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Tasca P, van den Berg BM, Rabelink TJ, Wang G, Heijs B, van Kooten C, de Vries APJ, Kers J. Application of spatial-omics to the classification of kidney biopsy samples in transplantation. Nat Rev Nephrol 2024:10.1038/s41581-024-00861-x. [PMID: 38965417 DOI: 10.1038/s41581-024-00861-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/06/2024] [Indexed: 07/06/2024]
Abstract
Improvement of long-term outcomes through targeted treatment is a primary concern in kidney transplant medicine. Currently, the validation of a rejection diagnosis and subsequent treatment depends on the histological assessment of allograft biopsy samples, according to the Banff classification system. However, the lack of (early) disease-specific tissue markers hinders accurate diagnosis and thus timely intervention. This challenge mainly results from an incomplete understanding of the pathophysiological processes underlying late allograft failure. Integration of large-scale multimodal approaches for investigating allograft biopsy samples might offer new insights into this pathophysiology, which are necessary for the identification of novel therapeutic targets and the development of tailored immunotherapeutic interventions. Several omics technologies - including transcriptomic, proteomic, lipidomic and metabolomic tools (and multimodal data analysis strategies) - can be applied to allograft biopsy investigation. However, despite their successful application in research settings and their potential clinical value, several barriers limit the broad implementation of many of these tools into clinical practice. Among spatial-omics technologies, mass spectrometry imaging, which is under-represented in the transplant field, has the potential to enable multi-omics investigations that might expand the insights gained with current clinical analysis technologies.
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Affiliation(s)
- Paola Tasca
- Center for Proteomics and Metabolomics, Leiden University Medical Center, Leiden, the Netherlands
- Leiden Transplant Center, Leiden University Medical Center, Leiden, the Netherlands
- Department of Pathology, Leiden University Medical Center, Leiden, the Netherlands
| | - Bernard M van den Berg
- Department of Internal Medicine, Division of Nephrology, Einthoven Laboratory of Vascular and Regenerative Medicine, Leiden University Medical Center, Leiden, the Netherlands
| | - Ton J Rabelink
- Department of Internal Medicine, Division of Nephrology, Einthoven Laboratory of Vascular and Regenerative Medicine, Leiden University Medical Center, Leiden, the Netherlands
- The Novo Nordisk Foundation Center for Stem Cell Medicine (Renew), Leiden University Medical Center, Leiden, the Netherlands
| | - Gangqi Wang
- Department of Internal Medicine, Division of Nephrology, Einthoven Laboratory of Vascular and Regenerative Medicine, Leiden University Medical Center, Leiden, the Netherlands
- The Novo Nordisk Foundation Center for Stem Cell Medicine (Renew), Leiden University Medical Center, Leiden, the Netherlands
| | - Bram Heijs
- Center for Proteomics and Metabolomics, Leiden University Medical Center, Leiden, the Netherlands
- Bruker Daltonics GmbH & Co. KG, Bremen, Germany
| | - Cees van Kooten
- Leiden Transplant Center, Leiden University Medical Center, Leiden, the Netherlands
- Department of Internal Medicine, Division of Nephrology, Einthoven Laboratory of Vascular and Regenerative Medicine, Leiden University Medical Center, Leiden, the Netherlands
| | - Aiko P J de Vries
- Leiden Transplant Center, Leiden University Medical Center, Leiden, the Netherlands.
- Department of Internal Medicine, Division of Nephrology, Einthoven Laboratory of Vascular and Regenerative Medicine, Leiden University Medical Center, Leiden, the Netherlands.
| | - Jesper Kers
- Leiden Transplant Center, Leiden University Medical Center, Leiden, the Netherlands
- Department of Pathology, Leiden University Medical Center, Leiden, the Netherlands
- Department of Pathology, Amsterdam University Medical Centers, University of Amsterdam, Amsterdam, the Netherlands
- Center for Analytical Sciences Amsterdam, Van't Hoff Institute for Molecular Sciences, University of Amsterdam, Amsterdam, the Netherlands
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2
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Peng QY, An Y, Jiang ZZ, Xu Y. The Role of Immune Cells in DKD: Mechanisms and Targeted Therapies. J Inflamm Res 2024; 17:2103-2118. [PMID: 38601771 PMCID: PMC11005934 DOI: 10.2147/jir.s457526] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2024] [Accepted: 03/19/2024] [Indexed: 04/12/2024] Open
Abstract
Diabetic kidney disease (DKD), is a common microvascular complication and a major cause of death in patients with diabetes. Disorders of immune cells and immune cytokines can accelerate DKD development of in a number of ways. As the kidney is composed of complex and highly differentiated cells, the interactions among different cell types and immune cells play important regulatory roles in disease development. Here, we summarize the latest research into the molecular mechanisms underlying the interactions among various immune and renal cells in DKD. In addition, we discuss the most recent studies related to single cell technology and bioinformatics analysis in the field of DKD. The aims of our review were to explore immune cells as potential therapeutic targets in DKD and provide some guidance for future clinical treatments.
