1
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Li ZL, Li XY, Zhou Y, Wang B, Lv LL, Liu BC. Renal tubular epithelial cells response to injury in acute kidney injury. EBioMedicine 2024; 107:105294. [PMID: 39178744 DOI: 10.1016/j.ebiom.2024.105294] [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: 04/27/2024] [Revised: 07/19/2024] [Accepted: 08/06/2024] [Indexed: 08/26/2024] Open
Abstract
Acute kidney injury (AKI) is a clinical syndrome characterized by a rapid and significant decrease in renal function that can arise from various etiologies, and is associated with high morbidity and mortality. The renal tubular epithelial cells (TECs) represent the central cell type affected by AKI, and their notable regenerative capacity is critical for the recovery of renal function in afflicted patients. The adaptive repair process initiated by surviving TECs following mild AKI facilitates full renal recovery. Conversely, when injury is severe or persistent, it allows the TECs to undergo pathological responses, abnormal adaptive repair and phenotypic transformation, which will lead to the development of renal fibrosis. Given the implications of TECs fate after injury in renal outcomes, a deeper understanding of these mechanisms is necessary to identify promising therapeutic targets and biomarkers of the repair process in the human kidney.
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Affiliation(s)
- Zuo-Lin Li
- Institute of Nephrology, Zhongda Hospital, Southeast University School of Medicine, Nanjing, Jiangsu, China
| | - Xin-Yan Li
- Institute of Nephrology, Zhongda Hospital, Southeast University School of Medicine, Nanjing, Jiangsu, China
| | - Yan Zhou
- Institute of Nephrology, Zhongda Hospital, Southeast University School of Medicine, Nanjing, Jiangsu, China
| | - Bin Wang
- Institute of Nephrology, Zhongda Hospital, Southeast University School of Medicine, Nanjing, Jiangsu, China
| | - Lin-Li Lv
- Institute of Nephrology, Zhongda Hospital, Southeast University School of Medicine, Nanjing, Jiangsu, China.
| | - Bi-Cheng Liu
- Institute of Nephrology, Zhongda Hospital, Southeast University School of Medicine, Nanjing, Jiangsu, China.
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2
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Tran MA, Youssef D, Shroff S, Chowhan D, Beaumont KG, Sebra R, Mehrazin R, Wiklund P, Lin JJ, Horowitz A, Farkas AM, Galsky MD, Sfakianos JP, Bhardwaj N. Urine scRNAseq reveals new insights into the bladder tumor immune microenvironment. J Exp Med 2024; 221:e20240045. [PMID: 38847806 PMCID: PMC11157455 DOI: 10.1084/jem.20240045] [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: 01/07/2024] [Revised: 04/04/2024] [Accepted: 05/21/2024] [Indexed: 06/10/2024] Open
Abstract
Due to bladder tumors' contact with urine, urine-derived cells (UDCs) may serve as a surrogate for monitoring the tumor microenvironment (TME) in bladder cancer (BC). However, the composition of UDCs and the extent to which they mirror the tumor remain poorly characterized. We generated the first single-cell RNA-sequencing of BC patient UDCs with matched tumor and peripheral blood mononuclear cells (PBMC). BC urine was more cellular than healthy donor (HD) urine, containing multiple immune populations including myeloid cells, CD4+ and CD8+ T cells, natural killer (NK) cells, B cells, and dendritic cells (DCs) in addition to tumor and stromal cells. Immune UDCs were transcriptionally more similar to tumor than blood. UDCs encompassed cytotoxic and activated CD4+ T cells, exhausted and tissue-resident memory CD8+ T cells, macrophages, germinal-center-like B cells, tissue-resident and adaptive NK cells, and regulatory DCs found in tumor but lacking or absent in blood. Our findings suggest BC UDCs may be surrogates for the TME and serve as therapeutic biomarkers.
