineering, Center for Regenerative and Reconstructive Medicine, Med-X Institute, First Affiliated Hospital of Xi'an Jiaotong University, 124, 76 West Yanta Road, Xi'an 710061, China
| | - Xiao Bai
- Department of Nephrology, Xijing Hospital, Fourth Military Medical University, Xi'an 710032, China
| | - Shiren Sun
- Department of Nephrology, Xijing Hospital, Fourth Military Medical University, Xi'an 710032, China
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24
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Li JSY, Raghubar AM, Matigian NA, Ng MSY, Rogers NM, Mallett AJ. The Utility of Spatial Transcriptomics for Solid Organ Transplantation. Transplantation 2023; 107:1463-1471. [PMID: 36584371 DOI: 10.1097/tp.0000000000004466] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Spatial transcriptomics (ST) measures and maps transcripts within intact tissue sections, allowing the visualization of gene activity within the spatial organization of complex biological systems. This review outlines advances in genomic sequencing technologies focusing on in situ sequencing-based ST, including applications in transplant and relevant nontransplant settings. We describe the experimental and analytical pipelines that underpin the current generation of spatial technologies. This context is important for understanding the potential role ST may play in expanding our knowledge, including in organ transplantation, and the important caveats/limitations when interpreting the vast data output generated by such methodological platforms.
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Affiliation(s)
- Jennifer S Y Li
- Centre for Transplant and Renal Research, Westmead Institute for Medical Research, Westmead, NSW, Australia
- Sydney Medical School, University of Sydney, Sydney, NSW, Australia
| | - Arti M Raghubar
- Kidney Health Service, Royal Brisbane and Women's Hospital, QLD, Australia
- Conjoint Internal Medicine Laboratory, Pathology Queensland, Health Support Queensland, QLD, Australia
- Department of Anatomical Pathology, Pathology Queensland, Health Support Queensland, QLD, Australia
- Faculty of Medicine, University of Queensland, QLD, Australia
- Institute for Molecular Bioscience, University of Queensland, QLD, Australia
| | - Nicholas A Matigian
- QCIF Facility for Advanced Bioinformatics, The University of Queensland, QLD, Australia
| | - Monica S Y Ng
- Kidney Health Service, Royal Brisbane and Women's Hospital, QLD, Australia
- Conjoint Internal Medicine Laboratory, Pathology Queensland, Health Support Queensland, QLD, Australia
- Faculty of Medicine, University of Queensland, QLD, Australia
- Institute for Molecular Bioscience, University of Queensland, QLD, Australia
- Nephrology Department, Princess Alexandra Hospital, QLD, Australia
| | - Natasha M Rogers
- Centre for Transplant and Renal Research, Westmead Institute for Medical Research, Westmead, NSW, Australia
- Sydney Medical School, University of Sydney, Sydney, NSW, Australia
- Department of Renal Medicine, Westmead Hospital, Westmead, NSW, Australia
| | - Andrew J Mallett
- Faculty of Medicine, University of Queensland, QLD, Australia
- Institute for Molecular Bioscience, University of Queensland, QLD, Australia
- College of Medicine and Dentistry, James Cook University, QLD, Australia
- Department of Renal Medicine, Townsville University Hospital, QLD, Australia
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25
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Fangma Y, Liu M, Liao J, Chen Z, Zheng Y. Dissecting the brain with spatially resolved multi-omics. J Pharm Anal 2023; 13:694-710. [PMID: 37577383 PMCID: PMC10422112 DOI: 10.1016/j.jpha.2023.04.003] [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: 10/31/2022] [Revised: 04/04/2023] [Accepted: 04/06/2023] [Indexed: 08/15/2023] Open
Abstract
Recent studies have highlighted spatially resolved multi-omics technologies, including spatial genomics, transcriptomics, proteomics, and metabolomics, as powerful tools to decipher the spatial heterogeneity of the brain. Here, we focus on two major approaches in spatial transcriptomics (next-generation sequencing-based technologies and image-based technologies), and mass spectrometry imaging technologies used in spatial proteomics and spatial metabolomics. Furthermore, we discuss their applications in neuroscience, including building the brain atlas, uncovering gene expression patterns of neurons for special behaviors, deciphering the molecular basis of neuronal communication, and providing a more comprehensive explanation of the molecular mechanisms underlying central nervous system disorders. However, further efforts are still needed toward the integrative application of multi-omics technologies, including the real-time spatial multi-omics analysis in living cells, the detailed gene profile in a whole-brain view, and the combination of functional verification.
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Affiliation(s)
- Yijia Fangma
- Key Laboratory of Neuropharmacology and Translational Medicine of Zhejiang Province, School of Pharmaceutical Sciences, Zhejiang Chinese Medical University, Hangzhou, 310053, China
| | - Mengting Liu
- Key Laboratory of Neuropharmacology and Translational Medicine of Zhejiang Province, School of Pharmaceutical Sciences, Zhejiang Chinese Medical University, Hangzhou, 310053, China
| | - Jie Liao
- Pharmaceutical Informatics Institute, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Zhong Chen
- Key Laboratory of Neuropharmacology and Translational Medicine of Zhejiang Province, School of Pharmaceutical Sciences, Zhejiang Chinese Medical University, Hangzhou, 310053, China
| | - Yanrong Zheng
- Key Laboratory of Neuropharmacology and Translational Medicine of Zhejiang Province, School of Pharmaceutical Sciences, Zhejiang Chinese Medical University, Hangzhou, 310053, China
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26
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Maria Francis Y, Karunakaran B, Ashfaq F, Yahia Qattan M, Ahmad I, Alkhathami AG, Idreesh Khan M, Varadhan M, Govindan L, Ponnusamy Kasirajan S. Mercuric Chloride Induced Nephrotoxicity: Ameliorative Effect of Carica papaya Leaves Confirmed by Histopathology, Immunohistochemistry, and Gene Expression Studies. ACS OMEGA 2023; 8:21696-21708. [PMID: 37360438 PMCID: PMC10286259 DOI: 10.1021/acsomega.3c01045] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/24/2023] [Accepted: 05/08/2023] [Indexed: 06/28/2023]
Abstract
The present study analyzes the efficacy of the ethanolic extract of C. papaya leaves (ECP) against HgCl2-induced nephrotoxicity. The effects on the biochemical and percentage of body and organ weight against HgCl2-induced nephrotoxicity in female Wistar rats were studied. Wistar rats were divided into five groups with six animals in each group: control, HgCl2 (2.5 mg/kg b.w.), N-acetylcysteine (NAC 180 mg/kg) + HgCl2, ECP (300 mg/kg b.w.) + HgCl2, and ECP (600 mg/kg) + HgCl2 groups. After 28 days of study, animals were sacrificed on the 29th day to harvest the blood and kidneys for further analysis. The effect ECP was analyzed by immunohistochemistry (NGAL) and real-time PCR (KIM-1 and NGAL mRNA) in HgCl2-induced nephrotoxicity. The results revealed that the HgCl2 group showed prominent damage in the proximal tubules and glomerulus of nephrons and enormous expression of NGAL in immunohistochemistry and KIM-1 and NGAL in real-time PCR compared to the control group. The simultaneous pretreatment with NAC (180 mg/kg) and ECP (600 and 300 mg/kg) reduced renal damage and expression of NGAL in immunohistochemistry and KIM-1 and NGAL gene in real-time PCR. This study attests to the nephroprotective effect of ECP against HgCl2-induced toxicity.