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Affiliation(s)
- Qiu-Yue Peng
- Department of Endocrinology and Metabolism, the Affiliated Hospital of Southwest Medical University, Luzhou, Sichuan, People’s Republic of China
- Metabolic Vascular Disease Key Laboratory of Sichuan Province, Sichuan, People’s Republic of China
- Sichuan Clinical Research Center for Nephropathy, Luzhou, Sichuan, People’s Republic of China
| | - Ying An
- Department of Endocrinology and Metabolism, the Affiliated Hospital of Southwest Medical University, Luzhou, Sichuan, People’s Republic of China
- Metabolic Vascular Disease Key Laboratory of Sichuan Province, Sichuan, People’s Republic of China
- Sichuan Clinical Research Center for Nephropathy, Luzhou, Sichuan, People’s Republic of China
| | - Zong-Zhe Jiang
- Department of Endocrinology and Metabolism, the Affiliated Hospital of Southwest Medical University, Luzhou, Sichuan, People’s Republic of China
- Metabolic Vascular Disease Key Laboratory of Sichuan Province, Sichuan, People’s Republic of China
- Sichuan Clinical Research Center for Nephropathy, Luzhou, Sichuan, People’s Republic of China
| | - Yong Xu
- Department of Endocrinology and Metabolism, the Affiliated Hospital of Southwest Medical University, Luzhou, Sichuan, People’s Republic of China
- Metabolic Vascular Disease Key Laboratory of Sichuan Province, Sichuan, People’s Republic of China
- Sichuan Clinical Research Center for Nephropathy, Luzhou, Sichuan, People’s Republic of China
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Mao ZH, Gao ZX, Liu Y, Liu DW, Liu ZS, Wu P. Single-cell transcriptomics: A new tool for studying diabetic kidney disease. Front Physiol 2023; 13:1053850. [PMID: 36685214 PMCID: PMC9846140 DOI: 10.3389/fphys.2022.1053850] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2022] [Accepted: 12/16/2022] [Indexed: 01/05/2023] Open
Abstract
The kidney is a complex organ comprising various functional partitions and special cell types that play important roles in maintaining homeostasis in the body. Diabetic kidney disease (DKD) is the leading cause of end-stage renal disease and is an independent risk factor for cardiovascular diseases. Owing to the complexity and heterogeneity of kidney structure and function, the mechanism of DKD development has not been fully elucidated. Single-cell sequencing, including transcriptomics, epigenetics, metabolomics, and proteomics etc., is a powerful technology that enables the analysis of specific cell types and states, specifically expressed genes or pathways, cell differentiation trajectories, intercellular communication, and regulation or co-expression of genes in various diseases. Compared with other omics, RNA sequencing is a more developed technique with higher utilization of tissues or samples. This article reviewed the application of single-cell transcriptomics in the field of DKD and highlighted the key signaling pathways in specific tissues or cell types involved in the occurrence and development of DKD. The comprehensive understanding of single-cell transcriptomics through single-cell RNA-seq and single-nucleus RNA-seq will provide us new insights into the pathogenesis and treatment strategy of various diseases including DKD.