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Affiliation(s)
- Michelle A. Tran
- Division of Hematology and Medical Oncology, Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Dina Youssef
- Division of Hematology and Medical Oncology, Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Sanjana Shroff
- Department of Genomics, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Disha Chowhan
- Department of Genomics, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Kristin G. Beaumont
- Department of Genomics, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Robert Sebra
- Department of Genomics, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Reza Mehrazin
- Department of Urology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Peter Wiklund
- Department of Urology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Jenny J. Lin
- Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Amir Horowitz
- Department of Immunology and Immunotherapy, The Marc and Jennifer Lipschultz Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Oncological Sciences, Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Adam M. Farkas
- Division of Hematology and Medical Oncology, Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Matthew D. Galsky
- Division of Hematology and Medical Oncology, Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Urology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - John P. Sfakianos
- Department of Urology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Nina Bhardwaj
- Division of Hematology and Medical Oncology, Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Urology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Extramural Member, Parker Institute for Cancer Immunotherapy, San Francisco, CA, USA
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3
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Hinze C, Lovric S, Halloran PF, Barasch J, Schmidt-Ott KM. Epithelial cell states associated with kidney and allograft injury. Nat Rev Nephrol 2024; 20:447-459. [PMID: 38632381 DOI: 10.1038/s41581-024-00834-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/27/2024] [Indexed: 04/19/2024]
Abstract
The kidney epithelium, with its intricate arrangement of highly specialized cell types, constitutes the functional core of the organ. Loss of kidney epithelium is linked to the loss of functional nephrons and a subsequent decline in kidney function. In kidney transplantation, epithelial injury signatures observed during post-transplantation surveillance are strong predictors of adverse kidney allograft outcomes. However, epithelial injury is currently neither monitored clinically nor addressed therapeutically after kidney transplantation. Several factors can contribute to allograft epithelial injury, including allograft rejection, drug toxicity, recurrent infections and postrenal obstruction. The injury mechanisms that underlie allograft injury overlap partially with those associated with acute kidney injury (AKI) and chronic kidney disease (CKD) in the native kidney. Studies using advanced transcriptomic analyses of single cells from kidney or urine have identified a role for kidney injury-induced epithelial cell states in exacerbating and sustaining damage in AKI and CKD. These epithelial cell states and their associated expression signatures are also observed in transplanted kidney allografts, suggesting that the identification and characterization of transcriptomic epithelial cell states in kidney allografts may have potential clinical implications for diagnosis and therapy.
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Affiliation(s)
- Christian Hinze
- Department of Nephrology and Hypertension, Hannover Medical School, Hannover, Germany
| | - Svjetlana Lovric
- Department of Nephrology and Hypertension, Hannover Medical School, Hannover, Germany
| | - Philip F Halloran
- Alberta Transplant Applied Genomics Centre, Edmonton, Alberta, Canada
- Department of Medicine, Division of Nephrology and Transplant Immunology, University of Alberta, Edmonton, Alberta, Canada
| | - Jonathan Barasch
- Division of Nephrology, Columbia University, New York City, NY, USA
| | - Kai M Schmidt-Ott
- Department of Nephrology and Hypertension, Hannover Medical School, Hannover, Germany.