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Affiliation(s)
- Yuvaraj Maria Francis
- Department
of Anatomy, Saveetha Medical College and Hospital, Saveetha Institute of Medical and Technical Sciences, Chennai 602105, Tamil Nadu, India
| | - Balaji Karunakaran
- Department
of Anatomy, Saveetha Medical College and Hospital, Saveetha Institute of Medical and Technical Sciences, Chennai 602105, Tamil Nadu, India
| | - Fauzia Ashfaq
- Department
of Clinical Nutrition, College of Applied Medical Sciences, Jazan University, Jazan 45142, Saudi Arabia
| | - Malak Yahia Qattan
- Health
Sciences Departments, College of Applied Studies and Community Service, King Saud University, KSA-4545, Riyadh 11451, Saudi Arabia
| | - Irfan Ahmad
- Department
of Clinical Laboratory Sciences, College of Applied Medical Sciences, King Khalid University, Abha 61421, Saudi Arabia
| | - Ali G. Alkhathami
- Department
of Clinical Laboratory Sciences, College of Applied Medical Sciences, King Khalid University, Abha 61421, Saudi Arabia
| | - Mohammad Idreesh Khan
- Department
of Clinical Nutrition, College of Applied Health Sciences in Ar Rass, Qassim University, Ar Rass 51921, Saudi Arabia
| | - Mohan Varadhan
- Department
of Siddha, TN Dr. MGR Medical University,
Guindy, Chennai 600032, India
| | - Lakshmanan Govindan
- Department
of Anatomy, Saveetha Medical College and Hospital, Saveetha Institute of Medical and Technical Sciences, Chennai 602105, Tamil Nadu, India
| | - Sankaran Ponnusamy Kasirajan
- Department
of Anatomy, All India Institute of Medical
Sciences (AIIMS), Mangalagiri, Andhra Pradesh 522503, India
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27
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Deng B, Wang S, Zhou P, Ding F. New insights into immune cell diversity in acute kidney injury. Cell Mol Immunol 2023; 20:680-682. [PMID: 36973486 PMCID: PMC10229659 DOI: 10.1038/s41423-023-01003-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2023] [Accepted: 03/11/2023] [Indexed: 03/29/2023] Open
Affiliation(s)
- Bo Deng
- Division of Nephrology, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Sutian Wang
- State Key Laboratory of Livestock and Poultry Breeding, Guangdong Key Laboratory of Animal Breeding and Nutrition, Institute of Animal Science, Guangdong Academy of Agricultural Sciences, Guangzhou, China
| | - Peihui Zhou
- Division of Nephrology, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Feng Ding
- Division of Nephrology, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China.
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28
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Tang R, Jin P, Shen C, Lin W, Yu L, Hu X, Meng T, Zhang L, Peng L, Xiao X, Eggenhuizen P, Ooi JD, Wu X, Ding X, Zhong Y. Single-cell RNA sequencing reveals the transcriptomic landscape of kidneys in patients with ischemic acute kidney injury. Chin Med J (Engl) 2023; 136:1177-1187. [PMID: 37083129 PMCID: PMC10278705 DOI: 10.1097/cm9.0000000000002679] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2022] [Indexed: 04/22/2023] Open
Abstract
BACKGROUND Ischemic acute kidney injury (AKI) is a common syndrome associated with considerable mortality and healthcare costs. Up to now, the underlying pathogenesis of ischemic AKI remains incompletely understood, and specific strategies for early diagnosis and treatment of ischemic AKI are still lacking. Here, this study aimed to define the transcriptomic landscape of AKI patients through single-cell RNA sequencing (scRNA-seq) analysis in kidneys. METHODS In this study, scRNA-seq technology was applied to kidneys from two ischemic AKI patients, and three human public scRNA-seq datasets were collected as controls. Differentially expressed genes (DEGs) and cell clusters of kidneys were determined. Gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analysis, as well as the ligand-receptor interaction between cells, were performed. We also validated several DEGs expression in kidneys from human ischemic AKI and ischemia/reperfusion (I/R) injury induced AKI mice through immunohistochemistry staining. RESULTS 15 distinct cell clusters were determined in kidney from subjects of ischemic AKI and control. The injured proximal tubules (PT) displayed a proapoptotic and proinflammatory phenotype. PT cells of ischemic AKI had up-regulation of novel pro-apoptotic genes including USP47 , RASSF4 , EBAG9 , IER3 , SASH1 , SEPTIN7 , and NUB1 , which have not been reported in ischemic AKI previously. Several hub genes were validated in kidneys from human AKI and renal I/R injury mice, respectively. Furthermore, PT highly expressed DEGs enriched in endoplasmic reticulum stress, autophagy, and retinoic acid-inducible gene I (RIG-I) signaling. DEGs overexpressed in other tubular cells were primarily enriched in nucleotide-binding and oligomerization domain (NOD)-like receptor signaling, estrogen signaling, interleukin (IL)-12 signaling, and IL-17 signaling. Overexpressed genes in kidney-resident immune cells including macrophages, natural killer T (NKT) cells, monocytes, and dendritic cells were associated with leukocyte activation, chemotaxis, cell adhesion, and complement activation. In addition, the ligand-receptor interactions analysis revealed prominent communications between macrophages and monocytes with other cells in the process of ischemic AKI. CONCLUSION Together, this study reveals distinct cell-specific transcriptomic atlas of kidney in ischemic AKI patients, altered signaling pathways, and potential cell-cell crosstalk in the development of AKI. These data reveal new insights into the pathogenesis and potential therapeutic strategies in ischemic AKI.
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Affiliation(s)
- Rong Tang
- Department of Nephrology, Xiangya Hospital, Central South University, Changsha, Hunan 410008, China
- Key Laboratory of Biological Nanotechnology of National Health Commission, Xiangya Hospital, Central South University, Changsha, Hunan 410008, China
| | - Peng Jin
- Department of Organ Transplantation, Xiangya Hospital, Central South University, Changsha, Hunan 410008, China
| | - Chanjuan Shen
- Department of Hematology, The Affiliated Zhuzhou Hospital Xiangya Medical College, Central South University, Zhuzhou, Hunan 412007, China
| | - Wei Lin
- Key Laboratory of Biological Nanotechnology of National Health Commission, Xiangya Hospital, Central South University, Changsha, Hunan 410008, China
- Department of Pathology, Xiangya Hospital, Central South University, Changsha, Hunan 410008, China
| | - Leilin Yu
- Department of Nephrology, Xiangya Hospital, Central South University, Changsha, Hunan 410008, China
- Department of Nephrology, Jiujiang Hospital of Traditional Chinese Medicine, Jiujiang, Jiangxi 332099, China
| | - Xueling Hu
- Department of Nephrology, Xiangya Hospital, Central South University, Changsha, Hunan 410008, China
| | - Ting Meng
- Department of Nephrology, Xiangya Hospital, Central South University, Changsha, Hunan 410008, China
- Key Laboratory of Biological Nanotechnology of National Health Commission, Xiangya Hospital, Central South University, Changsha, Hunan 410008, China
| | - Linlin Zhang
- Department of Nephrology, Xiangya Hospital, Central South University, Changsha, Hunan 410008, China
| | - Ling Peng
- Department of Nephrology, Xiangya Hospital, Central South University, Changsha, Hunan 410008, China
| | - Xiangcheng Xiao
- Department of Nephrology, Xiangya Hospital, Central South University, Changsha, Hunan 410008, China
- Key Laboratory of Biological Nanotechnology of National Health Commission, Xiangya Hospital, Central South University, Changsha, Hunan 410008, China
| | - Peter Eggenhuizen
- Department of Medicine, Centre for Inflammatory Diseases, Monash Medical Centre, Monash University, Clayton, VIC 3168, Australia
| | - Joshua D. Ooi
- Department of Nephrology, Xiangya Hospital, Central South University, Changsha, Hunan 410008, China
- Department of Medicine, Centre for Inflammatory Diseases, Monash Medical Centre, Monash University, Clayton, VIC 3168, Australia
| | - Xueqin Wu
- Department of Nephrology, The Third Xiangya Hospital, Central South University, Changsha, Hunan 410013, China
| | - Xiang Ding
- Department of Organ Transplantation, Xiangya Hospital, Central South University, Changsha, Hunan 410008, China
| | - Yong Zhong
- Department of Nephrology, Xiangya Hospital, Central South University, Changsha, Hunan 410008, China
- Key Laboratory of Biological Nanotechnology of National Health Commission, Xiangya Hospital, Central South University, Changsha, Hunan 410008, China
- National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, Hunan 410008, China
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Wen Y, Xu L, Melchinger I, Thiessen-Philbrook H, Moledina DG, Coca SG, Hsu CY, Go AS, Liu KD, Siew ED, Ikizler TA, Chinchilli VM, Kaufman JS, Kimmel PL, Himmelfarb J, Cantley LG, Parikh CR. Longitudinal biomarkers and kidney disease progression after acute kidney injury. JCI Insight 2023; 8:e167731. [PMID: 36951957 PMCID: PMC10243801 DOI: 10.1172/jci.insight.167731] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2022] [Accepted: 03/15/2023] [Indexed: 03/24/2023] Open
Abstract
BACKGROUNDLongitudinal investigations of murine acute kidney injury (AKI) suggest that injury and inflammation may persist long after the initial insult. However, the evolution of these processes and their prognostic values are unknown in patients with AKI.METHODSIn a prospective cohort of 656 participants hospitalized with AKI, we measured 7 urine and 2 plasma biomarkers of kidney injury, inflammation, and tubular health at multiple time points from the diagnosis to 12 months after AKI. We used linear mixed-effect models to estimate biomarker changes over time, and we used Cox proportional hazard regressions to determine their associations with a composite outcome of chronic kidney disease (CKD) incidence and progression. We compared the gene expression kinetics of biomarkers in murine models of repair and atrophy after ischemic reperfusion injury (IRI).RESULTSAfter 4.3 years, 106 and 52 participants developed incident CKD and CKD progression, respectively. Each SD increase in the change of urine KIM-1, MCP-1, and plasma TNFR1 from baseline to 12 months was associated with 2- to 3-fold increased risk for CKD, while the increase in urine uromodulin was associated with 40% reduced risk for CKD. The trajectories of these biological processes were associated with progression to kidney atrophy in mice after IRI.CONCLUSIONSustained tissue injury and inflammation, and slower restoration of tubular health, are associated with higher risk of kidney disease progression. Further investigation into these ongoing biological processes may help researchers understand and prevent the AKI-to-CKD transition.FUNDINGNIH and NIDDK (grants U01DK082223, U01DK082185, U01DK082192, U01DK082183, R01DK098233, R01DK101507, R01DK114014, K23DK100468, R03DK111881, K01DK120783, and R01DK093771).