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Affiliation(s)
- Zi-Hui Mao
- Traditional Chinese Medicine Integrated Department of Nephrology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China,Institute of Nephrology, Zhengzhou University, Zhengzhou, China,Henan Province Research Center for Kidney Disease, Zhengzhou, China,Key Laboratory of Precision Diagnosis and Treatment for Chronic Kidney Disease in Henan Province, Zhengzhou, China
| | - Zhong-Xiuzi Gao
- Traditional Chinese Medicine Integrated Department of Nephrology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China,Institute of Nephrology, Zhengzhou University, Zhengzhou, China,Henan Province Research Center for Kidney Disease, Zhengzhou, China,Key Laboratory of Precision Diagnosis and Treatment for Chronic Kidney Disease in Henan Province, Zhengzhou, China
| | - Yong Liu
- Traditional Chinese Medicine Integrated Department of Nephrology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China,Institute of Nephrology, Zhengzhou University, Zhengzhou, China,Henan Province Research Center for Kidney Disease, Zhengzhou, China,Key Laboratory of Precision Diagnosis and Treatment for Chronic Kidney Disease in Henan Province, Zhengzhou, China
| | - Dong-Wei Liu
- Traditional Chinese Medicine Integrated Department of Nephrology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China,Institute of Nephrology, Zhengzhou University, Zhengzhou, China,Henan Province Research Center for Kidney Disease, Zhengzhou, China,Key Laboratory of Precision Diagnosis and Treatment for Chronic Kidney Disease in Henan Province, Zhengzhou, China
| | - Zhang-Suo Liu
- Traditional Chinese Medicine Integrated Department of Nephrology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China,Institute of Nephrology, Zhengzhou University, Zhengzhou, China,Henan Province Research Center for Kidney Disease, Zhengzhou, China,Key Laboratory of Precision Diagnosis and Treatment for Chronic Kidney Disease in Henan Province, Zhengzhou, China,*Correspondence: Peng Wu, ; Zhang-Suo Liu,
| | - Peng Wu
- Traditional Chinese Medicine Integrated Department of Nephrology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China,Institute of Nephrology, Zhengzhou University, Zhengzhou, China,Henan Province Research Center for Kidney Disease, Zhengzhou, China,Key Laboratory of Precision Diagnosis and Treatment for Chronic Kidney Disease in Henan Province, Zhengzhou, China,*Correspondence: Peng Wu, ; Zhang-Suo Liu,
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Shankland SJ, Wang Y, Shaw AS, Vaughan JC, Pippin JW, Wessely O. Podocyte Aging: Why and How Getting Old Matters. J Am Soc Nephrol 2021; 32:2697-2713. [PMID: 34716239 PMCID: PMC8806106 DOI: 10.1681/asn.2021050614] [Citation(s) in RCA: 31] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2021] [Accepted: 08/26/2021] [Indexed: 02/04/2023] Open
Abstract
The effects of healthy aging on the kidney, and how these effects intersect with superimposed diseases, are highly relevant in the context of the population's increasing longevity. Age-associated changes to podocytes, which are terminally differentiated glomerular epithelial cells, adversely affect kidney health. This review discusses the molecular and cellular mechanisms underlying podocyte aging, how these mechanisms might be augmented by disease in the aged kidney, and approaches to mitigate progressive damage to podocytes. Furthermore, we address how biologic pathways such as those associated with cellular growth confound aging in humans and rodents.
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Affiliation(s)
- Stuart J. Shankland
- Division of Nephrology, University of Washington, Seattle, Washington
- Institute for Stem Cell & Regenerative Medicine, University of Washington, Seattle, Washington
| | - Yuliang Wang
- Institute for Stem Cell & Regenerative Medicine, University of Washington, Seattle, Washington
- Paul G. Allen School of Computer Science and Engineering, University of Washington, Seattle, Washington
| | - Andrey S. Shaw
- Department of Research Biology, Genentech, South San Francisco, California
| | - Joshua C. Vaughan
- Department of Chemistry, University of Washington, Seattle, Washington
- Department of Physiology and Biophysics, University of Washington, Seattle, Washington
| | - Jeffrey W. Pippin
- Division of Nephrology, University of Washington, Seattle, Washington
| | - Oliver Wessely
- Lerner Research Institute, Department of Cardiovascular & Metabolic Sciences, Cleveland Clinic Foundation, Cleveland, Ohio
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Jiang M, Chen H, Guo G. Studying Kidney Diseases at the Single-Cell Level. KIDNEY DISEASES (BASEL, SWITZERLAND) 2021; 7:335-342. [PMID: 34604340 PMCID: PMC8443939 DOI: 10.1159/000517130] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/12/2021] [Accepted: 05/10/2021] [Indexed: 12/17/2022]
Abstract
BACKGROUND The kidney is a highly complex organ that performs diverse functions that are essential for health. Kidney disease occurs when the kidneys are damaged and fail to function properly. Single-cell analysis is a powerful technology that provides unprecedented insights into normal and abnormal kidney cell types and will transform our understanding of the mechanism underlying common kidney diseases. SUMMARY Our understanding of kidney disease pathogenesis is limited by the incomplete molecular characterization of cell types responsible for kidney functions. Application of single-cell technologies for the study of the kidney has revealed cellular heterogeneity, gene expression signatures, and molecular dynamics during the onset and development of kidney diseases. Single-cell analyses of kidney organoids and allograft tissues offer new insights into kidney organogenesis, disease mechanisms, and therapeutic outcomes. Collectively, a better understanding of kidney cell heterogeneity and the molecular dynamics of kidney diseases will improve diagnostic accuracy and facilitate the identification of novel treatment strategies in nephrology. KEY MESSAGE In this review article, we summarize recent single-cell studies on kidney diseases and discuss the impact of single-cell technology on both basic and clinical nephrology research.