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4
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Anandakrishnan N, Yi Z, Sun Z, Liu T, Haydak J, Eddy S, Jayaraman P, DeFronzo S, Saha A, Sun Q, Yang D, Mendoza A, Mosoyan G, Wen HH, Schaub JA, Fu J, Kehrer T, Menon R, Otto EA, Godfrey B, Suarez-Farinas M, Leffters S, Twumasi A, Meliambro K, Charney AW, García-Sastre A, Campbell KN, Gusella GL, He JC, Miorin L, Nadkarni GN, Wisnivesky J, Li H, Kretzler M, Coca SG, Chan L, Zhang W, Azeloglu EU. Integrated multiomics implicates dysregulation of ECM and cell adhesion pathways as drivers of severe COVID-associated kidney injury. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2024:2024.03.18.24304401. [PMID: 38562892 PMCID: PMC10984064 DOI: 10.1101/2024.03.18.24304401] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/04/2024]
Abstract
COVID-19 has been a significant public health concern for the last four years; however, little is known about the mechanisms that lead to severe COVID-associated kidney injury. In this multicenter study, we combined quantitative deep urinary proteomics and machine learning to predict severe acute outcomes in hospitalized COVID-19 patients. Using a 10-fold cross-validated random forest algorithm, we identified a set of urinary proteins that demonstrated predictive power for both discovery and validation set with 87% and 79% accuracy, respectively. These predictive urinary biomarkers were recapitulated in non-COVID acute kidney injury revealing overlapping injury mechanisms. We further combined orthogonal multiomics datasets to understand the mechanisms that drive severe COVID-associated kidney injury. Functional overlap and network analysis of urinary proteomics, plasma proteomics and urine sediment single-cell RNA sequencing showed that extracellular matrix and autophagy-associated pathways were uniquely impacted in severe COVID-19. Differentially abundant proteins associated with these pathways exhibited high expression in cells in the juxtamedullary nephron, endothelial cells, and podocytes, indicating that these kidney cell types could be potential targets. Further, single-cell transcriptomic analysis of kidney organoids infected with SARS-CoV-2 revealed dysregulation of extracellular matrix organization in multiple nephron segments, recapitulating the clinically observed fibrotic response across multiomics datasets. Ligand-receptor interaction analysis of the podocyte and tubule organoid clusters showed significant reduction and loss of interaction between integrins and basement membrane receptors in the infected kidney organoids. Collectively, these data suggest that extracellular matrix degradation and adhesion-associated mechanisms could be a main driver of COVID-associated kidney injury and severe outcomes.
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5
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Elwakiel A, Mathew A, Isermann B. The role of endoplasmic reticulum-mitochondria-associated membranes in diabetic kidney disease. Cardiovasc Res 2024; 119:2875-2883. [PMID: 38367274 DOI: 10.1093/cvr/cvad190] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/05/2022] [Revised: 07/03/2023] [Accepted: 07/07/2023] [Indexed: 02/19/2024] Open
Abstract
Diabetic kidney disease (DKD) is the leading cause of end-stage renal disease worldwide. The pathomechanisms of DKD are multifactorial, yet haemodynamic and metabolic changes in the early stages of the disease appear to predispose towards irreversible functional loss and histopathological changes. Recent studies highlight the importance of endoplasmic reticulum-mitochondria-associated membranes (ER-MAMs), structures conveying important cellular homeostatic and metabolic effects, in the pathology of DKD. Disruption of ER-MAM integrity in diabetic kidneys is associated with DKD progression, but the regulation of ER-MAMs and their pathogenic contribution remain largely unknown. Exploring the cell-specific components and dynamic changes of ER-MAMs in diabetic kidneys may lead to the identification of new approaches to detect and stratify diabetic patients with DKD. In addition, these insights may lead to novel therapeutic approaches to target and/or reverse disease progression. In this review, we discuss the association of ER-MAMs with key pathomechanisms driving DKD such as insulin resistance, dyslipidaemia, ER stress, and inflammasome activation and the importance of further exploration of ER-MAMs as diagnostic and therapeutic targets in DKD.