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Affiliation(s)
- Yumeng Wen
- Division of Nephrology, Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Leyuan Xu
- Section of Nephrology, Department of Medicine, Yale School of Medicine, New Haven, Connecticut, USA
| | - Isabel Melchinger
- Section of Nephrology, Department of Medicine, Yale School of Medicine, New Haven, Connecticut, USA
| | - Heather Thiessen-Philbrook
- Division of Nephrology, Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Dennis G. Moledina
- Section of Nephrology, Department of Medicine, Yale School of Medicine, New Haven, Connecticut, USA
| | - Steven G. Coca
- Division of Nephrology, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Chi-yuan Hsu
- Division of Nephrology, University of California, San Francisco, San Francisco, California, USA
- Kaiser Permanente Division of Research, Oakland, California, USA
| | - Alan S. Go
- Kaiser Permanente Division of Research, Oakland, California, USA
| | - Kathleen D. Liu
- Division of Nephrology, University of California, San Francisco, San Francisco, California, USA
| | - Edward D. Siew
- Division of Nephrology, Vanderbilt University, Nashville, Tennessee, USA
| | - T. Alp Ikizler
- Division of Nephrology, Vanderbilt University, Nashville, Tennessee, USA
| | - Vernon M. Chinchilli
- Division of Nephrology, Pennsylvania State University College of Medicine, Hershey, Pennsylvania, USA
| | - James S. Kaufman
- Division of Nephrology, New York University School of Medicine and VA New York Harbor Healthcare System, New York, New York, USA
| | - Paul L. Kimmel
- National Institute of Diabetes and Digestive and Kidney Diseases (NIDDK), National Institutes of Health (NIH), Bethesda, Maryland, USA
| | | | - Lloyd G. Cantley
- Section of Nephrology, Department of Medicine, Yale School of Medicine, New Haven, Connecticut, USA
| | - Chirag R. Parikh
- Division of Nephrology, Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
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30
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Song N, Xu Y, Paust HJ, Panzer U, de Las Noriega MM, Guo L, Renné T, Huang J, Meng X, Zhao M, Thaiss F. IKK1 aggravates ischemia-reperfusion kidney injury by promoting the differentiation of effector T cells. Cell Mol Life Sci 2023; 80:125. [PMID: 37074502 PMCID: PMC10115737 DOI: 10.1007/s00018-023-04763-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2022] [Revised: 03/10/2023] [Accepted: 03/20/2023] [Indexed: 04/20/2023]
Abstract
Ischemia-reperfusion injury (IRI) is one of the major causes of acute kidney injury (AKI), and experimental work has revealed detailed insight into the inflammatory response in the kidney. T cells and NFκB pathway play an important role in IRI. Therefore, we examined the regulatory role and mechanisms of IkappaB kinase 1 (IKK1) in CD4+T lymphocytes in an experimental model of IRI. IRI was induced in CD4cre and CD4IKK1Δ mice. Compared to control mice, conditional deficiency of IKK1 in CD4+T lymphocyte significantly decreased serum creatinine, blood urea nitrogen (BUN) level, and renal tubular injury score. Mechanistically, lack in IKK1 in CD4+T lymphocytes reduced the ability of CD4 lymphocytes to differentiate into Th1/Th17 cells. Similar to IKK1 gene ablation, pharmacological inhibition of IKK also protected mice from IRI. Together, lymphocyte IKK1 plays a pivotal role in IRI by promoting T cells differentiation into Th1/Th17 and targeting lymphocyte IKK1 may be a novel therapeutic strategy for IRI.
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Affiliation(s)
- Ning Song
- Department of Critical Care Medicine, The First Affiliated Hospital of Harbin Medical University, Youzheng St 23, Harbin, 150001, China
- III. Department of Medicine, University Medical Center Hamburg-Eppendorf, Martinistraße 52, Hamburg, 20246, Germany
| | - Yang Xu
- Department of General, Visceral and Thoracic Surgery, University Medical Center Hamburg-Eppendorf, Hamburg, 20246, Germany
| | - Hans-Joachim Paust
- III. Department of Medicine, University Medical Center Hamburg-Eppendorf, Martinistraße 52, Hamburg, 20246, Germany
| | - Ulf Panzer
- III. Department of Medicine, University Medical Center Hamburg-Eppendorf, Martinistraße 52, Hamburg, 20246, Germany
| | | | - Linlin Guo
- III. Department of Medicine, University Medical Center Hamburg-Eppendorf, Martinistraße 52, Hamburg, 20246, Germany
| | - Thomas Renné
- Institute for Clinical Chemistry and Laboratory Medicine, University Medical Center Hamburg-Eppendorf, Hamburg, 20246, Germany
- Irish Centre for Vascular Biology, School of Pharmacy and Biomolecular Sciences, Royal College of Surgeons in Ireland, Dublin, Ireland
- Center for Thrombosis and Hemostasis (CTH), Johannes Gutenberg University Medical Center, Mainz, 55131, Germany
| | - Jiabin Huang
- Institute for Medical Microbiology, Virology and Hygiene, University Medical Center Hamburg-Eppendorf, Hamburg, 20246, Germany
| | - Xianglin Meng
- Department of Critical Care Medicine, The First Affiliated Hospital of Harbin Medical University, Youzheng St 23, Harbin, 150001, China
- Cancer Institute, Fudan University Shanghai Cancer Center, Shanghai, 200032, People's Republic of China
- Heilongjiang Provincial Key Laboratory of Critical Care Medicine, The First Affiliated Hospital of Harbin Medical University, Harbin, 150001, China
| | - Mingyan Zhao
- Department of Critical Care Medicine, The First Affiliated Hospital of Harbin Medical University, Youzheng St 23, Harbin, 150001, China.
- Heilongjiang Provincial Key Laboratory of Critical Care Medicine, The First Affiliated Hospital of Harbin Medical University, Harbin, 150001, China.
| | - Friedrich Thaiss
- III. Department of Medicine, University Medical Center Hamburg-Eppendorf, Martinistraße 52, Hamburg, 20246, Germany.
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Devarajan P. Pathogenesis of intrinsic acute kidney injury. Curr Opin Pediatr 2023; 35:234-238. [PMID: 36482770 PMCID: PMC9992147 DOI: 10.1097/mop.0000000000001215] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
PURPOSE OF REVIEW This review focuses on the pathogenesis of intrinsic acute kidney injury (AKI), emphasizing recent advances that hold therapeutic promise. RECENT FINDINGS Enhanced endothelin and reduced endothelium-derived nitric oxide release in AKI can be blocked using endothelin receptor antagonists or nitric oxide supplementation. Vasodilatory agents such as theophylline and caffeine may prevent AKI. Free labile iron is a potent factor in the generation of reactive oxygen species and tubule damage in AKI. Apoptosis via induction of p53 is an important mechanism of cell death in AKI, which can be blocked using small interfering RNA. The AKI-driven reduction in nicotinamide adenine dinucleotide can be countered using oral supplements. Surviving tubule cells regenerate after AKI, by upregulating genes encoding growth factors, such as hepatocyte growth factor. Pro-angiogenic agents (statins and erythropoietin) that can mobilize endothelial progenitor cells after AKI are currently being tested. The inflammatory response in AKI, including activation of C5a, can be therapeutically targeted. Contemporary single cell profiling technologies have identified novel genes with altered expression, new signalling pathways and drug targets in AKI. SUMMARY Recent advances in the pathogenesis of intrinsic AKI have provided a better understanding of the clinical continuum and the rational deployment of promising therapeutics.