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Affiliation(s)
- Mengmeng Jiang
- Liangzhu Laboratory, Zhejiang University Medical Center, Hangzhou, China
- Center for Stem Cell and Regenerative Medicine, Zhejiang University School of Medicine, Hangzhou, China
| | - Haide Chen
- Center for Stem Cell and Regenerative Medicine, Zhejiang University School of Medicine, Hangzhou, China
- Zhejiang Provincial Key Lab for Tissue Engineering and Regenerative Medicine, Dr. Li Dak Sum & Yip Yio Chin, Center for Stem Cell and Regenerative Medicine, Hangzhou, China
| | - Guoji Guo
- Liangzhu Laboratory, Zhejiang University Medical Center, Hangzhou, China
- Center for Stem Cell and Regenerative Medicine, Zhejiang University School of Medicine, Hangzhou, China
- Zhejiang Provincial Key Lab for Tissue Engineering and Regenerative Medicine, Dr. Li Dak Sum & Yip Yio Chin, Center for Stem Cell and Regenerative Medicine, Hangzhou, China
- Bone Marrow Transplantation Center, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
- Institute of Hematology, Zhejiang University, Hangzhou, China
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Bülow RD, Dimitrov D, Boor P, Saez-Rodriguez J. How will artificial intelligence and bioinformatics change our understanding of IgA Nephropathy in the next decade? Semin Immunopathol 2021; 43:739-752. [PMID: 33835214 PMCID: PMC8551101 DOI: 10.1007/s00281-021-00847-y] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2021] [Accepted: 02/17/2021] [Indexed: 01/16/2023]
Abstract
IgA nephropathy (IgAN) is the most common glomerulonephritis. It is characterized by the deposition of immune complexes containing immunoglobulin A (IgA) in the kidney’s glomeruli, triggering an inflammatory process. In many patients, the disease has a progressive course, eventually leading to end-stage kidney disease. The current understanding of IgAN’s pathophysiology is incomplete, with the involvement of several potential players, including the mucosal immune system, the complement system, and the microbiome. Dissecting this complex pathophysiology requires an integrated analysis across molecular, cellular, and organ scales. Such data can be obtained by employing emerging technologies, including single-cell sequencing, next-generation sequencing, proteomics, and complex imaging approaches. These techniques generate complex “big data,” requiring advanced computational methods for their analyses and interpretation. Here, we introduce such methods, focusing on the broad areas of bioinformatics and artificial intelligence and discuss how they can advance our understanding of IgAN and ultimately improve patient care. The close integration of advanced experimental and computational technologies with medical and clinical expertise is essential to improve our understanding of human diseases. We argue that IgAN is a paradigmatic disease to demonstrate the value of such a multidisciplinary approach.
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Affiliation(s)
- Roman David Bülow
- University Hospital RWTH Aachen, Institute of Pathology, Aachen, Germany
| | - Daniel Dimitrov
- Faculty of Medicine, Heidelberg University, Heidelberg, Germany
- Institute for Computational Biomedicine, Heidelberg University Hospital, Bioquant, Heidelberg, Germany
| | - Peter Boor
- University Hospital RWTH Aachen, Institute of Pathology, Aachen, Germany.
- Department of Nephrology and Immunology, University Hospital RWTH Aachen, Aachen, Germany.
| | - Julio Saez-Rodriguez
- Faculty of Medicine, Heidelberg University, Heidelberg, Germany.
- Institute for Computational Biomedicine, Heidelberg University Hospital, Bioquant, Heidelberg, Germany.
- Faculty of Medicine, Joint Research Centre for Computational Biomedicine (JRC-COMBINE), 52074, RWTH Aachen University, Aachen, Germany.
- Molecular Medicine Partnership Unit, European Molecular Biology Laboratory and Heidelberg University, Heidelberg, Germany.
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