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Affiliation(s)
- Ahmed Elwakiel
- Institute of Laboratory Medicine, Clinical Chemistry and Molecular Diagnostics, University Hospital Leipzig, Paul-List-Straße 13/15, 04103 Leipzig, Germany
| | - Akash Mathew
- Institute of Laboratory Medicine, Clinical Chemistry and Molecular Diagnostics, University Hospital Leipzig, Paul-List-Straße 13/15, 04103 Leipzig, Germany
| | - Berend Isermann
- Institute of Laboratory Medicine, Clinical Chemistry and Molecular Diagnostics, University Hospital Leipzig, Paul-List-Straße 13/15, 04103 Leipzig, Germany
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6
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Martorella M, Kasela S, Garcia-Flores R, Gokden A, Castel SE, Lappalainen T. Evaluation of noninvasive biospecimens for transcriptome studies. BMC Genomics 2023; 24:790. [PMID: 38114913 PMCID: PMC10729488 DOI: 10.1186/s12864-023-09875-4] [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: 07/17/2023] [Accepted: 12/05/2023] [Indexed: 12/21/2023] Open
Abstract
Transcriptome studies disentangle functional mechanisms of gene expression regulation and may elucidate the underlying biology of disease processes. However, the types of tissues currently collected typically assay a single post-mortem timepoint or are limited to investigating cell types found in blood. Noninvasive tissues may improve disease-relevant discovery by enabling more complex longitudinal study designs, by capturing different and potentially more applicable cell types, and by increasing sample sizes due to reduced collection costs and possible higher enrollment from vulnerable populations. Here, we develop methods for sampling noninvasive biospecimens, investigate their performance across commercial and in-house library preparations, characterize their biology, and assess the feasibility of using noninvasive tissues in a multitude of transcriptomic applications. We collected buccal swabs, hair follicles, saliva, and urine cell pellets from 19 individuals over three to four timepoints, for a total of 300 unique biological samples, which we then prepared with replicates across three library preparations, for a final tally of 472 transcriptomes. Of the four tissues we studied, we found hair follicles and urine cell pellets to be most promising due to the consistency of sample quality, the cell types and expression profiles we observed, and their performance in disease-relevant applications. This is the first study to thoroughly delineate biological and technical features of noninvasive samples and demonstrate their use in a wide array of transcriptomic and clinical analyses. We anticipate future use of these biospecimens will facilitate discovery and development of clinical applications.
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Affiliation(s)
- Molly Martorella
- New York Genome Center, New York, NY, USA.
- Department of Systems Biology, Columbia University, New York, NY, USA.
| | - Silva Kasela
- New York Genome Center, New York, NY, USA
- Department of Systems Biology, Columbia University, New York, NY, USA
| | - Renee Garcia-Flores
- New York Genome Center, New York, NY, USA
- Department of Computer Science, Columbia University, New York, NY, USA
- Undergraduate Program On Genomic Sciences, National Autonomous University of Mexico, Cuernavaca, Morelos, Mexico
| | | | - Stephane E Castel
- New York Genome Center, New York, NY, USA.
- Department of Systems Biology, Columbia University, New York, NY, USA.
| | - Tuuli Lappalainen
- New York Genome Center, New York, NY, USA.
- Department of Systems Biology, Columbia University, New York, NY, USA.
- Science for Life Laboratory, Department of Gene Technology, KTH Royal Institute of Technology, Stockholm, Sweden.
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7
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Zhu J, Lu J, Weng H. Single-cell RNA sequencing for the study of kidney disease. Mol Med 2023; 29:85. [PMID: 37400792 DOI: 10.1186/s10020-023-00693-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2023] [Accepted: 06/27/2023] [Indexed: 07/05/2023] Open
Abstract
The kidney is an important organ for maintaining normal metabolism and stabilising the internal environment, in which, the heterogeneity of cell types has hindered the progress in understanding the mechanisms underlying kidney disease. In recent years the application of single-cell RNA sequencing (scRNA-seq) in nephrology has developed rapidly. In this review, we summarized the technical platform related to scRNA-seq and the role of this technology in investigating the onset and development of kidney diseases, starting from several common kidney diseases (mainly including lupus nephritis, renal cell carcinoma, diabetic nephropathy and acute kidney injury), and provide a reference for the application of scRNA-seq in the study of kidney disease diagnosis, treatment and prognosis.
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Affiliation(s)
- Jiayi Zhu
- The College of Medical Technology, Shanghai University of Medicine & Health Sciences, 279 Zhouzhu Highway, Pudong New Area, 201318, Shanghai, China
| | - Jinrong Lu
- The College of Medical Technology, Shanghai University of Medicine & Health Sciences, 279 Zhouzhu Highway, Pudong New Area, 201318, Shanghai, China
| | - Huachun Weng
- The College of Medical Technology, Shanghai University of Medicine & Health Sciences, 279 Zhouzhu Highway, Pudong New Area, 201318, Shanghai, China.