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Affiliation(s)
- Prasad Devarajan
- Nephrology and Hypertension, Cincinnati Children's Hospital Medical Center, University of Cincinnati School of Medicine, Cincinnati, Ohio, USA
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32
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Charytonowicz D, Brody R, Sebra R. Interpretable and context-free deconvolution of multi-scale whole transcriptomic data with UniCell deconvolve. Nat Commun 2023; 14:1350. [PMID: 36906603 PMCID: PMC10008582 DOI: 10.1038/s41467-023-36961-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2022] [Accepted: 02/27/2023] [Indexed: 03/13/2023] Open
Abstract
We introduce UniCell: Deconvolve Base (UCDBase), a pre-trained, interpretable, deep learning model to deconvolve cell type fractions and predict cell identity across Spatial, bulk-RNA-Seq, and scRNA-Seq datasets without contextualized reference data. UCD is trained on 10 million pseudo-mixtures from a fully-integrated scRNA-Seq training database comprising over 28 million annotated single cells spanning 840 unique cell types from 898 studies. We show that our UCDBase and transfer-learning models achieve comparable or superior performance on in-silico mixture deconvolution to existing, reference-based, state-of-the-art methods. Feature attribute analysis uncovers gene signatures associated with cell-type specific inflammatory-fibrotic responses in ischemic kidney injury, discerns cancer subtypes, and accurately deconvolves tumor microenvironments. UCD identifies pathologic changes in cell fractions among bulk-RNA-Seq data for several disease states. Applied to lung cancer scRNA-Seq data, UCD annotates and distinguishes normal from cancerous cells. Overall, UCD enhances transcriptomic data analysis, aiding in assessment of cellular and spatial context.
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Affiliation(s)
- Daniel Charytonowicz
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Rachel Brody
- Department of Pathology, Molecular and Cell-Based Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Robert Sebra
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
- Icahn Genomics Institute, New York, NY, USA.
- Black Family Stem Cell Institute, New York, NY, USA.
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Inhibition of ALKBH5 attenuates I/R-induced renal injury in male mice by promoting Ccl28 m6A modification and increasing Treg recruitment. Nat Commun 2023; 14:1161. [PMID: 36859428 PMCID: PMC9977869 DOI: 10.1038/s41467-023-36747-y] [Citation(s) in RCA: 21] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2022] [Accepted: 02/15/2023] [Indexed: 03/03/2023] Open
Abstract
Ischemia reperfusion injury (IRI) is a common cause of acute kidney injury (AKI). The role of N6-methyladenosine (m6A) modification in AKI remains unclear. Here, we characterize the role of AlkB homolog 5 (ALKBH5) and m6A modification in an I/R-induced renal injury model in male mice. Alkbh5-knockout mice exhibit milder pathological damage and better renal function than wild-type mice post-IRI, whereas Alkbh5-knockin mice show contrary results. Also conditional knockout of Alkbh5 in the tubular epithelial cells alleviates I/R-induced AKI and fibrosis. CCL28 is identified as a target of ALKBH5. Furthermore, Ccl28 mRNA stability increases with Alkbh5 deficiency, mediating by the binding of insulin-like growth factor 2 binding protein 2. Treg recruitment is upregulated and inflammatory cells are inhibited by the increased CCL28 level in IRI-Alkbh5fl/flKspCre mice. The ALKBH5 inhibitor IOX1 exhibits protective effects against I/R-induced AKI. In summary, inhibition of ALKBH5 promotes the m6A modifications of Ccl28 mRNA, enhancing its stability, and regulating the Treg/inflammatory cell axis. ALKBH5 and this axis is a potential AKI treatment target.
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Bartos K, Moor MB. FGFR regulator Memo1 is dispensable for FGF23 expression by osteoblasts during folic acid-driven kidney injury. Physiol Rep 2023; 11:e15650. [PMID: 36967231 PMCID: PMC10040316 DOI: 10.14814/phy2.15650] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2022] [Revised: 03/04/2023] [Accepted: 03/07/2023] [Indexed: 03/28/2023] Open
Abstract
Loss of the mediator Of cell motility 1 (Memo1) in mice caused kidney disease and a bone disease with diminished osteoblast and osteoclast biomarkers in serum, resembling alterations occurring in adynamic bone disease in humans with chronic kidney disease or in Klotho-deficient mice. Here, we investigated whether Memo1 expression in osteoblasts is required for normal bone structure and FGF23 expression. We deleted Memo1 in the osteoblast-osteocyte lineage in Memo fl/fl mice using a Cre under Col1a1 promotor to obtain osteoblast-specific knockout (obKO) mice. We studied organs by micro-computed tomography, qPCR, and western blot. We challenged mice with folic acid for acute kidney injury (AKI) and analyzed organs. Memo obKO were viable without changes in gross anatomy, serum electrolytes, or circulating FGF23 concentrations compared to controls. Memo1 expression was blunted in bones of Memo obKO, whereas it remained unchanged in other organs. Micro-CT revealed no differences between genotypes in bone structure of vertebrae, femur, and tibia. During AKI, Fgf23 expression in calvaria, and renal transcriptional changes were comparable between genotypes. However, renal injury marker expression, circulating FGF23, and parathyroid hormone revealed a sex difference with more severely affected females than males of either genotype. The present data imply that Memo1 in osteoblasts is dispensable for bone structure and expression of Fgf23. Moreover, we found evidence of potential sex differences in murine folic acid nephropathy similar to other experimental models of renal injury that are important to consider when using this experimental model of renal injury.
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Affiliation(s)
- Katalin Bartos
- Department of Nephrology and HypertensionBern University HospitalBernSwitzerland
- Department of Biomedical ResearchUniversity of BernBernSwitzerland
- National Center of Competence in Research (NCCR) Kidney Control of Homeostasis (Kidney.CH), University of ZurichZurichSwitzerland
| | - Matthias B. Moor
- Department of Nephrology and HypertensionBern University HospitalBernSwitzerland
- Department of Biomedical ResearchUniversity of BernBernSwitzerland
- National Center of Competence in Research (NCCR) Kidney Control of Homeostasis (Kidney.CH), University of ZurichZurichSwitzerland
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35
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Akalay S, Hosgood SA. How to Best Protect Kidneys for Transplantation-Mechanistic Target. J Clin Med 2023; 12:jcm12051787. [PMID: 36902572 PMCID: PMC10003664 DOI: 10.3390/jcm12051787] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2023] [Revised: 02/15/2023] [Accepted: 02/17/2023] [Indexed: 02/25/2023] Open
Abstract
The increasing number of patients on the kidney transplant waiting list underlines the need to expand the donor pool and improve kidney graft utilization. By protecting kidney grafts adequately from the initial ischemic and subsequent reperfusion injury occurring during transplantation, both the number and quality of kidney grafts could be improved. The last few years have seen the emergence of many new technologies to abrogate ischemia-reperfusion (I/R) injury, including dynamic organ preservation through machine perfusion and organ reconditioning therapies. Although machine perfusion is gradually making the transition to clinical practice, reconditioning therapies have not yet progressed from the experimental setting, pointing towards a translational gap. In this review, we discuss the current knowledge on the biological processes implicated in I/R injury and explore the strategies and interventions that are being proposed to either prevent I/R injury, treat its deleterious consequences, or support the reparative response of the kidney. Prospects to improve the clinical translation of these therapies are discussed with a particular focus on the need to address multiple aspects of I/R injury to achieve robust and long-lasting protective effects on the kidney graft.
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Affiliation(s)
- Sara Akalay
- Department of Development and Regeneration, Laboratory of Pediatric Nephrology, KU Leuven, 3000 Leuven, Belgium
| | - Sarah A. Hosgood
- Department of Surgery, University of Cambridge, Cambridge CB2 0QQ, UK
- Correspondence:
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Vanrobaeys Y, Peterson ZJ, Walsh EN, Chatterjee S, Lin LC, Lyons LC, Nickl-Jockschat T, Abel T. Spatial transcriptomics reveals unique gene expression changes in different brain regions after sleep deprivation. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.01.18.524406. [PMID: 36712009 PMCID: PMC9882298 DOI: 10.1101/2023.01.18.524406] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
Sleep deprivation has far-reaching consequences on the brain and behavior, impacting memory, attention, and metabolism. Previous research has focused on gene expression changes in individual brain regions, such as the hippocampus or cortex. Therefore, it is unclear how uniformly or heterogeneously sleep loss affects the brain. Here, we use spatial transcriptomics to define the impact of a brief period of sleep deprivation across the brain. We find that sleep deprivation induced pronounced differences in gene expression across the brain, with the greatest changes in the hippocampus, neocortex, hypothalamus, and thalamus. Both the differentially expressed genes and the direction of regulation differed markedly across regions. Importantly, we developed bioinformatic tools to register tissue sections and gene expression data into a common anatomical space, allowing a brain-wide comparison of gene expression patterns between samples. Our results suggest that distinct molecular mechanisms acting in discrete brain regions underlie the biological effects of sleep deprivation.