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8
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Pregizer S, Vreven T, Mathur M, Robinson LN. Multi-omic single cell sequencing: Overview and opportunities for kidney disease therapeutic development. Front Mol Biosci 2023; 10:1176856. [PMID: 37091871 PMCID: PMC10113659 DOI: 10.3389/fmolb.2023.1176856] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2023] [Accepted: 03/21/2023] [Indexed: 04/09/2023] Open
Abstract
Single cell sequencing technologies have rapidly advanced in the last decade and are increasingly applied to gain unprecedented insights by deconstructing complex biology to its fundamental unit, the individual cell. First developed for measurement of gene expression, single cell sequencing approaches have evolved to allow simultaneous profiling of multiple additional features, including chromatin accessibility within the nucleus and protein expression at the cell surface. These multi-omic approaches can now further be applied to cells in situ, capturing the spatial context within which their biology occurs. To extract insights from these complex datasets, new computational tools have facilitated the integration of information across different data types and the use of machine learning approaches. Here, we summarize current experimental and computational methods for generation and integration of single cell multi-omic datasets. We focus on opportunities for multi-omic single cell sequencing to augment therapeutic development for kidney disease, including applications for biomarkers, disease stratification and target identification.
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9
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Deoliveira M, Sikri H, Yu SMW, He JC. Viral Glomerulopathy. GLOMERULAR DISEASES 2023; 3:148-154. [PMID: 37901695 PMCID: PMC10601964 DOI: 10.1159/000531434] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/10/2022] [Accepted: 04/26/2023] [Indexed: 10/31/2023]
Abstract
Background The association between viral infections and glomerular diseases, commonly known as "viral glomerulopathies," has been described in various clinical scenarios for decades. Despite advancements in diagnostic tools, it remains challenging to establish a causative link fully. Summary Data from mouse models have substantiated clinical observations and implicate direct viral infection in the pathogenesis of viral glomerulopathy, particularly in human immunodeficiency virus-associated nephropathy. In addition to the traditional concept of direct viral effects on kidneys, other factors such as APOL1 risk alleles can further modify the clinical outcomes or presentations of different viral glomerulopathies. Newly developed antiviral drugs are now applicable to a wider range of patients with lower kidney function and fewer side effects. Key Message Efforts focusing on vaccines and antiviral treatments have significantly reduced the incidence of viral glomerulopathies. However, the most recent pandemic caused by severe acute respiratory syndrome coronavirus 2 infection complicated by COVID-associated nephropathy illustrates our susceptibility to novel viruses. Ongoing research is pivotal to deciphering the mechanisms behind viral glomerulopathies and discovering therapeutics in a collaborative approach.
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Affiliation(s)
- Margaret Deoliveira
- Division of Nephrology, Department of Medicine, Mount Sinai School of Medicine, New York, NY, USA
| | - Hridyesh Sikri
- Division of Nephrology, Department of Medicine, Mount Sinai School of Medicine, New York, NY, USA
| | - Samuel Mon-Wei Yu
- Division of Nephrology, Department of Medicine, Mount Sinai School of Medicine, New York, NY, USA
| | - John Cijiang He
- Division of Nephrology, Department of Medicine, Mount Sinai School of Medicine, New York, NY, USA
- Department of Pharmacological Sciences, Mount Sinai School of Medicine, New York, NY, USA
- James J. Peters Veteran Administration Medical Center, New York, NY, USA
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10
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Klocke J, Kim SJ, Skopnik CM, Hinze C, Boltengagen A, Metzke D, Grothgar E, Prskalo L, Wagner L, Freund P, Görlich N, Muench F, Schmidt-Ott KM, Mashreghi MF, Kocks C, Eckardt KU, Rajewsky N, Enghard P. Urinary single-cell sequencing captures kidney injury and repair processes in human acute kidney injury. Kidney Int 2022; 102:1359-1370. [PMID: 36049643 DOI: 10.1016/j.kint.2022.07.032] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2022] [Revised: 07/06/2022] [Accepted: 07/27/2022] [Indexed: 01/12/2023]
Abstract
Acute kidney injury (AKI) is a major health issue, the outcome of which depends primarily on damage and reparative processes of tubular epithelial cells. Mechanisms underlying AKI remain incompletely understood, specific therapies are lacking and monitoring the course of AKI in clinical routine is confined to measuring urine output and plasma levels of filtration markers. Here we demonstrate feasibility and potential of a novel approach to assess the cellular and molecular dynamics of AKI by establishing a robust urine-to-single cell RNA sequencing (scRNAseq) pipeline for excreted kidney cells via flow cytometry sorting. We analyzed 42,608 single cell transcriptomes of 40 urine samples from 32 patients with AKI and compared our data with reference material from human AKI post-mortem biopsies and published mouse data. We demonstrate that tubular epithelial cells transcriptomes mirror kidney pathology and reflect distinct injury and repair processes, including oxidative stress, inflammation, and tissue rearrangement. We also describe an AKI-specific abundant urinary excretion of adaptive progenitor-like cells. Thus, single cell transcriptomics of kidney cells excreted in urine provides noninvasive, unprecedented insight into cellular processes underlying AKI, thereby opening novel opportunities for target identification, AKI sub-categorization, and monitoring of natural disease course and interventions.
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Affiliation(s)
- Jan Klocke
- Department of Nephrology and Medical Intensive Care, Charité-Universitätsmedizin, Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany; Deutsches Rheuma-Forschungszentrum, an Institute of the Leibniz Foundation, Berlin, Germany.
| | - Seung Joon Kim
- Systems Biology of Gene-Regulatory Elements, Berlin Institute for Medical Systems Biology (BIMSB), Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin, Germany
| | - Christopher M Skopnik
- Department of Nephrology and Medical Intensive Care, Charité-Universitätsmedizin, Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany; Deutsches Rheuma-Forschungszentrum, an Institute of the Leibniz Foundation, Berlin, Germany
| | - Christian Hinze
- Department of Nephrology and Medical Intensive Care, Charité-Universitätsmedizin, Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany; Molecular and Translational Kidney Research, Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin, Germany; Department of Nephrology and Hypertension, Hannover Medical School, Hannover, Germany
| | - Anastasiya Boltengagen
- Systems Biology of Gene-Regulatory Elements, Berlin Institute for Medical Systems Biology (BIMSB), Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin, Germany
| | - Diana Metzke
- Department of Nephrology and Medical Intensive Care, Charité-Universitätsmedizin, Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany; Deutsches Rheuma-Forschungszentrum, an Institute of the Leibniz Foundation, Berlin, Germany
| | - Emil Grothgar
- Department of Nephrology and Medical Intensive Care, Charité-Universitätsmedizin, Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany; Deutsches Rheuma-Forschungszentrum, an Institute of the Leibniz Foundation, Berlin, Germany
| | - Luka Prskalo
- Department of Nephrology and Medical Intensive Care, Charité-Universitätsmedizin, Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany; Deutsches Rheuma-Forschungszentrum, an Institute of the Leibniz Foundation, Berlin, Germany
| | - Leonie Wagner
- Department of Nephrology and Medical Intensive Care, Charité-Universitätsmedizin, Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany; Deutsches Rheuma-Forschungszentrum, an Institute of the Leibniz Foundation, Berlin, Germany