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Affiliation(s)
- Yann Vanrobaeys
- Interdisciplinary Graduate Program in Genetics, University of Iowa, 357 Medical Research Center Iowa City, IA 52242, USA
- Iowa Neuroscience Institute, Carver College of Medicine, 169 Newton Road, 2312 Pappajohn Biomedical Discovery Building, University of Iowa, Iowa City, IA 52242, USA
- Department of Neuroscience and Pharmacology, Carver College of Medicine, 51 Newton Road, 2-417B Bowen Science Building, University of Iowa, Iowa City, IA 52242, USA
| | - Zeru J. Peterson
- Iowa Neuroscience Institute, Carver College of Medicine, 169 Newton Road, 2312 Pappajohn Biomedical Discovery Building, University of Iowa, Iowa City, IA 52242, USA
- Department of Psychiatry, University of Iowa, Iowa City, IA, USA
| | - Emily. N. Walsh
- Iowa Neuroscience Institute, Carver College of Medicine, 169 Newton Road, 2312 Pappajohn Biomedical Discovery Building, University of Iowa, Iowa City, IA 52242, USA
- Department of Neuroscience and Pharmacology, Carver College of Medicine, 51 Newton Road, 2-417B Bowen Science Building, University of Iowa, Iowa City, IA 52242, USA
- Interdisciplinary Graduate Program in Neuroscience, University of Iowa, 356 Medical Research Center, Iowa City, IA 52242, USA
| | - Snehajyoti Chatterjee
- Iowa Neuroscience Institute, Carver College of Medicine, 169 Newton Road, 2312 Pappajohn Biomedical Discovery Building, University of Iowa, Iowa City, IA 52242, USA
- Department of Neuroscience and Pharmacology, Carver College of Medicine, 51 Newton Road, 2-417B Bowen Science Building, University of Iowa, Iowa City, IA 52242, USA
| | - Li-Chun Lin
- Iowa Neuroscience Institute, Carver College of Medicine, 169 Newton Road, 2312 Pappajohn Biomedical Discovery Building, University of Iowa, Iowa City, IA 52242, USA
- Department of Neuroscience and Pharmacology, Carver College of Medicine, 51 Newton Road, 2-417B Bowen Science Building, University of Iowa, Iowa City, IA 52242, USA
- Department of Neurology, University of Iowa, Iowa City, IA, USA
| | - Lisa C. Lyons
- Program in Neuroscience, Department of Biological Science, Florida State University, Tallahassee, FL, USA
| | - Thomas Nickl-Jockschat
- Iowa Neuroscience Institute, Carver College of Medicine, 169 Newton Road, 2312 Pappajohn Biomedical Discovery Building, University of Iowa, Iowa City, IA 52242, USA
- Department of Neuroscience and Pharmacology, Carver College of Medicine, 51 Newton Road, 2-417B Bowen Science Building, University of Iowa, Iowa City, IA 52242, USA
- Department of Psychiatry, University of Iowa, Iowa City, IA, USA
| | - Ted Abel
- Iowa Neuroscience Institute, Carver College of Medicine, 169 Newton Road, 2312 Pappajohn Biomedical Discovery Building, University of Iowa, Iowa City, IA 52242, USA
- Department of Neuroscience and Pharmacology, Carver College of Medicine, 51 Newton Road, 2-417B Bowen Science Building, University of Iowa, Iowa City, IA 52242, USA
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Fan Z, Luo Y, Lu H, Wang T, Feng Y, Zhao W, Kim P, Zhou X. SPASCER: spatial transcriptomics annotation at single-cell resolution. Nucleic Acids Res 2023; 51:D1138-D1149. [PMID: 36243975 PMCID: PMC9825565 DOI: 10.1093/nar/gkac889] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2022] [Revised: 09/21/2022] [Accepted: 10/13/2022] [Indexed: 01/30/2023] Open
Abstract
In recent years, the explosive growth of spatial technologies has enabled the characterization of spatial heterogeneity of tissue architectures. Compared to traditional sequencing, spatial transcriptomics reserves the spatial information of each captured location and provides novel insights into diverse spatially related biological contexts. Even though two spatial transcriptomics databases exist, they provide limited analytical information. Information such as spatial heterogeneity of genes and cells, cell-cell communication activities in space, and the cell type compositions in the microenvironment are critical clues to unveil the mechanism of tumorigenesis and embryo differentiation. Therefore, we constructed a new spatial transcriptomics database, named SPASCER (https://ccsm.uth.edu/SPASCER), designed to help understand the heterogeneity of tissue organizations, region-specific microenvironment, and intercellular interactions across tissue architectures at multiple levels. SPASCER contains datasets from 43 studies, including 1082 sub-datasets from 16 organ types across four species. scRNA-seq was integrated to deconvolve/map spatial transcriptomics, and processed with spatial cell-cell interaction, gene pattern and pathway enrichment analysis. Cell-cell interactions and gene regulation network of scRNA-seq from matched spatial transcriptomics were performed as well. The application of SPASCER will provide new insights into tissue architecture and a solid foundation for the mechanistic understanding of many biological processes in healthy and diseased tissues.
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Affiliation(s)
- Zhiwei Fan
- West China School of Public Health and West China Fourth Hospital, Sichuan University, Chengdu 610041, China
- Center for Computational Systems Medicine, School of Biomedical Informatics, The University of Texas Health Science Center at Houston, Houston, TX 77030, USA
| | - Yangyang Luo
- West China Hospital, Sichuan University, Chengdu 610041, China
| | - Huifen Lu
- West China Hospital, Sichuan University, Chengdu 610041, China
| | - Tiangang Wang
- School of Life Science and Technology, Xidian University, Xi’an 710126, China
| | - YuZhou Feng
- West China Hospital, Sichuan University, Chengdu 610041, China
| | - Weiling Zhao
- Center for Computational Systems Medicine, School of Biomedical Informatics, The University of Texas Health Science Center at Houston, Houston, TX 77030, USA
| | - Pora Kim
- Center for Computational Systems Medicine, School of Biomedical Informatics, The University of Texas Health Science Center at Houston, Houston, TX 77030, USA
| | - Xiaobo Zhou
- Center for Computational Systems Medicine, School of Biomedical Informatics, The University of Texas Health Science Center at Houston, Houston, TX 77030, USA
- McGovern Medical School, The University of Texas Health Science Center at Houston, Houston, TX 77030, USA
- School of Dentistry, The University of Texas Health Science Center at Houston, Houston, TX 77030, USA
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Ospina O, Soupir A, Fridley BL. A Primer on Preprocessing, Visualization, Clustering, and Phenotyping of Barcode-Based Spatial Transcriptomics Data. Methods Mol Biol 2023; 2629:115-140. [PMID: 36929076 DOI: 10.1007/978-1-0716-2986-4_7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/18/2023]
Abstract
Recent developments in spatially resolved transcriptomics (ST) have resulted in a large number of studies characterizing the architecture of tissues, the spatial distribution of cell types, and their interactions. Furthermore, ST promises to enable the discovery of more accurate drug targets while also providing a better understanding of the etiology and evolution of complex diseases. The analysis of ST brings similar challenges as seen in other gene expression assays such as scRNA-seq; however, there is the additional spatial information that warrants the development of suitable algorithms for the quality control, preprocessing, visualization, and other discovery-enabling approaches (e.g., clustering, cell phenotyping). In this chapter, we review some of the existing algorithms to perform these analytical tasks and highlight some of the unmet analytical challenges in the analysis of ST data. Given the diversity of available ST technologies, we focus this chapter on the analysis of barcode-based RNA quantitation techniques.
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Affiliation(s)
- Oscar Ospina
- Department of Biostatistics and Bioinformatics, Moffitt Cancer Center, Tampa, FL, USA
| | - Alex Soupir
- Department of Biostatistics and Bioinformatics, Moffitt Cancer Center, Tampa, FL, USA
| | - Brooke L Fridley
- Department of Biostatistics and Bioinformatics, H. Lee Moffitt Cancer Center & Research Institute, Tampa, FL, USA.