| | - Paul Freund
- Department of Nephrology and Medical Intensive Care, Charité-Universitätsmedizin, Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany; Deutsches Rheuma-Forschungszentrum, an Institute of the Leibniz Foundation, Berlin, Germany
| | - Nina Görlich
- Department of Nephrology and Medical Intensive Care, Charité-Universitätsmedizin, Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany; Deutsches Rheuma-Forschungszentrum, an Institute of the Leibniz Foundation, Berlin, Germany
| | - Frédéric Muench
- Department of Nephrology and Medical Intensive Care, Charité-Universitätsmedizin, Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
| | - Kai M Schmidt-Ott
- Department of Nephrology and Medical Intensive Care, Charité-Universitätsmedizin, Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany; Molecular and Translational Kidney Research, Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin, Germany; Department of Nephrology and Hypertension, Hannover Medical School, Hannover, Germany
| | - Mir-Farzin Mashreghi
- Therapeutic Gene Regulation, Deutsches Rheuma-Forschungszentrum, an Institute of the Leibniz Foundation, Berlin, Germany
| | - Christine Kocks
- Systems Biology of Gene-Regulatory Elements, Berlin Institute for Medical Systems Biology (BIMSB), Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin, Germany
| | - Kai-Uwe Eckardt
- Department of Nephrology and Medical Intensive Care, Charité-Universitätsmedizin, Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
| | - Nikolaus Rajewsky
- Systems Biology of Gene-Regulatory Elements, Berlin Institute for Medical Systems Biology (BIMSB), Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin, Germany
| | - Philipp Enghard
- Department of Nephrology and Medical Intensive Care, Charité-Universitätsmedizin, Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany; Deutsches Rheuma-Forschungszentrum, an Institute of the Leibniz Foundation, Berlin, Germany
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11
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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: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 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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12
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Killian JT, Houp JA, Burkholder GA, Roman Soto SA, Killian AC, Ong SC, Erdmann NB, Goepfert PA, Hauptfeld-Dolejsek V, Leal SM, Zumaquero E, Nellore A, Agarwal G, Kew CE, Orandi BJ, Locke JE, Porrett PM, Levitan EB, Kumar V, Lund FE. COVID-19 Vaccination and Remdesivir are Associated With Protection From New or Increased Levels of Donor-Specific Antibodies Among Kidney Transplant Recipients Hospitalized With COVID-19. Transpl Int 2022; 35:10626. [PMID: 35928347 PMCID: PMC9343962 DOI: 10.3389/ti.2022.10626] [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: 05/08/2022] [Accepted: 06/20/2022] [Indexed: 02/05/2023]
Abstract
Alloimmune responses in kidney transplant (KT) patients previously hospitalized with COVID-19 are understudied. We analyzed a cohort of 112 kidney transplant recipients who were hospitalized following a positive SARS-CoV-2 test result during the first 20 months of the COVID-19 pandemic. We found a cumulative incidence of 17% for the development of new donor-specific antibodies (DSA) or increased levels of pre-existing DSA in hospitalized SARS-CoV-2-infected KT patients. This risk extended 8 months post-infection. These changes in DSA status were associated with late allograft dysfunction. Risk factors for new or increased DSA responses in this KT patient cohort included the presence of circulating DSA pre-COVID-19 diagnosis and time post-transplantation. COVID-19 vaccination prior to infection and remdesivir administration during infection were each associated with decreased likelihood of developing a new or increased DSA response. These data show that new or enhanced DSA responses frequently occur among KT patients requiring admission with COVID-19 and suggest that surveillance, vaccination, and antiviral therapies may be important tools to prevent alloimmunity in these individuals.