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Liu J, Tran V, Vemuri VNP, Byrne A, Borja M, Kim YJ, Agarwal S, Wang R, Awayan K, Murti A, Taychameekiatchai A, Wang B, Emanuel G, He J, Haliburton J, Oliveira Pisco A, Neff NF. Concordance of MERFISH spatial transcriptomics with bulk and single-cell RNA sequencing. Life Sci Alliance 2022; 6:6/1/e202201701. [PMID: 36526371 PMCID: PMC9760489 DOI: 10.26508/lsa.202201701] [Citation(s) in RCA: 21] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2022] [Revised: 09/27/2022] [Accepted: 09/28/2022] [Indexed: 12/23/2022] Open
Abstract
Spatial transcriptomics extends single-cell RNA sequencing (scRNA-seq) by providing spatial context for cell type identification and analysis. Imaging-based spatial technologies such as multiplexed error-robust fluorescence in situ hybridization (MERFISH) can achieve single-cell resolution, directly mapping single-cell identities to spatial positions. MERFISH produces a different data type than scRNA-seq, and a technical comparison between the two modalities is necessary to ascertain how to best integrate them. We performed MERFISH on the mouse liver and kidney and compared the resulting bulk and single-cell RNA statistics with those from the Tabula Muris Senis cell atlas and from two Visium datasets. MERFISH quantitatively reproduced the bulk RNA-seq and scRNA-seq results with improvements in overall dropout rates and sensitivity. Finally, we found that MERFISH independently resolved distinct cell types and spatial structure in both the liver and kidney. Computational integration with the Tabula Muris Senis atlas did not enhance these results. We conclude that MERFISH provides a quantitatively comparable method for single-cell gene expression and can identify cell types without the need for computational integration with scRNA-seq atlases.
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Affiliation(s)
| | | | | | | | | | | | | | - Ruofan Wang
- Chan Zuckerberg Biohub, San Francisco, CA, USA
| | - Kyle Awayan
- Chan Zuckerberg Biohub, San Francisco, CA, USA
| | - Abhishek Murti
- School of Medicine, University of California, San Francisco, CA, USA
| | | | - Bruce Wang
- School of Medicine, University of California, San Francisco, CA, USA
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40
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Li H, Dixon EE, Wu H, Humphreys BD. Comprehensive single-cell transcriptional profiling defines shared and unique epithelial injury responses during kidney fibrosis. Cell Metab 2022; 34:1977-1998.e9. [PMID: 36265491 PMCID: PMC9742301 DOI: 10.1016/j.cmet.2022.09.026] [Citation(s) in RCA: 43] [Impact Index Per Article: 21.5] [Reference Citation Analysis] [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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41
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L'Imperio V, Cazzaniga G, Vergani B, Smith AJ, Alberici F, Pagni F. Monoclonal Gammopathy of Renal Significance: A Molecular Middle Earth between Oncology, Nephrology, and Pathology. KIDNEY DISEASES (BASEL, SWITZERLAND) 2022; 8:446-457. [PMID: 36590677 PMCID: PMC9798844 DOI: 10.1159/000527056] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/08/2022] [Accepted: 09/06/2022] [Indexed: 11/05/2022]
Abstract
Background The renal biopsy represents a cornerstone in the definition of monoclonal gammopathy of renal significance (MGRS), helping in identifying patients with sub-detectable neoplastic clones (MGUS) that would deserve aggressive chemotherapies. However, the rising complexity of this onco-nephrology field is significantly challenging the daily work of nephrologists and nephropathologists, leading to the formation of ultra-specialized international centers with dedicated personnel/instrumentation and stressing the need for a better understanding of the underlying molecular landscape of these entities. Summary In this setting, the application of proteomic techniques, some with in situ capabilities (e.g., MALDI-MS imaging), for the investigation of the most challenging MGRS is progressively shedding light on the pathobiology of these diseases, providing new insights in the diagnosis and prognosis of these cases. This transformation is further enhanced by the application of next-generation digital pathology platforms, leading to a significant improvement of the cultural background for physicians thanks to second opinions, database and atlas creation, enhancement of diagnostic reports, with obvious repercussions for patients both in terms of turnaround time and appropriateness. Key Messages The present review is aimed at bridging the gap between clinical questions (i.e., a better characterization of MGRS) and the molecular landscape of onco-nephrology entities.
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Affiliation(s)
- Vincenzo L'Imperio
- Department of Medicine and Surgery, Pathology, ASST Monza, San Gerardo Hospital, University of Milan-Bicocca, Monza, Italy
| | - Giorgio Cazzaniga
- Department of Medicine and Surgery, Pathology, ASST Monza, San Gerardo Hospital, University of Milan-Bicocca, Monza, Italy
| | - Barbara Vergani
- Department of Medicine and Surgery, Pathology, ASST Monza, San Gerardo Hospital, University of Milan-Bicocca, Monza, Italy
| | - Andrew James Smith
- Department of Medicine and Surgery, Clinical Proteomics and Metabolomics Unit, University of Milano - Bicocca, Monza, Italy
| | - Federico Alberici
- Department of Medical and Surgical Specialties, Radiological Sciences and Public Health, University of Brescia, Brescia, Italy,Nephrology Unit, Spedali Civili Hospital, ASST Spedali Civili di Brescia, Brescia, Italy
| | - Fabio Pagni
- Department of Medicine and Surgery, Pathology, ASST Monza, San Gerardo Hospital, University of Milan-Bicocca, Monza, Italy,*Fabio Pagni,
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42
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Cheung MD, Erman EN, Moore KH, Lever JM, Li Z, LaFontaine JR, Ghajar-Rahimi G, Liu S, Yang Z, Karim R, Yoder BK, Agarwal A, George JF. Resident macrophage subpopulations occupy distinct microenvironments in the kidney. JCI Insight 2022; 7:e161078. [PMID: 36066976 PMCID: PMC9714795 DOI: 10.1172/jci.insight.161078] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2022] [Accepted: 09/02/2022] [Indexed: 11/17/2022] Open
Abstract
The kidney contains a population of resident macrophages from birth that expands as it grows and forms a contiguous network throughout the tissue. Kidney-resident macrophages (KRMs) are important in homeostasis and the response to acute kidney injury. While the kidney contains many microenvironments, it is unknown whether KRMs are a heterogeneous population differentiated by function and location. We combined single-cell RNA-Seq (scRNA-Seq), spatial transcriptomics, flow cytometry, and immunofluorescence imaging to localize, characterize, and validate KRM populations during quiescence and following 19 minutes of bilateral ischemic kidney injury. scRNA-Seq and spatial transcriptomics revealed 7 distinct KRM subpopulations, which are organized into zones corresponding to regions of the nephron. Each subpopulation was identifiable by a unique transcriptomic signature, suggesting distinct functions. Specific protein markers were identified for 2 clusters, allowing analysis by flow cytometry or immunofluorescence imaging. Following injury, the original localization of each subpopulation was lost, either from changing locations or transcriptomic signatures. The original spatial distribution of KRMs was not fully restored for at least 28 days after injury. The change in KRM localization confirmed a long-hypothesized dysregulation of the local immune system following acute injury and may explain the increased risk for chronic kidney disease.
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Affiliation(s)
- Matthew D. Cheung
- Department of Surgery
- Department of Nephrology Research and Training Center
| | - Elise N. Erman
- Department of Surgery
- Department of Nephrology Research and Training Center
| | - Kyle H. Moore
- Department of Surgery
- Department of Nephrology Research and Training Center
| | | | - Zhang Li
- Department of Cellular Developmental and Integrative Biology
| | | | - Gelare Ghajar-Rahimi
- Department of Nephrology Research and Training Center
- Department of Medicine, and
| | | | | | - Rafay Karim
- Department of Surgery
- Department of Nephrology Research and Training Center
| | | | - Anupam Agarwal
- Department of Nephrology Research and Training Center
- Department of Medicine, and
- Department of Veterans Affairs, University of Alabama at Birmingham, Birmingham, Alabama, USA
| | - James F. George
- Department of Surgery
- Department of Nephrology Research and Training Center
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43
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Semibulk RNA-seq analysis as a convenient method for measuring gene expression statuses in a local cellular environment. Sci Rep 2022; 12:15309. [PMID: 36097044 PMCID: PMC9468030 DOI: 10.1038/s41598-022-19391-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2022] [Accepted: 08/29/2022] [Indexed: 11/10/2022] Open
Abstract
When biologically interpretation of the data obtained from the single-cell RNA sequencing (scRNA-seq) analysis is attempted, additional information on the location of the single cells, behavior of the surrounding cells, and the microenvironment they generate, would be very important. We developed an inexpensive, high throughput application while preserving spatial organization, named “semibulk RNA-seq” (sbRNA-seq). We utilized a microfluidic device specifically designed for the experiments to encapsulate both a barcoded bead and a cell aggregate (a semibulk) into a single droplet. Using sbRNA-seq, we firstly analyzed mouse kidney specimens. In the mouse model, we could associate the pathological information with the gene expression information. We validated the results using spatial transcriptome analysis and found them highly consistent. When we applied the sbRNA-seq analysis to the human breast cancer specimens, we identified spatial interactions between a particular population of immune cells and that of cancer-associated fibroblast cells, which were not precisely represented solely by the single-cell analysis. Semibulk analysis may provide a convenient and versatile method, compared to a standard spatial transcriptome sequencing platform, to associate spatial information with transcriptome information.
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44
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Chen J, Luo P, Wang C, Yang C, Bai Y, He X, Zhang Q, Zhang J, Yang J, Wang S, Wang J. Integrated single-cell transcriptomics and proteomics reveal cellular-specific response and microenvironment remodeling in aristolochic acid nephropathy. JCI Insight 2022; 7:157360. [PMID: 35852860 PMCID: PMC9462482 DOI: 10.1172/jci.insight.157360] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2021] [Accepted: 07/14/2022] [Indexed: 11/30/2022] Open
Abstract
Aristolochic acid nephropathy (AAN) is characterized by acute proximal tubule necrosis and immune cell infiltration, contributing to the global burden of chronic kidney disease and urothelial cancer. Although the proximal tubule has been defined as the primary target of aristolochic acids I (AAI), the mechanistic underpinning of gross renal deterioration caused by AAI has not been explicitly explained, prohibiting effective therapeutic intervention. To this point, we employed integrated single-cell RNA-Seq, bulk RNA-Seq, and mass spectrometry–based proteomics to analyze the mouse kidney after acute AAI exposure. Our results reveal a dramatic reduction of proximal tubule epithelial cells, associated with apoptotic and inflammatory pathways, indicating permanent damage beyond repair. We found the enriched development pathways in other nephron segments, suggesting activation of reparative programs triggered by AAI. The divergent response may be attributed to the segment-specific distribution of organic anion channels along the nephron, including OAT1 and OAT3. Moreover, we observed dramatic activation and recruitment of cytotoxic T and macrophage M1 cells, highlighting inflammation as a principal contributor to permanent renal injury. Ligand-receptor pairing revealed that critical intercellular crosstalk underpins damage-induced activation of immune cells. These results provide potentially novel insight into the AAI-induced kidney injury and point out possible pathways for future therapeutic intervention.
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Affiliation(s)
- Jiayun Chen
- Artemisinin Research Center and Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, China
| | - Piao Luo
- Artemisinin Research Center and Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, China
| | - Chen Wang
- Artemisinin Research Center and Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, China
| | - Chuanbin Yang
- Department of Geriatrics, Shenzhen People’s Hospital (The Second Clinical Medical College, Jinan University; The First Affiliated Hospital, Southern University of Science and Technology), Shenzhen, Guangdong, China
| | - Yunmeng Bai
- Department of Geriatrics, Shenzhen People’s Hospital (The Second Clinical Medical College, Jinan University; The First Affiliated Hospital, Southern University of Science and Technology), Shenzhen, Guangdong, China
| | - Xueling He
- Artemisinin Research Center and Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, China
| | - Qian Zhang
- Artemisinin Research Center and Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, China
| | - Junzhe Zhang
- Artemisinin Research Center and Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, China
| | - Jing Yang
- Department of Geriatrics, Shenzhen People’s Hospital (The Second Clinical Medical College, Jinan University; The First Affiliated Hospital, Southern University of Science and Technology), Shenzhen, Guangdong, China
| | - Shuang Wang
- Department of Geriatrics, Shenzhen People’s Hospital (The Second Clinical Medical College, Jinan University; The First Affiliated Hospital, Southern University of Science and Technology), Shenzhen, Guangdong, China
| | - Jigang Wang
- Artemisinin Research Center and Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, China
- Department of Geriatrics, Shenzhen People’s Hospital (The Second Clinical Medical College, Jinan University; The First Affiliated Hospital, Southern University of Science and Technology), Shenzhen, Guangdong, China
- Center for Reproductive Medicine, Dongguan Maternal and Child Health Care Hospital, Southern Medical University, Dongguan, Guangdong, China
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45
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Raghubar AM, Pham DT, Tan X, Grice LF, Crawford J, Lam PY, Andersen SB, Yoon S, Teoh SM, Matigian NA, Stewart A, Francis L, Ng MSY, Healy HG, Combes AN, Kassianos AJ, Nguyen Q, Mallett AJ. Spatially Resolved Transcriptomes of Mammalian Kidneys Illustrate the Molecular Complexity and Interactions of Functional Nephron Segments. Front Med (Lausanne) 2022; 9:873923. [PMID: 35872784 PMCID: PMC9300864 DOI: 10.3389/fmed.2022.873923] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2022] [Accepted: 05/23/2022] [Indexed: 11/30/2022] Open
Abstract
Available transcriptomes of the mammalian kidney provide limited information on the spatial interplay between different functional nephron structures due to the required dissociation of tissue with traditional transcriptome-based methodologies. A deeper understanding of the complexity of functional nephron structures requires a non-dissociative transcriptomics approach, such as spatial transcriptomics sequencing (ST-seq). We hypothesize that the application of ST-seq in normal mammalian kidneys will give transcriptomic insights within and across species of physiology at the functional structure level and cellular communication at the cell level. Here, we applied ST-seq in six mice and four human kidneys that were histologically absent of any overt pathology. We defined the location of specific nephron structures in the captured ST-seq datasets using three lines of evidence: pathologist's annotation, marker gene expression, and integration with public single-cell and/or single-nucleus RNA-sequencing datasets. We compared the mouse and human cortical kidney regions. In the human ST-seq datasets, we further investigated the cellular communication within glomeruli and regions of proximal tubules–peritubular capillaries by screening for co-expression of ligand–receptor gene pairs. Gene expression signatures of distinct nephron structures and microvascular regions were spatially resolved within the mouse and human ST-seq datasets. We identified 7,370 differentially expressed genes (padj < 0.05) distinguishing species, suggesting changes in energy production and metabolism in mouse cortical regions relative to human kidneys. Hundreds of potential ligand–receptor interactions were identified within glomeruli and regions of proximal tubules–peritubular capillaries, including known and novel interactions relevant to kidney physiology. Our application of ST-seq to normal human and murine kidneys confirms current knowledge and localization of transcripts within the kidney. Furthermore, the generated ST-seq datasets provide a valuable resource for the kidney community that can be used to inform future research into this complex organ.
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Affiliation(s)
- Arti M. Raghubar
- Kidney Health Service, Royal Brisbane and Women's Hospital, Herston, QLD, Australia
- Conjoint Internal Medicine Laboratory, Chemical Pathology, Pathology Queensland, Health Support Queensland, Herston, QLD, Australia
- Faculty of Medicine, University of Queensland, Brisbane, QLD, Australia
- Anatomical Pathology, Pathology Queensland, Health Support Queensland, Herston, QLD, Australia
- Institute for Molecular Bioscience, University of Queensland, Brisbane, QLD, Australia
| | - Duy T. Pham
- Institute for Molecular Bioscience, University of Queensland, Brisbane, QLD, Australia
| | - Xiao Tan
- Institute for Molecular Bioscience, University of Queensland, Brisbane, QLD, Australia
| | - Laura F. Grice
- Institute for Molecular Bioscience, University of Queensland, Brisbane, QLD, Australia
- School of Biomedical Sciences, The University of Queensland, Brisbane, QLD, Australia
| | - Joanna Crawford
- Institute for Molecular Bioscience, University of Queensland, Brisbane, QLD, Australia
| | - Pui Yeng Lam
- Institute for Molecular Bioscience, University of Queensland, Brisbane, QLD, Australia
| | - Stacey B. Andersen
- Genome Innovation Hub, University of Queensland, Brisbane, QLD, Australia
- UQ Sequencing Facility, Institute for Molecular Bioscience, University of Queensland, Brisbane, QLD, Australia
| | - Sohye Yoon
- Genome Innovation Hub, University of Queensland, Brisbane, QLD, Australia
| | - Siok Min Teoh
- UQ Diamantina Institute, Faculty of Medicine, The University of Queensland, Woolloongabba, QLD, Australia
| | - Nicholas A. Matigian
- QCIF Facility for Advanced Bioinformatics, Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD, Australia
| | - Anne Stewart
- Anatomical Pathology, Pathology Queensland, Health Support Queensland, Herston, QLD, Australia
| | - Leo Francis
- Anatomical Pathology, Pathology Queensland, Health Support Queensland, Herston, QLD, Australia
| | - Monica S. Y. Ng
- Kidney Health Service, Royal Brisbane and Women's Hospital, Herston, QLD, Australia
- Conjoint Internal Medicine Laboratory, Chemical Pathology, Pathology Queensland, Health Support Queensland, Herston, QLD, Australia
- Faculty of Medicine, University of Queensland, Brisbane, QLD, Australia
- Institute for Molecular Bioscience, University of Queensland, Brisbane, QLD, Australia
- Nephrology Department, Princess Alexandra Hospital, Woolloongabba, QLD, Australia
| | - Helen G. Healy
- Kidney Health Service, Royal Brisbane and Women's Hospital, Herston, QLD, Australia
- Conjoint Internal Medicine Laboratory, Chemical Pathology, Pathology Queensland, Health Support Queensland, Herston, QLD, Australia
- Faculty of Medicine, University of Queensland, Brisbane, QLD, Australia
| | - Alexander N. Combes
- Department of Anatomy and Developmental Biology, Stem Cells and Development Program, Monash Biomedicine Discovery Institute, Monash University, Melbourne, VIC, Australia
| | - Andrew J. Kassianos
- Kidney Health Service, Royal Brisbane and Women's Hospital, Herston, QLD, Australia
- Conjoint Internal Medicine Laboratory, Chemical Pathology, Pathology Queensland, Health Support Queensland, Herston, QLD, Australia
- Faculty of Medicine, University of Queensland, Brisbane, QLD, Australia
| | - Quan Nguyen
- Institute for Molecular Bioscience, University of Queensland, Brisbane, QLD, Australia
- *Correspondence: Andrew J. Mallett
| | - Andrew J. Mallett
- Faculty of Medicine, University of Queensland, Brisbane, QLD, Australia
- Institute for Molecular Bioscience, University of Queensland, Brisbane, QLD, Australia
- College of Medicine & Dentistry, James Cook University, Townsville, Queensland, QLD, Australia
- Department of Renal Medicine, Townsville University Hospital, Townsville, Queensland, QLD, Australia
- Quan Nguyen
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46
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Deng J, Wu Z, He Y, Lin L, Tan W, Yang J. Interaction Between Intrinsic Renal Cells and Immune Cells in the Progression of Acute Kidney Injury. Front Med (Lausanne) 2022; 9:954574. [PMID: 35872775 PMCID: PMC9300888 DOI: 10.3389/fmed.2022.954574] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2022] [Accepted: 06/15/2022] [Indexed: 11/25/2022] Open
Abstract
A growing number of studies have confirmed that immune cells play various key roles in the pathophysiology of acute kidney injury (AKI) development. After the resident immune cells and intrinsic renal cells are damaged by ischemia and hypoxia, drugs and toxins, more immune cells will be recruited to infiltrate through the release of chemokines, while the intrinsic cells promote macrophage polarity conversion, and the immune cells will promote various programmed deaths, phenotypic conversion and cycle arrest of the intrinsic cells, ultimately leading to renal impairment and fibrosis. In the complex and dynamic immune microenvironment of AKI, the bidirectional interaction between immune cells and intrinsic renal cells affects the prognosis of the kidney and the progression of fibrosis, and determines the ultimate fate of the kidney.