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Affiliation(s)
- John T. Killian
- Department of Surgery, Heersink School of Medicine, University of Alabama at Birmingham, Birmingham, AL, United States
| | - Julie A. Houp
- Department of Surgery, Heersink School of Medicine, University of Alabama at Birmingham, Birmingham, AL, United States
| | - Greer A. Burkholder
- Department of Medicine, Heersink School of Medicine, University of Alabama at Birmingham, Birmingham, AL, United States
| | - Salomon A. Roman Soto
- Department of Surgery, Heersink School of Medicine, University of Alabama at Birmingham, Birmingham, AL, United States
| | - A. Cozette Killian
- Department of Surgery, Heersink School of Medicine, University of Alabama at Birmingham, Birmingham, AL, United States
| | - Song C. Ong
- Department of Medicine, Heersink School of Medicine, University of Alabama at Birmingham, Birmingham, AL, United States
| | - Nathaniel B. Erdmann
- Department of Medicine, Heersink School of Medicine, University of Alabama at Birmingham, Birmingham, AL, United States
| | - Paul A. Goepfert
- Department of Medicine, Heersink School of Medicine, University of Alabama at Birmingham, Birmingham, AL, United States
| | - Vera Hauptfeld-Dolejsek
- Department of Surgery, Heersink School of Medicine, University of Alabama at Birmingham, Birmingham, AL, United States
| | - Sixto M. Leal
- Department of Pathology, Heersink School of Medicine, University of Alabama at Birmingham, Birmingham, AL, United States
| | - Esther Zumaquero
- Department of Microbiology, Heersink School of Medicine, University of Alabama at Birmingham, Birmingham, AL, United States
| | - Anoma Nellore
- Department of Medicine, Heersink School of Medicine, University of Alabama at Birmingham, Birmingham, AL, United States
| | - Gaurav Agarwal
- Department of Medicine, Heersink School of Medicine, University of Alabama at Birmingham, Birmingham, AL, United States
| | - Clifton E. Kew
- Department of Medicine, Heersink School of Medicine, University of Alabama at Birmingham, Birmingham, AL, United States
| | - Babak J. Orandi
- Department of Surgery, Heersink School of Medicine, University of Alabama at Birmingham, Birmingham, AL, United States
| | - Jayme E. Locke
- Department of Surgery, Heersink School of Medicine, University of Alabama at Birmingham, Birmingham, AL, United States
| | - Paige M. Porrett
- Department of Surgery, Heersink School of Medicine, University of Alabama at Birmingham, Birmingham, AL, United States
| | - Emily B. Levitan
- School of Public Health, University of Alabama at Birmingham, Birmingham, AL, United States
| | - Vineeta Kumar
- Department of Medicine, Heersink School of Medicine, University of Alabama at Birmingham, Birmingham, AL, United States
| | - Frances E. Lund
- Department of Microbiology, Heersink School of Medicine, University of Alabama at Birmingham, Birmingham, AL, United States,*Correspondence: Frances E. Lund,
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13
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Cheung MD, Agarwal A, George JF. Where Are They Now: Spatial and Molecular Diversity of Tissue-Resident Macrophages in the Kidney. Semin Nephrol 2022; 42:151276. [PMID: 36435683 DOI: 10.1016/j.semnephrol.2022.10.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
Kidney resident macrophages (KRMs) are involved in homeostasis, phagocytosis, defense against infectious agents, response to insults, inflammation, and tissue repair. They also play critical roles in the pathogenesis and recovery from many kidney diseases such as acute kidney injury. KRMs historically have been studied as one homogenous population, but the wide-ranging roles and phenotypes observed suggest that there is greater heterogeneity than previously understood. Advancements in RNA sequencing technologies (single-cell RNA sequencing and spatial transcriptomics) have identified specific subsets of KRMs that are molecularly, functionally, and spatially distinct with dynamic changes after kidney injury. Multiple studies have identified unique markers that represent these subpopulations, permitting further characterization of the function and roles they play in the kidney. Understanding the diversity of KRM subpopulations will be key in the development of novel therapies used in treating kidney diseases and promoting kidney health.
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Affiliation(s)
- Matthew D Cheung
- Department of Surgery, University of Alabama at Birmingham Heersink School of Medicine, Birmingham, Alabama; Department of Medicine, University of Alabama at Birmingham Heersink School of Medicine, Birmingham, Alabama; Nephrology Research and Training Center, University of Alabama at Birmingham Heersink School of Medicine, Birmingham, Alabama
| | - Anupam Agarwal
- Department of Medicine, University of Alabama at Birmingham Heersink School of Medicine, Birmingham, Alabama; Nephrology Research and Training Center, University of Alabama at Birmingham Heersink School of Medicine, Birmingham, Alabama; Department of Veteran Affairs, University of Alabama at Birmingham Heersink School of Medicine, Birmingham, Alabama
| | - James F George
- Department of Surgery, University of Alabama at Birmingham Heersink School of Medicine, Birmingham, Alabama; Nephrology Research and Training Center, University of Alabama at Birmingham Heersink School of Medicine, Birmingham, Alabama.
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