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Affiliation(s)
- Junhui Deng
- The Third Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Zhifen Wu
- The Third Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Yun He
- The Fifth People's Hospital of Chongqing, Chongqing, China
| | - Lirong Lin
- The Third Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Wei Tan
- The Third Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Jurong Yang
- The Third Affiliated Hospital of Chongqing Medical University, Chongqing, China
- *Correspondence: Jurong Yang ;
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47
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Zhang Y, Cai J, Lu W, Xu S, Qu M, Zhao S, Ding X. Comprehensive Network-Based Analyses Reveal Novel Renal Function-Related Targets in Acute Kidney Injury. Front Genet 2022; 13:907145. [PMID: 35860471 PMCID: PMC9289212 DOI: 10.3389/fgene.2022.907145] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2022] [Accepted: 05/23/2022] [Indexed: 11/13/2022] Open
Abstract
Background: Acute kidney injury (AKI) is a common clinical syndrome with limited methods of treatment and diagnosis. Although several molecules associated with AKI have been discovered, molecular mechanisms underlying AKI still remain unclear. Weighted gene co-expression network analysis (WGCNA) is a novel method to uncover the relationship between co-expression genes and clinical traits at the system level. Methods: First, by employing WGCNA in transcriptional data on 30 patients with well/poor functioning kidney graft, we identified two co-expression modules that were significantly related to serum creatinine (SCr). Second, based on the modules, potential small molecular compound candidates for developing targeted therapeutics were obtained by connectivity map analysis. Furthermore, multiple validations of expression in space/time were carried out with two classical AKI models in vivo and other five databases of over 152 samples. Results: Two of the 14 modules were found to be closely correlated with SCr. Function enrichment analysis illustrated that one module was enriched in the immune system, while the other was in the metabolic process. Six key renal function-related genes (RFRGs) were finally obtained. Such genes performed well in cisplatin-induced or cecal ligation and puncture-induced AKI mouse models. Conclusion: The analysis suggests that WGCNA is a proper method to connect clinical traits with genome data to find novel targets in AKI. The kidney tissue with worse renal function tended to develop a “high immune but low metabolic activity” expression pattern. Also, ACSM2A, GLYAT, CORO1A, DPEP1, ALDH7A1, and EPHX2 are potential targets of molecular diagnosis and treatment in AKI.
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Affiliation(s)
- Yang Zhang
- Department of Nephrology, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Jieru Cai
- Department of Nephrology, Zhongshan Hospital, Fudan University, Shanghai, China
- Shanghai Medical Center of Kidney Disease, Shanghai, China
- Kidney and Dialysis Institute of Shanghai, Shanghai, China
- Kidney and Blood Purification Key Laboratory of Shanghai, Shanghai, China
| | - Wei Lu
- Department of Nephrology, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Sujuan Xu
- Department of Nephrology, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Mengdi Qu
- Department of Anesthesiology, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Shuan Zhao
- Department of Nephrology, Zhongshan Hospital, Fudan University, Shanghai, China
- Shanghai Medical Center of Kidney Disease, Shanghai, China
- Kidney and Dialysis Institute of Shanghai, Shanghai, China
- Kidney and Blood Purification Key Laboratory of Shanghai, Shanghai, China
- *Correspondence: Xiaoqiang Ding, ; Shuan Zhao,
| | - Xiaoqiang Ding
- Department of Nephrology, Zhongshan Hospital, Fudan University, Shanghai, China
- Shanghai Medical Center of Kidney Disease, Shanghai, China
- Kidney and Dialysis Institute of Shanghai, Shanghai, China
- Kidney and Blood Purification Key Laboratory of Shanghai, Shanghai, China
- *Correspondence: Xiaoqiang Ding, ; Shuan Zhao,
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48
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Spatially resolved transcriptomics and the kidney: Many opportunities. Kidney Int 2022; 102:482-491. [PMID: 35788360 DOI: 10.1016/j.kint.2022.06.011] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2022] [Revised: 06/10/2022] [Accepted: 06/20/2022] [Indexed: 01/31/2023]
Abstract
Defining changes in gene expression during health and disease is critical for the understanding of human physiology. In recent years, single cell/nuclei RNA sequencing (sc/snRNAseq) has revolutionized the definition and discovery of cell types and states, as well as the interpretation of organ and cell type specific signaling pathways. However, these advances require tissue dissociation to the level of the single cell or single nuclei level. Spatially resolved transcriptomics (SrT) now provides a platform to overcome this barrier in understanding the physiological contexts of gene expression and cellular microenvironment changes in development and disease. Some of these transcriptomic tools allow for high resolution mapping of hundreds of genes simultaneously in cellular and subcellular compartments. Other tools offer genome depth mapping, but at lower resolution. Here, we will review advances in SrT, considerations for using SrT in your own research, and applications for kidney biology.
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49
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Buse M, Moeller MJ, Stamellou E. What We Have Learned so far From Single Cell Sequencing in Acute Kidney Injury. Front Physiol 2022; 13:933677. [PMID: 35755431 PMCID: PMC9217124 DOI: 10.3389/fphys.2022.933677] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2022] [Accepted: 05/25/2022] [Indexed: 11/18/2022] Open
Abstract
Acute Kidney injury is a major clinical problem associated with increased morbidity and mortality. Despite, intensive research the clinical outcome remains poor and apart from supportive therapy no other specific therapy exists. Single cell technologies have enabled us to get deeper insights into the transcriptome of individual cells in complex tissues like the kidney. With respect to kidney injury, this would allow us to better define the unique role of individual cell populations in the pathophysiology of acute kidney injury and progression to chronic kidney disease. In this mini review, we would like to give an overview and discuss the current major findings in the field of acute kidney injury through Single-Cell technologies.
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Affiliation(s)
- Marc Buse
- Division of Nephrology and Clinical Immunology, RWTH Aachen University Hospital, Aachen, Germany
| | - Marcus J Moeller
- Division of Nephrology and Clinical Immunology, RWTH Aachen University Hospital, Aachen, Germany
| | - Eleni Stamellou
- Division of Nephrology and Clinical Immunology, RWTH Aachen University Hospital, Aachen, Germany
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50
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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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